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Biogeosciences, 21, 3523–3536, 2024
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Research article
Reefal ostracod assemblages from the Zanzibar
Archipelago (Tanzania)
Skye Yunshu Tian1, Martin Langer1, Moriaki Yasuhara2,3, and Chih-Lin Wei4
1Bonn Institute for Organismic Biologie, Paläontologie, Universität Bonn, Bonn, Germany
2School of Biological Sciences, Area of Ecology and Biodiversity, Swire Institute of Marine Science,
The University of Hong Kong, Hong Kong SAR, China
3State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
4Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
Correspondence: Skye Yunshu Tian (skyeystian@gmail.com) and Martin Langer (martin.langer@uni-bonn.de)
Received: 19 February 2024 – Discussion started: 13 March 2024
Revised: 2 June 2024 – Accepted: 12 June 2024 – Published: 6 August 2024
Abstract. Tropical reefs encompass tremendous biodiversity
yet are imperiled by increasing natural and anthropogenic
disturbances worldwide. Meiobenthic biota on coral reefs,
for example, ostracods, may experience substantial diver-
sity loss and compositional changes even before being ex-
amined. In this study, we investigated the reefal ostracod as-
semblages from the highly diverse and productive ecosystem
in the Zanzibar Archipelago (Pemba, Zanzibar, and Mafia is-
lands), Tanzania, to understand how their diversity and fau-
nal structure vary in response to water depth, benthic com-
munity type, and human impacts. We characterized four dis-
tinct ostracod faunas associated with different benthic habi-
tats, which were deep fore reefs, shallow fringing reefs, de-
graded fringing reefs, and algae-covered intertidal flats. We
identified typical ostracod associations, i.e., Bairdiidae ver-
sus Loxoconchidae–Xestoleberididae, that showed affinities
towards hard corals or algae on the reef platforms, respec-
tively. The highest diversity was found on shallow fringing
reefs where coral-affined and algae-affined taxa exhibited
maximum overlap of their distributional ranges, while the
sand flats, mangrove, and marginal reefs within the intertidal
zone had much lower diversity with a high dominance of eu-
ryhaline taxa. Along the western coast of Zanzibar Island,
coastal development likely resulted in a unique faunal com-
position and comparatively low diversity of ostracod assem-
blages among those in reefal habitats, in conjunction with
overall reef ecosystem degradation. This study represents the
first large-scale assessment of shallow-marine ostracods in
the Zanzibar Archipelago. It lays a solid foundation for fu-
ture research into the ecological significance of ostracods on
coral reefs.
1 Introduction
Coral reefs as the most diverse ecosystem in the marine
realm hold great ecological and economic values, yet our
knowledge of their enormous biodiversity is far from com-
plete. Compared with well-studied, conspicuous macrofauna
(Souza et al., 2023), meiofauna on coral reefs are highly
under-represented in current research despite being ecolog-
ically essential components and contributing significantly
to total biodiversity (Leray and Knowlton, 2015; Plaisance
et al., 2011). Ostracoda (Crustacea) among all meioben-
thos has a tight association with reef environments tracing
back to the lower Paleozoic (Whatley and Watson, 1988).
It is considered a useful model organism in modern- and
paleo-biodiversity research because of its high fossilization
potential, high abundance, and ubiquity in almost all ma-
rine ecosystems (Yasuhara et al., 2017). However, ostracods
on coral reefs are poorly understood. Do ostracods exhibit
higher diversity in reefal habitats compared with other soft-
sediment environments? What are the characteristic ostracod
taxa occupying different niches on coral reefs? Answers to
these questions are important for a holistic understanding of
the reef ecosystem and may hint at the underlying mecha-
nisms that support such extraordinary reef diversity. With
intensifying anthropogenic disturbances at local to global
Published by Copernicus Publications on behalf of the European Geosciences Union.
3524 S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
scales, the need to examine reefal ostracods before they per-
ish is pressing.
Studies targeting tropical shallow-marine ostracods on
coral reefs are surprisingly deficient. Across the circumtrop-
ical belt, the central Indo-Pacific receives the most attention
for its diverse reefal ostracods, with pioneering studies iden-
tifying distinct faunas associated with depth habitats from the
shallow intertidal to deep reefal zones (Whatley and Wat-
son, 1988; Babinot and Degaugue-Michalski, 1996). Apart
from bathymetry, the distribution of reefal ostracods seems
also related to benthic community type (coral reefs versus
seagrass/algal beds) and sediment type (i.e., sandy versus
muddy deposits), in addition to local hydrology (i.e., ex-
posure to wave energy) (Weissleader et al., 1989; Whatley
and Watson, 1988; Babinot and Degaugue-Michalski, 1996;
Tabuki, 1990, 1987). However, most of these works are con-
fined to small geographic areas and based on limited (sub-
)fossil materials. An extensive regional-scale survey of reefal
ostracods has never been conducted. More importantly, the
focus of previous studies mainly revolved around taxonomy,
as well as biogeography to a lesser degree, while quantita-
tive assessments of biodiversity are largely lacking (Tabuki,
1987, 1990; Mostafawi et al., 2005). The highest species
richness (S=74) was reported for a reef slope environment
in Pulau Seribu, Java (Whatley and Watson, 1988), in con-
trast to much lower values at lagoons (S=27–42) (Babinot
and Degaugue-Michalski, 1996; Weissleader et al., 1989)
and reef flats (S=34) (Mostafawi et al., 2005).
Reefal ostracods are even less known in other tropical re-
gions outside of the central Indo-Pacific. Along the eastern
coast of Africa, where the reef ecosystem is productive and
biodiverse, the only studies on ostracod assemblages are per-
haps Hartmann (1974) and Jellinek (1993) that document
more than 200 species inhabiting the algae facies and reefal
facies across the littoral zone in Kenya. Here we present
the first large-scale study on reefal ostracods from the Zanz-
ibar Archipelago, Tanzania, a biodiversity hotspot of great
conservation interests and vulnerability to increasing anthro-
pogenic impacts (Grimsditch et al., 2009). We investigated
the geographical structure of ostracod diversity and compo-
sition in relation to environmental habitats among the three
major islands of Pemba, Zanzibar, and Mafia. We compared
the patterns with those of benthic foraminifera (Thissen and
Langer, 2017) to explore complex environmental controls on
the two groups of meiobenthos. This study is a major step
towards better understanding tropical shallow-marine ostra-
cods in eastern Africa and provides valuable insight into the
ostracod–reef association in general.
