This is an author produced version of an Open Access paper accepted for publication
in Oceanography and Marine Biology: An Annual Review, Volume 60. This paper has
been peer-reviewed but does not include the final publisher proof-corrections or
Citation for the accepted paper:
Skinner, C., Cobain, M.R.D., Zhu, Y., Wyatt, A.S.J., Polunin, N.V.C.
“Progress and direction in the use of stable isotopes to understand complex coral reef
ecosystems: a review.”
Oceanography and Marine Biology: An Annual Review, 2022, Volume 60. In press.
Published online with permission from: Routledge, Taylor & Francis Group
Progress and direction in the use of stable isotopes to understand complex coral reef
ecosystems: a review.
C. Skinner1*§, M. R. D. Cobain2,3*, Y. Zhu2,4, A. S. J. Wyatt1, N. V. C. Polunin2
1 = Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering,
Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Kowloon, Hong
2 = School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU,
3 = School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
4 = Institute of Marine Research, NO-5005 Bergen, Norway
* the first two authors contributed equally to this work.
§ = corresponding author = email@example.com
Coral reef ecosystems are exceptionally complex with a myriad of trophic pathways and consumer
relationships. The application of stable isotopes (SIs) offers numerous advantages over traditional methods
towards understanding these intricate systems. We summarize current knowledge derived from the rapidly
increasing SI literature base and identify potential gaps and future directions for the use of SI in coral reef
ecosystem studies. Using topic modelling, a form of text mining, on 236 identified published works, we
determined that SI research on coral reefs broadly falls into five major topics. 1) Organic matter dynamics:
SI analyses (SIA) have quantified substantial variability in autochthonous (internal) and allochthonous
(external) fluxes across coral reefs. 2) Holobiont metabolism: Coral nutrient acquisition, translocation and
partitioning, and coral responses to various endogenous and exogenous factors, have been explored
through SIA. 3) Trophic niches: SIA has indicated that considerable variation in resource use facilitates co-
occurrence of high densities of consumers, emphasising that many trophic categorisations on reefs are
often too simplistic. 4) Fish diet variation and habitat connectivity: SIA has revealed how ontogenetic,
larval, and mobile predator movements link adjacent ecosystems. 5) Environmental drivers (both natural
and anthropogenic): SIA can track anthropogenic nutrient inputs, revealing impacts of human-derived
pollutants on reef systems. There are a number of important knowledge gaps however. Few studies
compare feeding strategies across guilds and the literature is biased towards reef fish and hard corals.
Furthermore, few studies examine multiple taxonomic groups in situ or consider multiple environmental
drivers. Studies also tend to ignore the underlying, but potentially substantial, spatiotemporal variation in
SI baselines as demonstrated from 741 mean SI values extracted from the literature, making inferences
based on small variations in SI values problematic. Given that coral reefs face global decline, knowledge
gaps need to be addressed while acknowledging the limitations of SIA; careful application of SIs can
enhance understanding of processes driving environmental change in these iconic marine ecosystems.
1. INTRODUCTION ........................................................................................................................................... 3
2. KEY PATTERNS AND TOPICS IN SI APPROACHES TO CORAL REEFS ................................................................ 8
3. ORGANIC MATTER DYNAMICS ................................................................................................................... 10
3.1. BACKGROUND................................................................................................................................. 10
3.2. INTERNAL AND EXTERNAL FLUXES OF DOM AND POM .......................................................................... 12
3.3. SPATIAL AND TEMPORAL VARIATIONS .................................................................................................. 14
3.4. ISOTOPIC INSIGHTS INTO THE ROLE OF DETRITUS ................................................................................... 16
4. HOLOBIONT METABOLISM......................................................................................................................... 17
4.1. BACKGROUND................................................................................................................................. 17
4.2. EXTERNAL NUTRIENT ACQUISITION ..................................................................................................... 18
4.3. INTERNAL NUTRIENT TRANSLOCATION AND PARTITIONING ...................................................................... 21
4.4. DRIVERS OF MIXOTROPHY ................................................................................................................. 23
4.4.1. Exogenous factors .............................................................................................................................. 23
4.4.2. Endogenous factors ............................................................................................................................ 24
4.5. METABOLISM IN NON-HARD CORAL SYMBIOSES .................................................................................. 26
5. TROPHIC NICHES ........................................................................................................................................ 28
5.1. BACKGROUND................................................................................................................................. 28
5.2. ISOTOPIC NICHES ............................................................................................................................. 29
5.3. DRIVERS OF ISOTOPIC NICHE VARIATION .............................................................................................. 35
6. FISH DIET VARIATION AND HABITAT CONNECTIVITY .................................................................................. 36
6.1. BACKGROUND................................................................................................................................. 36
6.2. ONTOGENETIC HABITAT SHIFTS .......................................................................................................... 37
6.3. BODY SIZE ...................................................................................................................................... 38
6.4. RESIDENCY AND POPULATION CONNECTIVITY ........................................................................................ 40
6.5. HABITAT CONNECTIVITY .................................................................................................................... 41
7. ENVIRONMENTAL DRIVERS ........................................................................................................................ 44
7.1. BACKGROUND................................................................................................................................. 44
7.2. NATURAL DRIVERS ........................................................................................................................... 45
7.3. ANTHROPOGENIC DRIVERS ................................................................................................................ 49
8. KNOWLEDGE GAPS, CAVEATS, LIMITATIONS, AND FUTURE DIRECTIONS ................................................... 53
8.1 KNOWLEDGE GAPS AND OPPORTUNITIES .............................................................................................. 53
8.2 CAVEATS AND LIMITATIONS ................................................................................................................ 57
9. CONCLUSIONS ........................................................................................................................................... 59
10. ACKNOWLEDGEMENTS ............................................................................................................................ 61
11. REFERENCES ............................................................................................................................................. 61
Knowledge of the energy fluxes and networks of consumer relationships that constitute whole ecosystems
has long been considered crucial to understanding their structure (e.g. Lindeman 1942, Teal 1962),
functioning (e.g. Patten 1959, Slobodkin 1959, Ulanowicz 1972, Bellwood et al. 2019) and sustainable use
(e.g. Ryther 1969 , Friedland et al. 2012, Link and Watson 2019). This is particularly challenging where the
range of sources, diversity of consumers, and number of trophic levels are large (Link 2002). The high
species diversity of coral reefs therefore presents a huge obstacle to any attempt to understand the
ecosystem, especially as the ecologies of the majority of species are known only from short bursts of
research activity at particular locations and points in time (e.g. Odum and Odum 1955, Hiatt and Strasburg
1960, Randall 1967, Vivien 1973, Hobson 1974, Harmelin-Vivien 1981, Sano et al. 1984). This creates great
uncertainty in understanding coral reef functionality.
Ecosystem function relies on the movement and storage of energy and nutrients. As such, the exceptional
productivity and biodiversity of coral reef ecosystems in mostly oligotrophic tropical surface waters has
long been considered a paradox (Darwin 1842). The array of potential pathways sustaining these iconic
ecosystems are only now being explored in the detail that their present plight demands – there is a
plethora of threats to coral reefs, including multiple consequences of climate change (Hughes et al. 2003,
Graham et al. 2011, Hoegh-Guldberg et al. 2017, Hughes et al. 2017) and impacts of fishery exploitation
(Newton et al. 2007, MacNeil et al. 2015, Bozec et al. 2016).
Coral reef primary production sources (all bold words appear in the glossary, Table 1) can include algae,
phytoplankton, various sponges and cnidarians which are partially photosynthetic or chemosynthetic, and
suspended and sedimentary particulate and dissolved organic materials derived from these. The nature of
these sources is complex, so characterising consumer relationships is non-trivial. For example, the
macroalgal matrix that nominally herbivorous fish feed on may also include microbes, detritus, and animal
material (Wilson and Bellwood 1997). Many herbivores may also feed opportunistically on the faeces of
zooplanktivorous fishes (Robertson 1982). Corallivores and spongivores, which include nominal herbivores
(e.g. Burkepile et al. 2019), actually ingest material of mixotrophic origin. This is because the coral or
sponge holobiont is composed of the host animal tissue but also symbiotic dinoflagellates (often from the
clade Symbiodiniaceae) and other potential prokaryotic symbionts, hereafter referred to as
“endosymbionts”. Marine symbioses such as these are particularly common in nutrient-poor environments
such as coral reefs (Ferrier-Pagès and Leal 2019) and present another layer of complexity in understanding
these ecosystems. Zooplankton have long been considered an important resource for reefs, but assessing
their role is complicated by the fact that pelagic plankton are continuously advected over reefs, in
conjunction with distinct reef plankton living amongst the reef substrata, with some only emerging at night
(Hobson 1974). Free-living bacteria also represent an important resource in coral reefs. They experience
high rates of growth and production through feeding on abundant dissolved organic matter, providing a
food source to higher trophic level consumers including zooplankton and corals, thereby transferring
energy and contributing to reef productivity (Sorokin 1973a, b, Sorokin et al. 1985, Ferrier-Pagès and
Gattuso 1998). While detritus constitutes an important flux (e.g. Crossman et al. 2005), the origins and
lability of the materials involved are diverse and little studied.
Even at this low level, understanding these diverse and complex relationships is hedged with uncertainty.
Traditionally, tools used to tackle these knowledge gaps have included in situ behavioural and stomach-
contents analyses, mass-balanced modelling, genetics, and “omics” methods (i.e. proteomics and
metabolomics). Feeding observations offer considerable resolution in some aspects of a consumer’s diet
but, without costly extension, provide data over only small temporal and spatial scales. They also generally
do not allow quantification of some hard to observe but significant dietary components such as microbes
and plankton, and they may provide only a modest measure of what is assimilated into consumer tissues.
Additionally, for interactions among marine symbioses, it is not possible to track nutrient exchanges
visually. For modelling approaches, the scope is vast but severely constrained by the accuracy of
parameterisation and key assumptions such as the rate of primary production and trophic transfer
efficiencies (e.g. Polovina 1984, Polunin and Klumpp 1990, Arias-González et al. 1997). While “omics”
methods are important for disentangling metabolic relationships in marine symbioses, they cannot trace
nutrient exchanges or identify original sources well (Ferrier-Pagès and Leal 2019).
Although coral reef ecosystem functioning has been considered since the early 1800s (Darwin 1842), stable
isotope (SI) approaches (see Text box 1) are a relatively recent addition to this endeavour, having only been
applied readily since the early 1980s (e.g. Fry et al. 1982), although there are some examples of earlier
works (Stephens 1960, Sorokin 1973a, Goreau 1977). These approaches fall into two categories: 1)
measuring natural abundances of stable isotopes in a sample, and 2) tracing the artificial addition of
heavier isotopes through a system of interest, known as isotope labelling. SI approaches have many
strengths (Text box 1; Fry 2006). SI compositions are time-integrated so potentially represent material
assimilation by consumers over time scales of days to months, whereas behavioural and gut content
analyses capture at most hours to days. SI ratios in a consumer’s tissues also contain information about
what has been assimilated from the diet, not merely ingested. This means the nutritional role of a
particular source can be clarified rather than having to be assumed. This extends to quantifying the
importance of materials such as gelatinous plankton and dissolved organic matter, which may be estimated
poorly, or not at all, via traditional gut contents analyses. This also extends to primary producers, with
tissue SIs relating to the nutrients taken up for fixation along with the fixation pathway itself. SI analyses
(SIA) offer ways of tracking distinct production sources and testing ideas about how the importance of
different pathways may vary in space and time, or in relation to other factors such as body size. SI ratios
can provide a chemical proxy of trophic position (TP) and a means of estimating trophic niche widths and
volumes, providing an opportunity to test ideas about overlaps in these parameters. Because of their
snapshot character, gut-contents analyses tend to require much larger sample sizes than those needed for
SIA, while SI data can be derived from non-lethal sampling. Inherent in each of these strengths are
important constraints, however. This includes those of the isotope ratio mass spectrometry technology
involved (e.g. Mill et al. 2008), the fact that SI ratios can only be used to track sources and trophic pathways
that are isotopically distinct, and that derived metrics such as TP rely on assumptions regarding isotopic
discrimination which can vary across space, time and trophic levels (Hussey et al. 2014).
There are still many opportunities to add value to SI studies, including through: 1) the use of elements
other than carbon and nitrogen (such as sulphur); 2) the use of fast and slow turnover tissues to represent
feeding over different time scales; 3) the use of archived materials to test ideas about past changes; 4)
improved parameterisation of niche topology (Jackson et al. 2011); 5) development of SI mixing models
allowing better differentiation of different production sources and trophic pathways (e.g. Parnell et al.
2013); 6) estimation of key processes such as food chain transfer efficiency from relationships between TP
and body size (Jennings et al. 2002); and 7) accurate characterization of enrichment factors between
consumers and their diet, especially for holobionts. The ability to gain SI information on specific
compounds rather than just bulk tissue homogenate has further expanded our ability to understand coral
reef ecosystems by better resolving different sources and pathways (e.g. McMahon et al. 2016, Fox et al.
2019, Skinner et al. 2021). While important for contextual understanding, the purpose of this review is not
to summarise or explain recent advances in SI methodologies and techniques (for that, we point readers to
Text box 1 and, among others, e.g. Boecklen et al. 2011, McMahon et al. 2013, Vander Zanden et al. 2015,
Pethybridge et al. 2018, Ferrier-Pagès and Leal 2019, McCormack et al. 2019, Whiteman et al. 2019, Shipley
and Matich 2020, Tsui et al. 2020). Instead, in light of the expanding but often disparate research occurring
on coral reefs that utilises SIs and the lack of a comprehensive synthesis of general findings, we sought to
summarise the current knowledge of coral reefs that has been advanced through the application of SI
Undertaking a more systematic approach to guide this review, we conducted an extensive literature search
for studies utilising SI approaches in coral reef ecosystems and organisms. We screened and extracted key
information pertaining to each study including the focal taxa, when and where the study was conducted,
along with SI measurements of baseline sources. We then analysed the text in article abstracts using topic
modelling (a form of text mining which identifies clusters of words e.g. topics; Griffiths and Steyvers 2004,
Grün and Hornik 2011). This approach facilitates the objective identification of recurring themes in the
articles within the extensive literature (see Supplements S1 for detailed methods). Specifically, here we:
1) characterise the biological, geographical, and methodological foci of SI applications in published works,
2) quantify the isotopic variability observed among production sources across coral reef systems globally,
and 3) identify the principal topics to which SI data have been applied. We summarise the extent to which
current knowledge of coral reef ecosystems has been advanced through SIA, highlight the main areas for
growth, emphasise considerations that are essential when interpreting SI data from coral reef ecosystems,
and identify future challenges for obtaining fuller understanding of this complex system.
2. Key patterns and topics in SI approaches to coral reefs
By combining a traditional literature search with mining of pertinent information from identified articles,
and topic modelling of their abstracts, we were able to identify patterns and recurring themes in the SI
coral reef studies published to date (1980 – 2019 inclusive). Of 341 articles identified through
WebOfScience and 964 identified through GoogleScholar, a total of 238 were retained after careful
screening (Table S1). Of those, 236 had abstracts and were used in the subsequent topic modelling analysis
(see Supplements S1 for detailed methods). We also extracted key information from all 238 articles (Table
S1), including basic article information, study-specific information (e.g. spatial and temporal information;
Table S2 for definitions), sample information (e.g. single or multi-tissue, tissue type, isotopes, focal taxa etc;
see Table S3 for definitions), and, when reported, SI values of baseline sources (Table S6). It is worth noting
here that although we combined extensive literature searches across two different databases, the final 238
articles are likely not an exhaustive list of published SI studies on coral reefs. However, our literature search
generated an extensive, comprehensive, and representative suite of coral reef SI studies using an objective
Topic modelling identified five topics, which were named based on the highest weighted words occurring
within each (Table 2). Generally, similar numbers of articles were assigned to each topic, with Topic 2
(Holobiont metabolism) having the highest number of articles (n = 55) and Topic 1 (Organic matter
dynamics) the lowest number of articles (n = 41). Although topic popularity has fluctuated over time (Fig.
1), the distribution of topics across regions is fairly equitable (Fig. 2). These five topics were used as a guide
to construct the remainder of this review. The topics appear in a logical order which reflects the structure
of the coral reef ecosystem; starting from the basal production sources (Topic 1: Organic Matter
Dynamics), moving onto key primary producers and consumers (Topic 2: Holobiont Metabolism), food web
and community structure (Topic 3: Trophic Niches), higher-level consumers and the energetic linkages they
construct (Topic 4: Fish Diet Variation/Habitat Connectivity), and finally considering external drivers of
coral reef systems (Topic 5: Environmental Drivers) (Fig. 3). It should be acknowledged however that there
is some inherent cross-over between topics.
