Respiration in the open ocean

Microbial community respiration kinetics and their dynamics in coastal seawater

Oxygen (O2) concentrations in coastal seawater have been declining for decades and models predict continued deoxygenation into the future. As O2 declines, metabolic energy use is progressively channelled from higher trophic levels into microbial community respiration, which in turn influences coastal ecology and biogeochemistry. Despite its critical role in deoxygenation and ecosystem functioning, the kinetics of microbial respiration at low O2 concentrations in coastal seawater remain uncertain and are mostly modeled based on parameters derived from laboratory cultures and a limited number of environmental observations. To explore microbial responses to declining O2, we measured respiration kinetics in coastal microbial communities in Hong Kong over the course of an entire year. We found the mean maximum respiration rate (Vmax) ranged between 560 ± 280 and 5930 ± 800 nmol O2 L-1 h-1, with apparent half-saturation constants (Km) for O2 uptake of between 50 ± 40 and 310 ± 260 nmol O2 L-1. These kinetic parameters vary seasonally in association with shifts in microbial community composition that were linked to nutrient availability, temperature, and biological productivity. In general, coastal communities in Hong Kong exhibited low affinities for O2, yet communities in the dry season had higher affinities, which may play a key role in shaping the relationship between community size, biomass, and O2 consumption rates through respiration. Overall, parameters derived from these experiments can be employed in models to predict the expansion of deoxygenated waters and associated effects on coastal ecology and biogeochemistry.

The global distribution and climate resilience of marine heterotrophic prokaryotes

Heterotrophic Bacteria and Archaea (prokaryotes) are a major component of marine food webs and global biogeochemical cycles. Yet, there is limited understanding about how prokaryotes vary across global environmental gradients, and how their global abundance and metabolic activity (production and respiration) may be affected by climate change. Using global datasets of prokaryotic abundance, cell carbon and metabolic activity we reveal that mean prokaryotic biomass varies by just under 3-fold across the global surface ocean, while total prokaryotic metabolic activity increases by more than one order of magnitude from polar to tropical coastal and upwelling regions. Under climate change, global prokaryotic biomass in surface waters is projected to decline ~1.5% per °C of warming, while prokaryotic respiration will increase ~3.5% ( ~ 0.85 Pg C yr-1). The rate of prokaryotic biomass decline is one-third that of zooplankton and fish, while the rate of increase in prokaryotic respiration is double. This suggests that future, warmer oceans could be increasingly dominated by prokaryotes, diverting a growing proportion of primary production into microbial food webs and away from higher trophic levels as well as reducing the capacity of the deep ocean to sequester carbon, all else being equal.

Biogeography and dynamics of prokaryotic and microeukaryotic community assembly across 2600 km in the coastal and shelf ecosystems of the China Seas

Marine prokaryotes and microeukaryotes are essential components of microbial food webs, and drive the biogeochemical cycling. However, the underlying ecological mechanisms driving prokaryotic and microeukaryotic community assembly in large-scale coastal ecosystems remain unclear. In this study, we studied biogeographic patterns of prokaryotic and microeukaryotic communities in the coastal and shelf ecosystem of the China Seas. Results showed that prokaryotic richness was the highest in the Yangtze River Plume, whereas microeukaryotic richness decreased from south to north. Prokaryotic-microeukaryotic co-occurrence networks display greater complexity in the Yangtze River Plume compared to other regions, potentially indicating higher environmental heterogeneity. Furthermore, the cross-domain networks revealed that prokaryotes were more interconnected with each other than with microeukaryotes or between microeukaryotes, and all hub nodes were bacterial taxa, suggesting that prokaryotes may be more important for sustaining the stability and multifunctionality of coastal ecosystem than microeukaryotes. Variation Partitioning Analysis revealed that approximately equal proportions of environmental, biotic and spatial factors contribute to variations in microbial community composition. Temperature was the primary environmental driver of both prokaryotic and microeukaryotic communities across the China Seas. Additionally, stochastic processes (dispersal limitation) and deterministic processes (homogeneous selection) were two major ecological factors in shaping microeukaryotic and prokaryotic assemblages, respectively, suggesting their different environmental plasticity and evolutionary mechanisms. Overall, these results demonstrate both prokaryotic and microeukaryotic communities displayed a latitude-driven distribution pattern and different assembly mechanisms, improving our understanding of microbial biogeography patterns under global change and anthropogenic activity driven habitat diversification in the coastal and shelf ecosystem.

The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third

Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.

Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean

Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.

Decoding populations in the ocean microbiome

Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.

Copepod life history evolution under high- and low-food regimes

Copepods play a critical role in the carbon cycle of the planet - they mediate the sequestration of carbon into the deep ocean and are the trophic link between phytoplankton and marine food webs. Global change stressors that decrease copepod productivity create the potential for catastrophic positive feedback loops. Accordingly, a growing list of studies examine the evolutionary capacity of copepods to adapt to the two primary stressors associated with global change: warmer temperatures and lower pH. But the evolutionary capacity of copepods to adapt to changing food regimes, the third major stressor associated with global change, remains unknown. We used experimental evolution to explore how a 10-fold difference in food availability affects life history evolution in the copepod, Tisbe sp. over 2 years, and spanning 30+ generations. Different food regimes evoked evolutionary responses across the entire copepod life history: we observed evolution in body size, size-fecundity relationships and offspring investment strategies. Our results suggest that changes to food regimes reshape life histories and that cryptic evolution in traits such as body size is likely. We demonstrate that evolution in response to changes in ocean productivity will alter consumer life histories and may distort trophic links in marine foodchains. Evolution in response to changing phytoplankton productivity may alter the efficacy of the global carbon pump in ways that have not been anticipated until now.

Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean

Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.

