Jennifer E Smith

• PhD
• Professor (Full) at University of California, San Diego

High spatial or temporal variability in community composition makes it challenging for natural resource managers to predict ecosystem trajectories at scales relevant to management. This is commonly the case in nearshore marine environments, where the frequency and intensity of disturbance events vary at the sub-kilometer to meter scale, creating a...

Coral reef algae serve many important ecological functions, from primary production to nutrient uptake and reef stabilization, but our knowledge of longer-term effects of thermal stress on algae in situ is limited. While ocean warming can facilitate proliferation of algae and potential phase shifts from coral to macroalgal-dominated states, algal r...

Rhodolith beds are biogenic marine habitats formed by aggregations of free‐living crustose coralline algae. New descriptions of rhodolith beds fill the gaps in our understanding of the global distribution and ecological significance of these understudied habitats. We provide the first characterisation of a network of rhodolith beds associated with...

The red alga Asparagopsis taxiformis has recently been recognized for its unique ability to significantly reduce methane emissions from ruminant animals when fed in small quantities. The main obstacle in using this seaweed as a methane‐mitigating feed supplement is the lack of commercially available biomass. Little is known about how best to grow t...

Long-term monitoring of individual coral colonies is important for understanding variability between and within species over time in the context of thermal stress. Here, we analyze an 11-year time series of permanent benthic photoquadrats taken on Palmyra Atoll, central Pacific, from 2009 to 2019 to track the growth (i.e., increase in live planar a...

Climate change is transforming coral reefs by increasing the frequency and intensity of marine heatwaves, often leading to coral bleaching and mortality. Coral communities have demonstrated modest increases in thermal tolerance following repeated exposure to moderate heat stress, but it is unclear whether these shifts represent acclimatization of i...

In April and May of 2020, a large phytoplankton bloom composed primarily of the dinoflagellate Lingulodinium polyedra reached historic levels in geographic expanse, duration, and density along the coast of southern California, United States, and Baja California Norte, Mexico. Here, we report the water quality parameters of dissolved oxygen and pH o...

The inclusion Asparagopsis spp. into the diet of ruminant animals has produced compelling data regarding the mitigation of agricultural methane emissions. This reduction is achieved via the action of brominated halogenated compounds, predominantly bromoform, which act to inhibit methanogenic enzymes in ruminant digestion. As such, there is great in...

Marine heatwaves and regional coral bleaching events have become more frequent and severe across the world's oceans over the last several decades due to global climate change. Observational studies have documented spatiotemporal variation in the responses of reef-building corals to thermal stress within and among taxa across geographic scales. Alth...

Marine heatwaves are triggering coral bleaching events and devastating coral populations globally, highlighting the need to identify processes promoting coral survival. Here, we show that acceleration of a major ocean current and shallowing of the surface mixed layer enhanced localized upwelling on a central Pacific coral reef during the three stro...

Parrotfishes are conspicuous herbivores, microvores, and detritivores in coral reef ecosystems, and the impacts of their feeding, particularly their capacity to expose reef carbonate, have received much attention. In many cases, parrotfish assemblages have been shown to control algal proliferation and promote the settlement of corals and crustose c...

Ocean deoxygenation is predicted to threaten marine ecosystems globally. However, current and future oxygen concentrations and the occurrence of hypoxic events on coral reefs remain underexplored. Here, using autonomous sensor data to explore oxygen variability and hypoxia exposure at 32 representative reef sites, we reveal that hypoxia is already...

While green turtles (Chelonia mydas) were once abundant throughout the Caribbean, over-exploitation has dramatically reduced their numbers. We conducted a 168-day simulated grazing experiment to determine how loss of this once-abundant mega-herbivore could have affected the productivity and community composition of Thalassia testudinum-dominated se...

Methane is an extremely potent yet short-lived greenhouse gas and is thus recognized as a promising target for rapid climate change mitigation. About 35% of anthropogenic methane emissions are associated with livestock production, and most of these emissions are the outcome of enteric fermentation in ruminant animals. The red seaweed Asparagopsis i...

While green turtles (Chelonia mydas) were once abundant throughout the Caribbean, overexploitation has dramatically reduced their numbers. We conducted a 168-day simulated grazing experiment to determine how loss of this once-abundant mega-herbivore could have affected the productivity and community composition of Thalassia testudinum-dominated sea...

Methane is an extremely potent yet short-lived greenhouse gas and is thus recognized as a promising target for rapid climate change mitigation. About 35% of anthropogenic methane emissions are associated with livestock production, and most of these emissions are the outcome of enteric fermentation in ruminant animals. The red seaweed Asparagopsis i...