In terms of SI approaches used, natural abundances of SIs of bulk tissue (i.e. measuring a whole tissue type
such as muscle or liver) dominate the literature (84% of articles; Fig. 2B), with dual analysis of carbon and
nitrogen (i.e. δ13C and δ15N) the most popular approach (54% of articles; Fig 2B), followed by nitrogen on its
own (12% of articles; Fig. 2B). While SI studies using compound-specific stable isotope analysis (CSIA, i.e.
profiling individual compounds such as amino acids or fatty acids) are less frequent, they are increasing as
this methodology becomes more accessible (6%; Fig. 2B). Analyses on organism muscle tissue (n = 99),
holobiont host soft tissue (n = 79) and their endosymbionts (n = 46), and algal tissues (n = 66) constitute
the majority of studies, but there is a huge diversity of tissues that have been analysed. In addition to
various organs (liver n = 7; gonad n = 3; skin n = 3; digestive tract n = 2; heart n = 2), analyses have been
conducted on fish scales (n = 2) and gills (n = 2), faeces (n = 2), bone (n = 2), and sea cucumber respiratory
trees (n = 1). Most studies are field based (75%), with few relying on laboratory experiments (22%), and
fewer still combining both field and lab approaches (3%). While studies have been carried out around the
world, there is substantial disparity between regions (Fig. 2): the eastern Atlantic and eastern Pacific remain
poorly represented (n = 1 and n = 2, respectively), likely due to a lack of expansive coral reef systems in
these regions. Instead, western Atlantic studies dominate (28%), followed by the western Pacific (21%), and
the western Indian Ocean (20%), with notable foci localities in the Caribbean and Florida Keys, the Great
Barrier Reef, and the Red Sea, respectively.
Across the literature, a variety of sources have been sampled in the field, ranging from water nutrients and
organic matter through to macrophytes, zooplankton and holobionts, covering both the pelagic and
benthic and spanning the mangrove – seagrass – reef – offshore habitat continuum (Table 3). Of the 741
extracted values, macroalgae were the most repeatedly measured for both δ13C and δ15N (n = 145 and 203,
respectively). POM, zooplankton, algal turfs, SOM, and coral (both homogenate and separated fractions)
have also been well characterised across studies (n > 45). The global variability observed in δ13C and δ15N
across coral reef sources is substantial (Fig. 4), spanning from approximately -30‰ to -4‰ for δ13C and -5
to 15‰ for δ15N, with macroalgae specifically exhibiting considerable diversity in expressed SI
Sampling regimes of SI studies are dominated by limited temporal windows (single point, period, or season,
approximately 50% of screened articles), with only ~13% of studies designed to observe changes, if any,
between distinct seasons or years (multi-season, monthly, annually, and interannual studies) (Fig. 5A). Of
considerable concern is that 17% of studies screened failed to provide enough information to discern their
sampling regime, with examples found across all major regions of study. The focal taxa of studies are
heavily, but unsurprisingly, skewed towards reef fish and hard corals, which combined comprise over 60%
of all SI studies globally. This bias is particularly notable in the Western Indian region, whereas studies
based in the Western Atlantic appear to be more evenly dispersed across focal taxa groups (Fig. 5B). Barring
hard coral, there is limited focus on other coral reef sources (although they are often measured within
other studies, Table 3, and Fig. 4). Encouragingly however, studies that explore SIs in multiple components
of the ecosystem thereby employing a more holistic approach to understanding whole coral reef systems,
consist of over 5% of the observed literature.
3. Organic matter dynamics
The dynamics of organic matter and remineralized constituents over and within coral reef ecosystems, and
hence the food and dissolved nutrient resources available to reef consumers, have long been enigmatic.
Odum and Odum (1955) suggested that the “changes in dissolved organic matter (DOM) in the vast flow of
water crossing [a] reef” posed a central question in reef productivity. Quantifying variability in material
fluxes into and within reefs was recognised in early studies as essential to understanding how reefs
function in oligotrophic oceanic settings (Sargent and Austin 1954, Odum and Odum 1955, Sorokin 1973b).
However, reef food-webs possess a large range of potential sources, both autochthonous (hereafter
“internal”) and allochthonous (hereafter “external”), and these are likely to vary spatially along with
hydrodynamics and zonation of community structure (Fig. 3; Fig. 4; Table 3). SI studies investigating these
fluxes have predominantly been conducted in the western (n = 12) and central (n = 9) Pacific, western
Atlantic (n = 11), and western Indian Ocean (n = 10), with particular foci on Japan (n = 7), the Caribbean (n =
7), and the Red Sea (n = 5) respectively (Fig. 2). The eastern Pacific, eastern Indian, and eastern Atlantic are
poorly represented with few, if any, studies conducted (n = 0 of the papers assigned to this topic from our
High reef productivity despite low ambient nutrient concentrations has been attributed to both internal
and external processes: high rates of internal recycling or atmospheric nitrogen fixation, and therefore
nutrient retention (e.g. Odum and Odum 1955, Johannes et al. 1972, Webb et al. 1975), versus flow-driven
inputs of external oceanic nutrients (Odum and Odum 1955, Andrews and Gentien 1982, Atkinson 1992,
Atkinson 2011, Wyatt et al. 2012a). The high rate of respiration, with net productivity often close to zero,
indicates effective recycling within reef systems (Kinsey 1985, Crossland et al. 1991, Tribble et al. 1994).
However, the fluxes of materials over reefs (both internal and external) and their uses by consumers have
rarely been examined at ecosystem-scales. This makes it difficult to make accurate predictions regarding
the future function of reefs subject to change. Indeed, non-isotope studies, mostly in mesocosms or
incubations, have indicated that DOM may be a significant resource (Tanaka et al. 2009, Nakajima et al.
2010, Naumann et al. 2010a, Tanaka et al. 2011a, Naumann et al. 2012). However, these are generally
hampered by a lack of understanding of hydrodynamic influences on DOM fluxes over natural reef systems
(but see Wild et al. 2012, Thibodeau et al. 2013). SI data offer great potential to identify organic matter
sources over natural reefs and measure the gross fluxes of this material, providing insights into reef
functioning that are essential for predictions for the future. To date, the focal taxa of studies investigating
these fluxes (n = 41) are typically reef fish (n = 13), other invertebrates (n = 6), and hard corals (n = 5). While
seawater is also frequently sampled (n = 9), there has been little focus on benthic algae (macroalgae n = 4;
turf algae n = 0) regarding organic matter dynamics, despite their generally large surface area, important
role in nutrient uptake and as a resource for many reef consumers (Fig. 5B).
3.2. Internal and external fluxes of DOM and POM
Organic matter in the ocean is dominated by dissolved organic matter (DOM), concentrations of which are
far greater on average (1 to 2 orders of magnitude) than particulate organic matter (POM) (e.g. Libes 2009,
Barrón and Duarte 2015). In contrast to the refractory nature and low availability of oceanic DOM to reef
consumers, much of the DOM produced by reef communities is labile and rapidly remineralized (e.g., one
month for ~80% of total organic carbon in coral mucus to be mineralized; Tanaka et al. 2011b). SI data have
demonstrated that corals can release significant amounts of DOM; background concentrations of DOC and
DON rose from 100 µM and 15 µM to 300 – 1700 and 120 µM, respectively, above coral colonies (Ferrier-
Pagès et al. 1998b), as well as POM (see below). Isotope labelling is often used to trace DOM fluxes; highly
isotopically enriched nutrients are supplied and subsequently traced through the various metabolic
pathways within the holobiont. 13C-labelling of reef-building corals Porites cylindrica and Acropora pulchra
suggested that the dissolved organic carbon (DOC) they release over reefs is derived from stored (> 90% of
total) rather than from newly synthesised organic C (< 10%) (Tanaka et al. 2008). One of the few ecosystem-
scale investigations of reef dissolved organic nitrogen (DON) cycling used spatial patterns in δ15N to
demonstrate that localised release of DON (potentially supported by N2 fixation in pristine benthic habitats)
is an important means of recycling N within reef communities (Thibodeau et al. 2013). The spatial
arrangement (see 3.3. Spatial and temporal variations below) of reef communities is therefore important in
determining rates of nutrient exchange across whole coral reef systems (Smith and Marsh 1973, Steven and
Atkinson 2003, Miyajima et al. 2007, Wyatt et al. 2012a, Wyatt et al. 2013).
While concentrations of DOM are greater, POM is more bioavailable (Lønborg et al. 2018), and therefore
POM dynamics are more readily studied on coral reefs. Several studies, including non-isotope approaches,
have identified significant inputs of external POM from the ocean by analysing gross fluxes of isolated
components of the external POM pool (particularly the smallest phyto- and bacterio-plankton) (Genin et al.
2009, Wyatt et al. 2010b, Patten et al. 2011, Akhand et al. 2021). While this may suggest a less prominent
role for tight recycling within reefs, rates of internal POM production have not been adequately quantified
across reef systems. Therefore, robust generalisations regarding the overall relative importance of external
versus internal POM inputs are lacking. Isotope labelling indicates that release of POM from corals may be
of a similar order or higher than that of DOM (average ratios of 0.6 and 0.5 for P. cylindrica and A. pulchra
respectively) (Tanaka et al. 2008). Macroalgae can also produce large amounts of POM; small incubation
chambers over intact reef habitats in Moorea (French Polynesia) have shown a dominance of algal material
within POM, with increased POM δ13C (−16.9 to -11.2‰) above ambient (− 20.6‰) indicative of the
contribution of algal exudates relative to 13C-depleted plankton (Haas et al. 2010). More enriched
nearshore δ13C values of POM samples (-18.3‰) in the Florida Keys were similarly taken to indicate the
degradation of seagrass detritus, while more depleted δ13C of the POM on the outer reef (-21.4‰)
suggested it was dominated by plankton (Lamb and Swart 2008), cf. Fig. 4. Few studies have quantified
rates of POM production over a natural reef. However, modelling of δ13C and δ15N data from Ningaloo Reef
in Western Australia, supported the premise that external POM inputs were balanced by correspondingly
high rates of gross internal POM release into water flowing over the reef crest and flat (Wyatt et al. 2013).
Measuring net concentration changes of, for example bulk POM, may therefore obscure the dynamics of
organic matter uptake and release over reefs, making SI evidence indispensable for disentangling internal
from external organic matter fluxes over reefs.
Organic mucus produced in abundance by corals may play a role in both internal cycling and external
inputs to reefs. Studies have used δ13C analyses to demonstrate that coral mucus can be both exported
from reefs but also re-enter reef food webs due to uptake by reef consumers (Naumann et al. 2010b, Wyatt
et al. 2013). Mucus itself can be a significant source of organic matter, especially in inner reef habitats with
decreased oceanic exposure (Wyatt et al. 2013). For example, it may enhance the flux of external particles
by trapping oceanic plankton in mucus aggregates, enhancing sedimentation rates onto reef habitats
(Naumann et al. 2009). Moreover, internal sources within reefs are not limited to the corals. For instance,
15N-labelling has shown significant rates of POM release from upside-down jellyfish Cassiopea sp. which can
be abundant in some reef systems and subsequently assimilated by zooplankton (Niggl et al. 2010).
Furthermore, non-isotope work has highlighted the important role of fish communities in supplying
(excretion) and storing (biomass) nutrients on coral reefs and adjacent habitats (Allgeier et al. 2014),
suggesting nutrient cycling is prevalent even at higher trophic levels. To date, there is limited SI work
exploring this aspect of organic matter dynamics on reefs (but see 6.5 Habitat connectivity).
Isotope labelling has been used to demonstrate a potentially major role for sponges in organic matter
uptake and retention within coral reefs. The combination of isotopic labelling (13C and 15N) and nanoscale
secondary ion mass spectrometry (NANOSIMS) has shown that sponge host tissues are capable of directly
utilising DOM in the water column through filter feeding (Achlatis et al. 2019). Indeed, some sponges are
more heterotrophic, as indicated by their bulk δ15N values (Fig. 4) (Weisz et al. 2007). For example, bulk
δ13C and δ15N indicate that coral cavity sponges typically feed on coral-derived materials (van Duyl et al.
2011, Slattery et al. 2013). Unlike other marine organisms, a few sponges show differential assimilation
mechanisms for different DOM sources, as revealed by stable isotope pulse‐chase experiments (13C and
15N); e.g. algal DOM is mainly used by symbiotic bacteria while coral DOM is assimilated by sponge cells (Rix
et al. 2017). de Goeij et al. (2008) used 13C-labelling to provide evidence that, in addition to POM, a coral
reef sponge, Halisarca caerulea, was able to incorporate DOM, thereby accessing an abundant source of
organic matter in reef waters. Later, using 13C- and 15N-labelled DOM, de Goeij et al. (2013) demonstrated
both in aquaria and in situ that DOM incorporation by sponges may facilitate DOM transfer to higher
trophic levels through detritus (POM) production. Using 13C- and 15N-labelling in the laboratory, DOM
uptake and POM production by sponges was further demonstrated to facilitate the transfer of coral-mucus-
derived DOM to detritivores on both warm and cold-water reefs (e.g. ophiuroids and polychaetes) (Rix et
al. 2016, Rix et al. 2018). These isotope studies on reef sponges have revealed an additional mechanism by
which organic matter produced on reefs may be internally retained within the system.
3.3. Spatial and temporal variations
Organic matter fluxes are likely to have strong spatial and temporal dynamics (Fig. 4). These will be
influenced by the hydrodynamic conditions and zonation of benthic communities over small spatial scales
of hundreds of metres or less (Haas et al. 2011, Kolasinski et al. 2011, Wyatt et al. 2012a), and larger-scale
stochastic events such as upwelling, storm disturbances, and coral bleaching events (Leichter et al. 2007,
Wild et al. 2008, Kolasinski et al. 2011, Radice et al. 2021). Further, large-scale urbanisation-eutrophication
gradients can be reflected through reef food webs, particularly as elevated δ15N (Kürten et al. 2014, Duprey
et al. 2020; and see 7. Environmental Drivers). Broad scale SI data or ‘isoscapes’, i.e. a spatial pattern of
isotopic values across a land or seascape (West et al. 2008, Bowen 2010), can reveal geographic patterns in
organic matter and nutrient dynamics over reefs. For instance, in the Red Sea, where 11% of all coral reef SI
studies have been conducted (Fig. 2), low organic matter δ15N values in the north (zooplankton δ15N: 1.3‰)
reflect the importance of N2 fixation, while the higher δ15N of organic matter in the south (zooplankton
δ15N: 5.8‰) reflects N inputs from the Indian Ocean (Kürten et al. 2014). Spatial and temporal variability of
organic matter over reefs is poorly understood, yet there is strong SI evidence of habitat-linked variations
in fluxes of DOM (Thibodeau et al. 2013), POM (Wyatt et al. 2013), and dissolved nutrients (Leichter et al.
2007). While these oceanographic drivers mean that external resource supply can be highly variable in
space and time (Wyatt et al. 2012a, Wyatt et al. 2013, Kürten et al. 2014), most SI reef studies are based on
just a single time point or period of sampling (44%), with few conducting repeat samplings across multiple
time points (19%) (Fig. 5A).
Mass coral spawning can periodically increase POM concentrations several fold on many reefs and SI data
have proven useful in examining the biogeochemical impact of these events. A lasting influence of
spawning on POM δ15N was seen on the Great Barrier Reef over a period of about 10 days (increases of ~ 5
‰, from 0.7 to 4.8-5.7 ‰), suggesting spawning-derived organic matter is rapidly transferred to higher
trophic levels (Wild et al. 2008). Similarly, in Kane’ohe Bay, Hawai’i, POM δ15N remained slightly elevated
(2-3 ‰) after spawning (> 10 days), indicating incorporation of spawn-derived organic matter into higher
trophic levels, but spawning impacts on water-column POM δ13C were short-lived (2-4 days post-spawning
returned to pre-spawning values) (Briggs et al. 2013). Briggs et al. (2013) also found that the δ13C of tissues
of the coral Montipora capitata increased by ~ 1 ‰ (-13.3 to -12.2 ‰) over the course of the spawning
season, with eggs having lower δ13C than host tissues (-14.5 ‰). This temporal change could reflect the
spawning physiology; the concentration of 13C-light wax esters and overall carbon content is higher in M.
capitata eggs compared to adults (Padilla-Gamiño et al. 2013), but it may also reflect changes in feeding or
relative rates of autotrophy and heterotrophy. This underscores the importance of having a good
understanding of baseline isotope variations when assessing the impacts of stochastic events like spawning
using tissue SI data.