2 Regional setting
The Zanzibar Archipelago is located along the eastern coast
of Tanzania in the western Indian Ocean (Fig. 1) (Thissen
and Langer, 2017). It belongs to the eastern African bio-
geographic province that stretches from Somalia to the
northeastern coast of South Africa (Costello et al., 2017;
Obura, 2012). The archipelago is strongly influenced by the
warm, westward-flowing South Equatorial Current and the
northward-flowing East African Coastal Current (Narayan et
al., 2022). The western coastlines are more protected, with
generally higher coral coverage, whereas the eastern coast-
lines are exposed to large physical disturbances and strong
wave energy (Thissen and Langer, 2017). Tides there are
semi-diurnal, with a maximum range of 4.5 m and a neap
tidal range of 0.9 m (Thissen and Langer, 2017; Narayan et
al., 2022). The islands possess a great variety of benthic habi-
tats from the littoral to open-water zone, with mangroves,
vegetated sand flats, and reef complexes. Reefs are mainly
fringing reefs that are situated on the narrow continental shelf
(Mafia, Zanzibar) or are separated from the African mainland
by the deep Pemba Channel (Pemba) (Thissen and Langer,
2017). Noticeably, the major islands are subject to very dif-
ferent degrees of human exploration, as Zanzibar is densely
populated and highly urbanized, while Mafia and Pemba are
largely uninhabited (Narayan et al., 2022). Stone Town and
Bawe, in particular, are faced with a direct discharge of un-
treated domestic sewage along the western coast of Zanz-
ibar Island, where moderate levels of reef deterioration have
been found with a decrease in diversity and coral cover loss
(Bravo et al., 2021; Larsen et al., 2023). Although extensive
long-term monitoring is still lacking, previous studies indi-
cate that the Pemba reefs are likely in pristine condition with
the highest coverage of live hard corals, while the Zanzibar
reefs are often dominated by dead corals intermingled with
algae and seagrass habitats (Ussi et al., 2019; Larsen et al.,
2023; Grimsditch et al., 2009). No quantitative assessment
of reef health has been conducted at Mafia Island, unfortu-
nately, but our field observations suggested moderate to good
conditions at our sampling sites.
3 Materials and methods
3.1 Samples
The 26 surface sediment samples were collected from 16
sites during two field campaigns in 2005 at the islands of
Zanzibar and Pemba and in 2012 at Mafia Island (Table S1
in the Supplement). Depositional depths of all samples range
from 0 to 42 m across the intertidal and subtidal zones. The
selected sampling sites cover all major types of benthic habi-
tats, including a nearshore mangrove habitat; coastal sand
flats; and fringing, fore, and back reefs (Table 1). Note that
the mangrove habitat may be underrepresented in the current
study as we have only one such site, however. Samples were
collected by scuba diving to scrape along the seabed and fill
plastic containers with surface sediments from the top 2 cm
in order to avoid the loss of finer particles due to suspension.
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S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania) 3525
Table 1. Ostracod assemblage information including raw species richness, number of counted individuals, and abundance per gram sediment
in addition to a characterization of benthic habitat in terms of sediment type and algae coverage at each location.
Sample Species No. Abundance Habitat Sediment type Algae
richness individuals (per g) coverage
Haramu Passage20 37 69 1.645 fore reef bioclastic sand low
Haramu Passage30 35 60 4.212 fore reef bioclastic sand low
Kokota Reef25 64 235 4.176 fringing reef bioclastic sand low
Kokota Reef16 78 364 50.845 fringing reef bioclastic sand low
Mapenduzi wall40 60 235 37.337 fore reef bioclastic sand low
Mapenduzi wall42 55 188 22.212 fore reef bioclastic sand low
Misali Island20 65 254 29.480 fore reef bioclastic sand low
Ras Nungwi peak12 56 296 14.775 fringing reef bioclastic sand medium
Ras Nungwi peak12-14 46 116 7.635 fringing reef bioclastic sand medium
Ras Nungwi peak20 81 311 67.845 fringing reef bioclastic sand low
Ras Nungwi16 92 408 40.674 fringing reef bioclastic sand medium
Ras Nungwi20 37 76 16.497 fringing reef bioclastic sand low
Mnemba Atoll30 33 87 45.218 sand flat bioclastic sand medium
Ocean Paradise3 46 231 57.750 back reef bioclastic sand high
Bawe Island9-30 80 410 102.015 fringing reef bioclastic sand high
Bawe Island grob 64 308 13.077 fringing reef bioclastic sand high
Stone Town12 77 519 176.291 fringing reef bioclastic sand high
Stone Town20 66 361 158.542 fringing reef bioclastic sand high
Menai Bay1 36 241 21.294 mangrove fine-grained sand high
Kizimkazi Beach1 24 59 27.949 sand flat fine-grained sand high
Mafia outside21 44 94 20.764 fore reef bioclastic sand medium
Mafia outside20 82 347 96.657 fore reef bioclastic sand medium
Chole Bay18-21 27 74 3.664 back reef bioclastic sand medium
Chole Bay15-18 77 241 55.658 fringing reef bioclastic sand medium
Chole Bay20 72 281 69.383 fringing reef bioclastic sand medium
Mafia Lodge0–3 62 397 65.576 fringing reef fine-grained sand high
Most sampling sites were fine- to medium-grained
carbonate-rich, bioclastic sands and deposits with some reef
rubble. Sediments were washed through a 63 µm sieve and
oven dried at 50 °C. The residue was dry sieved over a
150 µm mesh sieve, and ostracods were picked from the
>150 µm size fraction because smaller individuals are usu-
ally early juveniles that are not preserved and/or are diffi-
cult to identify (Yasuhara et al., 2017). Large-volume sam-
ples were split into aliquot fractions using a microsplitter.