Functional and structural responses of plankton communities toward consecutive experimental heatwaves in Mediterranean coastal waters

The frequency of marine heatwaves (HWs) is projected to increase in the Mediterranean Sea over the next decades. An in situ mesocosm experiment was performed in a Mediterranean lagoon for 33 days. Three mesocosms were used as controls following the natural temperature of the lagoon. In three others, two HWs of + 5 °C compared to the controls were applied from experimental day (d) 1 to d5 (HW1) and from d11 to d15 (HW2). High-frequency data of oxygen, chlorophyll-a (chl-a), temperature, salinity and light from sensors immersed in all mesocosms were used to calculate gross primary production (GPP), respiration (R) and phytoplankton growth (µ) and loss (L) rates. Nutrients and phytoplankton community structure from pigments were also analyzed. HW1 significantly increased GPP, R, chl-a, µ and L by 7 to 38%. HW2 shifted the system toward heterotrophy by only enhancing R. Thus, the effects of the first HW resulted in the attenuation of those of a second HW on phytoplankton processes, but not on community respiration, which was strongly regulated by temperature. In addition, natural phytoplankton succession from diatoms to haptophytes was altered by both HWs as cyanobacteria and chlorophytes were favored at the expense of haptophytes. These results indicate that HWs have pronounced effects on Mediterranean plankton communities.

Vision-based techniques for automatic marine plankton classification

Plankton are an important component of life on Earth. Since the 19th century, scientists have attempted to quantify species distributions using many techniques, such as direct counting, sizing, and classification with microscopes. Since then, extraordinary work has been performed regarding the development of plankton imaging systems, producing a massive backlog of images that await classification. Automatic image processing and classification approaches are opening new avenues for avoiding time-consuming manual procedures. While some algorithms have been adapted from many other applications for use with plankton, other exciting techniques have been developed exclusively for this issue. Achieving higher accuracy than that of human taxonomists is not yet possible, but an expeditious analysis is essential for discovering the world beyond plankton. Recent studies have shown the imminent development of real-time, in situ plankton image classification systems, which have only been slowed down by the complex implementations of algorithms on low-power processing hardware. This article compiles the techniques that have been proposed for classifying marine plankton, focusing on automatic methods that utilize image processing, from the beginnings of this field to the present day.

Bioactivity Profiling and Untargeted Metabolomics of Microbiota Associated with Mesopelagic Jellyfish Periphylla periphylla

The marine mesopelagic zone extends from water depths of 200 m to 1000 m and is home to a vast number and diversity of species. It is one of the least understood regions of the marine environment with untapped resources of pharmaceutical relevance. The mesopelagic jellyfish Periphylla periphylla is a well-known and widely distributed species in the mesopelagic zone; however, the diversity or the pharmaceutical potential of its cultivable microbiota has not been explored. In this study, we isolated microorganisms associated with the inner and outer umbrella of P. periphylla collected in Irminger Sea by a culture-dependent approach, and profiled their chemical composition and biological activities. Sixteen mostly gram-negative bacterial isolates were selected and subjected to an OSMAC cultivation regime approach using liquid and solid marine broth (MB) and glucose-yeast-malt (GYM) media. Their ethyl acetate (EtOAc) extracts were assessed for cytotoxicity and antimicrobial activity against fish and human pathogens. All, except one extract, displayed diverse levels of antimicrobial activities. Based on low IC₅₀ values, four most bioactive gram-negative strains; Polaribacter sp. SU124, Shewanella sp. SU126, Psychrobacter sp. SU143 and Psychrobacter sp. SU137, were prioritized for an in-depth comparative and untargeted metabolomics analysis using feature-based molecular networking. Various chemical classes such as diketopiperazines, polyhydroxybutyrates (PHBs), bile acids and other lipids were putatively annotated, highlighting the biotechnological potential in P. periphylla-associated microbiota as well as gram-negative bacteria. This is the first study providing an insight into the cultivable bacterial community associated with the mesopelagic jellyfish P. periphylla and, indeed, the first to mine the metabolome and antimicrobial activities of these microorganisms.

Emiliania huxleyi-Bacteria Interactions under Increasing CO2 Concentrations

The interactions established between marine microbes, namely phytoplankton-bacteria, are key to the balance of organic matter export to depth and recycling in the surface ocean. Still, their role in the response of phytoplankton to rising CO₂ concentrations is poorly understood. Here, we show that the response of the cosmopolitan Emiliania huxleyi (E. huxleyi) to increasing CO₂ is affected by the coexistence with bacteria. Specifically, decreased growth rate of E. huxleyi at enhanced CO₂ concentrations was amplified in the bloom phase (potentially also related to nutrient concentrations) and with the coexistence with Idiomarina abyssalis (I. abyssalis) and Brachybacterium sp. In addition, enhanced CO₂ concentrations also affected E. huxleyi's cellular content estimates, increasing organic and decreasing inorganic carbon, in the presence of I. abyssalis, but not Brachybacterium sp. At the same time, the bacterial isolates only survived in coexistence with E. huxleyi, but exclusively I. abyssalis at present CO₂ concentrations. Bacterial species or group-specific responses to the projected CO₂ rise, together with the concomitant effect on E. huxleyi, might impact the balance between the microbial loop and the export of organic matter, with consequences for atmospheric carbon dioxide.

Microbial ecology of the Southern Ocean

The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.

