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Abstract Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.

Hydrothermal vents emit hot fluids enriched in energy sources for microbial life. Here, we compare the ecological and biogeochemical effects of hydrothermal venting of two recently discovered volcanic seamounts, Polaris and Aurora of the Gakkel Ridge, in the ice-covered Central Arctic Ocean. At both sites, persistent hydrothermal plumes increased up to 800 m into the deep Arctic Ocean. In the two non-buoyant plumes, rates of microbial carbon fixation were strongly elevated compared to background values of 0.5–1 μmol m−3 day−1 in the Arctic deep water, which suggests increased chemoautotrophy on vent-derived energy sources. In the Polaris plume, free sulfide and up to 360 nM hydrogen enabled microorganisms to fix up to 46 μmol inorganic carbon (IC) m−3 day−1. This energy pulse resulted in a strong increase in the relative abundance of SUP05 by 25% and Candidatus Sulfurimonas pluma by 7% of all bacteria. At Aurora, microorganisms fixed up to 35 μmol IC m−3 day−1. Here, metal sulfides limited the bioavailability of reduced sulfur species, and the putative hydrogen oxidizer Ca. S. pluma constituted 35% and SUP05 10% of all bacteria. In accordance with this data, transcriptomic analysis showed a high enrichment of hydrogenase-coding transcripts in Aurora and an enrichment of transcripts coding for sulfur oxidation in Polaris. There was neither evidence for methane consumption nor a substantial increase in the abundance of putative methanotrophs or their transcripts in either plume. Together, our results demonstrate the dominance of hydrogen and sulfide as energy sources in Arctic hydrothermal vent plumes.

The Aurora hydrothermal field (Arctic Ocean) is hosted in volcanic rocks but also shows evidence of mantle rock influence in the shallow sub-surface. Our discovery is pertinent to disciplines from marine mining to the search for life beyond Earth.

Abyssal plain communities rely on the overlying water column for a settling flux of organic matter. The origin and rate of this flux as well as the controls on its fine-scale spatial distribution following seafloor settlement are largely unquantified. This is particularly true across regions where anthropogenically-induced seafloor disturbance has occurred. Here, we observed, quantified and mapped a mass deposition event of gelatinous zooplankton carcasses (pyrosomes) in July-September 2015 across one such physically disturbed region in the Peru Basin polymetallic nodule province (4150 m). Seafloor in this area was disturbed with a plough harrow in 1989 (as part of the DISCOL experiment) causing troughs in the sediment. Other parts were disturbed with an epibenthic sled (EBS) during a cruise in 2015 resulting in steep-walled, U-shaped troughs. We investigated two hypotheses: a) gelatinous food falls contribute significantly to the abyssal plain carbon pump and b) physical seafloor disturbance influences abyssal distribution of organic matter. We combined optical and bathymetric seafloor observations, to analyze pyrosome distribution on seabeds with different levels of disturbance. 2954 pyrosome colonies and associated taxa were detected in > 14,000 seafloor images. The mean regional carbon (C) deposition associated with pyrosome carcasses was significant compared to the flux of particulate organic C (182 to 1543%), and the total respired benthic C flux in the DISCOL Experimental Area (39 to 184%). EBS-disturbed seafloor tracks contained 72 times more pyrosome-associated C than an undisturbed reference site, and up to 4 times more than an area disturbed in 1989. Deposited pyrosomes collected had a higher proportion of labile fatty acids compared to the sediment. We document the temporal and spatial extent of an abyssal food fall event with unprecedented detail and show that physical seafloor disturbance results in the accumulation of detrital material. Such accumulation may reduce oxygen availability and alter benthic community structure. Understanding both the relevance of large food falls and the fine scale topography of the seafloor, is necessary for impact assessment of technologies altering seafloor integrity (e.g. as a result of bottom-trawling or deep seabed mining) and may improve their management on a global scale.