The high spatiotemporal variability in resources means that adequately quantifying the isotopic
composition of material supplied to reefs can be a non-trivial undertaking (Fig. 4; Table 3; Table S6). For
instance, variability in the isotopic composition of dissolved inorganic N (e.g. nitrate) can be high across the
water column (3.5 to 5.5 ‰ between 50 – 242 m) just due to small-scale patchiness in N cycling (Leichter et
al. 2007). Internal production can also be highly variable, with organic carbon released by benthic algae on
reefs at Moorea demonstrating distinct seasonality, including δ13C variation of ~ 5 ‰ (Haas et al. 2010).
This variability is likely why few studies to date have used isoscapes on coral reefs, or tropical waters in
general (but see MacKenzie et al. 2019); those in marine settings have mostly been conducted in temperate
shelf regions (MacKenzie et al. 2014, Kurle and McWhorter 2017, St. John Glew et al. 2019). However,
isoscapes can provide spatial (and potentially temporal) context to more general questions about
community ecology, animal migration, and nutrient cycling (Hobson et al. 2010, McMahon et al. 2013,
Cheesman and Cernusak 2016). In one of the few studies employing an isoscape approach on coral reefs,
δ15N values of long-lived benthic bivalves were used to create a nitrogen isoscape in New Caledonia that
highlighted regions of eutrophication (δ15N of 11.7 ‰ compared to 4.3 ‰ in lagoon), characterising the
anthropogenic nitrogen footprint of the area (Thibault et al. 2020). Thus, isoscapes of coral reef ecosystems
that account for sufficient natural variation could offer insight into the complex processes that might
influence coral reef trophodynamics and SI values across various locations (Fig. 3; Fig. 4; Table 3). Given
that environmental conditions are fluctuating due to climate change, isoscape studies would further benefit
from the inclusion of SI data across both space and time where possible (McMahon et al. 2013).
3.4. Isotopic insights into the role of detritus
Detritus (i.e. non-living organic matter) is an abundant and potentially significant food resource over reefs,
but its variable lability makes it challenging to characterise (Fig. 4; Table 3; Table S6). Isotopes offer an
opportunity to better trace and quantify fluxes of this material. Indeed, there is substantial isotopic
evidence of a prominent role for detritus in reef food webs. While detrital pools are higher (1.6 times) in
low energy back reef habitats where benthic material accumulates (evidenced by enriched mean δ13C -
16.83 ‰), input rates are higher (1.7 – 2.9 times) over dynamic forereefs due to oceanic detritus supply
(evidenced by depleted mean δ13C - 19.84 ‰) (Max et al. 2013). Thus while detritus can be a nutritious
food source, its availability fluctuates with hydrodynamics (Max et al. 2013). Isotope labelling (13C and 15N)
has demonstrated that detritivores, such as ophiuroid brittle stars, can play an important role in the
recycling of nutritionally poor detritus to higher trophic levels (Rix et al. 2018). There is also increasing
evidence of a high degree of detritivory in reef fishes previously assumed to be largely herbivorous. For
instance, parrotfish like Chlorurus sordidus are often classified as herbivores. Stomach and feeding
observations have suggested that this species may be better described as a detritivore (Choat et al. 2002)
but bulk and CSIA data indicate it might be principally detritivorous across both oceanic and inshore reefs
(Wyatt et al. 2012b, McMahon et al. 2016). In agreement with observational and morphological studies
(Choat et al. 2002, Choat et al. 2004), CSIA data identified that the surgeonfish Ctenochaetus striatus is also
predominantly detritivorous (73%; McMahon et al. 2016). Dietary plasticity at the individual level
(McMahon et al. 2016), or spatial changes in the importance of detritivory (Wyatt et al. 2012b), require
more detailed investigation. However, it appears likely that the importance of detritus, and therefore
microbial reworking, in reef food webs has been underestimated (McMahon et al. 2016). As described in
detail in 3.2 Internal and external fluxes of DOM and POM, sponges also play a key role in reworking
detritus on coral reefs through the ‘sponge loop’: coral mucus carbon and nitrogen is transferred into
sponge tissues and subsequently released as detritus (de Goeij et al. 2013, Rix et al. 2016).
4. Holobiont metabolism
Hermatypic (reef-building) scleractinian corals play a foundational role providing essential habitat for reef
organisms (Coker et al. 2014), so it is only natural that considerable efforts have focussed on their ecology
and the metabolic dependency between them and their symbiotic dinoflagellates in the family
Symbiodiniaceae (Fig. 3). Holobiont metabolism had the largest number of studies principally assigned to it
(n = 55) among SI coral reef topics. Likewise, of all 238 identified SI studies, 26% (n = 62) have had coral as
their focal taxa, second only to fishes (36%, n = 85) (Fig. 5B). Studies focusing on this topic contributed a
major proportion of the earliest SI works on coral reefs (Fig. 1). As SIs act as natural (or artificial) tracers for
elucidating energetic pathways, they are ideally placed to resolve questions regarding nutrient acquisition,
translocation, and utilisation within and between holobionts and their symbiotic microbiomes (Fig. 3). This
is highlighted by the fact that most isotope labelling studies were assigned to the topic of ‘Holobiont
metabolism’ (28 of 37 total). Geographically, there has been a particular focus on holobiont metabolism
regionally in the western Indian Ocean (notably experimental work in the Red Sea) and the western Pacific
(Fig. 2B; 5B). Key aspects revolve around the nature of nutrients that are taken up by holobionts; how they
are proportioned internally between hosts and symbionts; and drivers of variation in the relative utilisation
of photo- or chemosynthetically fixed material (autotrophy) and secondarily sourced production
(heterotrophy), known as mixotrophy. Here we expand upon these ideas to demonstrate the
understanding achieved using SIs, before considering studies whose focus is on the symbiotic relationships
found in organisms other than those of hermatypic corals.
4.2. External nutrient acquisition
As highlighted in the previous section, there is a wealth of external nutrient sources that are potentially
available to corals and other holobionts to underpin their metabolism, as well as those of their
endosymbionts to form photosynthates. This is despite coral reef ecosystems traditionally being viewed as
restricted to oligotrophic tropical surface waters (Darwin 1842). Early work by Risk et al. (1994) suggested
increasing reliance on terrigenous carbon sources by corals and their endosymbionts after observing
increasing δ13C tissue values (from -16 to -11 ‰) with increasing distance from shore in the Great Barrier
Reef. Spatially varying nutrient acquisition has also been observed with reef zonation, with varying coral
tissue δ15N values along an offshore to mid-shelf to inshore barrier reef transect attributed to cold-water
upwellings, algae-based nitrogen fixation and terrigenous sources respectively (Sammarco et al. 1999, Erler
et al. 2014). Elsewhere, across a reef atoll system in the Maldives, nitrates from deep ocean water that are
enriched in 15N have been shown to be incorporated into coral tissues via seasonal upwelling (Radice et al.
2019). In the Cook Islands in the South Pacific Subtropical Gyre, nitrogen inputs to corals also vary
seasonally, with δ15N in coral skeletons suggesting nitrogen sources originate from groundwater during wet
seasons and from N2 fixation during dry seasons (Erler et al. 2019). These studies highlight the
environmental and temporal context dependency of patterns in coral nutrient uptake, but it is worth noting
that increases in coral and endosymbiont δ13C values may also be related to spatial gradients in, for
example, turbidity affecting coral photosynthesis rates or endosymbiont genera.
Direct nutrient uptake from the water column is likely influenced by its form; nitrogen is primarily available
as nitrate or ammonium, where ammonium appears to be principally taken up by the endosymbiotic algae.
Eight week-long 15N-labelled ammonium enrichment experiments revealed a 10-fold increase in ammonium
uptake rates by hosted dinoflagellates compared to coral tissue (Grover et al. 2002). However, overall
ammonium uptake is reduced in fed versus starved hosts (Grover et al. 2002), which may suggest
secondary reliance on ammonium as a nitrogen source compared to heterotrophic feeding. Similar
patterns were found for nitrate using 15N-labelled nitrate and ammonium; nitrate is principally taken up by
the endosymbionts, with uptake rate independent of prior nutrient acclimatisation, but significantly lower
under high ammonium regimes (Grover et al. 2003). The metabolic response of dinoflagellate
endosymbionts to external nutrient enrichment is rapid; significant uptake occurs within an hour of
exposure to either ammonium or nitrate 15N-enriched seawater (Pernice et al. 2012, Kopp et al. 2013). This
suggests direct uptake and fixation of ammonium by endosymbionts from seawater filling the coelenteron
rather than nutrient transfer from hosts to algae (Pernice et al. 2012, Kopp et al. 2013). Such a rapid
response is facilitated by temporary nitrogen storage in intracellular uric acid crystals that can then be
remobilised in the following hours (Kopp et al. 2013). Similar temporary intracellular storage structures
have also been identified for carbon using pulse chase isotopic labelling of 13C-bicarbonate, whereby
seawater bicarbonate is rapidly (~ 15 minutes) taken up by dinoflagellates and fixed into lipid droplets and
starch granules (Kopp et al. 2015).
The uptake of water column nutrients can be further facilitated by recycling pathways, as has been
revealed by isotope tracer experiments using artificially 15N-labelled bacteria to track their incorporation
into coral larvae (Ceh et al. 2013). Isotopic labelling (15N) has further shown that nitrogen-fixing
diazotrophic bacteria may also be taken up directly into the epidermal layers of coral larvae (Lema et al.
2016), potentially helping to meet their nitrogen demands. Nitrogen fixation can also occur within the
endolithic diazotrophs found between coral tissues and their carbonate skeleton, as demonstrated with
15N-labelling (Grover et al. 2014, Yang et al. 2019). However, the importance of this pathway varies
according to coral metabolic status (i.e. whether they are more auto- or hetero-trophic) and with depth
(Bednarz et al. 2017). Bulk SI work (δ13C and δ15N) has however shown a lack of nutrient exchange between
coral polyps and adjoining epilithic algal turfs, demonstrating that at least some potential nutrient
pathways are not utilised (Titlyanov et al. 2008).
Heterotrophic feeding by coral polyps further expands the potential nutrient sources available for these
holobionts, with a diversity of trophic interactions being observed (see Houlbrèque and Ferrier-Pagès 2009
for a detailed review on coral heterotrophy). Lai et al. (2013) used 15N-labelled seagrass to experimentally
show that corals can directly consume seagrass material, both in particulate and dissolved form. This
highlights a direct nutritional link between corals and adjacent seagrass meadows, which can export large
quantities of fresh and detrital material. Other experimental bulk SI work (δ13C and δ18O) has highlighted
how grazing on zooplankton can lead to substantial increases in various measures of coral fitness, such as
tissue chlorophyll concentrations, compared to when heterotrophic feeding is restricted (e.g. Reynaud et
al. 2002). Furthermore, grazing experiments using 3H-labelled bacteria and ciliates showed that although
coral grazing rates decrease as light intensity increases, heterotrophy still contributes to coral nutrition,
suggesting it complements autotrophy even under high light conditions in Stylophora sp. (Ferrier-Pagès et
al. 1998a). More recent SI finger-printing techniques using δ13C of essential amino acids (CSIA)
demonstrates the significant contribution of heterotrophic feeding to coral hosts, with an average of 41%
contribution to assimilated material determined for the widespread Indo-Pacific scleractinian coral
Pocillopora meandrina (Fox et al. 2019). Similar proportions of heterotrophic nutrient uptake have also
been verified experimentally using 15N-labelled rotifers to quantify nitrogen incorporation rates in another
common Indo-Pacific coral Porites lutea (Rangel et al. 2019). However, the degree of heterotrophic feeding
may be a species-specific trait; paired bulk (δ13C and δ15N) and amino acid CSIA (δ13CAA, δ15NAA) revealed
that Montipora capitata did not change their nutritional strategies under different experimental nutrition
regimes (Wall et al. 2021), suggesting a lack of trophic plasticity.
4.3. Internal nutrient translocation and partitioning
The fate of nutrients once assimilated into host tissues underpins the symbiotic relationship between coral
and Symbiodiniaceae – basal products need to be supplied to algal cells for autotrophy and likewise
photosynthates shuttled elsewhere for energetic demands of the host (Fig. 3). Isotopic labelling
experiments tracing the various metabolic pathways within the holobiont constitute some of the earliest
uses of SIs on coral reefs. For example, feeding experiments with 14C revealed that six species of coral were
able to feed on DOM and planktonic bacteria, actively consuming organic phosphorus bound in the cells of
the latter (Sorokin 1973a). Other studies have attempted to understand carbon translocation and turnover
within coral colonies. Crossland et al. (1980) saw a 50-60% loss of photosynthetically fixed 14C from
isotopically labelled and replanted coral colonies during their first 40h back on the reef. However, rather
than the coral colonies translocating fixed carbon from outer branches to basal regions, the authors
suggested that the coral tissues had released mucus and dissolved organic carbon into the environment
(Crossland et al. 1980). Similarly, Rinkevich and Loya (1983) used 14C sodium bicarbonate in the field to
demonstrate limited translocation of photosynthetic products across coral colonies over the course of a
month (from bases to branch tips), despite lower incorporation rates in the growing tip regions.
Under more controlled laboratory settings, high precision tracing can be conducted to elucidate internal
translocation of metabolites over short timescales, further revealing the complexities of this symbiotic
relationship. Following 13C-labelled bicarbonate enriched seawater incubation, Tremblay et al. (2012)
calculated that 60% of carbon fixed by endosymbionts in the scleractinian Stylophora pistillata is
translocated to host tissue within 15 minutes, with approximately 50% of fixed carbon being respired by
the holobiont as a whole. Whole nitrogen budgets have also been determined through 15N enrichment,
showing that a majority (50-83%) of nitrogen utilized by endosymbionts is derived from coral hosts, with
host species-level differences attributed to different N-biomasses per unit surface area of coral host species
(Tanaka et al. 2015, Tanaka et al. 2018). One of the few studies to combine both δ13CAA and δ15NAA to
explore the nutritional exchanges between coral hosts and their endosymbionts confirmed that
endosymbionts do benefit from host heterotrophy (Ferrier-Pagès et al. 2021). Furthermore, this
relationship is not one way but tightly coupled. Combining 13C- and 15N-labelling showed that the coral host
derived 99% of its total nitrogen from the endosymbiont, suggesting the host “farms” the endosymbionts
to efficiently exploit both C and N (Tanaka et al. 2018).
Interestingly, the fate of acquired nutrients appears to depend upon the source of the material. Isotope
labelling (13C and 15N) reveals that heterotrophic sources exhibit considerable internal exchange and
retention within the coral-algae symbiosis, whereas inorganic nutrients (that are photosynthetically fixed
by endosymbionts) are rapidly used and respired to meet more immediate metabolic demands (Hughes et
al. 2010, Tremblay et al. 2015). The release of DOM by corals can constitute a considerable loss of fixed
material, corresponding to approximately 5% of net photosynthetic production of endosymbionts as shown
by 13C tracer accumulation experiments (Tanaka et al. 2009). This has been corroborated elsewhere; similar
work has estimated coral carbon losses due to DOM release is equivalent of 28% of gross carbon fixation
(Tremblay et al. 2012).
With the advent of ever more-sophisticated technology, exploring the spatial structuring of metabolic
processes within coral tissues is now possible. Notably, the combination of isotopic labelling and nanoscale
secondary ion mass spectrometry (i.e. NANOSIMS) has revealed the variation in net carbon fixation rates
between individual cells of Symbiodiniaceae, with an average sixfold decrease between upper and lower
tissue layers within individual polyps (Wangpraseurt et al. 2016). These combined technologies have also
helped disentangle the rapid nutrient uptake dynamics within endosymbionts (Kopp et al. 2013, Kopp et al.
2015). Such approaches can be further expanded with, e.g. simultaneous immunofluorescent microscopy to
correlate presence of isotopically-labelled labile nutrients with associated proteins and enzymes to further
elucidate metabolic pathways (Loussert-Fonta et al. 2020). These technological advances have the potential
to greatly expand current understanding of the molecular-level underpinning of coral-algae symbioses.
4.4. Drivers of mixotrophy
The mechanisms that influence the strength of coral-algae symbiosis are key to the wider coral reef
ecosystem. Therefore, understanding how coral mixotrophy changes with different factors provides insight
into how they may be best managed and conserved in a changing world. SI studies that explore potential
drivers of mixotrophy in corals can generally be categorised by the nature of the driver(s) of interest:
whether mixotrophy is impacted by the external environment (exogenous) or influenced by traits that are
particular to the studied host or symbiont (endogenous).
4.4.1. Exogenous factors
Given the photosynthetic underpinning of coral-algae symbiosis, depth represents a strong natural abiotic
gradient which can impact autotrophic efficiency due to, among other things, diminishing ambient light
levels (see 7.2 Environmental Drivers: Natural Drivers). The nutritional history of host corals (fed versus
starved), which is driven by the temporal dynamics of prey availability, may also play a role in mixotrophy.
