Episodic organic carbon fluxes from surface ocean to abyssal depths during long-term monitoring in NE Pacific

Community differences and potential function along the particle size spectrum of microbes in the twilight zone

BACKGROUND

The twilight zone, which extends from the base of the euphotic zone to a depth of 1000 m, is the major area of particulate organic carbon (POC) remineralization in the ocean. However, little is known about the microbial community and metabolic activity that are directly associated with POC remineralization in this consistently underexplored realm. Here, we utilized a large-volume in situ water transfer system to collect the microbes on different-sized particles from the twilight zone in three regions and analyzed their composition and metabolic function by metagenomic analysis.

RESULTS

Distinct prokaryotic communities with significantly lower diversity and less endemic species were detected on particles in the South East Asian Time-series Study (SEATS) compared with the other two regions, perhaps due to the in situ physicochemical conditions and low labile nutrient availability in this region. Observable transitions in community composition and function at the upper and lower boundaries of the twilight zone suggest that microbes respond differently to (and potentially drive the transformation of) POC through this zone. Substantial variations among different particle sizes were observed, with smaller particles typically exhibiting lower diversity but harboring a greater abundance of carbon degradation-associated genes than the larger particles. Such a pattern might arise due to the relatively larger surface area of the smaller particles relative to their volume, which likely provides more sites for microbial colonization, increasing their chance of being remineralized. This makes them less likely to be transferred to the deep ocean, and thus, they contribute more to carbon recycling than to long-term sequestration. Both contig-based and metagenome-assembled genome-(MAG-) based analyses revealed a high diversity of the Carbohydrate-Active enZymes (CAZy) family. This indicates the versatile carbohydrate metabolisms of the microbial communities associated with sinking particles that modulate the remineralization and export of POC in the twilight zone.

CONCLUSION

Our study reveals significant shifts in microbial community composition and function in the twilight zone, with clear differences among the three particle sizes. Microbes with diverse metabolic potential exhibited different responses to the POC entering the twilight zone and also collectively drove the transformation of POC through this zone. These findings provided insights into the diversity of prokaryotes in sinking particles and their roles in POC remineralization and export in marine ecosystems. Video Abstract.

Sensing flow gradients is necessary for learning autonomous underwater navigation

Aquatic animals are much better at underwater navigation than robotic vehicles. Robots face major challenges in deep water because of their limited access to global positioning signals and flow maps. These limitations, and the changing nature of water currents, support the use of reinforcement learning approaches, where the navigator learns through trial-and-error interactions with the flow environment. But is it feasible to learn underwater navigation in the agent's Umwelt, without any land references? Here, we tasked an artificial swimmer with learning to reach a specific destination in unsteady flows by relying solely on egocentric observations, collected through on-board flow sensors in the agent's body frame, with no reference to a geocentric inertial frame. We found that while sensing local flow velocities is sufficient for geocentric navigation, successful egocentric navigation requires additional information of local flow gradients. Importantly, egocentric navigation strategies obey rotational symmetry and are more robust in unfamiliar conditions and flows not experienced during training. Our work expands underwater robot-centric learning, helps explain why aquatic organisms have arrays of flow sensors that detect gradients, and provides physics-based guidelines for transfer learning of learned policies to unfamiliar and diverse flow environments.

Ecological dynamics explain modular denitrification in the ocean

Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is multistep denitrification (NO3-→NO2-→NO→N2O→N2), which dominates OMZ bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain subsets ("modules") of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when organic matter (OM) limits growth, which explains the viability of populations respiring NO2- and N2O in a NO3--filled ocean. Results predict denitrifier community succession along environmental gradients: Pathway length increases as the limiting substrate shifts from OM to N, suggesting a niche for the short NO3-→NO2- module in free-living, OM-limited communities, and for the complete pathway in organic particle-associated communities, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3-→NO2- module. Results also capture observations that NO3- is the dominant source of N2O. Our framework advances the mechanistic understanding of the relationship between microbial ecology and N loss in the ocean and can be extended to other processes and environments.