Large-scale sampling of the freshwater microbiome suggests pollution-driven ecosystem changes

Freshwater microbes play a crucial role in the global carbon cycle. Anthropogenic stressors that lead to changes in these microbial communities are likely to have profound consequences for freshwater ecosystems. Using field data from the coordinated sampling of 617 lakes, ponds, rivers, and streams by citizen scientists, we observed linkages between microbial community composition, light and chemical pollution, and greenhouse gas concentration. All sampled water bodies were net emitters of CO₂, with higher concentrations in running waters, and increasing concentrations at higher latitudes. Light pollution occurred at 75% of sites, was higher in urban areas and along rivers, and had a measurable effect on the microbial alpha diversity. Genetic elements suggestive of chemical stress and antimicrobial resistances (IntI1, blaOX₅₈) were found in 85% of sites, and were also more prevalent in urban streams and rivers. Light pollution and CO₂ were significantly related to microbial community composition, with CO₂ inversely related to microbial phototrophy. Results of synchronous nationwide sampling indicate that pollution-driven alterations to the freshwater microbiome lead to changes in CO₂ production in natural waters and highlight the vulnerability of running waters to anthropogenic stressors.

Climate Change Impacts on the Marine Cycling of Biogenic Sulfur: A Review

A key component of the marine sulfur cycle is the climate-active gas dimethylsulfide (DMS), which is synthesized by a range of organisms from phytoplankton to corals, and accounts for up to 80% of global biogenic sulfur emissions. The DMS cycle starts with the intracellular synthesis of the non-gaseous precursor dimethylsulfoniopropionate (DMSP), which is released to the water column by various food web processes such as zooplankton grazing. This dissolved DMSP pool is rapidly turned over by microbially mediated conversion using two known pathways: demethylation (releasing methanethiol) and cleavage (producing DMS). Some of the formed DMS is ventilated to the atmosphere, where it undergoes rapid oxidation and contributes to the formation of sulfate aerosols, with the potential to affect cloud microphysics, and thus the regional climate. The marine phase cycling of DMS is complex, however, as heterotrophs also contribute to the consumption of the newly formed dissolved DMS. Interestingly, due to microbial consumption and other water column sinks such as photolysis, the amount of DMS that enters the atmosphere is currently thought to be a relatively minor fraction of the total amount cycled through the marine food web-less than 10%. These microbial processes are mediated by water column temperature, but the response of marine microbial assemblages to ocean warming is poorly characterized, although bacterial degradation appears to increase with an increase in temperature. This review will focus on the potential impact of climate change on the key microbially mediated processes in the marine cycling of DMS. It is likely that the impact will vary across different biogeographical regions from polar to tropical. For example, in the rapidly warming polar oceans, microbial communities associated with the DMS cycle will likely change dramatically during the 21st century with the decline in sea ice. At lower latitudes, where corals form an important source of DMS (P), shifts in the microbiome composition have been observed during thermal stress with the potential to alter the DMS cycle.

Niche differentiation of ammonia-oxidizing archaea and related autotrophic carbon fixation potential in the water column of the South China Sea

The significant primary production by ammonia-oxidizing archaea (AOA) in the ocean was reported, but the carbon fixation process of AOA and its community composition along the water depth remain unclear. Here, we investigated the abundance, community composition, and potential carbon fixation of AOA in water columns of the South China Sea. Higher abundances of the amoA and accA genes of AOA were found below the euphotic zone. Similarly, higher carbon fixation potential of AOA, evaluated by the ratios of amoA to accA gene, was also observed below euphotic zone and the ratios increased with increasing water depth. The vertical niche differentiation of AOA was further evidenced, with the dominant genus shifting from Nitrosopelagicus in the epipelagic zone to uncultured genus in the meso- and bathypelagic zones. Our findings highlight the higher carbon fixation potential of AOA in deep water and the significance of AOA to the ocean carbon budget.

Microbial metabolites in the marine carbon cycle

One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.

Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake

Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO₂ to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6-23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8-28.4%), pyruvate (9.5%; 4.2-14.8%), and leucine (5.9%; 0.1-11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO₂ from respiration unbalanced by net primary production was by 3.69 × 10⁹ g CO₂ lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.

Transformations of Diatom-Derived Dissolved Organic Matter by Bacillus pumilus Under Warming and Acidification Conditions

Heterotrophic bacteria are assumed to play an important role in processing of phytoplankton-derived dissolved organic matter (DOM). Although the algae-derived organic matter is commonly studied, the transformation and processing of DOM by epiphytic bacteria for phytoplankton have rarely been investigated, especially under warming and acidification. In this study, Bacillus pumilus is used to explore the ecologically important marine diatom Skeletonema dohrnii-derived DOM under different conditions (temperature, 27°C and 31°C; pCO2, 400 and 1,000 ppm), utilizing fluorescence excitation-emission matrix (EEM) combined with parallel factor analysis (EEM-PARAFAC). Fluorescence regional integration and the peak selecting method are used to generate B, T, N, A, M, and C peaks in the EEM fluorescence spectroscopy. The main known fluorophores including that protein-like components (peaks B and T), unknown components (peak N), and humic-like component (peaks A, M, and C). Our experimental results showed that under higher temperature and pressure of CO2 (pCO2) conditions, S. dohrnii-derived DOM fluorescence was dominated by a protein-like signal that slower waning throughout the experiment, becoming an increasingly humic-like substance, implying that processing by the epiphytic bacteria (B. pumilus) produced more complex molecules. In addition, spectroscopic indices (e.g., fluorescence index, biological index, freshness index β/α, and humification index) were changed in varying degrees. This study reveals and confirms the direct participation of heterotrophic bacteria in the transformation and generation of algae-derived DOM in the laboratory, underlining the influence of global warming and ocean acidification on this process.

Accounting for variation in temperature and oxygen availability when quantifying marine ecosystem metabolism

It is critical to understand how human modifications of Earth's ecosystems are influencing ecosystem functioning, including net and gross community production (NCP and GCP, respectively) and community respiration (CR). These responses are often estimated by measuring oxygen production in the light (NCP) and consumption in the dark (CR), which can then be combined to estimate GCP. However, the method used to create "dark" conditions-either experimental darkening during the day or taking measurements at night-could result in different estimates of respiration and production, potentially affecting our ability to make integrative predictions. We tested this possibility by measuring oxygen concentrations under daytime ambient light conditions, in darkened tide pools during the day, and during nighttime low tides. We made measurements every 1-3 months over one year in southeastern Alaska. Daytime respiration rates were substantially higher than those measured at night, associated with higher temperature and oxygen levels during the day and leading to major differences in estimates of GCP calculated using daytime versus nighttime measurements. Our results highlight the potential importance of measuring respiration rates during both day and night to account for effects of temperature and oxygen-especially in shallow-water, constrained systems-with implications for understanding the impacts of global change on ecosystem metabolism.