In isolation, 15N labelling indicates that nutritional history does not appear to affect the assimilation
efficiency of heterotrophic feeding by corals (Piniak and Lipschultz 2004). However, δ13C of fatty acids
reveals that recent starvation, when compounded with thermal stress, leads to reductions in chlorophyll
and maximal photosynthetic efficiency in coral tissues, resulting in respiration of storage fatty acids in order
to maintain coral metabolism (Tolosa et al. 2011). This highlights the compounding nature of
environmental factors (see 7.2 Environmental Drivers: Natural Drivers).
Bleaching events, which are induced by a variety of external stresses, are projected to continue to increase
with ongoing climate change (Hughes et al. 2017). Given the loss of the autotrophic symbionts during such
episodes, the impact on host energetics is likely to be significant. Early SI work suggested however that
bleaching does not alter the ratio of heterotrophic vs autotrophic dependency. This was inferred from
similar δ13C values in two corals (Porites compressa and Montipora verrucosa) and their endosymbionts
taken from paired samples of bleached and non-bleached tissue in the field in Hawai’i (Grottoli et al. 2004).
This was in contrast to pulse-chase experiments (13C) on the same species (P. compressa) and a congener
(Montipora verrucosa cf. M. capitata) that showed reduced assimilation of autotrophically derived carbon
in bleached corals, but with assimilation of heterotrophic sources remaining similar in bleached versus non-
bleached corals (Hughes et al. 2010). More recent work using bulk SI data (δ13C and δ15N) on the same two
species also did not indicate increased heterotrophic nutrition post-bleaching (Wall et al. 2019). The δ13C
data also suggest corals may undergo biomass compositional changes when bleached and directly after
(Wall et al. 2019), possibly as they catabolize their stores of 13C-enriched lipids (Grottoli and Rodrigues
2011). Heterotrophic carbon sources are likely important for coral recovery as they are predominantly used
to replenish coral lipids (Baumann et al. 2014), which are used to maintain metabolism during thermal
stresses (Tolosa et al. 2011). For longer-term responses of corals to bleaching, see 7.2 Environmental
Drivers: Natural Drivers.
4.4.2. Endogenous factors
The diversity in form observed across Scleractinia, and even within species across for example depth
gradients (Einbinder et al. 2009), suggests ecological trade-offs associated with different host
morphologies. Previous non-SI work exploring coral morphology-feeding relationships suggested that coral
surface to volume ratio (S/V) and polyp size might determine the importance of light or zooplankton
capture. Branching corals have maximum S/V ratios and small polyps so are best suited for light capture,
while corals with lower S/V ratios generally have larger polyps suiting them to zooplankton capture (Porter
1974, Porter 1976). Subsequent non-SI work by Wellington (1982) corroborated that tentacle size was
important for determining the degree of hetero- or autotrophy (i.e. corals with larger tentacles use more
zooplankton), but could not confirm the coral morphology-feeding relationships. Some SI data have now
supported this hypothesis. δ13C values in coral tissues and endosymbionts from 14 Red Sea coral species
indicated increased relative rates of autotrophy in branching corals with smaller polyps compared to
massive species with larger polyps, attributed to reductions in carbon-limitation associated with increasing
surface area (Levy et al. 2006). Such a trend with host morphology has been further corroborated by Xu et
al. (2020) using δ13C. However, in contrast, a non-isotope feeding study found no relationship between
coral feeding rates and polyp size (Palardy et al. 2005), while Hoogenboom et al. (2015) using bulk δ13C and
δ15N found that feeding rates were instead highest in branching corals with smaller polyp sizes. This
suggests more research is needed to disentangle coral morphology-feeding relationships. More recently,
corals that were more autotrophic, implied by similarity in host tissue and symbiont bulk δ13C and δ15N,
had a negative relationship with polyp size but also bleaching resistance, suggesting they may be more
susceptible to increasing water temperatures (Conti-Jerpe et al. 2020).
While less conspicuous, the different genera within Symbiodiniaceae that form symbioses with corals can
also influence host metabolism due to their differing functional responses to environmental conditions. For
example, isotope labelling (13C and 15N) revealed that holobionts hosting former clade C (genus
Cladocopium) have increased uptake rates of inorganic nitrogen under non-thermal stress conditions
compared to holobionts with former clade D (genus Durusdinium) (Baker et al. 2013a). This can lead to the
competitive exclusion of clade D under normal conditions despite this clade resulting in increased carbon
acquisition during periods of thermal stress (Baker et al. 2013a). Similarly, Ezzat et al. (2017) demonstrated
increased carbon acquisition by holobionts with clade C symbionts compared to clade A under low
irradiance levels using isotope labelling (13C and 15N), but this appeared to be due to increased
heterotrophic capacity by corals hosting clade C endosymbionts. However, other non-isotope studies did
not find an influence of symbiont genus on host metabolism (Matthews et al. 2020). Endosymbiont
communities do influence coral SI values though. Coral colonies dominated by clade D have lower δ13C in
both host and symbiont tissues compared to colonies dominated by clade C (clade C host and
endosymbiont δ13C 1.6 and 1.5 ‰ higher than clade D in summer); but these differences were inferred to
be driven by light availability rather than coral feeding (Wall et al. 2020).
The strong focus on adult coral colonies can ignore the importance of vulnerable larval stages that support
the maintenance of coral reefs through successful recruitment and ontogenetic development. In an effort
to better understand planktonic coral larvae metabolism, Alamaru et al. (2009b) conducted feeding
experiments with various potential food sources – phytoplankton, zooplankton and bacteria - but failed to
observe active feeding or heterotrophic uptake via δ13C and δ15N SI data. This is despite planulae larvae
having an oral opening. They therefore inferred that coral larvae rely wholly on lipid reserves or
photosynthates from symbionts that are already present in the endoderm. This was further elaborated by
pulse-chase experiments using labelled 13C-bicarbonate and 15N-nitrate conducted by Kopp et al. (2016),
who determined that there is minimal contribution by symbionts to host metabolism, demonstrating that
coral larvae are essentially lecithotrophic pre-settlement.
4.5. Metabolism in Non-Hard Coral Symbioses
A significant number of SI studies have explored the metabolic underpinning of other non-coral symbiotic
groups, revealing complex physiologies. Sponges possess an intricate symbiotic system due to the diversity
of the microbiomes they can host, including photosymbionts (Davy et al. 2002, Weisz et al. 2010). However,
the strength of the symbiotic dependency appears to vary between host sponge species, with both tight
and weak metabolic couplings being observed (Freeman et al. 2015). Isotopically enriched seawater with
13C and 15N tracers has been used to demonstrate nutrient transfer between microbes and host sponges,
the rate of which appears dependent on symbiont identity and irradiance rather than overall symbiont
abundance (Freeman et al. 2013). Interestingly, labelled 15N-ammonium and 13C-bicarbonate revealed that
coral-excavating sponges often host both Symbiodiniaceae and prokaryotic symbionts, with the former
undertaking significant inorganic nutrient fixation and transfer to host bioeroding sponges, but the latter
not contributing to nutrient assimilation (Achlatis et al. 2018). Conversely, 13C- and 15N-enriched DOM show
that sponge hosts can directly take up and utilise DOM and subsequently transfer significant dissolved
organic waste products to symbionts (Achlatis et al. 2019). This can constitute the entire nitrogen budget of
hosted algae (Davy et al. 2002), in a similar fashion to coral hosts. Pulse chase experiments with isotopically
labelled 13C‐ and 15N‐enriched coral‐ and algal‐derived DOM show that various sources of DOM are utilised
by sponges, but algal derived sources are predominantly transferred to the microbiome while coral derived
DOM is used directly by the sponge host (Rix et al. 2017). Interestingly, bulk SI (δ13C and δ15N) and isotope
labelling (13C and 15N) revealed that the encrusting sponge, Terpios hoshinota, which kills corals by
overgrowing them, does so for space, not food; in the new sponge tissues only 9.5% of the C and 16.9% of
the N was derived from the corals underneath (Syue et al. 2021). In contrast, contact association with
macroalgae appears to competitively inhibit sponges, with SI enrichment experiments (13C and 15N)
demonstrating nitrogen transfer from sponge to macroalgae (Easson et al. 2014). As with coral holobionts,
changes in the surrounding environment can alter the dependency of sponge hosts on photoautotrophic
symbiont production. Recent bulk and amino acid CSIA work in the Caribbean demonstrated increasing
heterotrophy with depth for sponges, but highlighted species-specific trends in host utilisation of POM and
DOM, and internal translocation of these (Macartney et al. 2020).
The host-symbiont relationship in gorgonians has been the focus of more recent interest in holobiont
metabolism utilising SIs, likely due to their increasing presence in some coral reef systems (Rossi et al.
2020). While overall autotrophic reliance varies seasonally and with species, endosymbionts can deliver the
majority of energetic demands (> 95%), with heterotrophically acquired carbon sources contributing less
than 5% year-round for gorgonian species examined in the Caribbean (Rossi et al. 2020). Conversely,
gorgonians examined in Taiwan appear to be highly dependent on heterotrophic inputs based on host and
symbiont δ13C and δ15N values, with relatively little energetic benefit garnered from their endosymbionts
(Hsu et al. 2020). Similarly, recent work on Antipatharian soft corals (black corals) using isotope labelling
(13C and 15N) has demonstrated that they can use a range of different food sources, likely allowing them to
exploit seasonal fluctuations in prey concentrations (Rakka et al. 2020). These studies highlight the diversity
in energy acquisition within this group. While environmental sensitivities to gorgonian symbioses have yet
to be thoroughly explored, depth appears to have little impact on gorgonian tissue δ15N values (change in
only 1.4 ‰ over 20 m), implying limiting physiological effects associated with ambient light (Baker et al.
2011). Further, short-term (seven day) nutrient enrichment does not appear to significantly impair the
symbiosis between gorgonians and their dinoflagellate endosymbionts, but can result in increased
chlorophyll content and algal densities within hosts (McCauley and Goulet 2019).
Other forms of symbiotic relationships, while lesser studied, are likely commonplace on coral reefs and
constitute important components to ecosystem functioning (Pinnegar and Polunin 2006). Anemones may
also host Symbiodinium as a source of autotrophic nutrition, however SI labelling (13C and 15N) highlights
the competitive nature of resource acquisition by both host and endosymbiont, implying a less stable
symbiotic association compared to true coral holobionts (Radecker et al. 2018). Carbon and nitrogen SI
data from both lab and field isotope-labelling feeding experiments have been used to demonstrate nutrient
transfer from anemonefishes to both fish-hosting anemones and their endosymbionts forming a tripartite
symbiosis (Cleveland et al. 2011). Parmentier and Das (2004) examined relationships between four species
of apparently parasitic carapid fishes and their echinoderm hosts using bulk SIs, but only found evidence
for feeding on host tissues for one species (Echeliophis gracilis), suggesting commensal associations for the
other three fishes. Similarly, while shallow-water black corals host a variety of macrosymbionts, bulk δ13C
and δ15N reveal that they do not use their host as a main food source, but instead use the coral’s structure
to access nutrition from the water column (Terrana et al. 2019). True parasitic-host relationships have also
been explored using bulk SIs in reef fish and gnathiid ectoparasites (Demopoulos and Sikkel 2015). Finally,
upscaling from individual metabolic processes to whole community metabolic functioning can be facilitated
through SI approaches. Spatial differences in isotopic discrimination of overlying seawater DIC are
attributable to the varying ratio of calcification:primary production of the underlying ecological community;
e.g. ~5‰ higher δ13CDIC discrimination for portions of the reef with more non-calcifiers compared to
portions of the reef with more calcifiers (Koweek et al. 2019).
5. Trophic niches
Ecological niches are multidimensional spaces defined by environmental conditions and resource
utilisations that are occupied by an organism (or population) where their survival curves are optimised
(Hutchinson 1957). The trophic niche relates to the array of food items consumed by an organism, which
constitutes a subset of its overall ecological niche. Understanding an animal’s resource use, and how this
varies within and among species and guilds, helps determine its trophic function within an ecosystem and
how this might respond to environmental change. Increasingly, studies are using SI to estimate an animal’s
trophic niche. Isotope data are typically presented on a bi-plot using the isotope values (δ‐values) as
coordinates (Fig. 3) (although note that tri-isotope plots are now being used; Skinner et al. 2019a). The area
(δ‐space) of these coordinates is determined to be the animal’s isotopic niche, providing an understanding
of its trophic ecology by reflecting some aspects of their trophic niche (Fig. 3) (Newsome et al. 2007). For
example, the size of the isotopic niche and position of the individual coordinates indicate intraspecific
variation in resource use, known as the niche width (Bearhop et al. 2004). SI approaches to trophic niche
determination are the newest of our defined topics to emerge in SIs on coral reefs (first paper published in
2007) and it has expanded rapidly since then (n = 48; Fig. 1). This is likely due to the instrumental Layman et
al. (2007) and Jackson et al. (2011) papers which have brought community SIA into the foreground.
However, although related, trophic niches and isotopic niches are not interchangeable, and care should be
taken when using these terms (see Reddin et al. 2018, Hette-Tronquart 2019). In some cases, variation in SI
values may be independent of diet, e.g. where habitat-derived isotopic baselines differ (Fig. 3; Fig. 4).
Organism foraging behaviour and habitat use must also be considered before converting an isotopic niche
to an ecological or trophic niche (Flaherty and Ben-David 2010).
5.2. Isotopic niches
To date, coral reef isotopic niche studies have predominantly explored resource partitioning within guilds,
likely as the high densities of species with seemingly similar functional roles raises questions as to the
mechanisms of their coexistence. This can be elucidated by SI data, revealing dietary variation and
intricacies which were previously overlooked. For example, while traditional techniques suggest that
herbivorous surgeonfish and parrotfish consume similar production sources on reefs, bulk δ13C and δ13N SI
data reveal complex trophic ecologies, indicating a high level of functional diversity (Plass-Johnson et al.
2013, Dromard et al. 2015). Similarly, isotopic niche overlap (see Fig. 3) among sympatric spotted
(Panulirus guttatus) and Caribbean (P. argus) spiny lobsters is minimal, with each utilising different food
sources and occupying unique TPs (evidenced by δ15N) in the food web (Segura-García et al. 2016). Higher
up the food chain, coral reefs have high biomasses of predators with seemingly similar traits and trophic
ecologies. Yet δ13C and δ13N reveal that sympatric species of coral trout Plectropomus laevis and P.
leopardus, have resource uses that differ (Matley et al. 2017, Matley et al. 2018). They likewise also vary
from other predatory teleosts (Lethrinus miniatus and Lutjanus carponotatus), implying degrees of trophic
specialisation in coral reef mesopredators (Frisch et al. 2014). Indeed, in the Maldives, the resource uses of
seven sympatric teleost reef predators across multiple families vary both within and among species and
spatially, with δ34S acting as a useful third isotope further differentiating individual feeding behaviours
(Skinner et al. 2019a). Furthermore, on Bahamian reefs, while isotope biplot data (δ13C and δ15N) of the
invasive lionfish (Pterois spp) and a native snapper Lutjanus griseus appeared to overlap considerably, their
core isotopic niches did not, suggesting competition was not as high as initially perceived (Layman and
Allgeier 2012). These predators appear to occupy the same functional roles within their guilds, but by
partitioning trophic resources both spatially and temporally, inter- and intraspecific competition is likely
reduced, thereby facilitating their coexistence and altering previously assumed ecological roles (Dale et al.
2011, Gallagher et al. 2017, Matich et al. 2017, Curnick et al. 2019, Skinner et al. 2019a).
Individual specialisation within a population is a mechanism through which sympatric individuals within an
age or size class may reduce competition for resources by focusing on a narrower set of resources than that
of the population as a whole (Bolnick et al. 2003, Araújo et al. 2007, Araújo et al. 2011). Occurrences of
individual specialisation are expected to be greater where resource diversity is high, as there is increased
ecological opportunity (Semmens et al. 2009, Araújo et al. 2011). Coral reefs, with their high rates of
biodiversity, should therefore be prime locations for occurrences of individual specialisation. This is
compounded for populations with access to two or more adjacent resource pools (e.g. benthic and pelagic)
or habitats (e.g. reef and seagrass), as there is a greater array of potential resources (Araújo et al. 2011,
Matich et al. 2019). SIs are a powerful tool which can quantify these specialisations and are less costly and
labour-intensive than long-term dietary records (Newsome et al. 2009). To date, studies investigating
individual specialisation using SI on coral reefs have concentrated on elasmobranchs and large predatory
teleosts (Shipley et al. 2018, Shiffman et al. 2019, Skinner et al. 2019a, Wyatt et al. 2019). The degree of
specialisation across lower trophic levels is little explored. However, 34% of SI coral reef studies involve a
single species, which suggests there is sufficient opportunity to investigate individual specialisation more
generally on coral reefs. Indeed, there is some evidence of such specialisation at lower trophic levels; bulk
δ13C and δ13N SI show that damselfish, Dascyllus aruanus, are more specialised when colonies are larger,
suggesting local abundances drive intra-group competition, which is then modulated by individual
specialisation (Frédérich et al. 2010). Groups of damselfish with narrower trophic niches (evidenced by
their isotopic niches using δ13C, δ13N, and δ34S) also have lower genetic diversity, highlighting potential links
between population- and trophic ecology (Gajdzik et al. 2018). Exceptional variation in feeding strategies
from heterotrophy to autotrophy at scales of metres to kilometres among colonies of the hard coral
Pocillopora meandrina has also been identified using δ13C of essential amino acids, showing no relationship
with site or depth (Fox et al. 2019). Although consumer dietary specialisation does not occur in all systems
or between all species (Gallagher et al. 2017), it warrants further study, particularly in systems where
resources are fluctuating. If consumers partition resources, their ecological roles may be vastly different,
which could be masked by traditional species- or guild-level categorisations.