Marine sinking particles sequester atmospheric carbon dioxide to the deep ocean via the biological carbon pump. Understanding how environmental shifts drive changes in the microbial composition of particles, and how these affect the export of organic matter from the surface to the deep ocean, is critical, especially in the rapidly changing Arctic Ocean. Here, we applied next generation sequencing of the 18S and 16S rRNA genes to sediment trap samples from around 200 m water depth in the eastern Fram Strait, covering a time frame of more than one decade (2000-2012). The aim was to characterize their microbial composition during annual highest particulate organic carbon flux events. The bimodal annual spring and summer export fluxes were representative of the strong seasonality in the region. Furthermore, the study period was characterized by considerable interannual variation, marked especially by a warm water anomaly between 2005 and 2007. During this period changes in the hydrography and sea ice cover also led to measurable changes in the microbial composition of particles. The warm water period was marked by a decrease in diatoms affiliated with Chaetoceros, an increase of small phytoplankton and an increase in sequence abundance of the bacterial taxa Oceanospirillales, Alteromonadales and Rhodobacterales on the particles. The resulting changes in microbial composition and the associated microbial network structure suggest the emergence of a more developed retention system in the surface ocean. Our results provide the first long-term assessment of the microbial composition of sinking particles in the Arctic Ocean, and stress the importance of sea ice and hydrography for particle composition and subsequent flux of organic matter to deeper waters.

This study presents a large-scale analysis of microbial diversity in deep-sea sponges. They show that sponge microbial abundance status, geographic distance, sponge phylogeny and the physical-biogeochemical environment drive microbiome composition, in descending order of relevance. The uniqueness of each deep-sea sponge ground stresses the need for their strategic preservation.

The North Atlantic biological pump has the most intense absorption of C globally, but how this will fare in light of climate changes (especially sea-ice melting) is poorly understood. Here the authors present a 24-month continuous time series of physical, chemical, and biological observations in the Fram Strait.

Fadeev et al. explore carbon export dynamics along the water column using microscopic analysis, 16S rRNA gene amplicon sequencing, and physical modeling of data from long-term sediment traps in the Fram Strait. Their results indicate that larger aggregates from sea-ice and under-ice diatom blooms are responsible for higher export efficiency and vertical microbial connectivity, suggesting that continuous sea-ice loss may result in decreased pelagic-benthic coupling, with resultant impacts on marine food webs.

The central Arctic Ocean is rapidly changing due to amplified warming and sea ice retreat. Nonetheless, it remains challenging to document and decipher impacts on key ecosystem processes such as primary production and pelagic-benthic coupling, due to limited observations in this remote area. Here we investigated environmental changes at the Laptev Sea continental slope (60-3400 m water depth) from the surface to the seafloor, by replicating sample transects two decades apart. Mean break-up of sea ice occurred earlier and mean freeze-up occurred later in 2012 compared to 1993, extending the ice-free period by more than 30 days. On average, observations and model results showed an annual increase in primary production of 30% and more in the study area in 2012. In contrast, calculated and modelled fluxes of particulate organic carbon (POC) to the seafloor were only slightly higher in 2012 and did not extend as far into the deep Laptev Sea as the increase in primary production, possibly due to a more developed retention system. Nevertheless, benthic surveys revealed a substantial increase in phytodetritus availability at the seafloor along the entire transect from the shelf edge to the deep sea. This calls for carbon input by lateral advection from the shelves, additional input from sea ice, and/or a late summer bloom. We also investigated the composition and activity of bacterial communities at the seafloor and potential linkages to the observed environmental changes. While bacterial abundance, biomass and overall community structure showed no systematic differences between the two contrasting years at all depths, extracellular enzymatic activities had increased as a result of higher food availability. This was partly reflected in higher benthic oxygen uptake, indicating a moderate impact on benthic remineralization rates at the time of sampling. Our results show considerable effects of ocean warming and sea ice loss on the ecosystem from the surface ocean to the seafloor in the Laptev Sea, which are likely to continue in the coming decades.