Fate of dissolved black carbon in the deep Pacific Ocean

Black carbon (BC), a byproduct of biomass and fossil fuel combustion, may impact the climate because it can be stored on Earth's surface for centuries to millennia. Dissolved BC (DBC) occurs ubiquitously in the ocean. However, the DBC cycle in the ocean has not been well constrained. Here, we show the basin-scale distribution of DBC in the Pacific Ocean and find that the DBC concentrations in the deep Pacific Ocean decrease along with deep-ocean meridional circulation. The DBC concentration is negatively correlated with apparent oxygen utilization, a proxy of the integrated flux of sinking particles, in the deep Pacific Ocean, implying that DBC is removed from the deep ocean to abyssal sediments through sorption onto sinking particles. The burial flux of BC to abyssal sediments is estimated to be 0.040-0.085 PgC yr^-1, corresponding to 1.5-3.3% of the anthropogenic CO₂ uptake by the ocean.

Mercury concentrations and stable isotope ratios (δ13C and δ15N) in pelagic nekton assemblages of the south-western Indian Ocean

Mercury (Hg) concentrations and stable isotope values (δ¹³C and δ¹⁵N) were investigated in micronekton collected from La Pérouse and MAD-Ridge seamounts, Reunion Island and the southern Mozambique Channel. Organisms occupying epipelagic habitats showed lower Hg concentrations relative to deeper dwelling benthopelagic ones. Increasing Hg concentrations with increasing body size were recorded in the Mozambique Channel and Reunion Island. Positive relationships were observed between Hg levels and δ¹⁵N values in pelagic nekton assemblages collected at MAD-Ridge seamount and the southern Mozambique Channel, suggesting biomagnification of Hg. Concentrations of Hg in organisms across the south-western Indian Ocean were within the same range of values. Total Hg concentrations depend on a range of factors linked to habitat range, body size and trophic position of the individuals. To our knowledge, this is the first study investigating the patterns of Hg concentrations in pelagic nekton assemblages from the south-western Indian Ocean.

Ontology-Enriched Specifications Enabling Findable, Accessible, Interoperable, and Reusable Marine Metagenomic Datasets in Cyberinfrastructure Systems

Marine microbial ecology requires the systematic comparison of biogeochemical and sequence data to analyze environmental influences on the distribution and variability of microbial communities. With ever-increasing quantities of metagenomic data, there is a growing need to make datasets Findable, Accessible, Interoperable, and Reusable (FAIR) across diverse ecosystems. FAIR data is essential to developing analytical frameworks that integrate microbiological, genomic, ecological, oceanographic, and computational methods. Although community standards defining the minimal metadata required to accompany sequence data exist, they haven’t been consistently used across projects, precluding interoperability. Moreover, these data are not machine-actionable or discoverable by cyberinfrastructure systems. By making ‘omic and physicochemical datasets FAIR to machine systems, we can enable sequence data discovery and reuse based on machine-readable descriptions of environments or physicochemical gradients. In this work, we developed a novel technical specification for dataset encapsulation for the FAIR reuse of marine metagenomic and physicochemical datasets within cyberinfrastructure systems. This includes using Frictionless Data Packages enriched with terminology from environmental and life-science ontologies to annotate measured variables, their units, and the measurement devices used. This approach was implemented in Planet Microbe, a cyberinfrastructure platform and marine metagenomic web-portal. Here, we discuss the data properties built into the specification to make global ocean datasets FAIR within the Planet Microbe portal. We additionally discuss the selection of, and contributions to marine-science ontologies used within the specification. Finally, we use the system to discover data by which to answer various biological questions about environments, physicochemical gradients, and microbial communities in meta-analyses. This work represents a future direction in marine metagenomic research by proposing a specification for FAIR dataset encapsulation that, if adopted within cyberinfrastructure systems, would automate the discovery, exchange, and re-use of data needed to answer broader reaching questions than originally intended.

Hydrothermal plumes as hotspots for deep-ocean heterotrophic microbial biomass production

Carbon budgets of hydrothermal plumes result from the balance between carbon sinks through plume chemoautotrophic processes and carbon release via microbial respiration. However, the lack of comprehensive analysis of the metabolic processes and biomass production rates hinders an accurate estimate of their contribution to the deep ocean carbon cycle. Here, we use a biogeochemical model to estimate the autotrophic and heterotrophic production rates of microbial communities in hydrothermal plumes and validate it with in situ data. We show how substrate limitation might prevent net chemolithoautotrophic production in hydrothermal plumes. Elevated prokaryotic heterotrophic production rates (up to 0.9 gCm^-2y^-1) compared to the surrounding seawater could lead to 0.05 GtCy^-1 of C-biomass produced through chemoorganotrophy within hydrothermal plumes, similar to the Particulate Organic Carbon (POC) export fluxes reported in the deep ocean. We conclude that hydrothermal plumes must be accounted for as significant deep sources of POC in ocean carbon budgets.