Attempts by ecologists to categorise species functional traits to better understand ecosystem function
conflicts with the natural variability inherent in complex systems such as coral reefs. SI data have
successfully been used to refute some strict dietary classifications of reef organisms derived from
traditional ecological studies using gut contents data and in situ observations. For example, in Papua New
Guinea, of seven damselfish species sampled, their δ13C and δ15N SI values and corresponding isotopic
niches, indicated that none were strict herbivores, despite traditionally being classified as such (Eurich et al.
2019). In fact, using δ13C and δ13N damselfish have relatively distinct isotopic niches, reflecting varying
degrees of planktonic to benthic reliance (Frédérich et al. 2009, Lepoint et al. 2016, Olivier et al. 2019).
Similarly, cardinalfishes, thought to be generalist carnivores based on stomach contents data, are sustained
by production sources from across a benthic-planktonic gradient, and δ13C and δ13N indicate distinct
species-specific isotopic niches using (Frederich et al. 2017). Indeed, community-wide δ13C and δ15N data
show that many strictly categorised reef fish rely on production sources outside their putative diet source
and this spans multiple trophic levels (Zhu et al. 2019), highlighting how narrow functional group
categorisations should be applied with caution. However, care should be taken when interpreting isotopic
spread as solely due to diet variation; spatiotemporal differences in production source isotopic baselines
and a myriad of other drivers may also cause such variations (Fig. 3 and Fig. 4; and see 7. Environmental
In some cases, there may be greater redundancy among different guilds rather than within them; δ13C and
δ15N SI values of muscle tissue from reef sharks and large teleost mesopredators indicated that they occupy
the same isotopic niche on the Great Barrier Reef, suggesting they perform similar functional roles (Frisch
et al. 2016). Similarly, in the Hawaiian archipelago, there was considerable overlap in the δ13C and δ15N
values of reef sharks and larger teleosts, highlighting a degree of functional redundancy which could
contribute to ecosystem stability (Hilting et al. 2013, Roff et al. 2016). However, a study further north on
the Great Barrier Reef using multi-tissue δ13C and δ13N data (muscle, blood, and plasma) to compare
resource use of reef sharks and large predatory teleosts identified significant trophic separation (Espinoza
et al. 2019). While Frisch et al. (2016) call for apex predator reef sharks to be reassigned as high-level
mesopredators, Espinoza et al. (2019) suggested there is substantial diversity in their trophic ecologies and
likely wider functional roles. This suggests that different localities may have populations with different
behaviours. Beyond these studies of reef mesopredators, few studies compare isotopic niches among
differing guilds on coral reefs, likely because they are expected to have different dietary strategies. For
example, overall, the structure of the reef fish assemblage remains fairly consistent, with herbivores
occupying lower trophic levels (reflected by low δ15N), while carnivores and piscivores feed across a
broader range of trophic levels and resources (Carassou et al. 2008, Yang et al. 2012). Most studies
comparing niches and categorisations do so across similar species groups; of the 47 articles assigned to the
Trophic Niche topic, 64% focus on reef fish and 15% on elasmobranchs. Few, if any, compare resource use
across broader groupings (e.g. some invertebrates may feed on the same prey as some reef fish; Zapata-
Hernández et al. 2021), so wider competitive feeding relationships may be missed.
Multi-tissue SI data can reveal detailed feeding strategies and how these fluctuate over different
timescales, particularly regarding individual specialization within a population (Bond et al. 2016). For
example, a multi-tissue (plasma, cartilage, and faeces), multi-isotope approach identified consistent
individual specialization on either oceanic or coastal prey in whale sharks, Rhincodon typus (Wyatt et al.
2019). Yet, they are infrequently utilised on coral reefs. Of the 29% of identified SI reef studies employing a
multi-tissue approach, only 9% measure multiple whole tissue types, e.g. muscle and liver, of the same
individual consumer to elucidate short- and longer-term fluctuations in resource use. Instead, 20% of multi-
tissue studies focus on exploring the trophic niches of mixotrophic holobionts, e.g. host soft tissue and
endosymbionts. For example, the degree of overlap in the isotopic niches (determined using bulk δ13C and
δ15N) of seven different genera of coral hosts and their endosymbionts was linked to coral trophic strategy;
higher overlap indicated resource sharing between host and endosymbionts (i.e. greater host autotrophy)
while lower overlap indicated less resource sharing (i.e. greater host heterotrophy) (Conti-Jerpe et al.
2020). While multi-tissue analyses may offer additional insight, comparing isotopic niches among guilds
helps understanding of how resource use and partitioning are structured within the wider community. One
of the few studies using SIA to investigate trophic interactions at the community level confirmed previous
hypotheses that the sea cucumber Stichopus herrmanni has a top-down influence (consistently higher δ15N
across seasons) on its meiobenthic prey in a lagoon system on the Great Barrier Reef (Wolfe et al. 2021).
For inferences to be made about resource use and trophic positions with confidence, knowledge on diet-
tissue discrimination factors (hereafter ‘trophic discrimination factor’ (TDF), usual notation is Δ) between a
consumer and their diet are necessary (see reviews referenced in 1. Introduction; Boecklen et al. 2011,
McCormack et al. 2019, Whiteman et al. 2019). The standard TDFs that are typically applied to bulk carbon
(~0.5) and nitrogen (~3.4) are averages drawn from broader syntheses of laboratory experiments, but are
known to vary among species, by life stage and season, among other factors (Wyatt et al. 2010a, Wyatt et
al. 2019). For example, the estimated Δ15N between the hard coral Porites lutea and its food source is only
1‰ (Rangel et al. 2019), three times lower than the commonly applied value. Average TDF values may be
appropriate for studies at the ecosystem level, but greater resolution specificity is required for individual
species. To date, very few studies (n ≈ 5) have empirically determined species-specific TDF for coral reef
organisms, despite a call for more lab studies to do so over a decade ago (Wyatt et al. 2010a). Evidence
suggests that typically employed TDFs may not be wholly applicable to coral reef ecosystems: feeding
observations and modelling indicated that three herbivorous reef fish have consistently higher Δ15N (model
estimates ranged from 4.30‰ to 5.68‰) than the accepted value of 3.4‰ (Mill et al. 2007). Furthermore,
a comprehensive study using CSIA of >200 samples from 47 species of marine teleosts including many reef
fish found that the estimated TDFAA was significantly lower (2‰) than previously accepted values for CSIA
(Bradley et al. 2015). Given the huge diversity of organisms on coral reefs, a greater understanding of how
these values vary among species and compounds, and with other factors such as seasonality, is required
(Whiteman et al. 2019) to improve understanding of coral reef trophic interactions. One such avenue might
involve parasites (an understudied group on coral reefs), which often reflect their host’s feeding ecology
and TP (indicated by their δ13C and δ15N values) (Jenkins et al. 2018). This suggests future research could
explore this relationship to better understand the complex trophic interactions and feeding strategies that
could affect reef organism’s TDF values, but SI data between fish hosts and their parasites are likely to be
complicated (Pinnegar et al. 2001).
As time-integrated values of the major source reliance and TP of an organism in the food web, SI data
cannot generally be used to identify specific prey. For example, while bulk δ13C and δ15N values were
similar across four species of mesopredatory teleosts, stomach contents data revealed substantial
differences in the types of prey taxa consumed (Ashworth et al. 2014). Similarly, among 21 species of
butterflyfish, gut contents data and in situ feeding observations were required to resolve finer scale
differences in prey items (Nagelkerken et al. 2009). SIs are therefore not necessarily suitable at
differentiating ecological niche differences that vary over smaller scales, especially when isotopic
differences between sources are small. SIs are also unable to distinguish between behavioural differences
in feeding: two sympatric species of fish that have approximately the same diet, but with one feeding
nocturnally while the other diurnally, would occupy the same position in isotopic space (given the same
TDFs). It is therefore often useful to combine multiple methodologies to obtain a comprehensive overview
of the complexities of an organism’s feeding strategies across different temporal and spatial scales on coral
reefs. As researchers become more accustomed to using SI data to understand food webs, the number of
isotopic niche studies on coral reefs is increasing, but other data, including traditional techniques, often
complement and add to the inferences deduced from SI data alone (e.g. inclusion of fatty acids, see Dethier
et al. 2013).
5.3. Drivers of isotopic niche variation
Isotopic niches may vary spatially, particularly in diverse systems such as coral reefs, helping to explain how
species partition resources (Fig. 3). This variation can occur across relatively large scales: across the
Southern Line Islands, isotopic niche widths (from δ13C and δ15N) of reef fish populations change in relation
to available primary production (Miller et al. 2019). They may also change at much smaller scales: bulk δ13C
and δ15N data show that several reef shark species have different patterns of resource use among coastal
areas of Florida (Shiffman et al. 2019) and dolphins have varying levels of coastal vs offshore resource use
in Panama (Barragan-Barrera et al. 2019). While isotopic niche variation can be driven by factors other than
dietary preference (Fig. 3), understanding the relationships between SI values and these drivers is non-
trivial. For example, predator biomass influences the dietary diversity (represented by the δ13C and δ15N
isotopic niche area) of two herbivorous reef fish in the Florida Keys, likely by causing a change in their
group foraging activities and perceived predation risk (Catano et al. 2014). Other biotic influences on
isotopic niches include the presence of parasites: ectoparasitic isopods affect the resource use (inferred
through δ13C and δ15N) of grunts, likely causing them to feed in different localities to uninfected fish, and
changing their condition (Welicky et al. 2017). On reefs in New Caledonia, partitioning of resources
indicated by bulk δ13C and δ15N data by two species of sea krait indicated habitat-based dietary divergence
(Brischoux et al. 2010). Environmental conditions may also influence isotopic niches: various flow
conditions led to differing physiological adaptations of two sympatric bonefish species based on δ13C and
δ18O data (Haak et al. 2018). These studies highlight how a range of factors may influence an organism’s
isotopic niche at any one time and underline the inherent difficulty in extrapolating findings from one
location to another. Other factors which may influence isotopic niches include growth rate, metabolism,
and diet quality, however to our knowledge, there are no studies investigating these relationships on coral
reefs to date. With few studies investigating the effect of multiple variables or drivers, or the indirect
relationships occurring between them, the ability to generalise such patterns across coral reef ecosystems
Anthropogenic impacts can influence isotopic niches and resource use, as habitats degrade or prey groups
fluctuate, but such responses vary among species. For example, corallivores had smaller δ13C and δ15N
isotopic niches at a degraded reef site compared to a healthy reef site, likely reflecting a narrower pool of
available resources from a loss of live coral cover (Letourneur et al. 2017). In contrast, invertivores had
larger isotopic niches, and herbivores and zooplanktivores displayed no difference (Letourneur et al. 2017).
Similarly, δ15N in spiny lobster muscle tissue did not differ between reefs of different levels of degradation,
with no apparent trend with the loss of habitat structural complexity (Lozano-Álvarez et al. 2017). The
impact of reef habitat degradation on organic matter sources and the trophic ecology of reefs in the
Caribbean (where 14% of SI reef studies have been conducted; Fig. 2) was quantified by Morillo-Velarde et
al. (2018), on the basis of switches or widening in carbon sources as evidenced by reef fish δ13C in degraded
habitats. This indicates that there is a degree of trophic plasticity, with some groups potentially adapting to
degradation while others do not, but there may be a cost to this adaptation. As the biomass of planktonic
damselfish decreased on a degraded reef, δ13C and δ15N of the spotted coral grouper, Plectropomus
maculatus, indicated it switched to foraging on herbivorous damselfish. This was linked to long-term
declines in the groupers’ growth rate, fecundity, and survivorship (Hempson et al. 2017, Hempson et al.
2018), highlighting potential negative, long-term consequences of anthropogenic impacts across the wider
coral reef food web.
6. Fish diet variation and habitat connectivity
In coral reef SI studies, reef fish are the dominant focal taxa (36% of all articles; Fig. 5B) and a major area of
research involves using SIs to determine how their habitat and resource use varies spatially and throughout
their life cycle (n = 44 identified studies; Fig. 3). Although this topic includes one of the earliest known
papers using SIs on coral reefs (Fry 1982), much of the bulk of the work on fish trophodynamics was
conducted from the late 2000s onwards, with a focus on the western Atlantic (n = 16) (Fig. 2B). While there
are thousands of fish living on coral reefs, only few have been the focus of multiple SI studies, namely the
whitetail damselfish Dascyllus aruanus (n = 5), leopard coral grouper Plectropomus leopardus (n = 6),
blackspot snapper Lutjanus ehrenbergii (n = 5) and the red lionfish Pterois volitans (n = 5). Similarly, coral
reef SI studies focus on common groups (e.g. damselfish, surgeonfish, groupers, snappers), with few to
none investigating the trophodynamics of well understood and often cryptic groups such as blennies and
6.2. Ontogenetic habitat shifts
Ontogenetic habitat shifts are common in marine organisms as they strive to maximize their fitness
strategies (Schmitt and Holbrook 1985, Holbrook and Schmitt 1988, Dahlgren and Eggleston 2000). In coral
reef ecosystems, it is common for juvenile reef fishes to spend time in a nursery habitat such as mangroves
or seagrass meadows, prior to migrating to the reef (Fig. 3). SIA can be a cost-effective tool to pinpoint
when and how these changes occur by analysing the SI values of juveniles through to adults across the
nursery and reef habitats. This allows the timing of the ontogenetic habitat and diet shifts to be estimated
(Cocheret de la Morinière et al. 2003, Frédérich et al. 2012, McMahon et al. 2012, Berkström et al. 2013).
For example, the δ13C of juvenile snappers in mangroves reflect mangrove habitat (-23 to -17 ‰), while
individuals on the reef shift to a reef δ13C signature with increasing body size (-16 to -8 ‰), indicating that
the smaller individuals within reefs have migrated there from the mangroves (Nakamura et al. 2008).
Acoustic telemetry can be used to further support inferences from SI data; δ13C of fin tissue and acoustic
tracking of the schoolmaster snapper, Lutjanus apodus, revealed that they move from bays to coral reefs as
they get larger (i.e. smaller fish mean δ13C -16.7 ‰, larger fish -12.2 ‰) (Huijbers et al. 2015).
Fish otoliths, as an incrementally grown, metabolically inert biological structure, provide the ability to
determine when ontogenetic shifts occur within a single individual, and have been utilised across several
coral reef SI studies (n = 13). As surface otolith material is continuously deposited with age, a time-series of
SI data can be derived by sampling progressive segments from the core (reflecting larval life stages) to the
edge (age of the fish just prior to otolith sampling). Changes in SI values will reflect potential changes such
as in habitat, diet, or physiology. In the Red Sea, otolith δ13C essential amino acid values of the blackspot
snapper, Lutjanus ehrenbergii, across a gradient from coral reefs to seagrass were influenced by the
habitats the fish resided in, offering an opportunity to track their movements across the isoscape
(McMahon et al. 2011). In addition to δ13C, some studies (6%; Fig 2B) use oxygen isotopes (δ18O) in otolith
segments (Blamart et al. 2002), as they vary with temperature and salinity, thus providing information on
the external environment. Both δ13C and δ18O in otolith core and edge segments of the trumpet emperor,
Lethrinus miniatus, on the Great Barrier Reef revealed contrasting movements of juveniles across different
latitudes and corresponding isotopic environments (Currey et al. 2014). Similarly, δ13C and δ18O of gray,
Lutjanus griseus, and yellowtail, Ocyurus chrysurus, snapper sub-adult otoliths in Florida determined the
distinct nursery areas in the Florida Bay that the fish had migrated to the reef from (Gerard et al. 2015).