Automated sampling technologies can enhance the temporal and spatial resolution of marine microbial observations, particularly in remote and inaccessible areas. A critical aspect of automated microbiome sampling is the preservation of nucleic acids over long-term autosampler deployments. Understanding the impact of preservation method on microbial metabarcoding is essential for implementing genomic observatories into existing infrastructure, and for establishing best practices for the regional and global synthesis of data. The present study evaluates the effect of two preservatives commonly used in autosampler deployments (mercuric chloride and formalin) and two extraction kits (PowerWater and NucleoSpin) on amplicon sequencing of 16S and 18S rRNA gene over 50 weeks of sample storage. Our results suggest the combination of mercuric chloride preservation and PowerWater extraction as most adequate for 16S and 18S rRNA gene amplicon-sequencing from the same seawater sample. This approach provides consistent information on species richness, diversity and community composition in comparison to control samples (nonfixed, filtered and frozen) when stored up to 50 weeks at in situ temperature. Preservation affects the recovery of certain taxa, with specific OTUs becoming overrepresented (SAR11 and diatoms) or underrepresented (Colwellia and pico-eukaryotes) after preservation. In case eukaryotic sequence information is the sole target, formalin preservation and NucleoSpin extraction performed best. Our study contributes to the design of long-term autonomous microbial observations in remote ocean areas, allowing cross-comparison of microbiome dynamics across sampling devices (e.g., water and particle samplers) and marine realms.

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota, none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

The Arctic is impacted by climate warming faster than any other oceanic region on Earth. Assessing the baseline of microbial communities in this rapidly changing ecosystem is vital for understanding the implications of ocean warming and sea ice retreat on ecosystem functioning. Using CARD-FISH and semi-automated counting, we quantified 14 ecologically relevant taxonomic groups of bacterioplankton (Bacteria and Archaea) from surface (0–30 m) down to deep waters (2,500 m) in summer ice-covered and ice-free regions of the Fram Strait, the main gateway for Atlantic inflow into the Arctic Ocean. Cell abundances of the bacterioplankton communities in surface waters varied from 105 cells mL–1 in ice-covered regions to 106 cells mL–1 in the ice-free regions. Observations suggest that these were overall driven by variations in phytoplankton bloom conditions across the Strait. The bacterial groups Bacteroidetes and Gammaproteobacteria showed several-fold higher cell abundances under late phytoplankton bloom conditions of the ice-free regions. Other taxonomic groups, such as the Rhodobacteraceae, revealed a distinct association of cell abundances with the surface Atlantic waters. With increasing depth (>500 m), the total cell abundances of the bacterioplankton communities decreased by up to two orders of magnitude, while largely unknown taxonomic groups (e.g., SAR324 and SAR202 clades) maintained constant cell abundances throughout the entire water column (ca. 103 cells mL–1). This suggests that these enigmatic groups may occupy a specific ecological niche in the entire water column. Our results provide the first quantitative spatial variations assessment of bacterioplankton in the summer ice-covered and ice-free Arctic water column, and suggest that further shift toward ice-free Arctic summers with longer phytoplankton blooms can lead to major changes in the associated standing stock of the bacterioplankton communities.

Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical, and temporal turnover. Yet, recent studies showed that the Arctic marine ecosystem harbors unique microbial community members that are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study the taxonomic composition of microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample sets, but these typically originated from low-latitude environments. An explicit evaluation of primer-set performances in representing the microbial communities of the Arctic Ocean is currently lacking. To select a suitable primer set for studying microbiomes of various Arctic marine habitats (sea ice, surface water, marine snow, deep ocean basin, and deep-sea sediment), we have conducted a performance comparison between two widely used primer sets, targeting different hypervariable regions of the 16S rRNA gene (V3–V4 and V4–V5). We observed that both primer sets were highly similar in representing the total microbial community composition down to genus rank, which was also confirmed independently by subgroup-specific catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) counts. Each primer set revealed higher internal diversity within certain bacterial taxonomic groups (e.g., the class Bacteroidia by V3–V4, and the phylum Planctomycetes by V4–V5). However, the V4–V5 primer set provides concurrent coverage of the archaeal domain, a relevant component comprising 10–20% of the community in Arctic deep waters and the sediment. Although both primer sets perform similarly, we suggest the use of the V4–V5 primer set for the integration of both bacterial and archaeal community dynamics in the Arctic marine environment.

