Decoupling of respiration rates and abundance in marine prokaryoplankton.

The ocean-atmosphere exchange of CO2 largely depends on the balance between marine microbial photosynthesis and respiration. Despite vast taxonomic and metabolic diversity among marine planktonic bacteria and archaea (prokaryoplankton)1-3, their respiration usually is measured in bulk and treated as a 'black box' in global biogeochemical models4; this limits the mechanistic understanding of the global carbon cycle. Here, using a technology for integrated phenotype analyses and genomic sequencing of individual microbial cells, we show that cell-specific respiration rates differ by more than 1,000× among prokaryoplankton genera. The majority of respiration was found to be performed by minority members of prokaryoplankton (including the Roseobacter cluster), whereas cells of the most prevalent lineages (including Pelagibacter and SAR86) had extremely low respiration rates. The decoupling of respiration rates from abundance among lineages, elevated counts of proteorhodopsin transcripts in Pelagibacter and SAR86 cells and elevated respiration of SAR86 at night indicate that proteorhodopsin-based phototrophy3,5-7 probably constitutes an important source of energy to prokaryoplankton and may increase growth efficiency. These findings suggest that the dependence of prokaryoplankton on respiration and remineralization of phytoplankton-derived organic carbon into CO2 for its energy demands and growth may be lower than commonly assumed and variable among lineages.

Ontogenetic variation in the skull of Stenopterygius quadriscissus with an emphasis on prenatal development.

The availability of a large sample size from a range of ontogenetic stages makes Stenopterygius quadriscissus a good model to study ontogenetic variation in a fossil sauropsid. We qualitatively examined pre- and postnatal ontogenetic changes in the cranium of S. quadriscissus. The prenatal ossification sequence is similar to other diapsids, exhibiting delayed chondrocranial ossification compared to the dermatocranium. In the dermatocranium, the circumorbital area is more ossified earlier in development relative to other elements, especially those of the skull roof where ossification is comparatively weaker across prenatal stages. Perinatally all cranial elements are ossified, and many scarf and step joints are already closed. We propose four prenatal and three postnatal stages in S. quadriscissus on the basis of relative ossification, size and qualitative cranial characters pertaining to the jugal, parietal, frontal, pterygoid and surangular. These will provide a basis for determining ontogenetic stages in other ichthyosaurs. Moreover, our postnatal observations aid in refining ontogenetic characters for phylogenetic studies. Lastly, we observed that the antimeric sutures of the midline of the skull roof are open perinatally and that fusion of the midline only appears in the adult stage. We hypothesize that the loose connection of the midline functions as a fontanelle, limiting potential damage during birth.

Nutrient supply controls the linkage between species abundance and ecological interactions in marine bacterial communities.

Nutrient scarcity is pervasive for natural microbial communities, affecting species reproduction and co-existence. However, it remains unclear whether there are general rules of how microbial species abundances are shaped by biotic and abiotic factors. Here we show that the ribosomal RNA gene operon (rrn) copy number, a genomic trait related to bacterial growth rate and nutrient demand, decreases from the abundant to the rare biosphere in the nutrient-rich coastal sediment but exhibits the opposite pattern in the nutrient-scarce pelagic zone of the global ocean. Both patterns are underlain by positive correlations between community-level rrn copy number and nutrients. Furthermore, inter-species co-exclusion inferred by negative network associations is observed more in coastal sediment than in ocean water samples. Nutrient manipulation experiments yield effects of nutrient availability on rrn copy numbers and network associations that are consistent with our field observations. Based on these results, we propose a "hunger games" hypothesis to define microbial species abundance rules using the rrn copy number, ecological interaction, and nutrient availability.

On predicting particle capture rates in aquatic ecosystems.