Diversity and Biogeography of Bathyal and Abyssal Seafloor Bacteria and Archaea Along a Mediterranean-Atlantic Gradient

Seafloor sediments cover the majority of planet Earth and microorganisms inhabiting these environments play a central role in marine biogeochemical cycles. Yet, description of the biogeography and distribution of sedimentary microbial life is still too sparse to evaluate the relative contribution of processes driving this distribution, such as the levels of drift, connectivity, and specialization. To address this question, we analyzed 210 archaeal and bacterial metabarcoding libraries from a standardized and horizon-resolved collection of sediment samples from 18 stations along a longitudinal gradient from the eastern Mediterranean to the western Atlantic. Overall, we found that biogeographic patterns depended on the scale considered: while at local scale the selective influence of contemporary environmental conditions appeared strongest, the heritage of historic processes through dispersal limitation and drift became more apparent at regional scale, and ended up superseding contemporary influences at inter-regional scale. When looking at environmental factors, the structure of microbial communities was correlated primarily with water depth, with a clear transition between 800 and 1,200 meters below sea level. Oceanic basin, water temperature, and sediment depth were other important explanatory parameters of community structure. Finally, we propose increasing dispersal limitation and ecological drift with sediment depth as a probable factor for the enhanced divergence of deeper horizons communities.

Dynamic prokaryotic communities in the dark western Mediterranean Sea

Dark ocean microbial dynamics are fundamental to understand ecosystem metabolism and ocean biogeochemical processes. Yet, the ecological response of deep ocean communities to environmental perturbations remains largely unknown. Temporal and spatial dynamics of the meso- and bathypelagic prokaryotic communities were assessed throughout a 2-year seasonal sampling across the western Mediterranean Sea. A common pattern of prokaryotic communities' depth stratification was observed across the different regions and throughout the seasons. However, sporadic and drastic alterations of the community composition and diversity occurred either at specific water masses or throughout the aphotic zone and at a basin scale. Environmental changes resulted in a major increase in the abundance of rare or low abundant phylotypes and a profound change of the community composition. Our study evidences the temporal dynamism of dark ocean prokaryotic communities, exhibiting long periods of stability but also drastic changes, with implications in community metabolism and carbon fluxes. Taken together, the results highlight the importance of monitoring the temporal patterns of dark ocean prokaryotic communities.

Temporal dynamics of carbon sequestration in coastal North Atlantic fjord system as seen through dissolved organic matter characterisation

Fjord systems in higher latitudes are unique coastal water ecosystems that facilitate the study of dissolved organic matter (DOM) dynamics from surface to deeper waters. The current work was undertaken in the Trondheim fjord characterized by North Atlantic waters, and compared DOM fractions from three depths - surface (3 m), intermediate (225 m) and deep (440 m) in four seasons, from late spring to winter in 2017. The high-resolution mass spectrometry data showed that DOM composition varies significantly in different seasons rather than in different depths in the fjord systems. The bacterial community composition was comparable except at spring surface and summer intermediate depths. Bacterial production was minimal below the euphotic layer, even with sufficient availability of inorganic nutrients. The bacterial production rate in the surface waters was about 7 times and over 50 times higher than that of the aphotic zone in the winter and the summer seasons, respectively. The surface heterotrophic microbial communities might have rapidly consumed the available labile DOM, with the production of more refractory DOM limiting bacterial production in aphotic layers. The greater number of CRAM-like formulas determined in the surface waters compared to other depths supports our hypothesis. The refractory DOM sequestered in the water column may either be exported into sediments attached to particulate matter and marine gels, or may escape into the atmosphere as carbon dioxide/monoxide during the photochemical oxidation pathways, suggesting that it is involved in climate change scenarios.

The impact of eutrophication towards selected bacterial process rates in tropical coastal waters

The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R² ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.

Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions

The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes.

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean's compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain

Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24-34°C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94-1.38 d-1, was very similar (0.34 ± 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38-24.4 d-1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.

New insights into mechanisms of sunlight- and dark-mediated high-temperature accelerated diurnal production-degradation of fluorescent DOM in lake waters

The production of fluorescent dissolved organic matter (FDOM) by phytoplankton and its subsequent degradation, both of which occur constantly under diurnal-day time sunlight and by night time dark-microbial respiration processes in the upper layer of surface waters, influence markedly several biogeochemical processes and functions in aquatic environments and can be feasibly related to global warming (GW). In this work sunlight-mediated high-temperature was shown to accelerate the production of FDOM, but also its complete disappearance over a 24-h diurnal period in July at the highest air and water temperatures (respectively, 41.1 and 33.5 °C), differently from lower temperature months. Extracellular polymeric substances (EPS), an early-state DOM, were produced by phytoplankton in July in the early morning (6:00-9:00), then they were degraded into four FDOM components over midday (10:00-15:00), which was followed by simultaneous production and almost complete degradation of FDOM with reformation of EPS during the night (2:00-6:00). Such transformations occurred simultaneously with the fluctuating production of nutrients, dissolved organic carbon (DOC), dissolved organic nitrogen (DON) and the two isotopes (δ¹⁵N and δ¹⁸O) of NO₃^-. It was estimated that complete degradation of FDOM in July was associated with mineralization of approximately 15% of the initial DOC, which showed a nighttime minimum (00:00) in comparison to a maximum at 13:00. FDOM identified by excitation-emission matrix spectroscopy combined with parallel factor analysis consisted of EPS, autochthonous humic-like substances (AHLS) of C- and M-types, a combined form of C- and M-types of AHLS, protein-like substances (PLS), newly-released PLS, tryptophan-like substances, tyrosine-like substances (TYLS), a combined form of TYLS and phenylalanine-like substances (PALS), and their degradation products. Finally, stepwise degradation and production processes are synthesized in a pathway for FDOM components production and their subsequent transformation under different diurnal temperature conditions, which provided a broader paradigm for future impacts on GW-mediated DOM dynamics in lake water.