The sample materials were primarily death assemblages, al-
though a very small number of specimens were preserved
with soft parts (less than 1 % among all observed individu-
als), indicating they were alive at the time of collection. Both
live and dead specimens were included in the total count
to represent time-averaged assemblages; this method effec-
tively defines reef habitats and provides general environmen-
tal and diversity data useful in paleoecology (Glenn-Sullivan
and Evans, 2001; Langer and Lipps, 2003). A single valve or
a carapace was considered one individual, which is a stan-
dard counting method in ostracod research (Yasuhara et al.,
2017). Selected specimens were imaged using a scanning
electron microscope (SEM).
3.2 Quantitative analysis
We used Hill numbers (i.e., the effective number of equally
abundant species) parameterized by a diversity order qto es-
timate ostracod diversity in each sample and island (Hill,
1973). Hill numbers have several major advantages over
other diversity indices and have been increasingly adopted
by ecologists (Chao et al., 2020). For example, the Hill num-
bers will double when combining two identically distributed
but distinct communities, so they obey the “doubling prop-
erty” and behave like species richness (Chao et al., 2014b).
In other words, the unit of Hill numbers is also “species”
and thus is more ecologically meaningful than other tradi-
tional diversity indices. Also, the order qof the Hill num-
bers controls the sensitivity of the diversity metric to species
relative abundance. When the order q=0, the Hill num-
ber (0D) reduces to species richness; when the order q=1,
the Hill number (1D) measures the diversity of the abun-
dant species; and when the order q=2, the Hill number
(2D) measures the diversity of dominant species (Chao et al.,
2014b). Therefore, besides species richness, the Hill num-
bers also estimate the effective (or hypothetical) number
of abundant and dominant species. Coincidentally, the Hill
https://doi.org/10.5194/bg-21-3523-2024 Biogeosciences, 21, 3523–3536, 2024
3526 S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Figure 1. Locality map showing three major islands of the Zanzibar
Archipelago with sample sites.
numbers 1Dand 2Dare equivalent to the exponential of
Shannon entropy and Simpson index (hereafter referred to
as Shannon and Simpson diversity), respectively (Chao et
al., 2014b), making them conceptually easy to understand by
ecologists. To make a fair comparison among multiple as-
semblages, we standardized the Hill numbers with rarefac-
tion or extrapolation to the largest sample completeness pos-
sible across samples (82.5 %) and across islands (98.6 %)
(Chao et al., 2020). The standard error and 95 % confidence
intervals of the Hill numbers were estimated by bootstrap re-
sampling, which was repeated 1000 times. Species evenness,
qE3(p) =(qD−1)/(S −1), where qDdenotes Hill numbers
of order qand Sdenotes species richness, was quantified
using the continuous profiles of Hill numbers as functions
of order q(Chao and Ricotta, 2019). A gradual profile sug-
gests a more even community in which the species richness
and number of abundant and dominant species are similar.
In contrast, a steep profile indicates an uneven community
comprised of one or a few dominant species (Mamo et al.,
2023).
To distinguish biofacies associated with different benthic
habitats, we conducted hierarchical cluster analysis based on
Ward’s minimum variance and three Hill-number-based dis-
similarity indices, including Sørensen (q=0), Horn (q=1),
and Morisita–Horn (q=2), to estimate the effective propor-
tion of unshared species in the ostracod assemblages (Chao
et al., 2014a). Similarly, the order qcontrols the sensitiv-
ity of the Hill-number-based dissimilarities to species rela-
tive abundance. While the classic Sørensen dissimilarity is
presence–absence based, the latter two indices are designed
to quantify the compositional dissimilarities of abundant and
dominant species, respectively. Ward’s algorithm is preferred
for delineating biofacies because it minimizes the error sum
of squares within clusters and generates more balanced clus-
ters. The number of clusters was determined by considering
both the structure of the dendrograms and the average silhou-
ette width, with a higher value indicating greater cohesion
and separation of clusters. We also performed a non-metric
multidimensional scaling (nMDS) to visualize and summa-
rize faunal similarities among ostracod assemblages in two-
dimensional space. Stress values were calculated to quantita-
tively weigh the “goodness of fit” between the original input
data matrix and the ultrametric matrix of the resultant nMDS
scatter plots (Hong et al., 2022; Kruskal, 1964). We used
a compositional heat map to illustrate the relationships be-
tween samples by Horn dissimilarities and between species
by Hellinger distances.
All analyses were implemented in RStudio. We used the
package “iNEXT” to estimate diversity (Chao et al., 2014a;
Hsieh et al., 2016) and “vegan” for our multivariate analyses
(Oksanen et al., 2020). Figures and maps were constructed
using “ggplot2” (Wickham, 2020).
4 Results
4.1 Diversity
A total of 6262 ostracods were recovered from 26 samples
at 16 locations around the Zanzibar Archipelago. They rep-
resent remarkably diverse ostracod assemblages comprised
of 235 species under 77 genera. An exceedingly high abun-
dance was found at Stone Town, while sites at Bawe Is-
land and Mafia outside were also abundant in contrast to the
lowest abundance at Haramu Passage and Chole Bay 1 (Ta-
ble 1). Considering the alpha diversity of individual samples
as measured by the Hill number of different orders q, the spa-
tial diversity patterns were relatively consistent for rare (i.e.,
species richness, 0D) and abundant (1D) species. The highest
values were recorded for fringing reefs at Chole Bay 2 and
Ras Nungwi, followed by fringing reefs at Mafia outside and
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S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania) 3527
Ras Nungwi peak (Figs. 2a and 3a, b). Moderately high levels
of diversity were observed at fore-reef sites at Pemba Island
and fringing reefs at Bawe, Stone Town, and Mafia Lodge.
In terms of the diversity of dominant (2D) species, there was
a more homogenous distribution with similarly high values
found at various fringing and fore reefs, including Chole
Bay 2, Mafia outside, Haramu Passage, Bawe Island, Ras
Nungwi, and Ras Nungwi peak (Figs. 2a and 3c). All re-
maining localities (Chole Bay 1, Mnemba Atoll, Ocean Par-
adise, and Kizimkazi Beach) characterized by sand flat and
back reef habitats had consistently low diversity across all or-
ders q, especially Menai Bay that was lined with mangrove
stands (Figs. 2a and 3). Evenness was highest at Haramu Pas-
sage and lowest at Menai Bay for both orders q=1 and
q=2 (Figs. 2b and S1 in the Supplement). With respect
to the gamma diversity of each island, Mafia and Zanzibar
were almost equally diverse across all orders q, while Pemba
had significantly lower diversity for abundant and dominant
species (Figs. 2c and S2 in the Supplement).