Sea ice in the Arctic Ocean (AO) has been undergoing dramatic changes during the last two decades. In addition, the water temperature of the inflow of Atlantic water masses at the gateway Fram Strait has recently increased. Long-term data may help to evaluate the impact of these physical changes on the biological processes in surface waters. Over a 25-year period, and mostly in summer, water samples were collected at discrete depths within the uppermost 100 m of the Fram Strait and other regions of the AO to investigate chlorophyll a (Chl a) and particulate organic carbon (POC) standing stocks. Stations sampled from 1991 to 2015 were located in the Fram Strait, Barents Sea (BS), on the Eurasian shelf, and over the Nansen, Amundsen, and parts of the Amerasian basins (AB). Discrete Chl a and POC measurements obtained during 33 and 24 expeditions, respectively, were integrated over the upper 100 m of the water column to monitor spatial and interannual variations in distribution patterns of standing stocks. In general, the highest Chl a and POC standing stocks were observed in the eastern Fram Strait (EFS) and in the BS, while the lowest biomasses were observed in the heavily ice-covered regions of the central AO, mainly in the Amundsen and ABs. Whereas summertime Chl a stocks sharply decreased northward from the Fram Strait and Barents Sea toward high latitudes, the decline in POC standing stocks was less pronounced. Over the sampling period, summertime Chl a stocks slightly increased in the EFS but remained more or less constant in the central AO. In contrast to Chl a, standing stocks of POC eventually increased over the last 25 years in the central AO, possibly as an effect of increasing air temperatures, decreasing sea ice extent and thickness, and increasing light availability. Moreover, variations in riverine discharge and in sea ice export within the Transpolar Drift may have contributed to the enhanced POC stock in the central AO surface waters. Overall, the objective of the present study was to provide baseline datasets of Chl a and POC to better track the effects of environmental changes due to global warming on the Arctic pelagic system.

Over the last decades, the Arctic Ocean has suffered a substantial decline in sea ice cover due to global warming. The impacts of these variations on primary productivity, fluxes of dissolved and particulate organic matter (OM) and turnover at the seafloor are still poorly understood. Here we focus on the characteristics and dynamics of the pool of marine dissolved OM (DOM) in surface sediments of the Arctic Ocean. To investigate spatial and temporal variations of DOM in relation to particulate OM input and benthic microbial community parameters, sediment porewater and overlying bottom water were collected from the long-term observatory HAUSGARTEN in June 2013 and 2014. The study area in the Fram Strait, which is partially covered by sea ice, was sampled along a bathymetric transect (1050–5500 m water depth), from east to west (7°0.2′ E to 5°17′ W), and from south to north (78°37’ to 79°43’ N). Molecular data on solid phase extracted DOM obtained via Fourier Transform Ion Cyclotron Resonance Mass Spectrometric analysis and a suite of bulk chemical parameters were related to benthic biogeochemical data. Our results demonstrate a close coupling between the production and input of OM from the surface ocean to the seafloor, and the concentration and composition of DOC/DOM in the deep sea. Surface porewaters collected in 2013 from shallower stations (≤1500 m water depth) in the eastern Fram Strait, had a signal of a larger and more recent input of OM (higher concentrations of phytodetritus). This was associated with higher numbers of molecular formulas, abundances of unsaturated aliphatic and N-containing formulas, in concert with higher enzymatic activity, phospholipids, total organic carbon and protein content. In contrast, porewaters collected in 2014 from deeper stations and from the West, were associated with lower OM input, and showed higher abundances of aromatic and oxygen-poor compounds. Higher OM input was also reflected in higher DOC concentrations and fluxes from the sediment into the water column. Our study demonstrates that regional and temporal variations in OM input can quickly translate into changes in the quantity and quality of surface porewater DOM, the latter substantially altered by deep-sea sediment bacteria.