Recent advances in understanding the capture of moving suspended particles in aquatic ecosystems have opened up new possibilities for predicting rates of suspension feeding, larval settlement, seagrass pollination and sediment removal. Drawing on results from both highly-resolved computational fluid dynamics (CFD) simulations and existing experimental data, we quantify the controlling influence of flow velocity, particle size and collector size on rates of contact between suspended particles and biological collectors over the parameter space characterising a diverse range of aquatic ecosystems. As distinct from assumptions in previous modeling studies, the functional relationships describing capture are highly variable. Contact rates can vary in opposing directions in response to changes in collector size, an organism's size, the size of particles being intercepted (related to diet in the case of suspension feeders), and the flow strength. Contact rates shift from decreasing to increasing with collector diameter when particles become relatively large and there is vortex shedding in the collector wake. And in some ranges of the ecologically relevant parameter space, contact rates do not increase strongly with velocity or particle size. The understanding of these complex dependencies allows us to reformulate some hypotheses of selection pressure on the physiology and ecology of aquatic organisms. We discuss the benefits and limitations of CFD tools in predicting rates of particle capture in aquatic ecosystems. Finally, across the complete parameter space relevant to real aquatic ecosystems, all quantitative estimates of particle capture from our model are provided here.

Antibacterial Activity and Amphidinol Profiling of the Marine Dinoflagellate Amphidinium carterae (Subclade III).

Microalgae have received growing interest for their capacity to produce bioactive metabolites. This study aimed at characterising the antimicrobial potential of the marine dinoflagellate Amphidinium carterae strain LACW11, isolated from the west of Ireland. Amphidinolides have been identified as cytotoxic polyoxygenated polyketides produced by several Amphidinium species. Phylogenetic inference assigned our strain to Amphidinium carterae subclade III, along with isolates interspersed in different geographic regions. A two-stage extraction and fractionation process of the biomass was carried out. Extracts obtained after stage-1 were tested for bioactivity against bacterial ATCC strains of Staphylococcus aureus, Enterococcus faecalis, Escherichia coli and Pseudomonas aeruginosa. The stage-2 solid phase extraction provided 16 fractions, which were tested against S. aureus and E. faecalis. Fractions I, J and K yielded minimum inhibitory concentrations between 16 µg/mL and 256 µg/mL for both Gram-positive. A targeted metabolomic approach using UHPLC-HRMS/MS analysis applied on fractions G to J evidenced the presence of amphidinol type compounds AM-A, AM-B, AM-22 and a new derivative dehydroAM-A, with characteristic masses of m/z 1361, 1463, 1667 and 1343, respectively. Combining the results of the biological assays with the targeted metabolomic approach, we could conclude that AM-A and the new derivative dehydroAM-A are responsible for the detected antimicrobial bioactivity.

Spatial subsidies drive sweet spots of tropical marine biomass production.

Spatial subsidies increase local productivity and boost consumer abundance beyond the limits imposed by local resources. In marine ecosystems, deeper water and open ocean subsidies promote animal aggregations and enhance biomass that is critical for human harvesting. However, the scale of this phenomenon in tropical marine systems remains unknown. Here, we integrate a detailed assessment of biomass production in 3 key locations, spanning a major biodiversity and abundance gradient, with an ocean-scale dataset of fish counts to predict the extent and magnitude of plankton subsidies to fishes on coral reefs. We show that planktivorous fish-mediated spatial subsidies are widespread across the Indian and Pacific oceans and drive local spikes in biomass production that can lead to extreme productivity, up to 30 kg ha-1 day-1. Plankton subsidies form the basis of productivity "sweet spots" where planktivores provide more than 50% of the total fish production, more than all other trophic groups combined. These sweet spots operate at regional, site, and smaller local scales. By harvesting oceanic productivity, planktivores bypass spatial constraints imposed by local primary productivity, creating "oases" of tropical fish biomass that are accessible to humans.

Decreasing Phanerozoic extinction intensity as a consequence of Earth surface oxygenation and metazoan ecophysiology.