4.2 Multivariate analysis
First, cluster analyses based on Sørensen, Horn, and
Morisita–Horn dissimilarities delineated biofacies consider-
ing faunal composition in terms of species occurrence, rela-
tive abundance of abundant species, and relative abundance
of dominant species, respectively. The greatest average sil-
houette width suggested the division of samples into 10 clus-
ters for all three dissimilarity measures; however, it is be-
yond being interpretable having too many clusters given the
size of our dataset. We therefore referred to the structure of
the dendrograms based on three dissimilarity measures, de-
termining the optimum number of clusters to be four (Fig. S3
in the Supplement). The nMDS results showed a clear sep-
aration of four biofacies based on Horn and Morisita–Horn
dissimilarities but not Sørensen dissimilarity, which was cal-
culated with a relatively high stress value (0.26) (Fig. S4 in
the Supplement). Ostracod faunas at Pemba Island consti-
tuted a distinct group across all levels of faunal composition
from presence/absence to relative abundance (Biofacies 1;
Fig. 4). Ras Nungwi, Ras Nungwi peak, and nearby Mnemba
Atoll were congregated with different sites around Zanzibar
and Mafia in Biofacies 2, including Mafia outside and Chole
Bay 2 in Sørensen; Mafia outside, Chole Bay 1, and Chole
Bay 2 in Horn; and Ocean Paradise, Kizimkazi Beach, and
Mafia Lodge in Morisita–Horn analyses (Fig. 4). Samples
assigned to Biofacies 3 and 4 strongly varied depending on
the dissimilarity matrix used, indicating these biofacies have
different ecological meaning among the three cluster anal-
yses (Fig. 4). Specifically, they scattered around the entire
Zanzibar Island based on Sørensen dissimilarity. Biofacies
4 was distributed along the western coast of Zanzibar, in-
cluding Stone Town and Bawe, and Biofacies 3 covered the
remaining Zanzibar locations (Menai Bay, Ocean Paradise,
and Kizimkazi Beach) in addition to Mafia Lodge based on
Horn dissimilarity. On the other hand, when Morisita–Horn
dissimilarity was applied, Menai Bay was different from all
other sites as a distinctive Biofacies 3, while most Mafia sites
(Mafia outside, Chole Bay 1, and Chole Bay 2) aggregated
in Biofacies 4. Considering the performance of multivariate
analyses to reflect and interpret biological patterns, we think
that cluster and nMDS results based on Horn dissimilarity
most reasonably captured the underlying ecological signif-
icance of reefal versus non-reefal facies as determined by
benthic community, depth, and possible anthropogenic dis-
turbances (see the Discussion section). We therefore focus
on the four biofacies as divided by Horn-based analysis to
scrutinize their diversity and compositional structure in rela-
tion to a set of environmental variables.
Each biofacies based on Horn dissimilarity index was
demonstrated with the top 10 species of highest mean rel-
ative abundance as shown in Table 2 and Fig. 5. Noticeably,
the Pemba fauna in Biofacies 1 was dominated by genera
Neonesidea (N. cf. crepidula and N. schulzi) and Bosasella
(B. profunda and B. elongate), together with Paracytheridea
tschoppi (Fig. 6; Table 2). Biofacies 2 included the most
diverse sites in Zanzibar and Mafia, which all shared simi-
lar faunal structures with a high abundance of Loxocornicu-
lum sp. 2, Xestoleberis rotunda,Paracytheridea albatros, and
Loxoconcha sp. 3. Biofacies 3 composed of low-diversity
sites in Zanzibar and Mafia was distinguished by highly
abundant Perissocytheridea estuaria,Xestoleberis hanaii,
and three Loxoconcha species (L. sp. 3, L. ghardaqensis, and
L. lilljeborgii). Finally, the faunal structure of Biofacies 4 in
western Zanzibar showed some similarities to that of Biofa-
cies 1 in Pemba with many common species; however, they
clearly differed by the dominance of Xestoleberis hanaii and
Patrizia nucleuspersici in Biofacies 4.
5 Discussion
Through Hill number profile and multivariate analyses, we
quantified a highly diverse ostracod fauna in the Zanzibar
Archipelago composed of four distinct biofacies. The delin-
eation of biofacies varied considerably depending on the dis-
similarity matrix used, indicating inconsistent faunal struc-
tures across different levels of species information from oc-
currence to relative abundance (Fig. 4). In terms of the pres-
ence/absence of species (Sørensen dissimilarity), all Pemba
sites united in Biofacies 1, but the assignment of Zanzibar
and Mafia sites into Biofacies 1–4 seemingly conformed to
a noisy pattern (Fig. 4a). Accordingly, four biofacies inter-
sected with each other in nMDS space with a relatively high
stress value (Fig. S4a). A possible explanation is that the oc-
currence of individual species may be homogenous among
sites in similar environmental conditions within a finite ge-
ographic region. Many species are likely to be ubiquitous
across the entire neritic zone despite showing certain ecolog-
ical preferences, and the redeposition processes may further
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3528 S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Figure 2. Diversity results of the Zanzibar Archipelago ostracods. (a) Alpha diversity of each sample shown by Hill number profile based
on 82.5 % sample coverage. The overall elevation of the profile indicates the diversity based on hill number across different orders q. The
levelness of the line indicates species evenness of the assemblage because a completely leveled diversity profile would suggest that the
numbers of total, common, and dominant species are all the same. (b) Evenness of each sample as the normalized slope of Hill number
profile for orders q=1 and q=2 based on 82.5 % sample coverage. (c) Gamma diversity of each island shown by Hill number profile based
on 98.6 % sample coverage. The shaded area shows the 95% confidence interval of the profile.
facilitate the mixing of death assemblages to blur the spatial
signal at a local scale (Frenzel and Boomer, 2005). Conse-
quently, species presence in all available habitats may trans-
late to considerable faunal similarities among biofacies as
measured by the Sørensen index. When considering the com-
position of abundant species (Horn dissimilarity) (Fig. 4b),
the identification of four biofacies instead reflected signifi-
cant changes in ostracod assemblages along two important
environmental gradients, which are benthic community type
and water depth. Specifically, Biofacies 1 and 2 characterize
typical fore reefs in the deep subtidal zone (sampling depth
16–42 m) and fringing reefs in the shallow subtidal zone (12–
30 m), respectively (Fig. 6). Biofacies 3 indicates intertidal
habitats with plant cover (0–3 m), and finally Biofacies 4 fea-
tures degraded fringing reefs in the shallow subtidal zone (9–
30 m) (see discussion below).