ABSTRACT Cold seeps and hydrothermal vents deliver large amounts of methane and other gaseous alkanes into marine surface sediments. Consortia of archaea and partner bacteria thrive on the oxidation of these alkanes and its coupling to sulfate reduction. The inherently slow growth of the involved organisms and the lack of pure cultures have impeded the understanding of the molecular mechanisms of archaeal alkane degradation. Here, using hydrothermal sediments of the Guaymas Basin (Gulf of California) and ethane as the substrate, we cultured microbial consortia of a novel anaerobic ethane oxidizer, “Candidatus Ethanoperedens thermophilum” (GoM-Arc1 clade), and its partner bacterium “Candidatus Desulfofervidus auxilii,” previously known from methane-oxidizing consortia. The sulfate reduction activity of the culture doubled within one week, indicating a much faster growth than in any other alkane-oxidizing archaea described before. The dominance of a single archaeal phylotype in this culture allowed retrieval of a closed genome of “Ca. Ethanoperedens,” a sister genus of the recently reported ethane oxidizer “Candidatus Argoarchaeum.” The metagenome-assembled genome of “Ca. Ethanoperedens” encoded a complete methanogenesis pathway including a methyl-coenzyme M reductase (MCR) that is highly divergent from those of methanogens and methanotrophs. Combined substrate and metabolite analysis showed ethane as the sole growth substrate and production of ethyl-coenzyme M as the activation product. Stable isotope probing demonstrated that the enzymatic mechanism of ethane oxidation in “Ca. Ethanoperedens” is fully reversible; thus, its enzymatic machinery has potential for the biotechnological development of microbial ethane production from carbon dioxide. IMPORTANCE In the seabed, gaseous alkanes are oxidized by syntrophic microbial consortia that thereby reduce fluxes of these compounds into the water column. Because of the immense quantities of seabed alkane fluxes, these consortia are key catalysts of the global carbon cycle. Due to their obligate syntrophic lifestyle, the physiology of alkane-degrading archaea remains poorly understood. We have now cultivated a thermophilic, relatively fast-growing ethane oxidizer in partnership with a sulfate-reducing bacterium known to aid in methane oxidation and have retrieved the first complete genome of a short-chain alkane-degrading archaeon. This will greatly enhance the understanding of nonmethane alkane activation by noncanonical methyl-coenzyme M reductase enzymes and provide insights into additional metabolic steps and the mechanisms underlying syntrophic partnerships. Ultimately, this knowledge could lead to the biotechnological development of alkanogenic microorganisms to support the carbon neutrality of industrial processes.

Half of the Arctic Ocean is deep sea (>1000 m), and this area is currently transitioning from being permanently ice-covered to being seasonally ice-free. Despite these drastic changes, it remains unclear how organisms are distributed in the deep Arctic basins, and particularly what feeds them. Here, we summarize data on auto- and heterotrophic organisms in the benthic, pelagic, and sympagic realm of the Arctic Ocean basins from the past three decades and put together an organic carbon budget for this region. Based on the budget, we investigate whether our current understanding of primary and secondary production and vertical carbon flux are balanced by the current estimates of the carbon demand by deep-sea benthos. At first glance, our budget identifies a mismatch between the carbon supply by primary production (3–46 g C m−2 yr−1), the carbon demand of organisms living in the pelagic (7–17 g C m−2) and the benthic realm (< 5 g C m−2 yr−1) versus the low vertical carbon export (at 200 m: 0.1–1.5 g C m−2 yr−1, at 3000–4000 m: 0.01–0.73 g C m−2 yr−1). To close the budget, we suggest that episodic events of large, fast sinking ice algae aggregates, export of dead zooplankton, as well as large food falls need to be quantified and included. This work emphasizes the clear need for a better understanding of the quantity, phenology, and the regionality of carbon supply and demand in the deep Arctic basins, which will allow us to evaluate how the ecosystem may change in the future.