Seamounts generate efficient active transport loops to nourish the twilight ecosystem

Seamounts are ecological oases nurturing abundant fisheries resources and epibenthic megafauna in the vast oligotrophic ocean. Despite their significance, the formation mechanisms underlying these seamount ecological oases remain uncertain. To shed light on this phenomenon, this study conducted interdisciplinary in situ observations focusing on a shallow seamount in the oligotrophic ocean. The findings show that the seamount's topography interferes with the oceanic current to generate lee waves, effectively enhancing the nutrient supply to the euphotic layer downstream of the seamount. This continuous supply enhances phytoplankton biomass and subsequently the grazing and diurnal vertical migration of zooplankton, rapidly transporting the augmented phytoplankton biomass to the aphotic layer. Unlike the cyclonic eddies that move in the upper ocean, seamounts stand at fixed locations creating a more efficient and steady active transport loop. This active transport loop connects the euphotic and twilight zones, potentially conveying nourishment to benthic ecosystems to create stereoscopic oases in the oligotrophic ocean.

A deep-sea isopod that consumes Sargassum sinking from the ocean's surface

Most deep-ocean life relies on organic carbon from the surface ocean. While settling primary production rapidly attenuates in the water column, pulses of organic material can be quickly transported to depth in the form of food falls. One example of fresh material that can reach great depths across the tropical Atlantic Ocean and Caribbean Sea is the pelagic macroalgae Sargassum. However, little is known about the deep-ocean organisms able to use this food source. Here, we encountered the isopod Bathyopsurus nybelini at depths 5002-6288 m in the Puerto Rico Trench and Mid-Cayman Spreading Center using the Deep Submergence Vehicle Alvin. In most of the 32 observations, the isopods carried fronds of Sargassum. Through an integrative suite of morphological, DNA sequencing, and microbiological approaches, we show that this species is adapted to feed on Sargassum by using a specialized swimming stroke, having serrated and grinding mouthparts, and containing a gut microbiome that provides a dietary contribution through the degradation of macroalgal polysaccharides and fixing nitrogen. The isopod's physiological, morphological, and ecological adaptations demonstrate that vertical deposition of Sargassum is a direct trophic link between the surface and deep ocean and that some deep-sea organisms are poised to use this material.

Abyssal hydrothermal springs-Cryptic incubators for brooding octopus

Does warmth from hydrothermal springs play a vital role in the biology and ecology of abyssal animals? Deep off central California, thousands of octopus (Muusoctopus robustus) migrate through cold dark waters to hydrothermal springs near an extinct volcano to mate, nest, and die, forming the largest known aggregation of octopus on Earth. Warmth from the springs plays a key role by raising metabolic rates, speeding embryonic development, and presumably increasing reproductive success; we show that brood times for females are ~1.8 years, far faster than expected for abyssal octopods. Using a high-resolution subsea mapping system, we created landscape-scale maps and image mosaics that reveal 6000 octopus in a 2.5-ha area. Because octopuses die after reproducing, hydrothermal springs indirectly provide a food supplement to the local energy budget. Although localized deep-sea heat sources may be essential to octopuses and other warm-tolerant species, most of these unique and often cryptic habitats remain undiscovered and unexplored.

Dynamic robotic tracking of underwater targets using reinforcement learning

To realize the potential of autonomous underwater robots that scale up our observational capacity in the ocean, new techniques are needed. Fleets of autonomous robots could be used to study complex marine systems and animals with either new imaging configurations or by tracking tagged animals to study their behavior. These activities can then inform and create new policies for community conservation. The role of animal connectivity via active movement of animals represents a major knowledge gap related to the distribution of deep ocean populations. Tracking underwater targets represents a major challenge for observing biological processes in situ, and methods to robustly respond to a changing environment during monitoring missions are needed. Analytical techniques for optimal sensor placement and path planning to locate underwater targets are not straightforward in such cases. The aim of this study was to investigate the use of reinforcement learning as a tool for range-only underwater target-tracking optimization, whose promising capabilities have been demonstrated in terrestrial scenarios. To evaluate its usefulness, a reinforcement learning method was implemented as a path planning system for an autonomous surface vehicle while tracking an underwater mobile target. A complete description of an open-source model, performance metrics in simulated environments, and evaluated algorithms based on more than 15 hours of at-sea field experiments are presented. These efforts demonstrate that deep reinforcement learning is a powerful approach that enhances the abilities of autonomous robots in the ocean and encourages the deployment of algorithms like these for monitoring marine biological systems in the future.