The decline in background extinction rates of marine animals through geologic time is an established but unexplained feature of the Phanerozoic fossil record. There is also growing consensus that the ocean and atmosphere did not become oxygenated to near-modern levels until the mid-Paleozoic, coinciding with the onset of generally lower extinction rates. Physiological theory provides us with a possible causal link between these two observations-predicting that the synergistic impacts of oxygen and temperature on aerobic respiration would have made marine animals more vulnerable to ocean warming events during periods of limited surface oxygenation. Here, we evaluate the hypothesis that changes in surface oxygenation exerted a first-order control on extinction rates through the Phanerozoic using a combined Earth system and ecophysiological modeling approach. We find that although continental configuration, the efficiency of the biological carbon pump in the ocean, and initial climate state all impact the magnitude of modeled biodiversity loss across simulated warming events, atmospheric oxygen is the dominant predictor of extinction vulnerability, with metabolic habitat viability and global ecophysiotype extinction exhibiting inflection points around 40% of present atmospheric oxygen. Given this is the broad upper limit for estimates of early Paleozoic oxygen levels, our results are consistent with the relative frequency of high-magnitude extinction events (particularly those not included in the canonical big five mass extinctions) early in the Phanerozoic being a direct consequence of limited early Paleozoic oxygenation and temperature-dependent hypoxia responses.

Seagrass habitat suitability model for Redang Marine Park using multibeam echosounder data: Testing different spatial resolutions and analysis window sizes.

Integrating Multibeam Echosounder (MBES) data (bathymetry and backscatter) and underwater video technology allows scientists to study marine habitats. However, use of such data in modeling suitable seagrass habitats in Malaysian coastal waters is still limited. This study tested multiple spatial resolutions (1 and 50 m) and analysis window sizes (3 × 3, 9 × 9, and 21 × 21 cells) probably suitable for seagrass-habitat relationships in Redang Marine Park, Terengganu, Malaysia. A maximum entropy algorithm was applied, using 12 bathymetric and backscatter predictors to develop a total of 6 seagrass habitat suitability models. The results indicated that both fine and coarse spatial resolution datasets could produce models with high accuracy (>90%). However, the models derived from the coarser resolution dataset displayed inconsistent habitat suitability maps for different analysis window sizes. In contrast, habitat models derived from the fine resolution dataset exhibited similar habitat distribution patterns for three different analysis window sizes. Bathymetry was found to be the most influential predictor in all the models. The backscatter predictors, such as angular range analysis inversion parameters (characterization and grain size), gray-level co-occurrence texture predictors, and backscatter intensity levels, were more important for coarse resolution models. Areas of highest habitat suitability for seagrass were predicted to be in shallower (<20 m) waters and scattered between fringing reefs (east to south). Some fragmented, highly suitable habitats were also identified in the shallower (<20 m) areas in the northwest of the prediction models and scattered between fringing reefs. This study highlighted the importance of investigating the suitable spatial resolution and analysis window size of predictors from MBES for modeling suitable seagrass habitats. The findings provide important insight on the use of remote acoustic sonar data to study and map seagrass distribution in Malaysia coastal water.

Ecotoxicity of losartan potassium in aquatic organisms of different trophic levels.

The intensive use of the antihypertensive losartan potassium (LOS) has culminated in its high occurrence in aquatic environments. However, insufficient studies had investigated its effects in non-target organisms. In this study, ecotoxicity of LOS was assessed in aquatic organisms from distinct trophic levels (Desmodesmus subspicatus, Daphnia magna, and Astyanax altiparanae). Genotoxicity was assessed by the comet assay in D. magna and A. altiparanae, and biochemical biomarkers for the fish. LOS was more toxic to D. subspicatus (EC50(72h) = 27.93 mg L-1) than D. magna (EC50 = 303.69 mg L-1). Subsequently, this drug showed to induce more DNA damage in D. magna than A. altiparanae, when exposed to 2.5 mg L-1. No significant stress responses were observed by the fish biomarkers, suggesting that higher trophic levels organisms are more tolerant to LOS toxicity. LOS showed relatively low toxic potential for a short period of exposure, but with different patterns of toxicity for the organisms from distinct trophic levels, contributing to further risk assessment of LOS.

High hydrostatic pressure shapes the development and production of secondary metabolites of Mariana Trench sediment fungi.