Otolith SI values can be incorporated into spatial simulation models, revealing that the geographic
distribution of the nursery areas plays an important role driving the spatial distribution of the adults on the
reefs (Hujibers et al. 2013). Recently, fish eye lenses have also been advocated as an alternate,
metabolically stable, incrementally grown structure with which to track resource and habitat use shifts with
SIs across different life stages (Quaeck-Davies et al. 2018, Curtis et al. 2020, Vecchio and Peebles 2020).
Clearly, SI data can be used to delineate fish movement patterns, tracking animal movements in the
absence of electronic tagging, and identifying nursery habitats that should be prioritized for management;
habitat impacts may disproportionately affect certain life stages thus influencing populations elsewhere,
e.g. recruitment of juveniles to reefs. However, if the animals move through the habitat before an isotopic
signature can be recorded, or if the habitats are isotopically indistinguishable, then movement information
may be missed (McMahon et al. 2013). As such, use of traditional approaches in conjunction such as
tagging (e.g. Huijbers et al. 2015), spatial simulation (e.g. Hujibers et al. 2013), and fish size distribution
modelling (e.g. Mumby et al. 2004) should be considered.
6.3. Body size
Multiple studies indicate that variation in resource use may occur as a function of body size (e.g. Layman et
al. 2005, Romanuk et al. 2011). Indeed, many predatory fishes across various biomes tend to feed at higher
TP (evidenced by higher δ15N) as body size increases, a pattern that also holds true for coral reef systems
(Layman et al. 2005, Greenwood et al. 2010). For example, in Moorea, French Polynesia, plasma of blacktip
reef sharks, Carcharhinus melanopterus, was enriched in δ15N with increasing body size but there was no
change in δ13C, suggesting they were feeding on higher trophic level prey but reliant on the same basal
production sources (Matich et al. 2019). Such trends are however far from ubiquitous in coral reefs. For
blacktip reef sharks at Palmyra Atoll, there was a positive relationship between body size and δ15N in one
lagoon, but no relationship with body size at all in another, suggesting that the two shark populations have
different trophic ecologies despite their proximity to one another (Papastamatiou et al. 2010). Similarly, in
the Caribbean reef shark Carcharhinus perezi there was no relationship between δ15N and body size but a
significant positive relationship with δ13C, implying larger individuals relied more on lagoonal food sources
with increasing size rather than feeding at higher trophic levels (Bond et al. 2018). Clearly, relationships
between predator TP and body size are not always positive or absolute (Gallagher et al. 2017, Matley et al.
2017, Shipley et al. 2018, Skinner et al. 2019a, Eddy et al. 2020). This is demonstrated by the invasive
lionfish in the Caribbean, which are smaller than native Nassau groupers, yet occupy the highest TP in the
study region (represented isotopically by higher δ15N) (O'Farrell et al. 2014). These studies highlight how
trophic ecology of fishes can vary with body size, indicating that an organism’s ecological role may be
complex and life stage-, as well as species-specific. However, for most herbivorous reef fish, TP
(represented by δ15N) remains relatively unchanged as body size increases (Cocheret de la Morinière et al.
2003, Greenwood et al. 2010, Plass-Johnson et al. 2013, 2015a). This is likely as, although they may access
different resources with increasing body size, the δ15N of these basal production sources remains fairly
Despite being lesser studied, similar trends with body size have also been observed in invertebrates. The
fireworm, Hermodice carunculata, a facultative corallivore, is enriched in δ15N and has fluctuating δ13C with
increasing body size, potentially reflecting feeding at higher trophic levels while diversifying resource use
across ontogeny (Wolf et al. 2014). It should be noted, however, that body size relationships with SIs
assume there is minimal change in isotopic baselines and growth/metabolic influences on isotopes
independent of diet (e.g. constant TDFs across ontogeny). Intra-specific and life-stage feeding
specialisations, such as these, may help promote population resilience to environmental change, as
individuals and populations are reliant on a wider range of resources across ontogeny. However, given that
many of the anthropogenic impacts on reef-fishes are size- and species-selective, with many targeted fish
often larger and functionally important (Benoît and Swain 2008, Lokrantz et al. 2009, Plass-Johnson et al.
2015a), this may have serious consequences for the trophodynamics of the coral reef food web.
6.4. Residency and population connectivity
SIA can reveal an organism’s residency within a habitat at various life stages, representing a more cost-
effective approach than tagging or tracking. This can be useful for management of certain species when
assessing the efficacy of protected areas. In Australia, δ13C and δ15N values of reef fish liver and muscle
revealed three species were resident in the area, while others had migrated from coastal riverine habitats
(Davis et al. 2015). In western Australia, δ13C and δ15N of muscle tissue of several reef sharks in coastal
habitats confirmed residency was high across four species (Speed et al. 2012). Examination of δ13C and δ15N
in lionfish, Pterois volitans, muscle tissue showed they did not move between mangroves and reefs; in fact
there was no overlap in habitat or resource use of lionfish between habitats, confirming them as site-
attached opportunistic foragers (Pimiento et al. 2015). SI data can also help assess the importance of
different habitats to more mobile consumers that have larger home ranges; for example one of the few
studies to use δ13C, δ15N, and δ34S, to examine habitat residency determined that the reef manta ray,
Manta alfredi, was heavily dependent on lagoonal resources, suggesting long periods of residency in the
lagoon (McCauley et al. 2014). Combining SI data with fatty acids further revealed that M. alfredi are
secondary consumers that rely on both epipelagic and demersal zooplankton, reflecting their ability to
access disparate resources through vertical and horizontal movements (Couterier et al. 2013). While SI data
can provide much needed insight into movement patterns and habitat usage, it should be noted that
connectivity ultimately depends on the spatial configuration of the seascape (Nagelkerken et al. 2008,
Rooker et al. 2018).
Larval population dynamics are inherently more difficult to study; larvae are hard to follow due to their
high natural mortality and rapid dispersal by ocean currents (Cowen and Sponaugle 2009). Nevertheless, SI
approaches provide an opportunity to track larval dispersal and understand population connectivity more
easily. Transgenerational isotope labelling involves injecting adult female fish with labelled isotopes (137Ba)
and results in consistently and permanently marked larvae throughout a reproductive season. This method
has minimal impact on the fish, their eggs, and larvae as they develop, or to those that consume them
(Williamson et al. 2009a, Williamson et al. 2009b, Roy et al. 2012, Cuif et al. 2014). By analysing the SI
values of the otolith cores of the new cohorts, the degree of connectivity and self-recruitment within a
population can be determined. In New Caledonia, this approach revealed that self-recruitment of
damselfish Dascyllus aruanus varied significantly between months and years, but was independent of the
proportion of self-recruits within the population (Cuif et al. 2015). This suggests that self-recruitment can
successfully indicate population openness but may not relate to population persistence (Cuif et al. 2015).
6.5. Habitat connectivity
There are important exchanges of organisms and energetic material between coral reefs and other
adjacent habitats that can be difficult to measure (Polis and Strong 1996, Huxel and McCann 1998). SI data
offer distinct opportunities to identify these cross-system linkages and quantify fluxes across habitat
boundaries; the flow of nutrients into and across shallow coral reef ecosystems is increasingly being
documented (Fig. 3). In shallow-water reef habitats in the Caribbean, δ13C suggests that benthic algae and
seagrass contribute 48-76% of carbon to reef fish (Fry et al. 1982), but in Moreton Bay, in eastern Australia,
dietary proportions vary with distance to adjacent mangrove and seagrass habitats (Davis et al. 2014). Such
patterns are not necessarily surprising, however they highlight that contributions of various exogenous
materials to reefs are likely to be site-dependent due to varying seascapes (Briand et al. 2015).
Nevertheless, looking at the wider spatial context can reveal less intuitive habitat linkages. In the Chagos
Archipelago, it has been shown that rats interrupt nutrient flows between pelagic, coral reef, and island
ecosystems. Rat-free islands had significantly greater densities of seabirds and therefore larger deposits of
nitrogen and subsequent runoff, leading to higher δ15N in the soil, macroalgae, turf algae, and reef fish
compared to rat-infested islands where seabird densities were lower (Graham et al. 2018). Sulphur isotopes
(δ34S) have rarely been applied to infer habitat connectivity but they may be well placed to distinguish and
help identify sources produced under anaerobic conditions, e.g. decomposition of mangrove organic
matter, due to the strong fractionations that occur during such processes (Okada and Sasaki 1998, Granek
et al. 2009). More widely, mangrove, microalgae, macroalgae, and seagrass exhibited greater separation in
δ34S compared to δ13C in a study conducted in Bocas del Toro (Panama) (Granek et al. 2009). Used together,
δ34S and δ13C suggested that mangrove-coral reef nutrients contributed up to 57% to the biomass of sessile
reef invertebrates (Granek et al. 2009). SI data thus point to mangroves as an important source of nutrients
for adjacent reef consumers (Carreón-Palau et al. 2013, Briand et al. 2015) despite their apparent low labile
organic matter content and nutritional quality (Granek et al. 2009).
While common in the deep-sea, chemosynthesis has rarely been explored as a potential source of nutrient
exchange for shallow water marine food webs (Table 3), yet SI data point to chemosynthesis being
important for some consumer species on coral reefs. δ34S, together with δ13C and δ15N, provides evidence
that chemosynthesis in lucinid clams supports 20% of the diet of Caribbean spiny lobster (Higgs et al. 2016).
They therefore play an important part in transferring the chemosynthetically fixed carbon into reef food
webs (Higgs et al. 2016). While there are undoubtedly many energetic connections between coral reefs and
adjacent habitats, the intricacies of many have yet to be fully identified. This should be addressed going
forward given that such subsidies are expected to contribute to wider ecosystem resilience and stability
(Bascompte et al. 2005).
Predators, typically being more mobile, often have greater opportunity to feed across ecosystem
boundaries, playing an important ecological role connecting distinct food webs (Fig. 3). While tracking
studies can identify these predator movements (e.g. Papastamatiou et al. 2009, Heupel and Simpfendorfer
2015), they cannot in isolation define the role of predators in nutrient cycling. This is in contrast to SI data
that offer an opportunity to track these energetic linkages. In Palmyra atoll, δ13C and δ15N from muscle
tissue of blacktip reef sharks, Carcharhinus melanopterus, grey reef sharks, C. amblyrhynchos, and red
snapper, Lutjanus bohar, indicated they relied on pelagic production sources from outside their primary
forereef habitats, playing a key role providing ecological coupling as cross-system foragers (McCauley et al.
2012). The reef manta ray, Manta alfredi, also constructs an important link between adjacent pelagic and
reef/lagoonal systems (evidenced by δ13C and δ15N) by feeding on pelagic zooplankton, which is then
excreted over shallow reefs (Peel et al. 2019). In fact many reef predators are similarly subsidised by pelagic
inputs (evidenced by δ13C, δ15N, and δ34S), likely arising through their feeding on reef-based planktivorous
fish, suggesting they play an important role in reef-pelagic connectivity (Frisch et al. 2014, Frisch et al.
2016, Matley et al. 2018, Skinner et al. 2019b).
Energetic connections across depth ranges have also been identified using δ13C, δ15N, and δ15NAA in
combination with acoustic telemetry. Galapagos sharks, Carcharhinus galapagensis, and giant trevally,
Caranx ignobilis, forage in both shallow and deep water mesophotic reef habitats, transporting nutrients
between them (Papastamatiou et al. 2015). In some cases, these energetic linking movements may be
nocturnal. δ13C and δ15N data combined with acoustic telemetry revealed that the grunt, Haemulon
plumieri, in the Caribbean is predominantly sustained by organic matter from habitats it visited at night,
likely to minimize encounters with barracuda (Rooker et al. 2018). These studies highlight the potential for
SIs to complement and enhance inferences from acoustic telemetry or tracking data, by providing detailed
information on energy fluxes which may help elucidate organism movements. Although SI studies
documenting cross-system linkages are increasing, only 13% of the studies in this topic have focussed on
sharks, despite their acknowledged important role in nutrient transfer (Williams et al. 2018b). There is
therefore much that remains to be understood about energy subsidies to and from coral reefs, particularly
the generality of the role that these mobile organisms play in establishing them.
Production source use in coral reef consumers can be difficult to define compared to other, simpler
systems with fewer energy pathways. Significant overlap between the myriad of reef-associated sources
(Fig. 4; Table 3; and see 3. Organic matter dynamics) often makes it impossible to clearly identify for
example carbon sources over a reef using bulk δ13C data. As such, isotope modelling to confidently assign
consumers to energy sources in such ‘underdetermined’ systems becomes impractical (Fry 2013). The use
of CSIA of amino acids (CSIA-AA), particularly essential amino acid carbon isotopes (δ13CEAA), which exhibit
minimal discrimination between resources and consumers across the food web, has great potential to help
resolve carbon resources over reefs due to the increased dimensionality of the data. This technique
effectively separates benthic versus planktonic pathways, further separating the latter into distinct
nearshore reef-associated plankton and offshore pelagic plankton groups (Skinner et al. 2021). Analysis of
consumer tissue δ13CEAA allows the source of primary productivity supporting consumers to be identified
with more precision than is possible with bulk δ13C. Less consideration of variations in isotopic baselines
and TDFs is required when interpreting δ13CEAA data, which can often confound inferences from bulk SI
data. Surprisingly, δ13CEAA data suggest that even highly mobile top predators may rely predominantly on a
single carbon source at the base of the food web. For instance, in the Red Sea, δ13CEAA data suggested that
the snapper, Lutjanus ehrenbergii, and giant moray, Gymnothorax javanicus, may receive >70 % of their C
from a single end-member, phytoplankton, indicating quite tightly linked food chains supporting these
predators (McMahon et al. 2016). Similarly, in the Maldives, several species of grouper were primarily
supported by offshore pelagic plankton across an oceanic atoll (73-86%; Skinner et al. 2021). Contrasting
δ13CEAA within more wide-ranging apex predators like the tiger shark, Galeocerdo cuvier, could provide
important information on the role of mobility in integrating across ocean and reef food webs (Hilting et al.
2013, Frisch et al. 2016).
7. Environmental drivers
It is intuitive following the identification of spatial and temporal patterns in data for scientists to try and
elucidate the underlying processes and mechanisms that give rise to them. Despite the complexity of coral
reefs, SI-based studies focusing on particular components of these ecosystems often infer the key drivers at
play that underpin observed trends. This is evident in all of the preceding topics, where studies attribute
the importance of inherent environmental and biological factors (see, for example, 3.3. Organic matter
dynamics: Spatial and temporal variations and 4.4 Holobiont metabolism: Drivers of mixotrophy). However,
there are a collective of SI studies that specifically investigate the general role spatial and temporal forcings
play on coral reefs, providing context for other studies utilising SI approaches (n = 48 identified topics).
These environmental drivers can be broadly separated into two categories: natural drivers and
anthropogenic drivers (Fig. 3). The first category investigates how the isotopic composition of various
components of coral reef ecosystems responds to a range of natural variables such as depth, resource
availability, and salinity. Hard coral (n = 17) and reef fish (n = 5) are the dominant focal taxa in this regard,
with most studies conducted in the Caribbean (n = 10), the Red Sea (n = 6), or the Central Pacific (n = 6) (Fig.
2B). The latter category almost exclusively focusses on measuring SIs in structure forming organisms, that is
marine plants (n = 9), soft corals (n = 6), and hard corals (n = 6), to explore anthropogenic nutrient inputs to
coral reef communities but also considers the impacts of thermal stress. These are conducted mostly in the
Caribbean (n = 7) or the western Pacific (n = 6) (Fig. 2B).
7.2. Natural drivers
Environmental conditions and nutrient availability fluctuate across both fine and broad spatial and
temporal scales. Much like those of the holobionts (see 4. Holobiont metabolism), primary producer and
higher consumer SI values may reflect this variability (Fig. 4; Table 3; Table S6), as organisms alter their
resource use accordingly and/or integrate isotopic differences in production baselines. For example,
gradients in resource availability exist across coral reef habitats depending on their proximity to open
ocean resources (Wyatt et al. 2013). Primary producers have higher δ15N baseline values on outer reefs
compared to lagoon regions (Page et al. 2013) and many reef fish are increasingly reliant on oceanic
nutrients with proximity to the open ocean (Wyatt et al. 2012b, Gajdzik et al. 2016, McMahon et al. 2016).
In New Caledonia, δ13C provided clear evidence of spatial changes in the primary sources of carbon across a
reef habitat, with increased oceanic inputs on the outer slopes (grouped teleosts mean δ13C -17.9 ‰)
compared to increased internal subsidies in the lagoon (grouped teleosts mean -14.8 ‰) (Le Bourg et al.