Coastal upwelling drives ecosystem temporal variability from the surface to the abyssal seafloor

Long-term biological time series that monitor ecosystems across the ocean's full water column are extremely rare. As a result, classic paradigms are yet to be tested. One such paradigm is that variations in coastal upwelling drive changes in marine ecosystems throughout the water column. We examine this hypothesis by using data from three multidecadal time series spanning surface (0 m), midwater (200 to 1,000 m), and benthic (~4,000 m) habitats in the central California Current Upwelling System. Data include microscopic counts of surface plankton, video quantification of midwater animals, and imaging of benthic seafloor invertebrates. Taxon-specific plankton biomass and midwater and benthic animal densities were separately analyzed with principal component analysis. Within each community, the first mode of variability corresponds to most taxa increasing and decreasing over time, capturing seasonal surface blooms and lower-frequency midwater and benthic variability. When compared to local wind-driven upwelling variability, each community correlates to changes in upwelling damped over distinct timescales. This suggests that periods of high upwelling favor increase in organism biomass or density from the surface ocean through the midwater down to the abyssal seafloor. These connections most likely occur directly via changes in primary production and vertical carbon flux, and to a lesser extent indirectly via other oceanic changes. The timescales over which species respond to upwelling are taxon-specific and are likely linked to the longevity of phytoplankton blooms (surface) and of animal life (midwater and benthos), which dictate how long upwelling-driven changes persist within each community.

Phenology in the deep sea: seasonal and tidal feeding rhythms in a keystone octocoral

Biological rhythms are widely known in terrestrial and marine systems, where the behaviour or function of organisms may be tuned to environmental variation over periods from minutes to seasons or longer. Although well characterized in coastal environments, phenology remains poorly understood in the deep sea. Here we characterized intra-annual dynamics of feeding activity for the deep-sea octocoral Paragorgia arborea. Hourly changes in polyp activity were quantified using a time-lapse camera deployed for a year on Sur Ridge (1230 m depth; Northeast Pacific). The relationship between feeding and environmental variables, including surface primary production, temperature, acoustic backscatter, current speed and direction, was evaluated. Feeding activity was highly seasonal, with a dormancy period identified between January and early April, reflecting seasonal changes in food availability as suggested by primary production and acoustic backscatter data. Moreover, feeding varied with tides, which likely affected food delivery through cyclic oscillation in current speed and direction. This study provides the first evidence of behavioural rhythms in a coral species at depth greater than 1 km. Information on the feeding biology of this cosmopolitan deep-sea octocoral will contribute to a better understanding of how future environmental change may affect deep-sea coral communities and the ecosystem services they provide.

Tracing the path of carbon export in the ocean though DNA sequencing of individual sinking particles

Surface phytoplankton communities were linked with the carbon they export into the deep ocean by comparing 18 S rRNA gene sequence communities from surface seawater and individually isolated sinking particles. Particles were collected in sediment traps deployed at locations in the North Pacific subtropical gyre and the California Current. DNA was isolated from individual particles, bulk-collected trap particles, and the surface seawater. The relative sequence abundance of exported phytoplankton taxa in the surface water varied across functional groups and ecosystems. Of the sequences detected in sinking particles, about half were present in large (>300 μm), individually isolated particles and primarily belonged to taxa with small cell sizes (<50 µm). Exported phytoplankton taxa detected only in bulk trap samples, and thus presumably packaged in the smaller sinking size fraction, contained taxa that typically have large cell sizes (>500 μm). The effect of particle degradation on the detectable 18 S rRNA gene community differed across taxa, and differences in community composition among individual particles from the same location largely reflected differences in relative degradation state. Using these data and particle imaging, we present an approach that incorporates genetic diversity into mechanistic models of the ocean's biological carbon pump, which will lead to better quantification of the ocean's carbon cycle.

Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats

BACKGROUND

The deep sea harbors the majority of the microbial biomass in the ocean and is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches-the deepest part of the ocean.

RESULTS

In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. In total, 62 metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family, and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g., benzoate), polyaromatic hydrocarbons (e.g., fluorene), polychlorobiphenyl (e.g., 4-chlorobiphenyl), and organochlorine compounds (e.g., chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g., trehalose) and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits suggest that Chloroflexi may follow a "feast-or-famine" metabolic strategy, i.e., preferentially consume labile OM and store the energy intracellularly under OM-rich conditions, and utilize the stored energy or degrade recalcitrant OM for survival under OM-limited condition.

CONCLUSION

This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi and highlights their significance in deep-sea carbon, sulfur, and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for survival under variable and heterogenic OM inputs in the deep ocean. Video Abstract.

Microbes contribute to setting the ocean carbon flux by altering the fate of sinking particulates

Sinking particulate organic carbon out of the surface ocean sequesters carbon on decadal to millennial timescales. Predicting the particulate carbon flux is therefore critical for understanding both global carbon cycling and the future climate. Microbes play a crucial role in particulate organic carbon degradation, but the impact of depth-dependent microbial dynamics on ocean-scale particulate carbon fluxes is poorly understood. Here we scale-up essential features of particle-associated microbial dynamics to understand the large-scale vertical carbon flux in the ocean. Our model provides mechanistic insight into the microbial contribution to the particulate organic carbon flux profile. We show that the enhanced transfer of carbon to depth can result from populations struggling to establish colonies on sinking particles due to diffusive nutrient loss, cell detachment, and mortality. These dynamics are controlled by the interaction between multiple biotic and abiotic factors. Accurately capturing particle-microbe interactions is essential for predicting variability in large-scale carbon cycling.

Micro-scale microbial community dynamics can substantially alter the fate of sinking particulates in the ocean thus playing a key role in setting the vertical flux of particulate carbon in the ocean.

Trace Elemental Analysis of the Exoskeleton, Leg Muscle, and Gut of Three Hadal Amphipods

Hadal trenches are the deepest areas worldwide. Amphipods are considered a key factor in hadal ecosystems because of their important impacts on the hadal environment. Amphipods have benthic habits, and therefore, serve as good metal biomonitors. However, little is known about the hadal amphipod metal accumulations. In the present study, Alicella gigantea, Hirondellea gigas, and Scopelocheirus schellenbergi were sampled from the New Britain Trench (8824m, 7.02S 149.16E), Mariana Trench (10,839m, 11.38N 142.42E), and Marceau Trench (6690m, 1.42N 148.74E) in the West Pacific Ocean, respectively. The elemental concentrations of the three hadal amphipods were subsequently investigated. Nine trace elements (V, Cr, Mn, Co, Ni, Se, Mo, Ag, and Cd) of three tissues (exoskeleton, leg muscle, and gut) of the hadal amphipods were detected by using inductively coupled plasma mass spectrometry (ICP-MS) method. The concentrations of Cr, Cd, and Mn were comparably higher among those nine examined elements. The greatest accumulations of the elements Cr, Ag, and V in the exoskeleton and leg muscle were observed in H. gigas, and elements Mn, Co, and Se showed the highest accumulations in the gut in H. gigas among the three hadal amphipods. In addition, comparisons of the leg muscle trace element accumulation between the hadal amphipods and non-abyssal and shallow water decapoda and amphipoda species showed that the hadal amphipods possessed comparably higher concentrations of the trace elements Cd, Co, Mo, Ag, and V. This finding suggested a bottom-up effect of food availability and indicated the effects of human activities within the hadal environments. This study reveals the trace element bio-accumulation of three hadal amphipods, and suggests that deep-sea amphipods are potential indicator species for trace element bioavailability in the deep-sea environment.