Phytoplankton blooms create organic matter that stimulates entire marine ecosystems, including other components of the microbial community. How the ecosystem responds varies depending on the intensity, duration, and composition of the bloom. When the bloom has a direct or indirect negative impact on the ecosystem, it is termed a harmful algal bloom...

Decades of research have revealed relationships between the abundance of coral reef taxa and local conditions, especially at small scales. However, a rigorous test of covariation requires a robust dataset collected across wide environmental or experimental gradients. Here, we surveyed spatial variability in the densities of major coral reef functio...

Tropical reef communities contain spatial patterns at multiple scales, observable from microscope and satellite alike. Many of the smaller-scale patterns are generated physiologically (e.g., skeletal structures of corals at <1-m scale), while some of the larger patterns have been attributed to scale-dependent feedbacks (e.g., spur and groove reefs...

Global climate change, such as warming and ocean acidification (OA), are likely to negatively impact calcifying marine taxa. Abundant and ecologically important coralline algae may be particularly susceptible to OA, however multi‐stressor studies and those on articulated morphotypes are lacking. Here, we use field observations and laboratory experi...

The prevalence of coral bleaching due to thermal stress has been increasing on coral reefs worldwide. While many studies have documented how corals respond to warming, fewer have focused on benthic community responses over longer time periods or on the response of non-coral taxa (e.g., crustose coralline algae, macroalgae, or turf). Here, we quanti...

Standardized metrics that quantify a component of ecosystem functioning are essential for evaluating the current status of coastal marine habitats and for monitoring how ecologically important ecosystems are changing in response to global and local environmental change. Calcification accretion units (CAUs) are a standardized tool for quantifying ne...

Photosynthetic microalgae are an attractive source of food, fuel, or nutraceuticals, but commercial production of microalgae is limited by low spatial efficiency. In the present study we developed a simple photosynthetic hydrogel system that cultivates the green microalga, Marinichlorella kaistiae KAS603, together with a novel strain of the bacteri...

Plain Language Summary Mass bleaching events caused by warming oceans and intensifying marine heatwaves have killed millions of corals globally. In the central equatorial Pacific, coral reefs experienced three extreme heatwaves within 15 years, providing valuable insights into the mechanisms that could facilitate coral survival under global warming...

Ocean acidification (OA) is likely to differentially affect the biology and physiology of calcifying and non-calcifying taxa, thereby potentially altering key ecological interactions (e.g., facilitation, competition, predation) in ways that are difficult to predict from single-species experiments. We used a two-factor experimental design to investi...

The effects of nutrient pollution on coral reef ecosystems are multifaceted. Numerous experiments have sought to identify the physiological effects of nutrient enrichment on reef‐building corals, but the results have been variable and sensitive to choices of nutrient quantity, chemical composition and exposure duration. To test the effects of chron...

Photosynthetic microalgae are an attractive source of food, fuel or nutraceuticals, but commercial production of microalgae is limited by low spatial efficiency. In the present study, we developed a simple photosynthetic hydrogel system that cultivates the green microalga, Marinichlorella kaistiae KAS603, together with a novel strain of the bacteri...

Abstract In marine systems, algal abundance and community composition is often heavily influenced by top-down control by herbivores. As a result, examining the extent to which native herbivores exert grazing pressure on non-native marine algae can provide valuable insight into mechanisms controlling invasion success. The purpose of this study was t...

The impacts of sea-level rise (SLR) are likely to be the greatest for ecosystems that exist at the land-sea interface, where small changes in sea-level could result in drastic changes in habitat availability. Rocky intertidal ecosystems possess a number of characteristics which make them highly vulnerable to changes in sea-level, yet our understand...

Primary producers release oxygen as the by-product of photosynthetic light reactions during the day. However, a prevalent, globally-occurring nighttime spike in dissolved oxygen in the absence of light challenges the traditional assumption that biological oxygen production is limited to daylight hours, particularly in tropical coral reefs. Here we...

Field‐based cultivation of Kappaphycus and Eucheuma seaweeds is widespread across the tropics and is largely done to extract the polysaccharide carrageenan, which is used in commercial applications. Although such seaweed farming has been cited as a sustainable alternative livelihood to destructive fishing, there has not been a comprehensive review...

Upwelling is an important source of inorganic nutrients in marine systems, yet little is known about how gradients in upwelling affect primary producers on coral reefs. The Southern Line Islands span a natural gradient of inorganic nutrient concentrations across the equatorial upwelling region in the central Pacific. We used this gradient to test t...

Coral reefs are facing intensifying stressors, largely due to global increases in seawater temperature and decreases in pH. However, there is extensive environmental variability within coral reef ecosystems, which can impact how organisms respond to global trends. We deployed spatial arrays of autonomous sensors across distinct shallow coral reef h...