We summarized the ecological preferences of dominant
genera in each biofacies based on Horn dissimilarity (Ta-
ble 3 and Fig. 6) and investigated how key environmental
factors (benthic community type, water depth, and anthro-
pogenic disturbance) may control the distribution and diver-
sity of reefal ostracod assemblages. First of all, Neonesidea
and Paranesidea (family Bairdiidae) are typical reefal genera
that reach their maximum diversity and incidence on reefs
and reef-associated habitats in tropical shallow-marine en-
vironments (Whatley and Watson, 1988; Maddocks, 2013;
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S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania) 3529
Figure 3. Diversity maps of the Zanzibar Archipelago ostracods. Distributions of Hill numbers 0D(a q=0, species richness),1D(b q=1,
exponential Shannon), and 2D(c q=2, inversed Simpson). We used 82.5 % sample coverage to standardize the Hill number estimates.
Diversity and habitat are represented by color and shape as shown in the legends, respectively.
Table 2. List of the top 10 species of the highest mean relative abundance for Biofacies 1–4 based on Horn dissimilarity.
Species Biofacies 1 Biofacies 2 Biofacies 3 Biofacies 4
Neonesidea cf. crepidula 0.085857 n/a n/a n/a
Bosasella profunda 0.079436 n/a n/a 0.040846
Neonesidea schulzi 0.075285 0.032551 0.024322 0.041291
Paracytheridea tschoppi 0.035779 n/a n/a 0.028826
Loxocorniculum sp. 2 0.030562 0.063399 n/a n/a
Xestoleberis hanaii 0.028593 0.039954 0.084378 0.071834
Patrizia nucleuspersici 0.02842 n/a n/a 0.057965
Paranesidea cf. spongicola 0.026203 n/a n/a 0.029754
Xestoleberis sp. 1 0.023801 n/a n/a n/a
Bosasella elongata 0.023369 n/a 0.017579 n/a
Xestoleberis rotunda n/a 0.061861 n/a n/a
Paracytheridea albatros n/a 0.045056 0.037464 n/a
Loxoconcha sp. 3 n/a 0.041327 0.110386 n/a
Bosasella sp. 1 n/a 0.040122 n/a n/a
Macrocyprina maddocksae n/a 0.039264 n/a n/a
Caudites exmouthensis n/a 0.027832 n/a n/a
Paranesidea sp. 1 n/a 0.025497 n/a n/a
Perissocytheridea estuaria n/a n/a 0.157932 n/a
Loxoconcha ghardaqensis n/a n/a 0.073153 n/a
Hiltermannicythere rubrimaris n/a n/a 0.04805 n/a
Loxoconcha lilljeborgii n/a n/a 0.033061 n/a
Neohornibrookella lactea n/a n/a 0.018616 n/a
Neonesidea sp. 3 n/a n/a n/a 0.048331
Neonesidea paiki n/a n/a n/a 0.042016
Loxoconcha cf. gisellae n/a n/a n/a 0.035319
Perissocytheridea? sp. 2 n/a n/a n/a 0.029391
n/a: not applicable.
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3530 S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Figure 4. Distribution of ostracod Biofacies 1–4 based on (a)
Sørensen, (b) Horn, and (c) Morisita–Horn dissimilarities and
Ward’s minimum variance cluster analysis. Note that the color
schemes are independent among panels; thus, the biofacies based on
different dissimilarities are unrelated. Cluster and habitat are repre-
sented by color and shape as shown in the legends, respectively.
Titterton and Whatley, 1988). Their dominance in Biofacies
1 is consistent with our background understanding that the
Pemba reefs were pristine and healthy (Ussi et al., 2019;
Grimsditch et al., 2009). However, it should be noted that
individual species of these genera likely have different en-
vironmental tolerance. For example, N. cf. crepidula were
restricted to Biofacies 1, while N. schulzi were widespread
among four biofacies inhabiting both reef and algae habi-
tats (Fig. 6) (Mostafawi et al., 2005). Bosasella as another
prominent component of Biofacies 1 is also known to oc-
cur on coral reefs in the western Indian Ocean (Munef et
al., 2012; Jellinek, 1993). Paracytheridea and Caudites on
the other hand are loosely categorized as reefal genera, as
their dominance on coral reefs was reported but not stud-
ied in detail (Whatley and Watson, 1988; Keyser and Mo-
hammed, 2021). In this study, they were common on fore
and fringing reefs in Biofacies 1 and 2 (Fig. 6). Loxoconcha
and Loxocorniculum (family Loxoconchidae) as two phy-
logenetically related and ecologically similar genera exhib-
ited ubiquitous distribution around the Zanzibar Archipelago
with the highest relative abundance in Biofacies 3 followed
by Biofacies 2. As generalists, they thrive on a wide variety
of benthic habitats across the neritic zone and show affinities
towards plant substrates (algae and seagrass beds) in par-
ticular (Munef et al., 2012; Keyser and Mohammed, 2021;
Kamiya, 1988). The ecology of Xestoleberis is very similar
to that of Loxoconchidae, living both on coral reefs and al-
gal flats (Keyser and Mohammed, 2021; Munef et al., 2012;
Whatley and Watson, 1988; Kamiya, 1988). This genus was
almost equally weighted in all biofacies, although individual
species clearly preferred different environments, as X. hanaii
prevailed in Biofacies 3 and 4, whereas X. rotunda only did
in Biofacies 2 (Fig. 6). Patrizia is documented as a reefal
genus in the lower littoral zone along the eastern coast of
tropical Africa (Jellinek, 1993). It dominated the relatively
deep fringing-reef faunas of Biofacies 4, which were subject
to sewage-derived nutrient and trace metal pollution from
Zanzibar Town (Narayan et al., 2022; Bravo et al., 2021).