ABSTRACT Crude oil and gases in the seabed provide an important energy source for subsurface microorganisms. We investigated the role of archaea in the anaerobic degradation of non-methane alkanes in deep-sea oil seeps from the Gulf of Mexico. We identified microscopically the ethane and short-chain alkane oxidizers “Candidatus Argoarchaeum” and “Candidatus Syntrophoarchaeum” forming consortia with bacteria. Moreover, we found that the sediments contain large numbers of cells from the archaeal clade “Candidatus Methanoliparia,” which was previously proposed to perform methanogenic alkane degradation. “Ca. Methanoliparia” occurred abundantly as single cells attached to oil droplets in sediments without apparent bacterial or archaeal partners. Metagenome-assembled genomes of “Ca. Methanoliparia” encode a complete methanogenesis pathway including a canonical methyl-coenzyme M reductase (MCR) but also a highly divergent MCR related to those of alkane-degrading archaea and pathways for the oxidation of long-chain alkyl units. Its metabolic genomic potential and its global detection in hydrocarbon reservoirs suggest that “Ca. Methanoliparia” is an important methanogenic alkane degrader in subsurface environments, producing methane by alkane disproportionation as a single organism. IMPORTANCE Oil-rich sediments from the Gulf of Mexico were found to contain diverse alkane-degrading groups of archaea. The symbiotic, consortium-forming “Candidatus Argoarchaeum” and “Candidatus Syntrophoarchaeum” are likely responsible for the degradation of ethane and short-chain alkanes, with the help of sulfate-reducing bacteria. “Ca. Methanoliparia” occurs as single cells associated with oil droplets. These archaea encode two phylogenetically different methyl-coenzyme M reductases that may allow this organism to thrive as a methanogen on a substrate of long-chain alkanes. Based on a library survey, we show that “Ca. Methanoliparia” is frequently detected in oil reservoirs and may be a key agent in the transformation of long-chain alkanes to methane. Our findings provide evidence for the important and diverse roles of archaea in alkane-rich marine habitats and support the notion of a significant functional versatility of the methyl coenzyme M reductase.

Ultraslow spreading ridges account for one-third of the global mid-ocean ridges. Their impact on the diversity and connectivity of benthic deep-sea microbial assemblages is poorly understood, especially for hydrothermally inactive, magma-starved ridges. We investigated bacterial and archaeal diversity in sediments collected from an amagmatic segment (10°–17°E) of the Southwest Indian Ridge (SWIR) and in the adjacent northern and southern abyssal zones of similar water depths within one biogeochemical province of the Indian Ocean. Microbial diversity was determined by 16S ribosomal RNA (rRNA) gene sequencing. Our results show significant differences in microbial communities between stations outside and inside the SWIR, which were mostly explained by environmental selection. Community similarity correlated significantly with differences in chlorophyll a content and with the presence of upward porewater fluxes carrying reduced compounds (e.g., ammonia and sulfide), suggesting that trophic resource availability is a main driver for changes in microbial community composition. At the stations in the SWIR axial valley (3,655–4,448 m water depth), microbial communities were enriched in bacterial and archaeal taxa common in organic matter-rich subsurface sediments (e.g., SEEP-SRB1, Dehalococcoida, Atribacteria, and Woesearchaeota) and chemosynthetic environments (mainly Helicobacteraceae). The abyssal stations outside the SWIR communities (3,760–4,869 m water depth) were dominated by OM1 clade, JTB255, Planctomycetaceae, and Rhodospirillaceae. We conclude that ultraslow spreading ridges create a unique environmental setting in sedimented segments without distinct hydrothermal activity, and play an important role in shaping microbial communities and promoting diversity, but also in connectivity among deep-sea habitats.

This paper reviews the scientific motivation and challenges, development, and use of underwater robotic vehicles designed for use in ice-covered waters, with special attention paid to the navigation systems employed for under-ice deployments. Scientific needs for routine access under fixed and moving ice by underwater robotic vehicles are reviewed in the contexts of geology and geophysics, biology, sea ice and climate, ice shelves, and seafloor mapping. The challenges of under-ice vehicle design and navigation are summarized. The paper reviews all known under-ice robotic vehicles and their associated navigation systems, categorizing them by vehicle type (tethered, untethered, hybrid, and glider) and by the type of ice they were designed for (fixed glacial or sea ice and moving sea ice).