The hadal biosphere is one of the least understood ecosystems on our planet. Recent studies have revealed diverse and active communities of prokaryotes in hadal sediment. However, there have been few studies on fungi in hadal sediment. Here we report the first isolation and cultivation of 8 fungi from the Mariana Trench sediment. The individual colonies were isolated and identified as Stemphylium sp., Cladosporium sp., Arthrinium sp., Fusarium sp., Alternaria sp., and Aspergillus sp. High hydrostatic pressure (HHP) test was carried out to identify the piezophily of these hadal fungi. Among them, 7 out of the 8 fungal isolates exhibited the ability of germination after incubation under 40 MPa for 7 days. Vegetative growth of the isolates was also affected by HHP. Characterization of secondary metabolites under different pressure conditions was also performed. The production of secondary metabolites was affected by the HHP treatment, improving the potential of discovering novel natural products from hadal fungi. The antibacterial assay revealed the potential of discovering novel natural products. Our results suggest that fungal growth pressure plays an important role in the development and production of secondary metabolites of these hadal fungi under the extreme environment in the Mariana Trench.

From the individual to the colony: Marine invertebrates as models to understand levels of biological organization.

The developmental and evolutionary principles of coloniality in marine animals remain largely unexplored. Although many common traits have evolved independently in different groups of colonial animals, questions about their significance for colonial life histories remain unanswered. In 2018 (Nov. 25 - Dec. 8), the inaugural course on the Evolution of Coloniality and Modularity took place at the Center for Marine Biology of the University of São Paulo (CEBIMAR-USP), Brazil. During the intensive two-week graduate-level course, we addressed some of the historical ideas about animal coloniality by focal studies in bryozoans, tunicates, cnidarians, and sponges. We discussed many historical hypotheses and ways to test these using both extant and paleontological data, and we carried direct observations of animal colonies in the different phyla to address questions about coloniality. We covered topics related to multi-level selection theory and studied colonial traits, including modular miniaturization, polymorphism, brooding, and allorecognition. Course participants carried out short research projects using local species of animals to address questions on allorecognition and regeneration in ascidians and sponges, fusion and chimerism in anthoathecate hydrozoans, and evolution of polymorphism in bryozoans. Although many questions remain unanswered, this course served as a foundation to continue to develop a developmental and evolutionary synthesis of clonal and modular development in colonial marine organisms.

The contributions of a trematode parasite infectious stage to carbon cycling in a model freshwater system.

Parasites remainunderstudied members of most ecosystems, especially free-living infectious stages, such as the aquatic cercariae of trematodes (flatworms). Recent studies are shedding more light on their roles, particularly as prey for a diverse array of aquatic predators, but the possible fates of cercariae remain unclear. While this is critical to elucidate because cercariae represent a large potential source of energy and nutrients, determining the fate of cercariae-derived organic matter involves many logistical challenges. Previous studies utilized elemental and stable isotope analysis when examining host-parasite interactions, but none has used such approaches to track the movement of cercariae biomass within food webs. Here we report that Plagiorchis sp. cercariae were effectively labelled with 13C by introducing this compound in the food of their snail host. We then added 13C-labelled cercariae as a potential food source to experimental mesocosms containing a simplified model freshwater food web represented by diving beetles (Dytiscidae sp.), dragonfly larvae (Leucorrhinia intacta), oligochaete worms (Lumbriculus variegatus), and a zooplankton community dominated by Daphnia pulex. The oligochaetes had the highest ratio of 13C to 12C, suggesting benthic detritivores are substantial, but previously unrecognized, consumers of cercariae biomass. In an experiment where L. variegatus were fed mass equivalents of dead D. pulex or cercariae, growth was greater with the latter diet, supporting the importance of cercariae as food source for benthic organisms. Given the substantial cercariae biomass possible in natural settings, understanding their contributions to energy flow and nutrient cycling is important, along with developing methods to do so.

Diurnal Fe(II)/Fe(III) cycling and enhanced O2 production in a simulated Archean marine oxygen oasis.

The oxygenation of early Earth's atmosphere during the Great Oxidation Event, is generally accepted to have been caused by oceanic Cyanobacterial oxygenic photosynthesis. Recent studies suggest that Fe(II) toxicity delayed the Cyanobacterial expansion necessary for the GOE. This study investigates the effects of Fe(II) on two Cyanobacteria, Pseudanabaena sp. PCC7367 and Synechococcus sp. PCC7336, in a simulated shallow-water marine Archean environment. A similar Fe(II) toxicity response was observed as reported for closed batch cultures. This toxicity was not observed in cultures provided with continuous gaseous exchange that showed significantly shorter doubling times than the closed-culture system, even with repeated nocturnal addition of Fe(II) for 12 days. The green rust (GR) formed under high Fe(II) conditions, was not found to be directly toxic to Pseudanabaena sp. PCC7367. In summary, we present evidence of diurnal Fe cycling in a simulated shallow-water marine environment for two ancestral strains of Cyanobacteria, with increased O2 production under anoxic conditions.

Effect of polymer type on the colonization of plastic pellets by marine bacteria.

Plastic is omnipresent in the oceans and serves as a surface for biofilm-forming microorganisms. Plastic debris comprises different polymers, which may influence microbial colonization; here, we evaluated whether polymer type affects bacterial biofilm formation. Quantifying the biofilm on polyethylene (PE), polypropylene (PP) or polystyrene (PS) pellets by six marine bacterial strains (Vibrio,Pseudoalteromonas,Phaeobacter) demonstrated that each strain had a unique colonization behavior with either a preference for PS or PP over the other polymer types or no preference for a specific plastic type. PE, PP and PS pellets were exposed to natural seawater microbiota using free-living or total communities as inoculum. Microbial assembly as determined by 16S rRNA (V4) amplicon sequencing was affected by the composition of the initial inoculum and also by the plastic type. Known polymer and hydrocarbon degraders such as Paraglaciecola, Oleibacter and Hydrogenophaga were found in the plastic biofilms. Thus, on a community level, bacterial colonization on plastic is influenced by the microorganisms as well as the polymer type, and also individual strains can demonstrate polymer-specific colonization.

Feedback mechanisms stabilise degraded turf algal systems at a CO2 seep site.

Human activities are rapidly changing the structure and function of coastal marine ecosystems. Large-scale replacement of kelp forests and coral reefs with turf algal mats is resulting in homogenous habitats that have less ecological and human value. Ocean acidification has strong potential to substantially favour turf algae growth, which led us to examine the mechanisms that stabilise turf algal states. Here we show that ocean acidification promotes turf algae over corals and macroalgae, mediating new habitat conditions that create stabilising feedback loops (altered physicochemical environment and microbial community, and an inhibition of recruitment) capable of locking turf systems in place. Such feedbacks help explain why degraded coastal habitats persist after being initially pushed past the tipping point by global and local anthropogenic stressors. An understanding of the mechanisms that stabilise degraded coastal habitats can be incorporated into adaptive management to better protect the contribution of coastal systems to human wellbeing.

Recovery of tropical marine benthos after a trawl ban demonstrates linkage between abiotic and biotic changes.

Bottom trawling, which is highly detrimental to seabed habitats, has been banned in some jurisdictions to mitigate the problems of habitat destruction and overfishing. However, most reports of ecosystem responses to trawling impacts originate from temperate latitudes, focusing on commercial species, and recovery of invertebrate macrobenthos from trawl ban has hardly ever been studied in the tropics. In Hong Kong (lat. 22.4°N), a history of intensive trawling with various types of gears has long degraded coastal ecosystems. To facilitate the recovery of fisheries resources and associated benthic ecosystems, the Government of the Hong Kong Special Administrative Region implemented a territory-wide trawl ban on December 31, 2012. Comparison of surveys conducted in June 2012 (before the trawl ban) and June 2015 (2.5 years after the ban) revealed higher organic contents in sediment and lower suspended-solid loads in water column, as well as a significant increase in site-based abundance, species richness, functional diversity and among-site similarity of macrobenthos after the trawl ban. Our results suggest that the imposition of a trawl ban can be an effective measure for biodiversity conservation in tropical coastal waters.

1 °C warming increases spatial competition frequency and complexity in Antarctic marine macrofauna.