Influence of Seasonal Variability in Flux Attenuation on Global Organic Carbon Fluxes and Nutrient Distributions

The biological carbon pump is a key component of the marine carbon cycle. This surface-to-deep flux of carbon is usually assumed to follow a simple power law function, which imposes that the surface export flux is attenuated throughout subsurface waters at a rate dictated by the parameterization exponent. This flux attenuation exponent is widely assumed as constant. However, there is increasing evidence that the flux attenuation varies both spatially and seasonally. While the former has received some attention, the consequences of the latter have not been explored. Here we aim to fill the gap with a theoretical study of how seasonal changes in both flux attenuation and sinking speed affect nutrient distributions and carbon fluxes. Using a global ocean-biogeochemical model that represents detritus explicitly, we look at different scenarios for how these varies seasonally, particularly the relative "phase" with respect to solar radiation and the "strength" of seasonality. We show that the sole presence of seasonality in the model-imposed flux attenuation and sinking speed leads to a greater transfer efficiency compared to the non-seasonal flux attenuation scenario, resulting in an increase of over 140% in some cases when the amplitude of the seasonality imposed is 60% of the non-seasonal base value. This work highlights the importance of the feedback taking place between the seasonally varying flux attenuation, sinking speed and other processes, suggesting that the assumption of constant-in-time flux attenuation and sinking speed might underestimate how much carbon is sequestered by the biological carbon pump.

Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors

We investigated the Southern Ocean (SO) prokaryote community structure via zero‐radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn‐winter) sectors of the SO. At higher taxonomic levels (phylum‐family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus‐zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi‐ and bathy‐abyssopelagic water masses. Common surface bacteria were abundant in several deep‐water masses and vice‐versa suggesting connectivity between surface and deep‐water microbial assemblages. Bacteria from same‐sector Antarctic Bottom Water samples showed patchy, high beta‐diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep‐water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide‐scale SO ecosystem microbial modelling.

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.

Abyssal Benthic Rover, an autonomous vehicle for long-term monitoring of deep-ocean processes

[Figure: see text].

A Visual Tour of Carbon Export by Sinking Particles

To better quantify the ocean's biological carbon pump, we resolved the diversity of sinking particles that transport carbon into the ocean's interior, their contribution to carbon export, and their attenuation with depth. Sinking particles collected in sediment trap gel layers from four distinct ocean ecosystems were imaged, measured, and classified. The size and identity of particles was used to model their contribution to particulate organic carbon (POC) flux. Measured POC fluxes were reasonably predicted by particle images. Nine particle types were identified, and most of the compositional variability was driven by the relative contribution of aggregates, long cylindrical fecal pellets, and salp fecal pellets. While particle composition varied across locations and seasons, the entire range of compositions was measured at a single well-observed location in the subarctic North Pacific over one month, across 500 m of depth. The magnitude of POC flux was not consistently associated with a dominant particle class, but particle classes did influence flux attenuation. Long fecal pellets attenuated most rapidly with depth whereas certain other classes attenuated little or not at all with depth. Small particles (<100 μm) consistently contributed ∼5% to total POC flux in samples with higher magnitude fluxes. The relative importance of these small particle classes (spherical mini pellets, short oval fecal pellets, and dense detritus) increased in low flux environments (up to 46% of total POC flux). Imaging approaches that resolve large variations in particle composition across ocean basins, depth, and time will help to better parameterize biological carbon pump models.

Abyssal deposit feeders are secondary consumers of detritus and rely on nutrition derived from microbial communities in their guts

Trophic ecology of detrital-based food webs is still poorly understood. Abyssal plains depend entirely on detritus and are among the most understudied ecosystems, with deposit feeders dominating megafaunal communities. We used compound-specific stable isotope ratios of amino acids (CSIA-AA) to estimate the trophic position of three abundant species of deposit feeders collected from the abyssal plain of the Northeast Pacific (Station M; ~ 4000 m depth), and compared it to the trophic position of their gut contents and the surrounding sediments. Our results suggest that detritus forms the base of the food web and gut contents of deposit feeders have a trophic position consistent with primary consumers and are largely composed of a living biomass of heterotrophic prokaryotes. Subsequently, deposit feeders are a trophic level above their gut contents making them secondary consumers of detritus on the abyssal plain. Based on δ13C values of essential amino acids, we found that gut contents of deposit feeders are distinct from the surrounding surface detritus and form a unique food source, which was assimilated by the deposit feeders primarily in periods of low food supply. Overall, our results show that the guts of deposit feeders constitute hotspots of organic matter on the abyssal plain that occupy one trophic level above detritus, increasing the food-chain length in this detritus-based ecosystem.