2017). Interestingly, δ15N data did not demonstrate any differences in food chain length or trophic level,
supporting the idea of consistent food web structure across the reef scale despite differences in production
sources supporting that structure (Le Bourg et al. 2017). At a regional spatial scale, Zgliczynski et al. (2019)
similarly did not find strong isotopic evidence of shifts in foraging patterns in a range of species and
functional groups across the central Pacific. Isotopic changes were attributed to baseline changes across
the ~ 1000 km scale oceanographic gradient studied and taken as indicative of regional consistency in
foraging (Zgliczynski et al. 2019). This demonstrates that coral reef food webs will often reflect fluctuations
in resource availability and illustrates how SI data can be used to test ideas about spatial and temporal
variation in key trophodynamic processes at different scales, and the factors likely to be driving these.
If assessed in the context of well quantified temporal and spatial isotope baselines, SI data can
demonstrate spatial changes in organic resource use that have significant implications for reef food web
structure (Glass et al. 2020). Such changes can be exceedingly difficult to observe with traditional
techniques such as feeding studies. As an example, bulk δ13C and δ15N data suggested a switch between
planktivory and herbivory between fore and back reef environments for both nominally planktivorous and
herbivorous species (Ho et al. 2009, Wyatt et al. 2012b). At Ningaloo Reef (western Australia), δ13C and
δ15N modelling suggested that nominally herbivorous Stegastes spp derived over half their diet from the
plankton in more oceanic habitats while planktivores increased herbivory in the back reef (Wyatt et al.
2012b). On a reef flat in Okinawa (Japan), δ13C, δ15N, and fatty acid data showed that the algal gardening
damselfish Stegastes nigricans supplemented its diet with unexpectedly large amounts of animal material
for a herbivore (Hata and Umezawa 2011). This suggests that notions of resource reliance in reef
consumers may need to be more flexible. Using δ13CEAA, McMahon et al. (2016) showed that while S.
nigricans gained the majority (75%) of their dietary C from macroalgae, in more oceanic habitats 13%, and
up to 30% for some individuals, came from phytoplankton. Importantly, the error on the estimates from
the δ13CEAA data was much lower than from bulk SIA observations. It is not clear whether such changes
reflect real spatial differences in actual food web structure however (McMahon et al. 2016), as SI data
cannot distinguish between active consumption or incidental ingestion of particular sources that can be
influenced by exposure rates and therefore spatial proximity and foraging strategies.
Interactions between the complex topography of reefs and hydrodynamic processes that alter physical and
biogeochemical conditions such as internal waves and upwelling can lead to highly variable isotope ratios in
reef organisms across depth ranges at the same location. As light availability decreases with depth so,
generally, does coral autotrophy; coral host tissue δ13C values thus become closer to oceanic carbon values
through feeding (Muscatine et al. 1989, Gattuso et al. 1993, Lesser et al. 2010, Crandall et al. 2016). Coral
skeletal δ13C values also reflect fluctuations in light and heterotrophy because they are influenced by
metabolic fractionation; decreasing light and zooplankton levels resulted in significant decreases in coral
skeleton δ13C (Grottoli and Wellington 1999, Grottoli 2000). Furthermore, both host and endosymbionts
are depleted in 15N with depth, with impacts on endosymbiont growth rates (Muscatine and Kaplan 1994).
This pattern of trophic zonation (i.e. where coral heterotrophy increases with depth) is not always
consistent, however. Some evidence suggests that increasing depth does not necessarily result in increased
heterotrophy as is typically expected (Einbinder et al. 2009), with observed changes in δ13C along depth
axes potentially driven by internal carbon cycling processes once other biological traits are accounted for.
Controlled feeding experiments of Reynaud et al. (2009) found no effect of ambient light levels on internal
nutrient metabolism. They did however identify increased nitrogen cycling of host metabolic waste
products to endosymbionts when heterotrophic feeding was limited by tracing bulk δ15N through different
tissues. This is in contrast to carbon metabolism, which appears to change with irradiance levels when
heterotrophic feeding occurs, with increasing rates of photosynthesis and carbon translocation from
endosymbionts to coral host under high light conditions (Tremblay et al. 2014). At Palmyra Atoll, δ13C and
δ15N data suggested that increases in coral heterotrophy with depth were absent at sites where resources
were assumed to be readily available from extensive water mixing (Williams et al. 2018a). Similarly, in one
of the few studies to use both δ13CAA and δ15NAA, while autotrophy was the dominant source of carbon to
the hard coral Stylophora pistillata, heterotrophic energy contributions were equal across shallow (5 m)
and deep (60 m) reefs (Martinez et al. 2020). Furthermore, SI data reveal that some species are
heterotrophs throughout their depth ranges (Alamaru et al. 2009a, Crandall et al. 2016, Radice et al. 2019)
or vary in their degree of heterotrophy across depths based on sampling region (Santos et al. 2021). Even
within the same genus and at the same location, SI values (δ13C and δ18O) reveal that three species of
Madracis differ in their depth adaptations and ecological plasticity (Maier et al. 2003), indicating that this
phenomenon could depend on prey encounter, resource availability and resource acquisition (Maier et al.
2010, Plass-Johnson et al. 2015b, Fox et al. 2018, Santos et al. 2021). Indeed, Leichter et al. (2007)
suggested that depth gradients in reef macroalgal SI values can reflect gradients of exposure to offshore
nutrient sources, such as increased use of deep-water nitrate by macroalgae exposed to high-frequency
upwelling. Conversely, variability in SI values (δ13C, δ15N, and δ18O) in two abundant macroalgal species over
scales of 10s of metres were perhaps independent of depth and instead reflected large amounts of spatial
heterogeneity (Stokes et al. 2011). Clearly there are limited universal trends with depth that can be
identified thus far on coral reefs, which suggests that biological traits and their plasticity may play a
significant role buffering effects of physical drivers over a species’ observed distribution.
CSIA can be especially powerful in examining variability in resource use across environmental gradients that
could influence tissue SI signatures independent of diet changes. While primary producer bulk SI values
vary across regions and seasons (Fig. 4; Table 3; Table S6), which can confound interpretation of dietary
changes, CSIA measures individual compounds which are shaped by the biochemical processes of the
primary producers and are thought not to vary spatially, temporally, or with growth rates (Whiteman et al.
2019). Using CSIA, Papastamatiou et al. (2015) were able to discount the isotope baseline as a source of
variation in the bulk SI data of giant trevally (Caranx ignobilis) from deep water reefs on a Pacific atoll;
differences were due to individual trophic flexibility, with trophic positions determined with CSIA-AA
ranging from 3.5–4.6. Acoustic tracking demonstrated individual variability in diel migration and feeding
behaviour leading to a range of trophic positions, perhaps reflecting individual foraging preferences and
intra-specific competition (Papastamatiou et al. 2015). By demonstrating changes in δ15NAA derived TP of
spiny and slipper lobsters across large spatial scales in the north-western Hawaiian Islands, which were thus
independent of baseline isotope variation, O’Malley et al. (2012) robustly demonstrated that spatial
variability in growth was due to different responses between the two species to limited prey availability.
Resource availability across spatial gradients thus may be a driver of consumer SI values. Of two obligate
corallivore butterflyfish that both preferentially feed on Acropora coral, δ13CAA reveal that the specialist
Chaetodon baronessa is more selective with depth and continually seeks out Acropora despite decreased
availability, while the generalist Chaetodon octofasciatus becomes more flexible with depth (MacDonald et
al. 2019). Furthermore, while planktivores have a consistent feeding strategy across shallow to mesophotic
reefs, benthic invertivores and omnivores have significantly broader niches (with benthic invertivores also
occupying a higher TP) (Bradley et al. 2016). These studies highlight the trophic versatility of many reef
organisms along spatial gradients.
7.3. Anthropogenic drivers
Land and seascapes are under increasing pressure from human activities worldwide, and shallow coral reef
ecosystems are particularly vulnerable to these threats (Fig. 3); coral bleaching events are now occurring
every six years or less (Hughes et al. 2017). Bulk δ18O SI values can reveal when a coral has been subjected
to extreme thermal stress by directly relating the δ18O values to in situ temperature (Porter et al. 1989,
Mayal et al. 2009). SIs can also identify how the coral animal host and endosymbionts alter their trophic
strategies and resource use in response to bleaching events (see 4.4.1. Holobiont metabolism: Exogenous
factors). Over the longer term, pulse-chase experiments using 13C-labelled bicarbonate revealed that some
corals may increase their use of heterotrophic carbon for up to a year after bleaching, but it is not known
whether this is a sign of resilience or prolonged stress (Hughes and Grottoli 2013). Generally, it seems that
different coral species have different bleaching responses, with some maintaining energy reserves or
heterotrophic capacity, but most recovering within a year if the bleaching is a mild and isolated event
(Grottoli et al. 2017, Levas et al. 2018). There is currently little understanding of how coral and
endosymbionts trophic strategies will change through successive bleaching events, despite predictions that
these will occur ever more frequently. Furthermore, studies assessing thermal stress effects using SIs have
focussed on corals, with few, if any, investigating these impacts on other holobionts. For non-symbiotic
organisms, Vaughan et al. (2021) suggested increases in δ15N (~ 1 ‰) in natural and transplanted
macroalgae, Sargassum mangarevense, were linked to the release of coral-derived nutrients post-
bleaching. While a better understanding of SI changes in reef biogeochemical cycles post-bleaching is
required (but see Radice et al. 2021), it is crucial to understand and measure the underlying natural
variation in SI source data when making inferences, i.e. by measuring the underlying δ15N baseline.
Global bleaching events and declines in live coral cover have been linked to declines in structural
complexity, coral biodiversity, and the abundance and diversity of reef-associated fishes (Jones et al. 2004,
Carpenter et al. 2008, Pratchett et al. 2018). Overfishing also contributes to the latter, while simultaneously
reducing fish-mediated storage and supply of nutrients by up to 50% (Allgeier et al. 2016). These drivers
may be reflected in consumer SI values. For example, as the amount of rubble increases along a habitat
disturbance gradient, there are significant differences in the δ13C and δ15N ranges and the isotopic niche
area of the parrotfish Chlororus bleekeri, the foraging of which varies according to the surrounding habitat
(Plass-Johnson et al. 2018). Similarly, as prey densities fluctuate in response to declines in structural
complexity, the peacock grouper Cephalopholis argus maintains their TP (as indicated by their δ15N) by
switching foraging modes from ambush to widely active foraging (Karkarey et al. 2017). Loss of habitat
structural complexity is predicted to cause a 3-fold reduction in fishery productivity (Rogers et al. 2014).
However, some species such as the peacock grouper may be more resilient to habitat loss than previously
thought as their foraging plasticity may enable them to adapt to coral degradation (Karkarey et al. 2017). In
addition to habitat loss, ocean acidification (i.e. reductions in oceanic pH through elevations in partial
pressure of seawater CO2 (pCO2) due to increasing global carbon emissions) may negatively impact
calcifying marine organisms. By studying coral skeleton δ13C and δ18O values, Zhou et al. (2016) determined
that Acropora gemmifera photosynthesis and calcification were only impaired at the highest pCO2
treatment, with their microbial communities remaining stable. More recently, benthic communities were
exposed to increased pCO2 and warming in mesocosms to determine how trophic architecture (represented
by organism δ13C and δ15N) would respond under future scenarios (Nagelkerken et al. 2020). While trophic
pyramids and community structure (i.e. biomass and productivity) shifted, the food web architecture
remained inflexible and stabilising processes were absent suggesting a lack of adaptive capacity in the
ecosystem (Nagelkerken et al. 2020). SIs therefore offer a unique opportunity to study potential impacts of
changing environmental conditions on organism and whole food web trophic ecology (Plass-Johnson et al.
SI data offer great potential for exploring other anthropogenic impacts on coral reef food webs, notably the
role of human-derived pollutants in reef systems. By measuring SI values of various reef organisms, these
nutrient inputs can be identified to determine the extent of their impact on the local reef communities
(Yamamuro et al. 2003). Elevated δ15N values in sampled organisms have suggested artificial nutrient inputs
to reef communities pertaining to aquaculture (Herbeck et al. 2014), shoreline sewage (Todd et al. 2009,
Baker et al. 2017, Abaya et al. 2018, Lachs et al. 2019), stormwater discharge (Lapointe and Bedford 2011),
seepage water (Mwaura et al. 2017), river plume pollution (Risk et al. 2014), and even wood pulp effluent
(Schleyer et al. 2006). This highlights how spatially explicit context is required to determine the role of
pollution in nutrient cycling of nearshore reefs and flow on effects for other taxa like coral (Umezawa et al.
2002, Huang et al. 2013, Adam et al. 2021). While most of these studies use macroalgae as bio-indicators of
pollution, seagrass δ15N has also been proposed as a tool to monitor time-integrated changes over coral
reef habitats, as there are fewer seagrass species than the diverse macroalgae that are found across reefs,
facilitating both identification and standardisation (Yamamuro et al. 2003). Indirect incorporation of
anthropogenic inputs can result from connectivity to the pelagic food chain and reef planktivore grazing.
Lower δ13C and higher δ15N in two damselfishes demonstrated how POM released from nearby fish farms in
southern Taiwan can enter coral reef food webs (Jan et al. 2014). One of the few studies to employ sulphur
isotopes to examine anthropogenic inputs attributed decreasing δ34S in coral skeletons off Yoron Island to
rain-driven inputs of low δ34S terrestrial material from sugar cane dominated farmland (Otani and
Nakanishi 2019). Oxygen isotopes may also be useful in anthropogenic impact monitoring, with shifts in
δ13C and δ18O in coral skeleton correlating with local oil spills (Xu et al. 2018). However, studies need to be
cautious when using taxon-specific variations in tissue isotopes to infer nutrient fluxes based on SI data,
especially across small ranges that might be explained by metabolic or hydrodynamic variations (see 7.2
Natural drivers), which is especially the case for coral skeleton. Relationships between anthropogenic
nutrient inputs and SI data, and subsequent ecological effects may be more nuanced. For example, a long-
term experiment involving δ13C and δ15N in the hard corals Acropora palmata and Porites porites showed
that moderate doses of anthropogenic nutrients had no additional effects and the corals continued growing
(Allgeier et al. 2020). However, models revealed that nutrient and carbon flows were dominated by the
symbiont, leading to algal dominance in the holobiont and greater algal demand on coral resources, likely
increasing the corals’ future vulnerability to bleaching due to stress (Allgeier et al. 2020).
It should be emphasised that elevated δ15N values alone are insufficient evidence of anthropogenic
impacts over reef ecosystems. There is an extensive range in natural isotope abundances in the ocean in
the absence of anthropogenic inputs; isotope effects across the marine nitrogen cycle span approximately -
0.5 ‰ to +38 ‰ (Sigman et al. 2009). Increased macroalgal δ15N with depth can be indicative of upwelling
increasing dissolved nitrogen availability, rather than a sewage impact (Huang et al. 2013). Instead of
anthropogenic sources (e.g. Lapointe 1997, Lapointe et al. 2005), POM isotopic variations may reflect
mineralization of organic material and nitrification along with inputs of DIN from upwelling, runoff,
sediments, and the atmosphere (Lamb and Swart 2008). Natural N cycling and resultant isotopic variation
could account for δ15N variations in benthic components of the reef. For instance, Lapointe et al. (2005)
reported algal δ15N elevated by +2 ‰ as indicative of land-based pollution, however the range in POM δ15N
across the Florida Keys varies over a 20 ‰ range with a standard deviation of ± 3.6 ‰, apparently
independent of human influences (Lamb and Swart 2008). This underscores the importance of
understanding spatial and temporal variations in potential source isotopes (Fig. 4; Table 3), due to e.g.
water column sources and upwelling (Leichter et al. 2007), before invoking anthropogenic perturbation.
This is especially important where the variations are small (e.g. a few per mil or less) relative to a potential
natural range of SI data variations.
Due to their incremental growth, corals, and in particular gorgonians, provide an opportunity to investigate
long-term trends in anthropogenic nutrient inputs. The biochemistry of skeletal banding reflects the
ambient nutrient levels and can therefore be used to infer long-term pollution trends (Ward-Paige et al.
2005). Indeed, gorgonian δ15N values accurately reflect tourism levels over multiple years, with declines in
δ15N linked to declines in tourism and increases in δ15N linked to its recovery (Baker et al. 2013b). Hard
coral skeletons can track anthropogenic nitrogen fluctuations over decades with 15N enrichment linked to
increasing sewage levels and population density (Duprey et al. 2017, Duprey et al. 2020). Archived museum
samples may provide another means to monitor human pollution levels over longer time spans. Gorgonian
samples from a 143 year time span had δ13C and δ15N values which reflected increasing atmospheric CO2
and use of agricultural fertilizers respectively (Baker et al. 2010), while samples in Bermuda spanning 50
years reflected changes in management policies which were effective in reducing local pollution levels
(Baker et al. 2017). Despite the wealth of information they can convey on prior isotopic baselines, the use
of archival samples is exceedingly low across SI reef studies (n ≈ 3).