Environmental conditions of the Southern Ocean around Antarctica have varied little for >5 million years but are now changing. Here, we investigated how warming affects competition for space. Little considered in the polar regions, this is a critical component of biodiversity response. Change in competition in response to environment forcing might be detectable earlier than individual species presence/absence or performance measures (e.g. growth). Examination of fauna on artificial substrata in Antarctica's shallows at ambient or warmed temperature found that, mid-century predicted 1°C warming (throughout the year or just summer-only), increased the probability of individuals encountering spatial competition, as well as density and complexity of such interactions. 2°C, late century predicted warming, increased variance in the probability and density of competition, but overall, competition did not significantly differ from ambient (control) levels. In summary only 1°C warming increased probability, density and complexity of spatial competition, which seems to be summer-only driven.

Potential application values of a marine red yeast, Rhodosporidiums sphaerocarpum YLY01, in aquaculture and tail water treatment assessed by the removal of ammonia nitrogen, the inhibition to Vibrio spp., and nutrient composition.

In recent years, marine red yeasts have been increasingly used as feed diets for larviculture of aquatic animals mainly due to their rich nutrition and immunopotentiation, however little attention is given to their other probiotic profits. In this study, a marine red yeast strain YLY01 was isolated and purified from farming water and it was identified as a member of Rhodosporidiums sphaerocarpum by the phylogeny based on 18S rDNA sequence. The strain YLY01 could effectively remove ammonia nitrogen from an initial 9.8 mg/L to 1.3 mg/L in 48 h when supplemented with slight yeast extract and glucose in water samples and the removal rate of ammonia nitrogen was up to 86%. Shrimps (Litopenaeus vannamei) in experimental group incubated with the yeast YLY01 exhibited a higher survival rate than those in blank control group and positive control group challenged by Vibrio harveyi, and it manifested that the strain has high biosecurity to at least shrimps. The strain YLY01 could inhibit the growth of Vibrio cells when a small quantity of carbon source was added into farming water. In addition, a nutrition composition assay showed the contents of protein, fatty acids, and total carotenoids of the yeast YLY01 were 30.3%, 3.2%, and 1.2 mg/g of dry cell weight, respectively. All these results indicated that the marine red yeast YLY01 has a great potential to be used as a versatile probiotic in aquaculture and to be developed as a microbial agent for high-ammonia tail water treatment.

Chemicals sorbed to environmental microplastics are toxic to early life stages of aquatic organisms.

Microplastics are ubiquitous in aquatic ecosystems, but little information is currently available on the dangers and risks to living organisms. In order to assess the ecotoxicity of environmental microplastics (MPs), samples were collected from the beaches of two islands in the Guadeloupe archipelago, Petit-Bourg (PB) located on the main island of Guadeloupe and Marie-Galante (MG) on the second island of the archipelago. These samples have a similar polymer composition with mainly polyethylene (PE) and polypropylene (PP). However, these two samples are very dissimilar with regard to their contamination profile and their toxicity. MPs from MG contain more lead, cadmium and organochlorine compounds while those from PB have higher levels of copper, zinc and hydrocarbons. The leachates of these two samples of MPs induced sublethal effects on the growth of sea urchins and on the pulsation frequency of jellyfish ephyrae but not on the development of zebrafish embryos. The toxic effects are much more marked for samples from the PB site than those from the MG site. This work demonstrates that MPs can contain high levels of potentially bioavailable toxic substances that may represent a significant ecotoxicological risk, particularly for the early life stages of aquatic animals.

Emerging Solutions to Return Nature to the Urban Ocean.

Urban and periurban ocean developments impact 1.5% of the global exclusive economic zones, and the demand for ocean space and resources is increasing. As we strive for a more sustainable future, it is imperative that we better design, manage, and conserve urban ocean spaces for both humans and nature. We identify three key objectives for more sustainable urban oceans: reduction of urban pressures, protection and restoration of ocean ecosystems, and support of critical ecosystem services. We describe an array of emerging evidence-based approaches, including greening grayinfrastructure, restoring habitats, and developing biotechnologies. We then explore new economic instruments and incentives for supporting these new approaches and evaluate their feasibility in delivering these objectives. Several of these tools have the potential to help bring nature back to the urban ocean while also addressing some of the critical needs of urban societies, such as climate adaptation, seafood production, clean water, and recreation, providing both human and environmental benefits in some of our most impacted ocean spaces.