Different from all the above-discussed genera, Hiltermanni-
cythere and Perissocytheridea are restricted to shallow in-
tertidal environments as phytal and sediment-dwelling taxa,
respectively (Jellinek, 1993), which explains their abundance
in our Biofacies 3. Perissocytheridea is especially considered
a bioindicator of brackish water facies, adapting to euryha-
line conditions (Nogueira and Ramos, 2016; Keyser, 1977).
Furthermore, we revealed a more generalized pattern of the
compositional differences among biofacies with the top five
families of highest mean relative abundance in each biofacies
(Fig. 7).
Thus, our study indicates that the distribution of shallow-
marine ostracods in the Zanzibar Archipelago is character-
ized by three reefal facies and one intertidal facies. Yet
slight differences in bathymetry, benthic community type,
and anthropogenic impacts likely contributed to subtle fau-
nal changes among reefal Biofacies 1, 2, and 4. The fore
reefs in Pemba (Biofacies 1) were deepest with a high in-
cidence and diversity of live hard corals (Gavrilets and
Losos, 2009; Ussi et al., 2019), which accounted for the
definite dominance of ostracod reefal taxa (Bairdiidae and
Bosasella) over algal taxa (Loxoconchidae and Xestoleberi-
didae) (Figs. 6 and 7). Moderately high levels of diversity
in terms of rare, abundant, and dominant species were ob-
served for these ostracod assemblages (Fig. 3). The Pemba
reefs are thereby considered the most mature and authen-
tic reef ecosystem, serving as a natural reference for com-
paring with other sites. The fringing-reef fauna of west-
ern Zanzibar (Stone Town and Bawe, Biofacies 4) exhibited
certain similarities to the Pemba fauna as indicated by the
prevalence of Bosasella profunda,Paracytheridea tschoppi,
and Paranesidea cf. spongicola in both facies (Fig. 6). In-
deed, they were grouped together based on the composi-
tion of dominant species (Morisita–Horn analysis) (Fig. 4c).
Faunal similarities between Pemba and Stone Town make
sense as they are in comparable baseline conditions of wa-
ter depths and hydrology along the protected western coast
of the Zanzibar Archipelago in contrast to Ras Nungwi and
Chole Bay that are exposed to oceanic disturbances from the
east (Fig. 1). However, Biofacies 4 was differentiated from
Biofacies 1 by the dominance of Patrizia in conjunction with
the absence of Neonesidea cf. crepidula. It also had the high-
est relative abundance of Trachyleberididae genera among all
facies (Fig. 7), for example, Adencythere,Strobilocythere,
Biogeosciences, 21, 3523–3536, 2024 https://doi.org/10.5194/bg-21-3523-2024
S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania) 3531
Figure 5. Scanning electron microscopy images of the top 10 ostracod species of the highest mean relative abundance for Biofacies 1–4 based
on Horn dissimilarity. 1,Neonesidea cf. crepidula, RV (right valve), Kokota Reef25; 2,Neonesidea cf. crepidula, LV (left valve), Haramu
Passage30; 3,Neonesidea paiki, RV, Bawe Island9-30; 4,Neonesidea paiki, LV, Kokota Reef25; 5,Neonesidea schulzi, RV, Mapenduzi
wall42; 6,Neonesidea schulzi, LV, Kokota Reef25; 7,Neonesidea sp. 3, RV, Bawe Island9-30; 8,Neonesidea sp. 3, LV, Bawe Island9-
30; 9,Paranesidea cf. spongicola, RV, Bawe Island9-30; 10,Paranesidea cf. spongicola, LV, Kokota Reef25; 11,Paranesidea sp. 1, RV,
Chole Bay18-21; 12,Paranesidea sp. 1, LV, Chole Bay18-21; 13,Macrocyprina maddocksae, RV, Haramu Passage20; 14,Macrocyprina
maddocksae, LV, Kokota Reef16; 15,Perissocytheridea estuaria, RV, Menai Bay1; 16,Perissocytheridea estuaria, LV, Menai Bay1; 17,
Perissocytheridea? sp. 2, RV, Bawe Island grob; 18,Perissocytheridea? sp. 2, LV, Bawe Island9-30; 19,Bosasella elongate, RV, Haramu
Passage30; 20,Bosasella elongate, LV, Mapenduzi wall42; 21,Bosasella profunda, RV, Haramu Passage20; 22,Bosasella profunda, LV,
Mapenduzi wall42; 23,Bosasella sp. 1, RV, Kokota Reef25; 24,Bosasella sp. 1, LV, Kokota Reef16; 25,Caudites exmouthensis, LV, Ras
Nungwi16; 26,Loxoconcha ghardaqensis, RV, Mnemba Atoll30; 27,Loxoconcha ghardaqensis, LV, Ras Nungwi peak12; 28,Loxoconcha
cf. gisellae, RV, Bawe Island9-30; 29,Loxoconcha cf. gisellae, LV, Bawe Island9-30; 30,Loxoconcha lilljeborgii, RV, Bawe Island9-30; 31,
Loxoconcha lilljeborgii, LV, Bawe Island grob; 32,Loxoconcha sp. 3, RV, Stone Town20; 33,Loxoconcha sp. 3, LV, Stone Town20; 34,
Loxocorniculum sp. 2, RV, Haramu Passage30; 35,Loxocorniculum sp. 2, LV, Kokota Reef16; 36,Paracytheridea albatross, RV, Kokota
Reef25; 37,Paracytheridea albatross, LV, Kokota Reef16; 38,Paracytheridea tschoppi, RV, Kokota Reef25; 39,Paracytheridea tschoppi,
LV, Mapenduzi wall42; 40,Neohornibrookella lactea, RV, Misali Island20; 41,Hiltermannicythere rubrimaris, RV, Stone Town20; 42,
Patrizia nucleuspersici, RV, Stone Town20; 43,Patrizia nucleuspersici, LV, Stone Town12; 44,Xestoleberis hanaii, RV, Bawe Island9-30;
45,Xestoleberis hanaii, LV, Kokota Reef25; 46,Xestoleberis rotunda, LV, Ras Nungwi peak12; 47,Xestoleberis sp. 1, RV, Mapenduzi
wall42. All adults and lateral views.