Large deep-sea zooplankton biomass mirrors primary production in the global ocean

The biological pump transports organic carbon produced by photosynthesis to the meso- and bathypelagic zones, the latter removing carbon from exchanging with the atmosphere over centennial time scales. Organisms living in both zones are supported by a passive flux of particles, and carbon transported to the deep-sea through vertical zooplankton migrations. Here we report globally-coherent positive relationships between zooplankton biomass in the epi-, meso-, and bathypelagic layers and average net primary production (NPP). We do so based on a global assessment of available deep-sea zooplankton biomass data and large-scale estimates of average NPP. The relationships obtained imply that increased NPP leads to enhanced transference of organic carbon to the deep ocean. Estimated remineralization from respiration rates by deep-sea zooplankton requires a minimum supply of 0.44 Pg C y-1 transported into the bathypelagic ocean, comparable to the passive carbon sequestration. We suggest that the global coupling between NPP and bathypelagic zooplankton biomass must be also supported by an active transport mechanism associated to vertical zooplankton migration.

Ocean acidification modifies biomolecule composition in organic matter through complex interactions

The main source of marine organic carbon (OC) is autotrophic production, while heterotrophic degradation is its main sink. Increased anthropogenic CO₂ release leads to ocean acidification and is expected to alter phytoplankton community composition, primary production rates and bacterial degradation processes in the coming decades with potential consequences for dissolved and particulate OC concentration and composition. Here we investigate effects of increased pCO₂ on dissolved and particulate amino acids (AA) and carbohydrates (CHO), in arctic and sub-arctic planktonic communities in two large-scale mesocosm experiments. Dissolved AA concentrations responded to pCO₂/pH changes during early bloom phases but did not show many changes after nutrient addition. A clear positive correlation in particulate AA was detected in post-bloom phases. Direct responses in CHO concentrations to changing pCO₂/pH were lacking, suggesting that observed changes were rather indirect and dependent on the phytoplankton community composition. The relative composition of AA and CHO did not change as a direct consequence of pCO₂ increase. Changes between bloom phases were associated with the prevailing nutrient status. Our results suggest that biomolecule composition will change under future ocean conditions but responses are highly complex, and seem to be dependent on many factors including bloom phase and sampling site.

Let more big fish sink: Fisheries prevent blue carbon sequestration-half in unprofitable areas

Contrary to most terrestrial organisms, which release their carbon into the atmosphere after death, carcasses of large marine fish sink and sequester carbon in the deep ocean. Yet, fisheries have extracted a massive amount of this "blue carbon," contributing to additional atmospheric CO₂ emissions. Here, we used historical catches and fuel consumption to show that ocean fisheries have released a minimum of 0.73 billion metric tons of CO₂ (GtCO₂) in the atmosphere since 1950. Globally, 43.5% of the blue carbon extracted by fisheries in the high seas comes from areas that would be economically unprofitable without subsidies. Limiting blue carbon extraction by fisheries, particularly on unprofitable areas, would reduce CO₂ emissions by burning less fuel and reactivating a natural carbon pump through the rebuilding of fish stocks and the increase of carcasses deadfall.

Subtle bacterioplankton community responses to elevated CO2 and warming in the oligotrophic South Pacific gyre

Bacterioplankton play a critical role in primary production, carbon cycling, and nutrient cycling in the oligotrophic ocean. To investigate the effect of elevated CO₂ and warming on the composition and function of bacterioplankton communities in oligotrophic waters, we performed two trace-metal clean deck board incubation experiments during the New Zealand GEOTRACES transect of the South Pacific gyre (SPG). High-throughput amplicon sequencing of the 16S rRNA gene revealed that bacterioplankton community composition was distinct between the fringe and ultra-oligotrophic centre of the SPG and changed consistently in response to elevated CO₂ at the ultra-oligotrophic centre but not at the mesotrophic fringe of the SPG. The combined effects of elevated CO₂ and warming resulted in a high degree of heterogeneity between replicate communities. Community-level protein synthesis rates (³ H-Leucine incorporation) and bacterioplankton abundance were not affected by elevated CO₂ alone or in combination with warming at the fringe or ultra-oligotrophic centre of the SPG. These data suggest bacterioplankton community responses to elevated CO₂ may be modulated by nutrient regimes in open ocean ecosystems and highlight the need for further investigation in expanding oligotrophic subtropical gyres.

Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes

Lakes receive large amounts of terrestrially derived dissolved organic matter (tDOM). However, little is known about how aquatic microbial communities interact with tDOM in lakes. Here, by performing microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l). In response to tDOM addition, microbial biomass increased while dissolved organic carbon (DOC) decreased. The amount of DOC decrease did not show any significant correlation with salinity. However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Abundant taxa and copiotrophs were actively involved in tDOM transformation, suggesting their vital roles in lacustrine carbon cycle. Network analysis indicated that 66 operational taxonomic units (OTUs, affiliated with Alphaproteobacteria, Actinobacteria, Bacteroidia, Bacilli,  Gammaproteobacteria, Halobacteria, Planctomycetacia, Rhodothermia, and Verrucomicrobiae) were associated with degradation of CHO compounds, while four bacterial OTUs (affiliated with Actinobacteria, Alphaproteobacteria, Bacteroidia and Gammaproteobacteria) were highly associated with the degradation of CHOS compounds. Network analysis further revealed that tDOM transformation may be a synergestic process, involving cooperation among multiple species. In summary, our study provides new insights into a microbial role in transforming tDOM in saline lakes and has important implications for understanding the carbon cycle in aquatic environments.

Carbon recycling efficiency and phosphate turnover by marine nitrifying archaea

Thaumarchaeotal nitrifiers are among the most abundant organisms in the ocean, but still unknown is the carbon (C) yield from nitrification and the coupling of these fluxes to phosphorus (P) turnover and release of metabolites from the cell. Using a dual radiotracer approach, we found that Nitrosopumilus maritimus fixed roughly 0.3 mol C, assimilated 2 mmol P, and released ca. 10^-2 mol C and 10^-5 mol P as dissolved organics (DOC and DOP) per mole ammonia respired. Phosphate turnover may influence assimilation fluxes by nitrifiers in the euphotic zone, which parallel those of the dark ocean. Collectively, marine nitrifiers assimilate up to 2 Pg C year^-1 and 0.05 Pg P year^-1 and thereby recycle roughly 5% of mineralized C and P into marine biomass. Release of roughly 50 Tg DOC and 0.2 Tg DOP by thaumarchaea each year represents a small but fresh input of reduced substrates throughout the ocean.