Few studies have documented the spatial and temporal dynamics of highly invasive species in coral reef benthic communities. Here, we quantified the ecological dynamics of invasion by a corallimorph, Rhodactis howesii, at Palmyra Atoll in the central Pacific. A localized outbreak of this species was first observed following a shipwreck at Palmyra in...

Reef‐building corals are mixotrophic organisms that can obtain nutrition from endosymbiotic microalgae (autotrophy) and particle capture (heterotrophy). Heterotrophic nutrition is highly beneficial to many corals, particularly in times of stress. Yet, the extent to which different coral species rely on heterotrophic nutrition remains largely unknow...

Population distributions are affected by a variety of spatial processes, including dispersal, intraspecific dynamics, and habitat selection. Within reef‐building coral communities, these processes are especially important during the earliest life stages when reproduction provides mobility among sessile organisms and populations experience the great...

During 2015–2016, an El Niño and associated warm water event caused widespread coral bleaching across the equatorial Pacific. Here, we combine 8 yr of benthic monitoring data from permanent photoquadrats with remotely sensed and in situ temperature measurements to assess the impact of the warming event on benthic communities at Palmyra Atoll. We qu...

On coral reefs, microorganisms are essential for recycling nutrients to primary producers through the remineralization of benthic-derived organic matter. Diel investigations of reef processes are required to holistically understand the functional roles of microbial players in these ecosystems. Here we report a metagenomic analysis characterizing mi...

Rocky intertidal ecosystems may be particularly susceptible to sea-level rise impacts but few studies have explored community scale response to future sea-level scenarios. Combining remote-sensing with large-area imaging, we quantify habitat extent and describe biological community structure at two rocky intertidal study locations in California. We...

Mixotrophy is among the most successful nutritional strategies in terrestrial and marine ecosystems. The ability of organisms to supplement primary nutritional modes along continua of autotrophy and heterotrophy fosters trophic flexibility that can sustain metabolic demands under variable or stressful conditions. Symbiotic, reef-building corals are...

This document is part of the status report series of the Global Coral Reef Monitoring Network (GCRMN) founded in 1995 as part of the International Coral Reef Initiative (ICRI) to document the ecological conditions of coral reefs, to strengthen monitoring efforts, and to link existing organisations and people working with coral reefs around the worl...

Corals and humans represent two extremely disparate metazoan lineages and are therefore useful for comparative evolutionary studies. Two lipid-based molecules that are central to human immunity, platelet-activating factor (PAF) and Lyso-PAF were recently identified in scleractinian corals. To identify processes in corals that involve these molecule...

Depth is used often as a proxy for gradients in energetic resources on coral reefs and for predicting patterns of community energy use. With increasing depth, loss of light can lead to a reduced reliance on autotrophy and an increased reliance on heterotrophy by mixotrophic corals. However, the generality of such trophic zonation varies across cont...

Background The metabolic rate of consumers is a key driver of ecosystem dynamics. On coral reefs, herbivorous echinoids consume fleshy algae, facilitating the growth of reef-building calcified organisms; however, little is known about differences among species in their metabolic and functional ecology. Here, we used log-linear (log-log) regression...

Echinoid assay data. (DOCX)

Mean sizes of echinoids used in metabolic assays. (DOCX)

Mean microbial versus uncorrected echinoid oxygen consumption rates. (DOCX)

Comparisons of replicate metabolic assays. (DOCX)

Comparison of mass and volumetric scaling of metabolism. (DOCX)

To inform a community-based ocean zoning initiative, we conducted an intensive ecological assessment of the marine ecosystems of Barbuda, West Indies. We conducted 116 fish and 108 benthic surveys around the island, and measured the abundance and size structure of lobsters and conch at 52 and 35 sites, respectively. We found that both coral cover a...

Typical reef habitats common around Barbuda. (A, B) Low-relief carbonate flat forereef habitat (C, D) Higher-relief patch reef habitat with standing dead coral. (TIF)

Abundance of lobsters around Barbuda. (A) sublegal (<95mm carapace length) and (B) legal (>95 mm carapace length) lobsters. Values are the number of lobsters seen at each site. (TIF)

Fish community structure around Barbuda. NMDS plot of density of fish species present at >10% of sites. CONT is continuous reef and ISOL is patch reef. LR, MR, and HR are low (<1.5 m), medium (1.5–3 m), and high (>3 m) relief. Depth categories are shallow (<6 m), mid (6–18 m), and deep (>18 m). (TIF)

Pairwise scatterplots of key benthic and fish groups. Values for benthic groups (coral, cca [= crustose coralline algae], turf, and macroalgae) are in percent cover, while values for fish groups (tot_biomass [= total fish biomass] and parrot_biomass [= parrotfish biomass]) are in g per m2. Top panels show data and bottom panels show r2 and p-values...