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3532 S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Figure 6. Dendrograms based on Horn dissimilarity between samples and Hellinger distances between the top 10 species of highest mean
relative abundance in each cluster. The blue heatmap indicates the relative (%) abundance of each species in each sample. The side panel
shows water depth and habitat type of each sample (note that several samples are shown by their corresponding depth ranges).
Table 3. Autoecology summary of important ostracod genera.
Genus Predominant habitats References
Neonesidea coral reef Whatley and Watson (1988), Maddocks (2013), Titterton and Whatley (1988),
Maddocks (1969)
Paranesidea coral reef Titterton and Whatley (1988), Whatley and Watson (1988), Maddocks (1969)
Bosasella coral reef Munef et al. (2012)
Loxoconcha algal mat and reef Keyser and Mohammed (2021), Whatley and Watson (1988),
Munef et al. (2012), Kamiya (1988)
Loxocorniculum algal mat and reef Munef et al. (2012), Kamiya (1988)
Xestoleberis algal mat and reef Keyser and Mohammed (2021), Whatley and Watson (1988),
Munef et al. (2012), Kamiya (1988)
Patrizia coral reef Jellinek (1993)
Hiltermannicythere intertidal algal mat Jellinek (1993), Keyser and Mohammed (2021)
Paracytheridea coral reef Whatley and Watson (1988)
Caudites coral reef Whatley and Watson (1988), Keyser and Mohammed (2021)
Perissocytheridea intertidal sand flat, euryhaline Nogueira and Ramos (2016), Keyser (1977)
Bradyon, and Actinocythereis, but their ecologies are not
well understood. Stressful environmental conditions in terms
of overexploitation, tourism, and coastal pollution offer the
most possible explanation for such a unique faunal compo-
sition and the comparatively low diversity of Biofacies 4
(Fig. 3) (Bravo et al., 2021; Larsen et al., 2023). Consistently,
foraminifera and coral surveys indicated early stages of reef
degradation there (Narayan et al., 2022; Bravo et al., 2021;
Thissen and Langer, 2017). It is possible that ongoing anthro-
pogenic disturbances near Stone Town will eventually ex-
ceed the critical threshold levels and cause more pronounced
changes in ostracod faunal structures in terms of dominant
Biogeosciences, 21, 3523–3536, 2024 https://doi.org/10.5194/bg-21-3523-2024
S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania) 3533
Figure 7. Family composition of Biofacies 1–4 based on Horn dis-
similarity. The top five families of the highest percentage of relative
abundance in each biofacies are shown.
species through a shift in benthic habitat (Narayan et al.,
2022; Hong et al., 2022). Other than Biofacies 1 and 4, Biofa-
cies 2 mostly represented the different type of relatively shal-
low (12–20 m) fringing-back reef habitats of Ras Nungwi,
Chole Bay, and Mafia outside, in addition to the deeper
(30 m) sand flat of Mnemba Atoll (Fig. 6). Algal taxa (Loxo-
conchidae and Xestoleberididae) and reefal taxa (Bairdiidae,
Bosasella,Paracytheridea, and Caudites) reached equally
high levels of relative abundance there (Figs. 6 and 7). Mi-
crohabitats on the reef platforms of Biofacies 2 are believed
to be diverse and heterogenous with interlaced live and dead
corals, algae and seagrass, calcareous sands, and bare sub-
strate rock (Ussi et al., 2019; Larsen et al., 2023), which facil-
itated the coexistence of reefal and algal ostracods and con-
sequently the highest diversity of local assemblages (Fig. 3).
The remainder of Biofacies 3 corresponded to the shallow-
est intertidal habitats with various benthic communities, in-
cluding a marginal back reef, a marginal fringing reef, a
sand flat, and a mangrove habitat (Fig. 6). Typical reefal taxa
(Bairdiidae and Bosasella) dropped to their lowest relative
abundance in this facies, replaced by large numbers of Lox-
oconchidae, Perissocytheridea, and Hiltermannicythere that
are well-adapted to shallow euryhaline conditions (Figs. 6
and 7). Not surprisingly, the diversity of Biofacies 3 was
much lower than that of open-ocean reefal facies, as dras-
tic changes in temperature, salinity, dissolved oxygen, and
wave energy in the intertidal zone may be too challenging
for many marine taxa (Fig. 3) (Morley and Hayward, 2007;
Frenzel and Boomer, 2005). The mangrove habitat at Menai
Bay was unique concerning the absolute dominance of Peris-
socytheridea in line with its lowest diversity and evenness
(Figs. 2b and 3). It indeed constituted an independent biofa-
cies based on Morisita–Horn analysis (Fig. 4c).
The division scheme of four biofacies based on Horn
dissimilarity explicitly revealed spatial patterns of ostra-
cod distribution in the aspects of diversity and composi-
tion, as discussed above. Our results are generally concor-
dant with a previous study on benthic foraminifera, which
separated six clusters of Pemba, Stone Town, Mafia Bay, Ras
Nungwi, Mnemba Atoll, and Menai Bay (Fig. 8b) (Thissen
Figure 8. Distributions of benthic foraminifera: (a) diversity mea-
sured as Fisher alpha index; (b) cluster groups based on Q-mode
cluster analysis. Modified from Thissen and Langer (2017). Diver-
sity/cluster and habitat are represented by color and shape as shown
in the legends, respectively.