Disentangling the mechanisms shaping the surface ocean microbiota

BACKGROUND

The ocean microbiota modulates global biogeochemical cycles and changes in its configuration may have large-scale consequences. Yet, the underlying ecological mechanisms structuring it are unclear. Here, we investigate how fundamental ecological mechanisms (selection, dispersal and ecological drift) shape the smallest members of the tropical and subtropical surface-ocean microbiota: prokaryotes and minute eukaryotes (picoeukaryotes). Furthermore, we investigate the agents exerting abiotic selection on this assemblage as well as the spatial patterns emerging from the action of ecological mechanisms. To explore this, we analysed the composition of surface-ocean prokaryotic and picoeukaryotic communities using DNA-sequence data (16S- and 18S-rRNA genes) collected during the circumglobal expeditions Malaspina-2010 and TARA-Oceans.

RESULTS

We found that the two main components of the tropical and subtropical surface-ocean microbiota, prokaryotes and picoeukaryotes, appear to be structured by different ecological mechanisms. Picoeukaryotic communities were predominantly structured by dispersal-limitation, while prokaryotic counterparts appeared to be shaped by the combined action of dispersal-limitation, selection and drift. Temperature-driven selection appeared as a major factor, out of a few selected factors, influencing species co-occurrence networks in prokaryotes but not in picoeukaryotes, indicating that association patterns may contribute to understand ocean microbiota structure and response to selection. Other measured abiotic variables seemed to have limited selective effects on community structure in the tropical and subtropical ocean. Picoeukaryotes displayed a higher spatial differentiation between communities and a higher distance decay when compared to prokaryotes, consistent with a scenario of higher dispersal limitation in the former after considering environmental heterogeneity. Lastly, random dynamics or drift seemed to have a more important role in structuring prokaryotic communities than picoeukaryotic counterparts.

CONCLUSIONS

The differential action of ecological mechanisms seems to cause contrasting biogeography, in the tropical and subtropical ocean, among the smallest surface plankton, prokaryotes and picoeukaryotes. This suggests that the idiosyncrasy of the main constituents of the ocean microbiota should be considered in order to understand its current and future configuration, which is especially relevant in a context of global change, where the reaction of surface ocean plankton to temperature increase is still unclear. Video Abstract.

Nitrifier adaptation to low energy flux controls inventory of reduced nitrogen in the dark ocean

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013 to ∼2 × 1013 mol of C per year globally through the flux of ∼1 × 1014 to ∼2 × 1014 mol of N per year of the two steps of oxidation throughout the dark ocean.

Drivers of Microbial Carbon Fluxes Variability in Two Oligotrophic Mediterranean Coastal Systems

The carbon fluxes between phytoplankton and heterotrophic bacterioplankton were studied in two coastal oligotrophic sites in the NW Mediterranean. Phytoplankton and bacterial production rates were measured under natural conditions using different methods. In the Bay of Villefranche, the temporal variability revealed net heterotrophy in July-October and net autotrophy in December-March. The spatial variability was studied in the Bay of Palma, showing net autotrophic areas in the west and heterotrophic areas in the east. On average bacterial respiration, represented 62% of the total community respiration. Bacterial growth efficiency (BGE) values were significantly higher in autotrophic conditions than in heterotrophic ones. During autotrophic periods, dissolved primary production (DPP) was enough to sustained bacterial metabolism, although it showed a positive correlation with organic carbon stock (DOC). Under heterotrophic conditions, DPP did not sustain bacterial metabolism but bacterial respiration correlated with DPP and bacterial production with DOC. Temperature affected positively, DOC, BGE, bacterial respiration and production when the trophic status was autotrophic. To summarize, the response of bacterial metabolism to temperature and carbon sources depends on the trophic status within these oligotrophic coastal systems.

Rising CO2 enhances hypoxia tolerance in a marine fish

Global environmental change is increasing hypoxia in aquatic ecosystems. During hypoxic events, bacterial respiration causes an increase in carbon dioxide (CO2) while oxygen (O2) declines. This is rarely accounted for when assessing hypoxia tolerances of aquatic organisms. We investigated the impact of environmentally realistic increases in CO2 on responses to hypoxia in European sea bass (Dicentrarchus labrax). We conducted a critical oxygen (O2crit) test, a common measure of hypoxia tolerance, using two treatments in which O2 levels were reduced with constant ambient CO2 levels (~530 µatm), or with reciprocal increases in CO2 (rising to ~2,500 µatm). We also assessed blood acid-base chemistry and haemoglobin-O2 binding affinity of sea bass in hypoxic conditions with ambient (~650 μatm) or raised CO2 (~1770 μatm) levels. Sea bass exhibited greater hypoxia tolerance (~20% reduced O2crit), associated with increased haemoglobin-O2 affinity (~32% fall in P50) of red blood cells, when exposed to reciprocal changes in O2 and CO2. This indicates that rising CO2 which accompanies environmental hypoxia facilitates increased O2 uptake by the blood in low O2 conditions, enhancing hypoxia tolerance. We recommend that when impacts of hypoxia on aquatic organisms are assessed, due consideration is given to associated environmental increases in CO2.