Abundance of key species in Codrington Lagoon. Shown are the abundance of (A) mojarra, (B) schoolmaster snapper, (c) gray snapper, and (D) lobster at sites surveyed in Codrington Lagoon. Values are number of individuals per 100 m2. (TIF)

Mean biomass of fish species. Values are mean biomass of fish species from reef fish surveys, in g per m2. (PDF)

Abundance of conch around Barbuda. (A) subadult conch (i.e., conch lacking a flared lip) and (B) adult conch (i.e., conch with a flared lip). Values are in numbers per 100 m2. (TIF)

Biomass of key reef fish families around Barbuda. (A) groupers (Serranidae), (B) snappers (Lutjanidae), (C) parrotfish (Labridae: Scarinae), and (D) surgeonfish (Acanthuridae). Values are in g per m2. (TIF)

Live coral cover around Barbuda. Values represent percent benthic cover of live coral. (TIF)

Benthic cover in Codrington Lagoon. Frequency distributions of major benthic groups present in Codrington Lagoon. (TIF)

Turf algal assemblages are ubiquitous primary producers on coral reefs, but little is known about the response of this diverse group to ocean acidification (OA) across different temperatures. We tested the hypothesis that CO2 influences the functional response of epilithic and endolithic turf assemblages to increasing temperature. Replicate carbona...

For sessile organisms such as reef-building corals, differences in the degree of dispersion of individuals across a landscape may result from important differences in life-history strategies or may reflect patterns of habitat availability. Descriptions of spatial patterns can thus be useful not only for the identification of key biological and phys...

The relative rates of carbon fixed by primary producers vs. consumption by primary consumers shape the community of organisms in ecosystems. On coral reefs, it is important to understand the demography of algae, given known competitive dynamics with reef-building corals. Numerous studies have shown that fleshy algal abundance is enhanced in the abs...

The relative contributions of grazing versus microbial food webs to the production of mesozooplankton communities in coral reef ecosystems remains an important and understudied field of inquiry. Here, we investigated the biomass and production of component organisms within these two food webs, and compared them to those of mesozooplankton on a cora...

Primary production due to photosynthesis results in daytime oxygen production across marine and freshwater ecosystems. However, a prevalent, globally-occurring nighttime spike in dissolved oxygen (DO) challenges our traditional assumption that oxygen production is limited to daylight hours, particularly in tropical coral reefs. When considered in t...

Primary production due to photosynthesis results in daytime oxygen production across marine and freshwater ecosystems. However, a prevalent, globally-occurring nighttime spike in dissolved oxygen (DO) challenges our traditional assumption that oxygen production is limited to daylight hours, particularly in tropical coral reefs. When considered in t...

Background The demography of a coral colony is not a binary trajectory of life and death. Based on the flexibility afforded by colonial organization, most reef-building corals employ a variety of dynamic survival strategies, including growth and shrinkage. The demographic flexibility affects coral size, shape and reproductive output, among other fa...

Table of Porites superfusa demographic changes tallied by year and number of colonies Year transitions (2009–2010, 2010–2011, 2011–2012) are recorded because changes in numbers of colonies occurred from one year survey to the next. No resurrected recruits were counted in the 2009 to 2010 year transition because in order to ‘resurrect’ the colony mu...

Raw data of coral colony sizes over time, at each site

All statistical analysis code completed in R

Code for Tukey’s post hoc

Primary production due to photosynthesis results in daytime oxygen production across marine and freshwater ecosystems. However, a prevalent, globally-occurring nighttime spike in dissolved oxygen (DO) challenges our traditional assumption that oxygen production is limited to daylight hours, particularly in tropical coral reefs. When considered in t...

The accuracy and precision of ion sensitive field effect transistor (ISFET) pH sensors have been well documented, but primarily by ocean chemistry specialists employing the technology at single locations. Here we examine their performance in a network context through comparison to discrete measurements of pH, using different configurations of the H...

Patterns of species resource use provide insight into the functional roles of species and thus their ecological significance within a community. The functional role of herbivorous fishes on coral reefs has been defined through a variety of methods, but from a grazing perspective, less is known about the species-specific preferences of herbivores on...

Previous studies have suggested that Crown-of-Thorns starfish (COTS) larvae may be able to survive in the absence of abundant phytoplankton resources suggesting that they may be able to utilize alternative food sources. Here, we tested the hypothesis that COTS larvae are able to feed on coral-derived organic matter using labeled stable isotope trac...

Owing to a publisher processing error, the incorrect figure files for figures 5 and 6 were included in the published article [1]. The correct figures are included here.

Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean's complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments...