Should I stay or should I go? Coral bleaching from the symbionts' perspective

Coral bleaching, the stress-induced breakdown of coral-algal symbiosis, threatens reefs globally. Paradoxically, despite adverse fitness effects, corals bleach annually, even outside of abnormal temperatures. This generally occurs shortly after the once-per-year mass coral spawning. Here, we propose a hypothesis linking annual coral bleaching and the transmission of symbionts to the next generation of coral hosts. We developed a dynamic model with two symbiont growth strategies, and found that high sexual recruitment and low adult coral survivorship and growth favour bleaching susceptibility, while the reverse promotes bleaching resilience. Otherwise, unexplained trends in the Indo-Pacific align with our hypothesis, where reefs and coral taxa exhibiting higher recruitment are more bleaching susceptible. The results from our model caution against interpreting potential shifts towards more bleaching-resistant symbionts as evidence of climate adaptation-we predict such a shift could also occur in declining systems experiencing low recruitment rates, a common scenario on today's reefs.

Speed and degree of functional and compositional recovery varies with latitude and community age

Rates at which a community recovers after disturbance, or its resilience, can be accelerated by increased net primary productivity and recolonization dynamics such as recruitment. These mechanisms can vary across biogeographic gradients, such as latitude, suggesting that biogeography is likely important to predicting resilience. To test whether community resilience, informed by functional and compositional recovery, hinges on geographic location, we employed a standardized replicated experiment on marine invertebrate communities across four regions from the tropics to the subarctic zone. Communities assembled naturally on standardized substrate while experiencing distinct levels of biomass removal (no removal, low disturbance, and high disturbance), which opened space for new colonizers, thereby providing a pulse of limited resource to these communities. We then quantified functional (space occupancy and biomass) and compositional recovery from these repeated pulse disturbances across two community assembly timescales (early and late at 3 and 12 months, respectively). We documented latitudinal variation in resilience across 47° latitude, where speed of functional recovery was higher toward lower latitudes yet incomplete at late assembly in the tropics and subtropics. The degree of functional recovery did not coincide with compositional recovery, and regional differences in recruitment and growth likely contributed to functional recovery in these communities. While biogeographic variation in community resilience has been predicted, our results are among the first to examine functional and compositional recovery from disturbance in a single large-scale standardized experiment.

Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin

Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.

Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus

Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions, and we demonstrate contains extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in serially transferred cultures across a range of temperatures (16-25°C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.

Toward a More Comprehensive Approach for Dissolved Organic Matter Chemical Characterization Using an Orbitrap Fusion Tribrid Mass Spectrometer Coupled with Ion and Liquid Chromatography Techniques

Dissolved organic matter (DOM) represents one of the largest active organic carbon pools in the global carbon cycle. Although extensively studied, only <10% of DOM has been chemically characterized into individual dissolved compounds due to its molecular complexity. This study introduced a more comprehensive DOM characterization method by coupling both ion chromatography (IC) and liquid chromatography (LC) with high mass accuracy and resolution mass spectrometry. We presented a new on-the-fly mass calibration of the Orbitrap technique by utilizing the "lock mass" function in the Orbitrap Fusion Tribrid mass spectrometer (OT-FTMS), which assures high mass accuracy at every scan by a postcolumn introduction of internal labeled standards. With both IC and LC, tested unlabeled standards of amino acids, small peptides, and organic acids were consistently below 1.0 ppm mass error, giving the OT-FTMS the potential of reaching mass accuracy of the Fourier-transform ion cyclotron resonance mass spectrometer. In addition to mass accuracy, a pooled quality control sample (QC) was used to increase reproducibility by applying systematic error removal using random forest (SERRF). Using an untargeted mass spectrometry approach, estuarine DOM samples were analyzed by OT-FTMS coupled to IC in negative mode and LC in positive mode detection to cover a wide range of highly cationic to highly anionic molecules. As a proof of concept, we focused on elucidating the structures of three distinct DOM compound classes with varied acidities and basicities. In UPLC-OT-FTMS, a total of 915 compounds were detected. We putatively elucidated 44 small peptides and 33 deaminated peptides of these compounds. With IC-OT-FTMS, a total of 1432 compounds were detected. We putatively elucidated 20 peptides, 268 deaminated peptides, and 188 organic acids. Except for five compounds, all putatively elucidated compounds were uniquely detected in their corresponding chromatography technique. These results highlight the need for combining these two techniques to provide a more comprehensive method for DOM characterization. Application of the combined IC and LC techniques is not limited to DOM chemical characterization. It can analyze other complex compound mixtures, such as metabolites, and anthropogenic pollutants, such as pesticides and endocrine-disrupting chemicals, in environmental and biological samples.

Soundscape enrichment increases larval settlement rates for the brooding coral Porites astreoides

Coral reefs, hubs of global biodiversity, are among the world's most imperilled habitats. Healthy coral reefs are characterized by distinctive soundscapes; these environments are rich with sounds produced by fishes and marine invertebrates. Emerging evidence suggests these sounds can be used as orientation and settlement cues for larvae of reef animals. On degraded reefs, these cues may be reduced or absent, impeding the success of larval settlement, which is an essential process for the maintenance and replenishment of reef populations. Here, in a field-based study, we evaluated the effects of enriching the soundscape of a degraded coral reef to increase coral settlement rates. Porites astreoides larvae were exposed to reef sounds using a custom solar-powered acoustic playback system. Porites astreoides settled at significantly higher rates at the acoustically enriched sites, averaging 1.7 times (up to maximum of seven times) more settlement compared with control reef sites without acoustic enrichment. Settlement rates decreased with distance from the speaker but remained higher than control levels at least 30 m from the sound source. These results reveal that acoustic enrichment can facilitate coral larval settlement at reasonable distances, offering a promising new method for scientists, managers and restoration practitioners to rebuild coral reefs.

Distinct bacterial succession and functional response to alginate in the South, Equatorial, and North Pacific Ocean

The availability of alginate, an abundant macroalgal polysaccharide, induces compositional and functional responses among marine microbes, but these dynamics have not been characterized across the Pacific Ocean. We investigated alginate-induced compositional and functional shifts (e.g., heterotrophic production, glucose turnover, hydrolytic enzyme activities) of microbial communities in the South Subtropical, Equatorial, and Polar Frontal North Pacific in mesocosms. We observed that shifts in response to alginate were site-specific. In the South Subtropical Pacific, prokaryotic cell counts, glucose turnover, and peptidase activities changed the most with alginate addition, along with the enrichment of the widest range of particle-associated taxa (161 amplicon sequence variants; ASVs) belonging to Alteromonadaceae, Rhodobacteraceae, Phormidiaceae, and Pseudoalteromonadaceae. Some of these taxa were detected at other sites but only enriched in the South Pacific. In the Equatorial Pacific, glucose turnover and heterotrophic prokaryotic production increased most rapidly; a single Alteromonas taxon dominated (60% of the community) but remained low (<2%) elsewhere. In the North Pacific, the particle-associated community response to alginate was gradual, with a more limited range of alginate-enriched taxa (82 ASVs). Thus, alginate-related ecological and biogeochemical shifts depend on a combination of factors that include the ability to utilize alginate, environmental conditions, and microbial interactions.

Comparative physiology reveals heat stress disrupts acid-base homeostasis independent of symbiotic state in the model cnidarian Exaiptasia diaphana

Climate change threatens the survival of symbiotic cnidarians by causing photosymbiosis breakdown in a process known as bleaching. Direct effects of temperature on cnidarian host physiology remain difficult to describe because heatwaves depress symbiont performance, leading to host stress and starvation. The symbiotic sea anemone Exaiptasia diaphana provides an opportune system to disentangle direct versus indirect heat effects on the host, as it can survive indefinitely without symbionts. We tested the hypothesis that heat directly impairs cnidarian physiology by comparing symbiotic and aposymbiotic individuals of two laboratory subpopulations of a commonly used clonal strain of E. diaphana, CC7. We exposed anemones to a range of temperatures (ambient, +2°C, +4°C and +6°C) for 15-18 days, then measured their symbiont population densities, autotrophic carbon assimilation and translocation, photosynthesis, respiration and host intracellular pH (pHi). Symbiotic anemones from the two subpopulations differed in size and symbiont density and exhibited distinct heat stress responses, highlighting the importance of acclimation to different laboratory conditions. Specifically, the cohort with higher initial symbiont densities experienced dose-dependent symbiont loss with increasing temperature and a corresponding decline in host photosynthate accumulation. In contrast, the cohort with lower initial symbiont densities did not lose symbionts or assimilate less photosynthate when heated, similar to the response of aposymbiotic anemones. However, anemone pHi decreased at higher temperatures regardless of cohort, symbiont presence or photosynthate translocation, indicating that heat consistently disrupts cnidarian acid-base homeostasis independent of symbiotic status or mutualism breakdown. Thus, pH regulation may be a critical vulnerability for cnidarians in a changing climate.

The dimensionality of infection networks among viruses infecting microbial eukaryotes and bacteria

Diverse viruses and their hosts are interconnected through complex networks of infection, which are thought to influence ecological and evolutionary processes, but the principles underlying infection network structure are not well understood. Here we focus on network dimensionality and how it varies across 37 networks of viruses infecting eukaryotic phytoplankton and bacteria. We find that dimensionality is often strikingly low, with most networks being one- or two-dimensional, although dimensionality increases with network richness, suggesting that the true dimensionality of natural systems is higher. Low-dimensional networks generally exhibit a mixture of host partitioning among viruses and nestededness of host ranges. Networks of bacteria-infecting and eukaryote-infecting viruses possess comparable distributions of dimensionality and prevalence of nestedness, indicating that fundamentals of network structure are similar among domains of life and different viral lineages. The relative simplicity of many infection networks suggests that coevolutionary dynamics are often driven by a modest number of underlying mechanisms.

Environment-dependent metabolic investments in the mixotrophic chrysophyte Ochromonas

Mixotrophic protists combine photosynthesis and phagotrophy to obtain energy and nutrients. Because mixotrophs can act as either primary producers or consumers, they have a complex role in marine food webs and biogeochemical cycles. Many mixotrophs are also phenotypically plastic and can adjust their metabolic investments in response to resource availability. Thus, a single species's ecological role may vary with environmental conditions. Here, we quantified how light and food availability impacted the growth rates, energy acquisition rates, and metabolic investment strategies of eight strains of the mixotrophic chrysophyte, Ochromonas. All eight Ochromonas strains photoacclimated by decreasing chlorophyll content as light intensity increased. Some strains were obligate phototrophs that required light for growth, while other strains showed stronger metabolic responses to prey availability. When prey availability was high, all eight strains exhibited accelerated growth rates and decreased their investments in both photosynthesis and phagotrophy. Photosynthesis and phagotrophy generally produced additive benefits: In low-prey environments, Ochromonas growth rates increased to maximum, light-saturated rates with increasing light but increased further with the addition of abundant bacterial prey. The additive benefits observed between photosynthesis and phagotrophy in Ochromonas suggest that the two metabolic modes provide nonsubstitutable resources, which may explain why a tradeoff between phagotrophic and phototrophic investments emerged in some but not all strains.

Manipulation of the seagrass-associated microbiome reduces disease severity

Host-associated microbes influence host health and function and can be a first line of defence against infections. While research increasingly shows that terrestrial plant microbiomes contribute to bacterial, fungal, and oomycete disease resistance, no comparable experimental work has investigated marine plant microbiomes or more diverse disease agents. We test the hypothesis that the eelgrass (Zostera marina) leaf microbiome increases resistance to seagrass wasting disease. From field eelgrass with paired diseased and asymptomatic tissue, 16S rRNA gene amplicon sequencing revealed that bacterial composition and richness varied markedly between diseased and asymptomatic tissue in one of the two years. This suggests that the influence of disease on eelgrass microbial communities may vary with environmental conditions. We next experimentally reduced the eelgrass microbiome with antibiotics and bleach, then inoculated plants with Labyrinthula zosterae, the causative agent of wasting disease. We detected significantly higher disease severity in eelgrass with a native microbiome than an experimentally reduced microbiome. Our results over multiple experiments do not support a protective role of the eelgrass microbiome against L. zosterae. Further studies of these marine host-microbe-pathogen relationships may continue to show new relationships between plant microbiomes and diseases.

Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change

Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the "translation-compensation hypothesis" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N:P.

Microbiome ecological memory and responses to repeated marine heatwaves clarify variation in coral bleaching and mortality

Microbiomes are essential features of holobionts, providing their hosts with key metabolic and functional traits like resistance to environmental disturbances and diseases. In scleractinian corals, questions remain about the microbiome's role in resistance and resilience to factors contributing to the ongoing global coral decline and whether microbes serve as a form of holobiont ecological memory. To test if and how coral microbiomes affect host health outcomes during repeated disturbances, we conducted a large-scale (32 exclosures, 200 colonies, and 3 coral species sampled) and long-term (28 months, 2018-2020) manipulative experiment on the forereef of Mo'orea, French Polynesia. In 2019 and 2020, this reef experienced the two most severe marine heatwaves on record for the site. Our experiment and these events afforded us the opportunity to test microbiome dynamics and roles in the context of coral bleaching and mortality resulting from these successive and severe heatwaves. We report unique microbiome responses to repeated heatwaves in Acropora retusa, Porites lobata, and Pocillopora spp., which included: microbiome acclimatization in A. retusa, and both microbiome resilience to the first marine heatwave and microbiome resistance to the second marine heatwave in Pocillopora spp. Moreover, observed microbiome dynamics significantly correlated with coral species-specific phenotypes. For example, bleaching and mortality in A. retusa both significantly increased with greater microbiome beta dispersion and greater Shannon Diversity, while P. lobata colonies had different microbiomes across mortality prevalence. Compositional microbiome changes, such as changes to proportions of differentially abundant putatively beneficial to putatively detrimental taxa to coral health outcomes during repeated heat stress, also correlated with host mortality, with higher proportions of detrimental taxa yielding higher mortality in A. retusa. This study reveals evidence for coral species-specific microbial responses to repeated heatwaves and, importantly, suggests that host-dependent microbiome dynamics may provide a form of holobiont ecological memory to repeated heat stress.

Towards two decades of Atlantic Ocean mass and heat transports at 26.5° N

Continuous measurements of the Atlantic meridional overturning circulation (AMOC) and meridional ocean heat transport at 26.5° N began in April 2004 and are currently available through December 2020. Approximately 90% of the total meridional heat transport (MHT) at 26.5° N is carried by the zonally averaged overturning circulation, and an even larger fraction of the heat transport variability (approx. 95%) is explained by the variability of the zonally averaged overturning. A physically based separation of the heat transport into large-scale AMOC, gyre and shallow wind-driven overturning components remains challenging and requires new investigations and approaches. We review the major interannual changes in the AMOC and MHT that have occurred over the nearly two decades of available observations and their documented impacts on North Atlantic heat content. Changes in the flow-weighted temperature of the Florida Current (Gulf Stream) over the past two decades are now taken into account in the estimates of MHT, and have led to an increased heat transport relative to the AMOC strength in recent years. Estimates of the MHT at 26.5° N from coupled models and various surface flux datasets still tend to show low biases relative to the observations, but indirect estimates based on residual methods (top of atmosphere net radiative flux minus atmospheric energy divergence) have shown recent promise in reproducing the heat transport and its interannual variability. This article is part of a discussion meeting issue 'Atlantic overturning: new observations and challenges'.

Buoyancy forcing and the subpolar Atlantic meridional overturning circulation

The North Atlantic meridional overturning circulation and its variability are examined in terms of the overturning in density space and diapycnal water mass transformation. The magnitude of the mean overturning is similar to the surface water mass transformation, but the density and properties of these waters are modified by diapycnal mixing. Surface waters are progressively densified while circulating cyclonically around the subpolar gyre, with the densest waters and deepest convection occurring in the Labrador Sea and Nordic Seas. The eddy-driven interaction between the convective interior and boundary currents is a key to the export of dense waters from marginal seas. Due to the multitude of pathways of dense waters within the subpolar gyre, as well as mixing with older waters, waters exiting the subpolar gyre have a wide range of ages, with a mean age on the order of a decade. As a result, interannual changes in water mass transformation are mostly balanced locally and do not result in changes in export to the subtropics. Only persistent changes in water mass transformation result in changes in export to the subtropics. The dilution of signals from upstream water mass transformation suggests that variability in export of dense waters to the subtropics may be controlled by other processes, including interaction of dense waters with the energetic upper ocean. This article is part of a discussion meeting issue 'Atlantic overturning: new observations and challenges'.

Blood meal identification reveals extremely broad host range and host-bias in a temporary ectoparasite of coral reef fishes

Appreciation for the role of cryptofauna in ecological systems has increased dramatically over the past decade. The impacts blood-feeding arthropods, such as ticks and mosquitos, have on terrestrial communities are the subject of hundreds of papers annually. However, blood-feeding arthropods have been largely ignored in marine environments. Gnathiid isopods, often referred to as "ticks of the sea", are temporary external parasites of fishes. They are found in all marine environments and have many consequential impacts on host fitness. Because they are highly mobile and only associated with their hosts while obtaining a blood meal, their broader trophic connections are difficult to discern. Conventional methods rely heavily on detecting gnathiids on wild-caught fishes. However, this approach typically yields few gnathiids and does not account for hosts that avoid capture. To overcome this limitation, we sequenced blood meals of free-living gnathiids collected in light traps to assess the host range and community-dependent exploitation of Caribbean gnathiid isopods. Using fish-specific COI (cox1) primers, sequencing individual blood meals from 1060 gnathiids resulted in the identification of 70 host fish species from 27 families. Comparisons of fish assemblages to blood meal identification frequencies at four collection sites indicated that fishes within the families Haemulidae (grunts) and Lutjanidae (snappers) were exploited more frequently than expected based on their biomass, and Labrid parrotfishes were exploited less frequently than expected. The broad host range along with the biased exploitation of diel-migratory species has important implications for the role gnathiid isopods play in Caribbean coral reef communities.

Food for all? Wildfire ash fuels growth of diverse eukaryotic plankton

In December 2017, one of the largest wildfires in California history, the Thomas Fire, created a large smoke and ash plume that extended over the northeastern Pacific Ocean. Here, we explore the impact of Thomas Fire ash deposition on seawater chemistry and the growth and composition of natural microbial communities. Experiments conducted in coastal California waters during the Thomas Fire revealed that leaching of ash in seawater resulted in significant additions of dissolved nutrients including inorganic nitrogen (nitrate, nitrite and ammonium), silicic acid, metals (iron, nickel, cobalt and copper), organic nitrogen and organic carbon. After exposure to ash leachate at high (0.25 g ash l-1) and low (0.08 g ash l-1) concentrations for 4 days, natural microbial communities had 59-154% higher particulate organic carbon concentrations than communities without ash leachate additions. Additionally, a diverse assemblage of eukaryotic microbes (protists) responded to the ash leachate with taxa from 11 different taxonomic divisions increasing in relative abundance compared with control treatments. Our results suggest that large fire events can be important atmospheric sources of nutrients (particularly nitrogen) to coastal marine systems, where, through leaching of various nutrients, ash may act as a 'food for all' in protist communities.

Long-term coral microbial community acclimatization is associated with coral survival in a changing climate

The plasticity of some coral-associated microbial communities under stressors like warming and ocean acidification suggests the microbiome has a role in the acclimatization of corals to future ocean conditions. Here, we evaluated the acclimatization potential of coral-associated microbial communities of four Hawaiian coral species (Porites compressa, Porites lobata, Montipora capitata, and Pocillopora acuta) over 22-month mesocosm experiment. The corals were exposed to one of four treatments: control, ocean acidification, ocean warming, or combined future ocean conditions. Over the 22-month study, 33-67% of corals died or experienced a loss of most live tissue coverage in the ocean warming and future ocean treatments while only 0-10% died in the ocean acidification and control. Among the survivors, coral-associated microbial communities responded to the chronic future ocean treatment in one of two ways: (1) microbial communities differed between the control and future ocean treatment, suggesting the potential capacity for acclimatization, or (2) microbial communities did not significantly differ between the control and future ocean treatment. The first strategy was observed in both Porites species and was associated with higher survivorship compared to M. capitata and P. acuta which exhibited the second strategy. Interestingly, the microbial community responses to chronic stressors were independent of coral physiology. These findings indicate acclimatization of microbial communities may confer resilience in some species of corals to chronic warming associated with climate change. However, M. capitata genets that survived the future ocean treatment hosted significantly different microbial communities from those that died, suggesting the microbial communities of the survivors conferred some resilience. Thus, even among coral species with inflexible microbial communities, some individuals may already be tolerant to future ocean conditions. These findings suggest that coral-associated microbial communities could play an important role in the persistence of some corals and underlie climate change-driven shifts in coral community composition.

Metaproteogenomic Profile of a Mesopelagic Adenylylsulfate Reductase: Course-Based Discovery Using the Ocean Protein Portal

Adenylylsulfate reductase (Apr) is a flavoprotein with a dissimilatory sulfate reductase function. Its ability to catalyze the reverse reaction in sulfur oxidizers has propelled a complex phylogenetic history of transfers with sulfate reducers and made this enzyme an important protein in ocean sulfur cycling. As part of a graduate course, we analyzed metaproteomic data from the Ocean Protein Portal and observed evidence of Apr alpha (AprA) and beta (AprB) subunits in the Central Pacific Ocean. The protein was originally taxonomically attributed toChlorobium tepidum TLS, a green sulfur bacterium. However, our phylogenomic and oceanographic contextual analysis contradicted this label, instead showing that this protein is consistent with the genomic material from the newly discovered Candidatus Lambdaproteobacteriaclass, implying that the ecological role of this lineage in oxygen minimum twilight zones is underappreciated. This study illustrates how metaproteogenomic analysis can contribute to more accurate metagenomic/proteomic annotations and comprehensive ocean biogeochemical processes conducive to course-based research experiences.

Characterization of a sperm motility signalling pathway in a gonochoric coral suggests conservation across cnidarian sexual systems

Most stony corals liberate their gametes into the water column via broadcast spawning, where fertilization hinges upon the activation of directional sperm motility. Sperm from gonochoric and hermaphroditic corals display distinct morphological and molecular phenotypes, yet it is unknown whether the signalling pathways controlling sperm motility are also distinct between these sexual systems. Here, we addressed this knowledge gap using the gonochoric, broadcast spawning coral Astrangia poculata. We found that cytosolic alkalinization of sperm activates the pH-sensing enzyme soluble adenylyl cyclase (sAC), which is required for motility. Additionally, we demonstrate for the first time in any cnidarian that sAC activity leads to protein kinase A (PKA) activation, and that PKA activity contributes to sperm motility activation. Ultrastructures of A. poculata sperm displayed morphological homology with other gonochoric cnidarians, and sAC exhibited broad structural and functional conservation across this phylum. These results indicate a conserved role for pH-dependent sAC-cAMP-PKA signalling in sperm motility across coral sexual systems, and suggest that the role of this pathway in sperm motility may be ancestral in metazoans. Finally, the dynamics of this pH-sensitive pathway may play a critical role in determining the sensitivity of marine invertebrate reproduction to anthropogenic ocean acidification.

Tracking Fish Lifetime Exposure to Mercury Using Eye Lenses

Mercury (Hg) uptake in fish is affected by diet, growth, and environmental factors such as primary productivity or oxygen regimes. Traditionally, fish Hg exposure is assessed using muscle tissue or whole fish, reflecting both loss and uptake processes that result in Hg bioaccumulation over entire lifetimes. Tracking changes in Hg exposure of an individual fish chronologically throughout its lifetime can provide novel insights into the processes that affect Hg bioaccumulation. Here we use eye lenses to determine Hg uptake at an annual scale for individual fish. We assess the widely distributed benthic round goby (Neogobius melanostomus) from the Baltic Sea, Lake Erie, and the St. Lawrence River. We aged layers of the eye lens using proportional relationships between otolith length at age and eye lens radius for each individual fish. Mercury concentrations were quantified using laser ablation inductively coupled plasma mass spectrometry. The eye lens Hg content revealed that Hg exposure increased with age in Lake Erie and the Baltic Sea but decreased with age in the St. Lawrence River, a trend not detected using muscle tissues. This novel methodology for measuring Hg concentration over time with eye lens chronology holds promise for quantifying how global change processes like increasing hypoxia affect the exposure of fish to Hg.

Active sinking particles: sessile suspension feeders significantly alter the flow and transport to sinking aggregates

Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in wastewater treatment plants. In both these contexts, the sinking aggregates are 'active', since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories and mass transfer to these 'active sinking particles' has not previously been studied. Here, we use a novel scale-free vertical tracking microscope (a.k.a. gravity machine; Krishnamurthy et al. 2020 Nat. Methods 17, 1040-1051 (doi:10.1038/s41592-020-0924-7)) to follow model sinking aggregates (agar spheres) with attached protists (Vorticella convallaria), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached V. convallaria causes significant changes to the flow around aggregates in a dynamic manner and reshapes mass transport boundary layers. Further, we find that activity-mediated local flows along with sinking modify the encounter and plume cross-sections of the aggregate and induce sustained aggregate rotations. Overall, our work shows the important role of biological activity in shaping the near-field flows around aggregates with potentially important effects on aggregate fate and material fluxes.

Seasonal timing on a cyclical Earth: Towards a theoretical framework for the evolution of phenology

Phenology refers to the seasonal timing patterns commonly exhibited by life on Earth, from blooming flowers to breeding birds to human agriculture. Climate change is altering abiotic seasonality (e.g., longer summers) and in turn, phenological patterns contained within. However, how phenology should evolve is still an unsolved problem. This problem lies at the crux of predicting future phenological changes that will likely have substantial ecosystem consequences, and more fundamentally, of understanding an undeniably global phenomenon. Most studies have associated proximate environmental variables with phenological responses in case-specific ways, making it difficult to contextualize observations within a general evolutionary framework. We outline the complex but universal ways in which seasonal timing maps onto evolutionary fitness. We borrow lessons from life history theory and evolutionary demography that have benefited from a first principles-based theoretical scaffold. Lastly, we identify key questions for theorists and empiricists to help advance our general understanding of phenology.

Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints

The study of isotopic fingerprints in nitrate (δ15N, δ18O, Δ17O) has enabled pivotal insights into the global nitrogen cycle and revealed new knowledge gaps. Measuring populations of isotopic homologs of intact NO3 - ions (isotopologues) shows promise to advance the understanding of nitrogen cycling processes; however, we need new theory and predictions to guide laboratory experiments and field studies. We investigated the hypothesis that the isotopic composition of the residual nitrate pool is controlled by the N-O bond-breaking step in Nar dissimilatory nitrate reductase using molecular models of the enzyme active sites and associated kinetic isotope effects (KIEs). We integrated the molecular model results into reaction path models representing the reduction of nitrate under either closed-system or steady-state conditions. The predicted intrinsic KIE (15ε and 18ε) of the Nar active site matches observed fractionations in both culture and environmental studies. This is what would be expected if the isotopic composition of marine nitrate were controlled by dissimilatory nitrate reduction by Nar. For a closed system, the molecular models predict a pronounced negative 15N-18O clumping anomaly in residual nitrate. This signal could encode information about the amount of nitrate consumed in a closed system and thus constrain initial nitrate concentration and its isotopic composition. Similar clumped isotope anomalies can potentially be used to distinguish whether a system is open or closed to new nitrate addition. These mechanistic predictions can be tested and refined in combination with emerging ESI-Orbitrap measurements.

Fine-scale heterogeneity reveals disproportionate thermal stress and coral mortality in thermally variable reef habitats during a marine heatwave

Increasing ocean temperatures threaten coral reefs globally, but corals residing in habitats that experience high thermal variability are thought to be better adapted to survive climate-induced heat stress. Here, we used long-term ecological observations and in situ temperature data from Heron Island, southern Great Barrier Reef to investigate how temperature dynamics within various thermally variable vs. thermally stable reef habitats change during a marine heatwave and the resulting consequences for coral community survival. During the heatwave, thermally variable habitats experienced larger surges in daily mean and maxima temperatures compared to stable sites, including extreme hourly incursions up to 36.5 °C. The disproportionate increase in heat stress in variable habitats corresponded with greater subsequent declines in hard coral cover, including a three-times greater decline within the thermally variable Reef Flat (70%) and Deep Lagoon (83%) than within thermally stable habitats along sheltered and exposed areas of the reef slope (0.3-19%). Interestingly, the thermally variable Reef Crest experienced comparatively small declines (26%), avoiding the most severe tidal ponding and resultant heat stress likely due to proximity to the open ocean equating to lower seawater residence times, greater mixing, and/or increased flow. These results highlight that variable thermal regimes, and any acclimatization or adaptation to elevated temperatures that may lead to, do not necessarily equate to protection against bleaching and mortality during marine heatwaves. Instead, thermally stable habitats that have greater seawater exchange with the open ocean may offer the most protection to corals during the severe marine heatwaves that accompany a changing climate.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s00338-022-02328-6.

Genetic variation underlies plastic responses to global change drivers in the purple sea urchin, Strongylocentrotus purpuratus

Phenotypic plasticity and adaptive evolution enable population persistence in response to global change. However, there are few experiments that test how these processes interact within and across generations, especially in marine species with broad distributions experiencing spatially and temporally variable temperature and pCO2. We employed a quantitative genetics experiment with the purple sea urchin, Strongylocentrotus purpuratus, to decompose family-level variation in transgenerational and developmental plastic responses to ecologically relevant temperature and pCO2. Adults were conditioned to controlled non-upwelling (high temperature, low pCO2) or upwelling (low temperature, high pCO2) conditions. Embryos were reared in either the same conditions as their parents or the crossed environment, and morphological aspects of larval body size were quantified. We find evidence of family-level phenotypic plasticity in response to different developmental environments. Among developmental environments, there was substantial additive genetic variance for one body size metric when larvae developed under upwelling conditions, although this differed based on parental environment. Furthermore, cross-environment correlations indicate significant variance for genotype-by-environment interactive effects. Therefore, genetic variation for plasticity is evident in early stages of S. purpuratus, emphasizing the importance of adaptive evolution and phenotypic plasticity in organismal responses to global change.

Measuring dissolved black carbon in water via aqueous, inorganic, high-performance liquid chromatography of benzenepolycarboxylic acid (BPCA) molecular markers

Dissolved black carbon (DBC) is the condensed aromatic portion of dissolved organic matter produced from the incomplete combustion of biomass and other thermogenic processes. DBC quantification facilitates the examination of the production, accumulation, cycling, transformation, and effects of biologically recalcitrant condensed aromatic carbon in aquatic environments. Due to the heterogeneous nature of DBC molecules, concentrations are difficult to measure directly. Here, the method for DBC quantification consists of oxidizing condensed aromatic carbon to benzenepolycarboxylic acids (BPCAs), which are used as proxies for the assessment of DBC in the original sample. The concentrations of oxidation products (BPCAs) are quantified using high-performance liquid chromatography. DBC concentrations are determined from the concentration of BPCAs using a previously established conversion factor. Details and full descriptions of the preparative and analytical procedures and techniques of the BPCA method are usually omitted for brevity in published method sections and method-specific papers. With this step-by-step protocol, we aim to clarify the steps of DBC analysis, especially for those adopting or conducting the BPCA method for the first time.

Characterizing the secret diets of siphonophores (Cnidaria: Hydrozoa) using DNA metabarcoding

Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species' diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the 'jelly-web', and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems.

New Perspectives on the Marine Carbon Cycle-The Marine Dissolved Organic Matter Reactivity Continuum

This perspective challenges our current understanding of the marine carbon cycle, including an alternative explanation of bulk 14C-DOM measurements. We propose the adoption of the carbon reactivity continuum concept previously established for lakes and sediments for the oceans using kinetic data and term this the marine DOM reactivity continuum. We need to gain a fundamental understanding of the biogeochemical drivers of surface water DOM concentrations and reactivity, biological carbon pump efficiency, and the autotrophic communities that are the ultimate but variable sources of marine DOM. This perspective is intended to shift our focus to a more inclusive kinetic model and may lead us to a more accurate assessment of the active and dynamic role marine DOM plays in the global carbon cycle. Currently, the kinetic data to establish and validate such a marine DOM reactivity continuum model are still lacking, and their resolution depends on the discovery of new organic tracers that span large differences in reactivity and microbial degradation rates. We may need to refocus our efforts in deciphering the structure and reactivity of marine organic molecules in a kinetic context, including the microbial and physicochemical constraints on molecular reactivity that are present in the deep ocean.

Tail-dependent spatial synchrony arises from nonlinear driver-response relationships

Spatial synchrony may be tail-dependent, that is, stronger when populations are abundant than scarce, or vice-versa. Here, 'tail-dependent' follows from distributions having a lower tail consisting of relatively low values and an upper tail of relatively high values. We present a general theory of how the distribution and correlation structure of an environmental driver translates into tail-dependent spatial synchrony through a non-linear response, and examine empirical evidence for theoretical predictions in giant kelp along the California coastline. In sheltered areas, kelp declines synchronously (lower-tail dependence) when waves are relatively intense, because waves below a certain height do little damage to kelp. Conversely, in exposed areas, kelp is synchronised primarily by periods of calmness that cause shared recovery (upper-tail dependence). We find evidence for geographies of tail dependence in synchrony, which helps structure regional population resilience: areas where population declines are asynchronous may be more resilient to disturbance because remnant populations facilitate reestablishment.

Heritable variation and lack of tradeoffs suggest adaptive capacity in Acropora cervicornis despite negative synergism under climate change scenarios

Knowledge of multi-stressor interactions and the potential for tradeoffs among tolerance traits is essential for developing intervention strategies for the conservation and restoration of reef ecosystems in a changing climate. Thermal extremes and acidification are two major co-occurring stresses predicted to limit the recovery of vital Caribbean reef-building corals. Here, we conducted an aquarium-based experiment to quantify the effects of increased water temperatures and pCO2 individually and in concert on 12 genotypes of the endangered branching coral Acropora cervicornis, currently being reared and outplanted for large-scale coral restoration. Quantification of 12 host, symbiont and holobiont traits throughout the two-month-long experiment showed several synergistic negative effects, where the combined stress treatment often caused a greater reduction in physiological function than the individual stressors alone. However, we found significant genetic variation for most traits and positive trait correlations among treatments indicating an apparent lack of tradeoffs, suggesting that adaptive evolution will not be constrained. Our results suggest that it may be possible to incorporate climate-resistant coral genotypes into restoration and selective breeding programmes, potentially accelerating adaptation.

Purification and Physical-Chemical Characterization of Bromocresol Purple for Carbon System Measurements in Freshwaters, Estuaries, and Oceans

This work provides an algorithm to describe the salinity (S _P) and temperature (T) dependence of the equilibrium and molar absorptivity characteristics of purified bromocresol purple (BCP, a pH indicator) over a river-to-sea range of salinity (0 ≤ S _P ≤ 40). Based on the data obtained in this study, the pH of water samples can be calculated on the seawater pH scale as follows: pH_SW = -log(K ₂ e ₂) + log((R - e ₁)/(1 - Re ₄)) where -log(K ₂ e ₂) = 4.981 - 0.1710S _P ^0.5 + 0.09428S _P + 0.3794S _P ^1.5 + 0.0009129S _P ² + 310.2/T - 17.33S ^1.5/T - 0.05895S _P ^1.5 ln T - 0.0005730S _P ^0.5 T, e ₁ = 0.00049 ± 0.00029, and e ₄ = -7.101 × 10^-3 + 7.674 × 10^-5 T + 1.361 × 10^-5 S _P. The term pH_SW is the negative log of the hydrogen ion concentration determined on the seawater pH scale; R is the ratio of BCP absorbances (A) at 432 and 589 nm; K ₂ is the equilibrium constant for the second BCP dissociation step; and e ₁, e ₂, and e ₄ are BCP molar absorptivity ratios. A log(K ₂ e ₂) equation is also presented on the total pH scale. The e ₄ value determined for purified BCP in this study can be used with previously published procedures to correct BCP absorbance measurements obtained using off-the-shelf (unpurified) BCP. This work provides a method for purifying BCP, fills a critical gap in the suite of available purified sulfonephthalein indicators, enables high-quality spectrophotometric measurements of total alkalinity, and facilitates pH measurements in freshwater, estuarine, and ocean environments within the range 4.0 ≤ pH ≤ 7.5.

Surveillance of densoviruses and mesomycetozoans inhabiting grossly normal tissues of three Aotearoa New Zealand asteroid species

Asteroid wasting events and mass mortality have occurred for over a century. We currently lack a fundamental understanding of the microbial ecology of asteroid disease, with disease investigations hindered by sparse information about the microorganisms associated with grossly normal specimens. We surveilled viruses and protists associated with grossly normal specimens of three asteroid species (Patiriella regularis, Stichaster australis, Coscinasterias muricata) on the North Island / Te Ika-a-Māui, Aotearoa New Zealand, using metagenomes prepared from virus and ribosome-sized material. We discovered several densovirus-like genome fragments in our RNA and DNA metagenomic libraries. Subsequent survey of their prevalence within populations by quantitative PCR (qPCR) demonstrated their occurrence in only a few (13%) specimens (n = 36). Survey of large and small subunit rRNAs in metagenomes revealed the presence of a mesomycete (most closely matching Ichthyosporea sp.). Survey of large subunit prevalence and load by qPCR revealed that it is widely detectable (80%) and present predominately in body wall tissues across all 3 species of asteroid. Our results raise interesting questions about the roles of these microbiome constituents in host ecology and pathogenesis under changing ocean conditions.

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

The reconstruction and analysis of genome-scale metabolic models constitutes a powerful systems biology approach, with applications ranging from basic understanding of genotype-phenotype mapping to solving biomedical and environmental problems. However, the biological insight obtained from these models is limited by multiple heterogeneous sources of uncertainty, which are often difficult to quantify. Here we review the major sources of uncertainty and survey existing approaches developed for representing and addressing them. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity.

Persistent El Niño driven shifts in marine cyanobacteria populations

In the California Current Ecosystem, El Niño acts as a natural phenomenon that is partially representative of climate change impacts on marine bacteria at timescales relevant to microbial communities. Between 2014–2016, the North Pacific warm anomaly (a.k.a., the “blob”) and an El Niño event resulted in prolonged ocean warming in the Southern California Bight (SCB). To determine whether this “marine heatwave” resulted in shifts in microbial populations, we sequenced the rpoC1 gene from the biogeochemically important picocyanobacteria Prochlorococcus and Synechococcus at 434 time points from 2009–2018 in the MICRO time series at Newport Beach, CA. Across the time series, we observed an increase in the abundance of Prochlorococcus relative to Synechococcus as well as elevated frequencies of ecotypes commonly associated with low-nutrient and high-temperature conditions. The relationships between environmental and ecotype trends appeared to operate on differing temporal scales. In contrast to ecotype trends, most microdiverse populations were static and possibly reflect local habitat conditions. The only exceptions were microdiversity from Prochlorococcous HLI and Synechococcus Clade II that shifted in response to the 2015 El Niño event. Overall, Prochlorococcus and Synechococcus populations did not return to their pre-heatwave composition by the end of this study. This research demonstrates that extended warming in the SCB can result in persistent changes in key microbial populations.

Interactive effects of large- and local-scale environmental gradients on phenotypic differentiation

Intraspecific differentiation across a steep environmental gradient depends on the relative influences of evolutionary, organismal, and environmental processes. But steep environmental gradients may be nested within larger-scale, regional conditions that could influence these processes at the local scale. Therefore, we hypothesized that phenotypic differentiation along a steep environmental gradient would vary among regions. To test this hypothesis, we conducted a reciprocal transplant experiment on rocky intertidal shores, a habitat characterized by gradients in abiotic and biotic stress, in three regions of the Gulf of Maine. We used the ubiquitous and ecologically important rockweed species Fucus vesiculosus to quantify differentiation in growth, tissue nitrogen, and nitrogen productivity between upper and lower intertidal individuals. We found that phenotypic differentiation between tide heights varied among traits and regions. Although tissue nitrogen did not vary among any treatment combinations, growth and nitrogen productivity response were region specific. A strong effect of transplant height was found in all regions; however, an effect of home (source) height was only detectable in the central Gulf of Maine. Our study reveals that intraspecific responses to steep environmental gradients vary among populations, but the mechanisms underlying these patterns remain unknown. Given the roles that rockweeds play as food and habitat, these in situ patterns of growth and nitrogen productivity could have important community- and ecosystem-level consequences.

Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry

Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Phytoplankton transcriptomic and physiological responses to fixed nitrogen in the California current system

Marine phytoplankton are responsible for approximately half of photosynthesis on Earth. However, their ability to drive ocean productivity depends on critical nutrients, especially bioavailable nitrogen (N) which is scarce over vast areas of the ocean. Phytoplankton differ in their preferences for N substrates as well as uptake efficiencies and minimal N requirements relative to other critical nutrients, including iron (Fe) and phosphorus. In this study, we used the MicroTOOLs high-resolution environmental microarray to examine transcriptomic responses of phytoplankton communities in the California Current System (CCS) transition zone to added urea, ammonium, nitrate, and also Fe in the late summer when N depletion is common. Transcript level changes of photosynthetic, carbon fixation, and nutrient stress genes indicated relief of N limitation in many strains of Prochlorococcus, Synechococcus, and eukaryotic phytoplankton. The transcriptomic responses helped explain shifts in physiological and growth responses observed later. All three phytoplankton groups had increased transcript levels of photosynthesis and/or carbon fixation genes in response to all N substrates. However, only Prochlorococcus had decreased transcript levels of N stress genes and grew substantially, specifically after urea and ammonium additions, suggesting that Prochlorococcus outcompeted other community members in these treatments. Diatom transcript levels of carbon fixation genes increased in response to Fe but not to Fe with N which might have favored phytoplankton that were co-limited by N and Fe. Moreover, transcription patterns of closely related strains indicated variability in N utilization, including nitrate utilization by some high-light adapted Prochlorococcus. Finally, up-regulation of urea transporter genes by both Prochlorococcus and Synechococcus in response to filtered deep water suggested a regulatory mechanism other than classic control via the global N regulator NtcA. This study indicated that co-existing phytoplankton strains experience distinct nutrient stresses in the transition zone of the CCS, an understudied region where oligotrophic and coastal communities naturally mix.

Habitability of the marine serpentinite subsurface: a case study of the Lost City hydrothermal field

The Lost City hydrothermal field is a dramatic example of the biological potential of serpentinization. Microbial life is prevalent throughout the Lost City chimneys, powered by the hydrogen gas and organic molecules produced by serpentinization and its associated geochemical reactions. Microbial life in the serpentinite subsurface below the Lost City chimneys, however, is unlikely to be as dense or active. The marine serpentinite subsurface poses serious challenges for microbial activity, including low porosities, the combination of stressors of elevated temperature, high pH and a lack of bioavailable ∑CO₂. A better understanding of the biological opportunities and challenges in serpentinizing systems would provide important insights into the total habitable volume of Earth's crust and for the potential of the origin and persistence of life in Earth's subsurface environments. Furthermore, the limitations to life in serpentinizing subsurface environments on Earth have significant implications for the habitability of subsurface environments on ocean worlds such as Europa and Enceladus. Here, we review the requirements and limitations of life in serpentinizing systems, informed by our research at the Lost City and the underwater mountain on which it resides, the Atlantis Massif. This article is part of a discussion meeting issue 'Serpentinite in the Earth System'.

Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys

There are a few baseline reef-systems available for understanding the microbiology of healthy coral reefs and their surrounding seawater. Here, we examined the seawater microbial ecology of 25 Northern Caribbean reefs varying in human impact and protection in Cuba and the Florida Keys, USA, by measuring nutrient concentrations, microbial abundances, and respiration rates as well as sequencing bacterial and archaeal amplicons and community functional genes. Overall, seawater microbial composition and biogeochemistry were influenced by reef location and hydrogeography. Seawater from the highly protected 'crown jewel' offshore reefs in Jardines de la Reina, Cuba had low concentrations of nutrients and organic carbon, abundant Prochlorococcus, and high microbial community alpha diversity. Seawater from the less protected system of Los Canarreos, Cuba had elevated microbial community beta-diversity whereas waters from the most impacted nearshore reefs in the Florida Keys contained high organic carbon and nitrogen concentrations and potential microbial functions characteristic of microbialized reefs. Each reef system had distinct microbial signatures and within this context, we propose that the protection and offshore nature of Jardines de la Reina may preserve the oligotrophic paradigm and the metabolic dependence of the community on primary production by picocyanobacteria.

Alligators in the abyss: The first experimental reptilian food fall in the deep ocean

The high respiration rates of the deep-sea benthos cannot be sustained by known carbon supply pathways alone. Here, we investigate moderately-sized reptilian food falls as a potential alternative carbon pathway. Specifically, three individual carcasses of Alligator mississippiensis were deployed along the continental slope of the northern Gulf of Mexico at depths of ~2000m in early 2019. We posit the tough hide of alligators would impeded scavengers by limiting access to soft tissues of the alligator fall. However, the scavengers began consuming the food fall 43 hours post-deployment for one individual (198.2cm, 29.7kg), and the carcass of another individual (175.3 cm, 19.5kg) was completely devoid of soft tissue at 51 days post-deployment. A third individual (172.7cm, 18.5kg) was missing completely after 8 days, with only the deployment harness and weight remaining drug 8 meters away, suggesting a large elasmobranch scavenger. Additionally, bones recovered post-deployment reveal the first observations of the bone-eating Osedax in the Gulf of Mexico and are confirmed here as new to science. The findings of this study indicate the quick and successful utilization of terrestrial and aquatic-based carbon food sources in the deep marine environment, though outcome variability may be high.

Minireview: demystifying microbial reaction energetics

The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy ( Δ G r 0 ) define the direction and energy yield of a reaction; they do not. Δ G r 0 is one part of the actual Gibbs energy of a reaction (ΔGr ), with a second part accounting for deviations from the standard composition. It is also frequently assumed that Δ G r 0 applies only to 25 °C and 1 bar; it does not. Δ G r 0 is a function of temperature and pressure. Here, we review how to determine ΔGr as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔGr and highlighting the large effects when multi-valent ions are part of the reaction. We also calculate ΔGr for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.

Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges

BACKGROUND

Sponges are important suspension-feeding members of reef communities, with the collective capacity to overturn the entire water column on shallow Caribbean reefs every day. The sponge-loop hypothesis suggests that sponges take up dissolved organic carbon (DOC) and, via assimilation and shedding of cells, return carbon to the reef ecosystem as particulate organic carbon (POC). Sponges host complex microbial communities within their tissues that may play a role in carbon and nutrient cycling within the sponge holobiont. To investigate this relationship, we paired microbial community characterization (16S rRNA analysis, Illumina Mi-Seq platform) with carbon (DOC, POC) and nutrient (PO₄, NO_x, NH₄) flux data (specific filtration rate) for 10 common Caribbean sponge species at two distant sites (Florida Keys vs. Belize, ~ 1203 km apart).

RESULTS

Distance-based linear modeling revealed weak relationships overall between symbiont structure and carbon and nutrient flux, suggesting that the observed differences in POC, DOC, PO₄, and NO_x flux among sponges are not caused by variations in the composition of symbiont communities. In contrast, significant correlations between symbiont structure and NH₄ flux occurred consistently across the dataset. Further, several individual symbiont taxa (OTUs) exhibited relative abundances that correlated with NH₄ flux, including one OTU affiliated with the ammonia-oxidizing genus Cenarchaeum.

CONCLUSIONS

Combined, these results indicate that microbiome structure is uncoupled from sponge carbon cycling and does not explain variation in DOC uptake among Caribbean coral reef sponges. Accordingly, differential DOC assimilation by sponge cells or stable microbiome components may ultimately drive carbon flux in the sponge holobiont.

Sea urchins mediate the availability of kelp detritus to benthic consumers

Detritus can fundamentally shape and sustain food webs, and shredders can facilitate its availability. Most of the biomass of the highly productive giant kelp, Macrocystis pyrifera, becomes detritus that is exported or falls to the seafloor as litter. We hypothesized that sea urchins process kelp litter through shredding, sloppy feeding and egestion, making kelp litter more available to benthic consumers. To test this, we conducted a mesocosm experiment in which an array of kelp forest benthic consumers were exposed to 13C- and 15N-labelled Macrocystis with or without the presence of sea urchins, Strongylocentrotus purpuratus. Our results showed that several detritivore species consumed significant amounts of kelp, but only when urchins were present. Although they are typically portrayed as antagonistic grazers in kelp forests, sea urchins can have a positive trophic role, capturing kelp litter before it is exported and making it available to a suite of benthic detritivores.

Effect of ocean acidification on the nutritional quality of marine phytoplankton for copepod reproduction

Phytoplankton are the oceans' principal source of polyunsaturated fatty acids that support the growth and reproduction of consumers such as copepods. Previous studies have demonstrated ocean acidification (OA) can change the availability of polyunsaturated fatty acids to consumer diets which may affect consumer reproduction. Two laboratory experiments were conducted to examine the effects of feeding high-pCO2-reared phytoplankton on copepod egg production, hatching success, and naupliar survival. Marine phytoplankton Rhodomonas salina, Skeletonema marinoi, Prorocentrum micans, and Isochrysis galbana were exponentially grown in semi-continuous cultures at present (control) (400 ppm CO2, pH~8.1) and future (1,000 ppm CO2, pH~7.8) conditions and provided to Acartia tonsa copepods over 4 consecutive days as either nitrogen-limited (Exp. I) or nitrogen-depleted (Exp. II) mixed assemblage of phytoplankton. The composition of FAs in the phytoplankton diet was affected by pCO2 concentration and nitrogen deficiency; the ratio of essential fatty acids to total polyunsaturated fatty acids decreased in phytoplankton grown under high pCO2 and the mass of total fatty acids increased under nitrogen depletion. Additionally, total concentrations of essential fatty acids and polyunsaturated fatty acids in the diet mixtures were less under the high-pCO2 compared to the control-pCO2 treatments. Median egg production, hatching success, and naupliar survival were 48-52%, 4-87%, and 9-100% lower, respectively, in females fed high-pCO2 than females fed low-pCO2 phytoplankton, but this decrease in reproductive success was less severe when fed N-depleted, but fatty acid-rich cells. This study demonstrates that the effects of OA on the nutritional quality of phytoplankton (i.e., their cellular fatty acid composition and quota) were modified by the level of nitrogen deficiency and the resulting negative reproductive response of marine primary consumers.

Incubation and grazing effects on spirotrich ciliate diversity inferred from molecular analyses of microcosm experiments

We used an experimental approach of analyzing marine microcosms to evaluate the impact of both predation (top-down) and food resources (bottom-up) on spirotrich ciliate communities. To assess the diversity, we used two molecular methods–denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (HTS). We carried out two types of experiments to measure top-down (adult copepods as predators) and bottom-up effects (phytoplankton as food resources) on the spirotrich ciliates. We observed both strong incubation effects (untreated controls departed from initial assessment of diversity) and high variability across replicates within treatments, particularly for the bottom-up experiments. This suggests a rapid community turn-over during incubation and differential susceptibility to the effects of experimental manipulation. Despite the variability, our analyses reveal some broad patterns such as (1) increasing adult copepod predator abundance had a greater impact on spirotrich ciliates than on other microbial eukaryotes; (2) there was no evidence for strong food selection by the dominant spirotrich ciliates.

Short-term effect of simulated salt marsh restoration by sand-amendment on sediment bacterial communities

Coastal climate adaptation strategies are needed to build salt marsh resiliency and maintain critical ecosystem services in response to impacts caused by climate change. Although resident microbial communities perform crucial biogeochemical cycles for salt marsh functioning, their response to restoration practices is still understudied. One promising restoration strategy is the placement of sand or sediment onto the marsh platform to increase marsh resiliency. A previous study examined the above- and below-ground structure, soil carbon dioxide emissions, and pore water constituents in Spartina alterniflora-vegetated natural marsh sediments and sand-amended sediments at varying inundation regimes. Here, we analyzed samples from the same experiment to test the effect of sand-amendments on the microbial communities after 5 months. Along with the previously observed changes in biogeochemistry, sand amendments drastically modified the bacterial communities, decreasing richness and diversity. The dominant sulfur-cycling bacterial community found in natural sediments was replaced by one dominated by iron oxidizers and aerobic heterotrophs, the abundance of which correlated with higher CO2-flux. In particular, the relative abundance of iron-oxidizing Zetaproteobacteria increased in the sand-amended sediments, possibly contributing to acidification by the formation of iron oxyhydroxides. Our data suggest that the bacterial community structure can equilibrate if the inundation regime is maintained within the optimal range for S. alterniflora. While long-term effects of changes in bacterial community on the growth of S. alterniflora are not clear, our results suggest that analyzing the microbial community composition could be a useful tool to monitor climate adaptation and restoration efforts.

A ctenophore (comb jelly) employs vortex rebound dynamics and outperforms other gelatinous swimmers

Gelatinous zooplankton exhibit a wide range of propulsive swimming modes. One of the most energetically efficient is the rowing behaviour exhibited by many species of schyphomedusae, which employ vortex interactions to achieve this result. Ctenophores (comb jellies) typically use a slow swimming, cilia-based mode of propulsion. However, species within the genus Ocyropsis have developed an additional propulsive strategy of rowing the lobes, which are normally used for feeding, in order to rapidly escape from predators. In this study, we used high-speed digital particle image velocimetry to examine the kinematics and fluid dynamics of this rarely studied propulsive mechanism. This mechanism allows Ocyropsis to achieve size-adjusted speeds that are nearly double those of other large gelatinous swimmers. The investigation of the fluid dynamic basis of this escape mode reveals novel vortex interactions that have not previously been described for other biological propulsion systems. The arrangement of vortices during escape swimming produces a similar configuration and impact as that of the well-studied 'vortex rebound' phenomenon which occurs when a vortex ring approaches a solid wall. These results extend our understanding of how animals use vortex-vortex interactions and provide important insights that can inform the bioinspired engineering of propulsion systems.

Going with the flow: hydrodynamic cues trigger directed escapes from a stalking predator

In the coevolution of predator and prey, different and less well-understood rules for threat assessment apply to freely suspended organisms than to substrate-dwelling ones. Particularly vulnerable are small prey carried with the bulk movement of a surrounding fluid and thus deprived of sensory information within the bow waves of approaching predators. Some planktonic prey have solved this apparent problem, however. We quantified cues generated by the slow approach of larval clownfish ( Amphiprion ocellaris) that triggered a calanoid copepod ( Bestiolina similis) to escape before the fish could strike. To estimate water deformation around the copepod immediately preceding its jump, we represented the body of the fish as a rigid sphere in a hydrodynamic model that we parametrized with measurements of fish size, approach speed and distance to the copepod. Copepods of various developmental stages (CII-CVI) were sensitive to the water flow caused by the live predator, at deformation rates as low as 0.04 s-1. This rate is far lower than that predicted from experiments that used artificial predator-mimics. Additionally, copepods localized the source, with 87% of escapes directed away (greater than or equal to 90°) from the predator. Thus, copepods' survival in life-threatening situations relied on their detection of small nonlinear signals within an environment of locally linear deformation.

Integrating ecosystem services considerations within a GIS-based habitat suitability index for oyster restoration

Geospatial habitat suitability index (HSI) models have emerged as powerful tools that integrate pertinent spatial information to guide habitat restoration efforts, but have rarely accounted for spatial variation in ecosystem service provision. In this study, we utilized satellite-derived chlorophyll a concentrations for Pamlico Sound, North Carolina, USA in conjunction with data on water flow velocities and dissolved oxygen concentrations to identify potential restoration locations that would maximize the oyster reef-associated ecosystem service of water filtration. We integrated these novel factors associated with oyster water filtration ecosystem services within an existing, ‘Metapopulation Persistence’ focused GIS-based, HSI model containing biophysical (e.g., salinity, oyster larval connectivity) and logistical (e.g., distance to nearest restoration material stockpile site) factors to identify suitable locations for oyster restoration that maximize long-term persistence of restored oyster populations and water filtration ecosystem service provision. Furthermore, we compared the ‘Water Filtration’ optimized HSI with the HSI optimized for ‘Metapopulation Persistence,’ as well as a hybrid model that optimized for both water filtration and metapopulation persistence. Optimal restoration locations (i.e., locations corresponding to the top 1% of suitability scores) were identified that were consistent among the three HSI scenarios (i.e., “win-win” locations), as well as optimal locations unique to a given HSI scenario (i.e., “tradeoff” locations). The modeling framework utilized in this study can provide guidance to restoration practitioners to maximize the cost-efficiency and ecosystem services value of habitat restoration efforts. Furthermore, the functional relationships between oyster water filtration and chlorophyll a concentrations, water flow velocities, and dissolved oxygen applied in this study can guide field- and lab-testing of hypotheses related to optimal conditions for oyster reef restoration to maximize water quality enhancement benefits.