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.

Microbial dynamics of elevated carbon flux in the open ocean's abyss

The ocean’s “biological pump” exports sinking particles containing carbon, nutrients, and energy to the deep sea, contributing centrally to the global carbon cycle. Here, we identify key organisms and biological processes associated with elevated carbon flux to the abyss. Our analyses reveal that, during summer export, specific populations of photosynthetic algae, heterotrophic protists, and bacteria reach the abyss on sinking particles. Deep-sea bacteria respond rapidly to this elevated nutrient delivery to the abyss in summer. During other seasons, different organisms and processes appear responsible for particle export to the deep sea. Our analyses reveal key biota and biological processes that interconnect surface productivity, particle export, and the deep-sea ecosystem, thereby influencing the function and efficiency of the ocean’s biological pump.

In the open ocean, elevated carbon flux (ECF) events increase the delivery of particulate carbon from surface waters to the seafloor by severalfold compared to other times of year. Since microbes play central roles in primary production and sinking particle formation, they contribute greatly to carbon export to the deep sea. Few studies, however, have quantitatively linked ECF events with the specific microbial assemblages that drive them. Here, we identify key microbial taxa and functional traits on deep-sea sinking particles that correlate positively with ECF events. Microbes enriched on sinking particles in summer ECF events included symbiotic and free-living diazotrophic cyanobacteria, rhizosolenid diatoms, phototrophic and heterotrophic protists, and photoheterotrophic and copiotrophic bacteria. Particle-attached bacteria reaching the abyss during summer ECF events encoded metabolic pathways reflecting their surface water origins, including oxygenic and aerobic anoxygenic photosynthesis, nitrogen fixation, and proteorhodopsin-based photoheterotrophy. The abundances of some deep-sea bacteria also correlated positively with summer ECF events, suggesting rapid bathypelagic responses to elevated organic matter inputs. Biota enriched on sinking particles during a spring ECF event were distinct from those found in summer, and included rhizaria, copepods, fungi, and different bacterial taxa. At other times over our 3-y study, mid- and deep-water particle colonization, predation, degradation, and repackaging (by deep-sea bacteria, protists, and animals) appeared to shape the biotic composition of particles reaching the abyss. Our analyses reveal key microbial players and biological processes involved in particle formation, rapid export, and consumption, that may influence the ocean’s biological pump and help sustain deep-sea ecosystems.

Differential recruitment of opportunistic taxa leads to contrasting abilities in carbon processing by bathypelagic and surface microbial communities

Different factors affect the way dissolved organic matter (DOM) is processed in the ocean water column, including environmental conditions and the functional capabilities of the communities. Recent studies have shown that bathypelagic prokaryotes are metabolically flexible, but whether this versatility translates into a higher ability to process DOM has been barely explored. Here we performed a multifactorial transplant experiment to compare the growth, activity and changes in DOM quality in surface and bathypelagic waters inoculated with either surface or bathypelagic prokaryotic communities. The effect of nutrient additions to surface waters was also explored. Despite no differences in the cell abundance of surface and deep ocean prokaryotes were observed in any of the treatments, in surface waters with nutrients the heterotrophic production of surface prokaryotes rapidly decreased. Conversely, bathypelagic communities displayed a sustained production throughout the experiment. Incubations with surface prokaryotes always led to a significant accumulation of recalcitrant compounds, which did not occur with bathypelagic prokaryotes, suggesting they have a higher ability to process DOM. These contrasting abilities could be explained by the recruitment of a comparatively larger number of opportunistic taxa within the bathypelagic assemblages, which likely resulted in a broader community capability of substrate utilization.