and Langer, 2017). Each of these foraminifera clusters cor-
responded to major habitat types, as argued by the authors
(Thissen and Langer, 2017), and we accordingly point out
the consistent role of habitat factors in shaping the biogeog-
raphy of both ostracod and foraminifera biota. However, the
diversity patterns of these two groups were apparently dif-
ferent among reefal habitats (Figs. 3 and 8a). High, mod-
erate, and low levels of diversity were recorded on fore
reefs (Pemba), fringing reefs (Mafia and Zanzibar), and inter-
tidal zones (Zanzibar) for foraminifera in contrast to fringing
reefs (Mafia and Zanzibar), fore reefs (Pemba), and intertidal
zones (Zanzibar) for ostracods, respectively. Such discrep-
ancies may imply a tight association of foraminifera with
the reef ecosystem and their ultra-sensitivity to reef health,
since their diversity generally decreased from pristine, ma-
ture reefs to degraded, marginal reefs. Ostracods on the other
hand may be less confined or specific to reef habitats. The
occupation of coral and algae substrate by distinct faunal
groups allows them to thrive in the transitional zone between
marginal and true reefs. Another important factor account-
ing for the different distributional patterns between ostracods
and foraminifera is likely their tolerance to eutrophication
and pollution. Previous studies indicate that an intermediate
level of eutrophication is beneficial to ostracods and many
other soft-sediment benthos, which are also resistant to heavy
metal pollution in highly urbanized areas (Hong et al., 2022).
https://doi.org/10.5194/bg-21-3523-2024 Biogeosciences, 21, 3523–3536, 2024
3534 S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania)
Consistently, our sampling sites at Stone Town reported the
highest abundance of ostracods (Table 1). Foraminifera on
the other hand are susceptible to environmental stressors, as
shown by low taxonomic richness and high dominance of the
faunas in eutrophic conditions (Mamo et al., 2023). In our
case, it makes sense that the highest diversity of foraminifera
was found in pristine and oligotrophic Pemba waters.
Most importantly, this study established a clear ben-
thic community axis along which the composition and
diversity of ostracod assemblages vary, i.e., from coral
reefs to algae turfs. We identified typical reefal as-
sociation (Bairdiidae–Bosasella) versus algal association
(Loxoconchidae–Xestoleberididae) (Fig. 7), and their rela-
tive dominance may be used as a direct indication of ben-
thic community type. As there is a growing interest to
monitor the degradation of reef ecosystems from the coral-
dominated phase to the algae-dominated phase (Roth et al.,
2018; Knowlton and Jackson, 2008; Knowlton, 2012), our
finding is of potential conservation value. Ostracod species
diversity was higher on shallow fringing reefs than on deep
fore reefs, as the former ecosystem harbored evenly weighted
reefal and algal taxa within a dynamic mosaic of microhabi-
tats. Our results thus strongly indicate the importance of coral
reefs in harboring conspicuously high levels of meiobenthic
biodiversity, likely through finer niche partitioning (Kohn et
al., 1997; Fox and Bellwood, 2013). Along with the ben-
thic community factor, we quantified prominent changes in
faunal structure and diversity along a depth gradient, as the
intertidal euryhaline assemblages transited to subtidal fully
marine assemblages. It is widely recognized that shallow-
marine biota are especially susceptible to depth-associated
changes, such as temperature, salinity, wave action, and light
penetration (Carvalho et al., 2012; Tian et al., 2022). This
study showed that a narrow depth zone across the intertidal
and subtidal zones (∼40 m) was further divided and occu-
pied by distinct biofacies. Such a finely tuned vertical gradi-
ent of diversity and faunal composition added to an exceed-
ingly large regional species pool (235 species) in this trop-
ical shallow-marine setting. Last but not least, it should be
noted that the effects of depth and benthic community type
are often intertwined with each other in determining ostracod
assemblages, as the habitat-building corals and algae essen-
tially exhibit depth distributions. At a regional scale like the
Zanzibar Archipelago, the combined effects of water depth
and benthic community characteristics should be considered
in studying the spatial patterns of benthic organisms.
6 Conclusion
In conclusion, this study showed that the diversity and faunal
composition of reefal ostracod assemblages vary along ben-
thic community and bathymetric gradients, which may also
be altered by local anthropogenic disturbances. Ostracod fau-
nas on shallow fringing reefs were especially diverse, which
may be explained by high levels of habitat complexity and
heterogeneity. The relative dominance of reefal taxa (Bairdi-
idae) versus algal taxa (Loxoconchidae–Xestoleberididae) is
likely determined by the proportion of coral versus algae
cover on the reef platforms, though more extensive studies
beyond this region are needed to confirm the universality of
this pattern. Coral reefs worldwide are vulnerable to ongoing
climate changes and other human impacts at local to global
scales, and many reefal species are at risk of extinction. It is
of great importance that we inspect and understand the im-
mense biodiversity of meiobenthos on coral reefs as an indis-
pensable part of the ecosystem.
Data availability. Ostracod census data are available in the Supple-
ment.
Supplement. The supplement related to this article is available on-
line at: https://doi.org/10.5194/bg-21-3523-2024-supplement.
Author contributions. Each named author has participated suffi-
ciently in the work to take public responsibility for the content. SYT
and ML developed the concept. ML collected the samples. SYT per-
formed the research and collected the data. SYT and CLW analyzed
the data. SYT drafted the manuscript. ML, MY, and CLW reviewed
and edited the manuscript.
Competing interests. The contact author has declared that none of
the authors has any competing interests.
Disclaimer. Publisher’s note: Copernicus Publications remains
neutral with regard to jurisdictional claims made in the text, pub-
lished maps, institutional affiliations, or any other geographical rep-
resentation in this paper. While Copernicus Publications makes ev-
ery effort to include appropriate place names, the final responsibility
lies with the authors.
Acknowledgements. We thank Stephanie Pietsch, Jens Thissen,
Anna Weinmann, and Michael Kunert for their help with fieldwork
and Jingfang He for her help in the lab.
Financial support. This research has been supported by the
Alexander von Humboldt-Stiftung (Humboldt Research Fel-
lowship); the Deutsche Forschungsgemeinschaft (grant no. LA
884/10-1); the Research Grants Council, University Grants
Committee (grant nos. HKU 17306023 and G-HKU709/21); and
the National Science and Technology Council (grant no. NSTC
112-2611-M-002-011).
This open-access publication was funded
by the University of Bonn.
Biogeosciences, 21, 3523–3536, 2024 https://doi.org/10.5194/bg-21-3523-2024
S. Y. Tian et al.: Reefal ostracod assemblages from the Zanzibar Archipelago (Tanzania) 3535
Review statement. This paper was edited by Helge Niemann and
reviewed by Peter Frenzel, Ilaria Mazzini, and Andreas Haas.
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