8. Knowledge gaps, caveats, limitations, and future directions
Throughout this review we have summarised the key findings of studies that have used SIs to understand
coral reef ecosystems. In doing so, we have highlighted that there are still areas where research,
knowledge, and understanding are lacking. This should be taken as an opportunity to focus future research.
Below, we have included a numbered list of identified gaps and opportunities for future SI studies. Given
the logistical ease for researchers to now obtain and analyse SI data, we also emphasise why care must be
taken not to misuse or overinterpret SI data. The Knowledge gaps and opportunities section is followed by
important caveats and limitations which must be considered. We hope that these points serve as a
roadmap to direct future research involving SIs on coral reefs.
8.1 Knowledge gaps and opportunities
1. Improve characterisation of basal sources. Corals have been the focus of much SI research due to their
foundational importance, but the living proportion of whole reefs that they cover is generally low.
Conversely, ‘turf algae’ cover a greater surface area and are intensively grazed, but there is sparse
understanding of the fate of turf-derived fluxes in the ecosystem. Similarly, substantial fluxes of detritus
derive from benthic reef sources both directly (e.g. exudates) and secondarily (e.g. grazer defecation),
but the detrital pool, its origins and fluxes are little resolved. SI data, both bulk and CSIA, have a lot to
offer well-focussed investigations which can advance our understanding of these lesser studied fluxes
2. Extend sampling over longer time frames. Resource availability on coral reefs fluctuates through time
and consumer resource use may vary accordingly. However, to date, many coral reef SI studies sample
during a single time point or limited temporal window (Fig. 5A). Future studies exploring the dynamics
and stability of coral reef ecosystems should consider longer time periods over which inference can be
made. Multi-tissue approaches are one technique which may reveal dietary variations across a range of
timescales from a single individual, yet currently, only 9% of studies measured multiple tissues within
the same individual organism. Employing a multi-tissue approach by sampling faster turnover tissues
e.g. organs and blood, in addition to slower turnover tissues e.g. muscle tissue, could better discriminate
dietary consistency or the lack thereof (Wyatt et al. 2019).
3. Employ an isoscape approach. To date, and likely to due to their inherent complexity, there are few
studies employing an isoscape approach on coral reefs. However, isoscapes of coral reef ecosystems
could offer valuable insight into the complex processes that might influence coral reef trophodynamics
and SI values across various locations (Fig. 4; Table 3). For example, spatial variations in the relative
importance of different production sources to reef food webs are evident. Given that environmental
conditions are fluctuating due to climate change, there is a need for studies examining the drivers of
these likely differences in coral reef ecosystems, which could be facilitated by a broadening of the
spatial scale across which studies are conducted. Isoscapes provide a solid isotopic foundation of a
region, providing the context upon which other avenues of research can be conducted (McMahon et al.
4. Explore trophodynamics across the wider community. SI data have helped to highlight that categorising
reef consumers into simple trophic groups masks dietary specialisations and the complexities of this
dynamic system. However, few studies compare niche dynamics and resource partitioning outside of
species groups or guilds. For example, most studies that focus on reef fish do not consider how
invertebrates occupying the same TP may share similar resources (but see Zapata-Hernández et al.
2021). A better understanding of trophic interactions across the wider reef community is required. This
will help understand the importance of potential competitiveness among disparate taxa on coral reefs.
Given increased feasibility, this body of knowledge is expected to grow, and it will be important for
greater resolution to be assimilated into whole ecosystems models.
5. Quantify species-specific TDF and tissue turnover rates. To date, few studies have accurately quantified
species-specific TDF and isotopic turnover rates (i.e. the time it takes for a given consumer tissue to
reflect the isotopic composition of its diet) across different tissue types for coral reef consumers. While
this will be challenging to determine for species with longer turnover times (e.g. hard coral; Tanaka et al.
2008), it is highly recommended that more laboratory feeding studies be conducted. Where
environment- and species-specific TDF are not available, analyses must rely on TDF across a range of
values to account for uncertainty surrounding the inherent variability (e.g. likely ≥ 1 ‰ SD for Δ15N).
6. Consider parasites. Parasites may be involved in >50% of food web links but they are rarely considered
in food web science (Dunne et al. 2013). Indeed, on coral reefs, there are estimated to be ten times
more parasite species than fish species (Justine et al. 2012). In addition to their huge biodiversity,
parasites can affect food web structure indirectly by modifying their host’s behaviour and subsequent
resource use (Welicky et al. 2017). Despite their important ecological role shaping trophic interactions in
coral reef ecosystems, parasite trophodynamics on reefs are poorly understood. While several more
recent studies are beginning to address this knowledge gap (e.g. Jenkins et al. 2018, Jenkins et al. 2020,
Riekenberg et al. 2021), few have considered parasite life stage dietary shifts.
7. Measure other isotopes. Despite limited application on coral reefs to date, bulk δ34S shows promise for
distinguishing among reef production sources and revealing consumer habitat use (Connolly et al. 2004,
Granek et al. 2009, Skinner et al. 2019a). Moreover, recent advances in SI technology mean that δ13C,
δ15N, and δ34S can now be measured from the same sample aliquot with a high level of precision (Fourel
et al. 2015). Similarly, to our knowledge, there are currently no coral reef SI studies that utilise mercury
isotopes (δ202Hg), which can characterize resource partitioning and identify foraging depth separation
among predators in marine environments (Besnard et al. 2021). Given the myriad of co-occurring
predators on coral reefs, δ202Hg may offer a useful tool to understand resource partitioning across
depths. Finally, copper (δ65Cu) and zinc (δ66Zn) isotopes have recently been suggested as a proxy for
coral stress, as both increase in coral host and symbiont tissue at higher temperatures (Ferrier-Pagès et
al. 2018). Given the difficulty in disentangling the production sources and consumer resource use on
reefs, studies incorporating such additional isotopes are strongly encouraged.
8. Apply compound-specific SIA (CSIA). The number of studies employing CSIA on coral reefs is rapidly
increasing (of coral reef SI studies >5 in 2020 alone, compared to 15 between 1982 – 2019). This
advance will certainly offer new insights into the complexities of the coral reef ecosystem. Although
multiple isotope approaches show significant potential for better elucidation of organic matter fluxes
and resource use in this complex ecosystem, few studies combine CSIA of both carbon and nitrogen in
the compounds of interest. Given the depth of information they can provide on production sources and
trophic interactions, studies combining both are likely to provide a more holistic understanding of the
specific systems of interest.
9. Incorporate and explore relationships with environmental drivers. Laboratory studies generally focus
on manipulating one aspect of the environment, while field studies use SIs as indicators rather than
testing what drives changes in their values. Few studies consider the effect of multiple environmental
drivers, whether natural or anthropogenic, or the interactions occurring between them. Measuring
multiple environmental variables (e.g. nutrients, pH, temperature, salinity etc) and linking those with SI
values is a multi-method approach which could better explain spatial gradients (of human impacts) on
reef ecosystems (Teichberg et al. 2018).
10. Utilise archival samples. Analysis of archival samples, held in museums and other institutions across the
globe, can provide additional information on prior isotopic baselines and how they have shifted over
time. Soft and hard corals are common, slow growing, benthic organisms, which may comprise
important baselines against which current pollution levels can be monitored. This gives the historical
context against which the significance of contemporary isotope values can be compared. Archival
specimen preservation is a considerable cause for concern, however improved mass spectrometer
technology means that very little material is physically required to obtain SI data. Where possible, we
encourage researchers to incorporate archival or historical baseline samples. Such approaches are
particularly powerful when drawing conclusions about current anthropogenic impacts.
11. Conduct multiple analyses on the same sample material. There are logistical efforts involved with
collecting samples on coral reefs and conservation concerns involved with intensive sampling, especially
of threatened species. As such, we advocate for multiple analyses on the same sample material. Not
only would this facilitate more collaboration between different regions (which at present tend to
specialise on particular fields of research), but it would maximize the information derived from each
12. Adopt a multi-regional, aggregative research approach. There are now many SI studies (and therefore
data) conducted on coral reefs, but almost all are isolated to a single area. Further still, there are
regional disparities in research focus. Here, it is worth acknowledging that collecting SI data often
requires extensive sampling to which there may be substantial limitations, particularly in coral reef
regions (i.e. lack of access, funding, infrastructure, requiring specialist vessels or equipment, sampling
during extreme conditions to assess seasonality). Regardless, generality at the regional to global scale is
currently lacking. Moreover, inferences from different studies can be contradictory (e.g. see 5.2 Trophic
niches: Isotopic Niches). Given the number of studies now published, a more aggregative research
approach (i.e. meta-analyses) may help discern ubiquity in patterns and drivers of these.
Complementary to this, we advocate for larger, multi-region studies to detect, if any, general trends in
SIs (e.g. variability in production sources cf. Fig. 4) on coral reefs to act as ecological baselines. This
could help generate mechanistic theory of overall ‘typical’ coral reef SI functioning. Deviations from this
may point to interesting but currently not-yet-realised avenues of further study.
8.2 Caveats and limitations
1. Provide enough detail for SI data to be useful to others. Researchers should strive to clearly report
their sampling design and SI data so it can be used by others. Over 15% of identified articles did not
report when or over what period samples were taken (Fig. 5A), despite the high spatiotemporal
variability of SI data on coral reefs. Furthermore, when extracting SI baseline data (i.e. Table 3), we
found that many articles only published data in figures and/or did not provide sample sizes that are
required to understand data spread and error. More rigorous reporting will facilitate point 12 above,
allowing researchers to employ an aggregative approach to future coral reef SI studies.
2. Interpret SI data within the context of underlying SI baselines. Variation in SI baselines (values at the
base of the food web) must be considered when assessing variation in resource- and nutrient-use using
isotopes. There is a tendency to extrapolate from taxon-specific variations in tissue SI data to infer
biogeochemical rates or anthropogenic impacts, which is especially concerning across small ranges in
isotope values. These variations may be within ranges of a few permille or less, that alone can be
explained by discrimination and metabolic variations or simply to fluctuations in isotopic baselines. This
presents a high risk of overinterpretation, especially given the dynamic fluxes present on coral reefs.
Understanding natural variation in SI values is also needed when analysing the influence of stochastic
events (e.g. coral spawning, coral bleaching) with SIs, especially when SI perturbations are small relative
to the magnitude of the natural variance in SI baselines (see Fig. 4). We urge researchers to take careful
consideration when interpreting spatial and temporal heterogeneity in reef organism SI values and to
measure isotopic baselines wherever possible. This might involve comprehensive source sampling for
bulk SIA or the application of more source specific CSIA. Complementary data, e.g. acoustic telemetry or
nutrient concentrations, and data simulations prior to SIA (to estimate the likely impact e.g. TDF
variability could have on observed data) could also be hugely beneficial for considering SI variation in
context. In some cases, it may not be possible to measure baseline source values in situ. As a first
estimate, researchers should consider the source SI values presented herein (Fig. 4 and Table 3 for
interstudy means; Table S6 for study-specific values). The presented values integrate differences
attributable to spatiotemporal dynamics, biodiversity, and inter-laboratory differences, highlighting the
variability that has been observed across studies. For example, macroalgae SI values show high variance
(mean ± s.d. for δ13C = -15.68 ± 4.87 and δ15N = 3.93 ± 3.45; Table 3), especially between species, and, as
such, authors should consider some form of abundance weighting by species.
3. Isotopic niche ≠ trophic niche. While variability in SI data within a population may indicate there are
individuals with consistent differences in trophic ecology, low variability in SI data in a population does
not necessarily indicate a narrow trophic niche. In the latter case, because of the time integrating
character of the SI signatures, there are two possibilities: 1) individuals could be constantly feeding on
one production source or 2) they could be feeding on different sources in proportions or combinations
that happen to integrate to the same SI value. Specifically, how equivalent is the isotopic niche to the
trophic niche? What is the magnitude of isotopic variation expected from processes independent of
feeding variation (e.g. growth rates, diet quality)? Given the diversity of production sources available on
coral reefs, these questions and the discrepancy between the trophic niche and the isotopic niche may
be more of a problem in this ecosystem compared to others with less diversity in available sources for
consumers. Consequently, care must be taken when making inferences regarding trophic niches based
on isotopic niches on coral reefs.
SIA are an important tool that have elucidated many of the diverse and complex processes and
relationships occurring on coral reef ecosystems. By combining a traditional literature search of databases
with topic modelling of article abstracts, we identified recurring patterns and themes in the SI coral reef
studies published to date. Summarising how SIs have advanced our understanding of coral reefs is
challenging due to the inherent cross-over between studies, but the topic modelling approach partitioned
the article text data to generate non-biased categories, providing a clear guide on the most logical structure
for the review.
One of the fundamental components of SI advances for coral reef ecology, and also one of the challenges,
involves identifying the available energy fluxes to reef food webs and how these vary across different
scales. SIA have been used to successfully identify and quantify inputs to reefs, and releases of material
from reef organisms, showing that both are closely linked to the spatial arrangement of organisms and
hydrodynamics across reefs. Fluctuations in available resources, related to the structure and layout of the
seascape, are reflected in reef primary producer and consumer SI values. This is highlighted by the global
variability in reported SI baselines across the literature (Table 3, Fig. 4), emphasising the importance of
considering variations in when studying trophodynamics across coral reef food webs.
Corals represent one of the most studied organisms on coral reefs due to their instrumental role as
ecosystem engineers. SI studies have revealed just how complex their nutrient uptake and feeding
strategies are, often with stark contrasts between species and little consistency in their reliance on auto- or
hetero-trophic resources spatially and temporally. SI studies have also highlighted the importance of
previously underappreciated holobiont groups to the overall coral reef ecosystem, notably sponges that
underpin diverse pathways of in situ DOM and POM recycling. The myriad of interactions occurring
between the vast numbers of reef primary producers and consumers is challenging to explore, but SI data
has begun to disentangle some of these. For example, many isotopic niche studies have shown that
traditional dietary classifications mask individual-level variations in resource use. They suggest that many
reef organisms have more varying and flexible functional roles than those inferred from traditional
techniques. Such insight also points to the fact that a better understanding of wider feeding relationships
across guilds, not only within guilds, is required, particularly among invertebrates.
Coral reef ecosystems do not persist in isolation, and SI studies demonstrate energetic linkages with
adjacent habitats. These linkages are formed not only from ontogenetic shifts in habitat use of reef fishes,
from their nursery grounds in mangroves and seagrass beds to the reef, but also through the movement
patterns of larger, mobile predators. SIs also reveal vertical movement patterns across depth gradients,
highlighting the extent of connectivity between shallow and deeper reefs. Connectivity is not only
determined by energy flows however, with SIs providing a methodological means of transgenerational
tagging to follow larval distributions, highlighting the diversity of research questions that can be addressed
using SI techniques.
SIA have become an increasingly important tool for exploring anthropogenic impacts on coral reef food
webs; they can highlight nutrient inputs, ocean acidification effects, and thermal stress, although care is
needed not to conflate such effects with natural SI baseline variations. Climate change is increasing global
water temperatures, resulting in catastrophic bleaching of coral reefs worldwide. Such a loss of live coral
can impact associated food webs by reducing biodiversity and degrading habitats, resulting in lower trophic
complexity across the community (Gabara et al. 2021), as well as reduced ecological stability due to loss of
functional redundancy. SIA represents a crucial tool to increase our understanding of the complex trophic
interactions occurring on coral reefs that are modulated by environmental drivers and their associated
dynamics, including human induced climate change.
The number of SI reef studies has been increasing rapidly in recent years. By objectively drawing on the
published literature, we have synthesised the current knowledge and understanding acquired through the
application of SIA on coral reefs into five broad bodies of research focus. In doing so, we have highlighted
potential research avenues that warrant further exploration, including increasing the scale at which SI
studies are conducted (both through time and across space) in the hope of identifying more general
patterns and processes that underpin coral reef structure and functionality. While acknowledging the
considerations that need to be made when utilising SIs, we hope this review acts as a useful synthesis, and
will serve to bolster the expanding literature on ecological applications of SI approaches to coral reef
CS and ASJW were supported by funding from the Hong Kong Branch of the Southern Marine Science and
Engineering Guangdong Laboratory (Guangzhou) (SMSEGL20SC01) and the Research Grants Council (RGC)
of Hong Kong (RGC Project No. 26100120). MRDC was supported by the NERC-BMBF CAO Coldfish project
(NE/R012520/1) at Newcastle University and was funded by Irish Research Council Laureate Award
IRCLA/2017/186 to Andrew L Jackson, Trinity College Dublin. We thank Dr Veronica Radice, one other
anonymous reviewer, and the editor, Prof Peter Mumby, for their constructive comments.
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