Marine mercury-methylating microbial communities from coastal to Capbreton Canyon sediments (North Atlantic Ocean)

Microbial mercury (Hg) methylation transforms inorganic mercury to neurotoxic methylmercury (MeHg) mainly in aquatic anoxic environments. Sampling challenges in marine ecosystems, particularly in submarine canyons, leads to a lack of knowledge about the Hg methylating microbia in marine sediments. A previous study showed an enrichment of mercury species in sediments from the Capbreton Canyon where both geochemical parameters and microbial activities constrained the net MeHg production. In order to characterize Hg-methylating microbial communities from coastal to deeper sediments, we analysed the diversity of microorganisms' (16S rDNA-based sequencing) and Hg methylators (hgcA based cloning and sequencing). Both, 16S rDNA and hgcA gene analysis demonstrated that the putative Hg-methylating prokaryotes were likely within the Deltaproteobacteria, dominated by sulfur-compounds based reducing bacteria (mainly sulfate reducers). Additionally, others clades were also identified as carrying HgcA gene, such as, Chloroflexi, Spirochaetes, Elusimicrobia, PVC superphylum (Plantomycetes, Verrucomicrobia and Chlamydiae) and Euryarchaea. Nevertheless, 61% of the hgcA sequences were not assigned to specific clade, indicating that further studies are needed to understand the implication of new microorganisms carrying hgcA in the Hg methylation in marine environments. These first results suggest that sulfur cycle drives the Hg-methylation in marine ecosystem.

Controlled sampling of ribosomally active protistan diversity in sediment-surface layers identifies putative players in the marine carbon sink

Marine sediments are one of the largest carbon reservoir on Earth, yet the microbial communities, especially the eukaryotes, that drive these ecosystems are poorly characterised. Here, we report implementation of a sampling system that enables injection of reagents into sediments at depth, allowing for preservation of RNA in situ. Using the RNA templates recovered, we investigate the 'ribosomally active' eukaryotic diversity present in sediments close to the water/sediment interface. We demonstrate that in situ preservation leads to recovery of a significantly altered community profile. Using SSU rRNA amplicon sequencing, we investigated the community structure in these environments, demonstrating a wide diversity and high relative abundance of stramenopiles and alveolates, specifically: Bacillariophyta (diatoms), labyrinthulomycetes and ciliates. The identification of abundant diatom rRNA molecules is consistent with microscopy-based studies, but demonstrates that these algae can also be exported to the sediment as active cells as opposed to dead forms. We also observe many groups that include, or branch close to, osmotrophic-saprotrophic protists (e.g. labyrinthulomycetes and Pseudofungi), microbes likely to be important for detrital decomposition. The sequence data also included a diversity of abundant amplicon-types that branch close to the Fonticula slime moulds. Taken together, our data identifies additional roles for eukaryotic microbes in the marine carbon cycle; where putative osmotrophic-saprotrophic protists represent a significant active microbial-constituent of the upper sediment layer.

High Growth Potential of Long-Term Starved Deep Ocean Opportunistic Heterotrophic Bacteria

Experiments with bacteria in culture have shown that they often display "feast and famine" strategies that allow them to respond with fast growth upon pulses in resource availability, and enter a growth-arrest state when resources are limiting. Although feast responses have been observed in natural communities upon enrichment, it is unknown whether this blooming ability is maintained after long periods of starvation, particularly in systems that are energy limited like the bathypelagic ocean. Here we combined bulk and single-cell activity measurements with 16S rRNA gene amplicon sequencing to explore the response of a bathypelagic community, that had been starved for 1.6 years, to a sudden organic carbon supply. We observed a dramatic change in activity within 30 h, with leucine incorporation rates increasing over two orders of magnitude and the number of translationally active cells (mostly Gammaproteobacteria) increasing 4-fold. The feast response was driven by a single operational taxonomic unit (OTU) affiliated with the Marinobacter genus, which had remained rare during 7 months of starvation. Our work suggests that bathypelagic communities harbor a seed bank of highly persistent and resourceful "feast and famine" strategists that might disproportionally contribute to carbon fluxes through fast responses to occasional pulses of organic matter.