Organic sulfur was integral to the Archean sulfur cycle

The chemistry of the Early Earth is widely inferred from the elemental and isotopic compositions of sulfidic sedimentary rocks, which are presumed to have formed globally through the reduction of seawater sulfate or locally from hydrothermally supplied sulfide. Here we argue that, in the anoxic Archean oceans, pyrite could form in the absence of ambient sulfate from organic sulfur contained within living cells. Sulfides could be produced through mineralization of reduced sulfur compounds or reduction of organic-sourced sulfite. Reactive transport modeling suggests that, for sulfate concentrations up to tens of micromolar, organic sulfur would have supported 20 to 100% of sedimentary pyrite precipitation and up to 75% of microbial sulfur reduction. The results offer an alternative explanation for the low range of δ34S in Archean sulfides, and raise a possibility that sulfate scarcity delayed the evolution of dissimilatory sulfate reduction until the initial ocean oxygenation around 2.7 Ga.

Amino acids promote black carbon aggregation and microbial colonization in coastal waters off Vietnam

The combustion of fossil fuels and biomass produces pyrogenic organic matter usually known as 'black carbon' (BC), which are transported across the atmosphere as particulate aerosol, eventually deposited on land and oceans. Soil studies have investigated the potential microbial colonization and remineralization of BC particles, but this process has been seldom studied in marine waters. BC provides a significant input of organic carbon to the oceans, yet its fate and role in biogeochemical cycling remains unknown. Here we explored the microbial colonization of BC particles in coastal seawater samples collected in Halong Bay (northern Vietnam). Using high-resolution mass spectrometry and microscopy methods, we observed an increasing colonization of BC particles by marine microbes in the presence of amino acids. Our results suggest that natural organic matter (NOM) present in seawater may promote the microbial colonization and eventual remineralization of BC particles. Future experiments should explore the potential microbial remineralization of BC particles to unveil the role of this massive source of carbon to marine ecosystems.

Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. The active enzyme harbors the nickel(I) hydrocorphin coenzyme F-430 as a prosthetic group and catalyzes the reversible reduction of methyl-coenzyme M (CH₃–S-CoM) with coenzyme B (HS-CoM) to methane and CoM-S–S-CoB. MCR is also involved in anaerobic methane oxidation in reverse of methanogenesis and most probably in the anaerobic oxidation of ethane, propane, and butane. The challenging question is how the unreactive CH₃–S thioether bond in methyl-coenzyme M and the even more unreactive C–H bond in methane and the other hydrocarbons are anaerobically cleaved. A key to the answer is the negative redox potential (E_o′) of the Ni(II)F-430/Ni(I)F-430 couple below −600 mV and the radical nature of Ni(I)F-430. However, the negative one-electron redox potential is also the Achilles heel of MCR; it makes the nickel enzyme one of the most O₂-sensitive enzymes known to date. Even under physiological conditions, the Ni(I) in MCR is oxidized to the Ni(II) or Ni(III) states, e.g., when in the cells the redox potential (E′) of the CoM-S–S-CoB/HS-CoM and HS-CoB couple (E_o′ = −140 mV) gets too high. Methanogens therefore harbor an enzyme system for the reactivation of inactivated MCR in an ATP-dependent reduction reaction. Purification of active MCR in the Ni(I) oxidation state is very challenging and has been achieved in only a few laboratories. This perspective reviews the function, structure, and properties of MCR, what is known and not known about the catalytic mechanism, how the inactive enzyme is reactivated, and what remains to be discovered.

Unraveling the sources and fluorescence compositions of dissolved and particulate organic matter (DOM and POM) in Lake Taihu, China

Organic matter (OM), a complex entity with diverse functional groups and molecular sizes, has important effects on aquatic systems. We studied the optical compositions and sources of dissolved organic matter (DOM) and particulate organic matter (POM) in Lake Taihu, a large, shallow and eutrophic lake in China. Significant differences in optical compositions and sources occurred between the POM and DOM. The temporal-spatial distribution of the fluorescence indices suggested that the POM in Lake Taihu was mainly from autochthonous sources, but more exogenous characteristics were shown in POM in the river mouths compared with other regions. The chromophoric DOM in Lake Taihu mainly displayed autochthonous characteristics. The POM-DOM PARAFAC model was used to examine OM optical composition and five components were identified, which contained three protein-like components (C1, C2, and C5), a microbial humic-like component (C3), and a terrestrial humic-like component (C4). The POM was dominated by C5 in summer and autumn and C3 in winter and spring, and the DOM was dominated by protein-like components (C1, C2, and C5) through the entire year. The algae-dominated region had a relative higher contribution of tryptophan-like components of POM compared with the macrophyte-dominated region. A conceptual model based on the theory of "four phases of cyanobacteria bloom development" was proposed to fully describe the relationship between POM-DOM exchanges and cyanobacteria bloom development.

Plastic Accumulation in the Sea Surface Microlayer: An Experiment-Based Perspective for Future Studies

Plastic particles are ubiquitous in the marine environment. Given their low density, they have the tendency to float on the sea surface, with possible impacts on the sea surface microlayer (SML). The SML is an enriched biofilm of marine organic matter, that plays a key role in biochemical and photochemical processes, as well as controlling gas exchange between the ocean and the atmosphere. Recent studies indicate that plastics can interfere with the microbial cycling of carbon. However, studies on microplastic accumulation in the SML are limited, and their effects on organic matter cycling in the surface ocean are poorly understood. To explore potential dynamics in this key ocean compartment, we ran a controlled experiment with standard microplastics in the surface and bulk water of a marine monoculture. Bacterial abundance, chromophoric dissolved organic matter (CDOM), and oxygen concentrations were measured. The results indicate an accumulation of CDOM in the SML and immediate underlying water when microplastic particles are present, as well as an enhanced oxygen consumption. If extrapolated to a typical marine environment, this indicates that alterations in the quality and reactivity of the organic components of the SML could be expected. This preliminary study shows the need for a more integrated effort to our understanding the impact of microplastics on SML functioning and marine biological processes.

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.