Quantitative camera surveys of benthic megafauna were carried out during the expedition ARK-XXVII/3 to the Eastern Central Arctic Basins with the research icebreaker Polarstern in summer 2012 (2 August-29 September). Nine transects were performed for the first time in deep-sea areas previously fully covered by ice, four of them in the Nansen Basin (3571-4066m) and five in the Amundsen Basin (4041-4384m). At seven of these stations benthic Agassiz trawls were taken near the camera tracks for species identification. Observed Arctic deep-sea megafauna was largely endemic. Several taxa showed a substantially greater depth or geographical range than previously assumed. Variations in the composition and structure of megabenthic communities were analysed and linked to several environmental variables, including state of the sea ice and phytodetritus supply to the seafloor. Three different types of communities were identified based on species dominating the biomass. Among these species were the actiniarian Bathyphellia margaritacea and the holothurians Elpidia heckeri and Kolga hyalina. Variations in megafaunal abundance were first of all related to the proximity to the marginal ice zone. Stations located closer to this zone were characterized by relatively high densities and biomass of B. margaritacea. Food supply was higher at these stations, as suggested by enhanced concentrations of pigments, organic carbon, bacterial cell abundances and nutrients in the sediments. Fully ice-covered stations closer to the North Pole and partially under multi-year ice were characterized by lower concentrations of the same biogeochemical indicators for food supply. These stations nevertheless hosted relatively high density and biomass of the holothurians E. heckeri or K. hyalina, which were observed to feed on large food falls of the sea-ice colonial diatom Melosira arctica. The link between the community structure of megafauna and the extent and condition of the Central Arctic sea-ice cover suggests that future climate changes may substantially affect deep ocean biodiversity.

Climate models project that the Arctic Ocean may experience ice-free summers by the second half of this century. This may have severe repercussions on phytoplankton bloom dynamics and the associated cycling of carbon in surface waters. We currently lack baseline knowledge of the seasonal dynamics of Arctic microbial communities, which is needed in order to better estimate the effects of such changes on ecosystem functioning. Here we present a comparative study of polar summer microbial communities in the ice-free (eastern) and ice-covered (western) hydrographic regimes at the LTER HAUSGARTEN in Fram Strait, the main gateway between the Arctic and North Atlantic Oceans. Based on measured and modeled biogeochemical parameters, we tentatively identified two different ecosystem states (i.e., different phytoplankton bloom stages) in the distinct regions. Using Illumina tag-sequencing, we determined the community composition of both free-living and particle-associated bacteria as well as microbial eukaryotes in the photic layer. Despite substantial horizontal mixing by eddies in Fram Strait, pelagic microbial communities showed distinct differences between the two regimes, with a proposed early spring (pre-bloom) community in the ice-covered western regime (with higher representation of SAR11, SAR202, SAR406 and eukaryotic MALVs) and a community indicative of late summer conditions (post-bloom) in the ice-free eastern regime (with higher representation of Flavobacteria, Gammaproteobacteria and eukaryotic heterotrophs). Co-occurrence networks revealed specific taxon-taxon associations between bacterial and eukaryotic taxa in the two regions. Our results suggest that the predicted changes in sea ice cover and phytoplankton bloom dynamics will have a strong impact on bacterial community dynamics and potentially on biogeochemical cycles in this region.

In summer 2012, Arctic sea ice declined to a record minimum and, as a consequence of the melting, large amounts of aggregated ice-algae sank to the seafloor at more than 4,000 m depth. In this study, we assessed the composition, turnover and connectivity of bacterial and microbial eukaryotic communities across Arctic habitats from sea ice, algal aggregates and surface waters to the seafloor. Eukaryotic communities were dominated by diatoms, dinoflagellates and other alveolates in all samples, and showed highest richness and diversity in sea-ice habitats (∼400–500 OTUs). Flavobacteriia and Gammaproteobacteria were the predominant bacterial classes across all investigated Arctic habitats. Bacterial community richness and diversity peaked in deep-sea samples (∼1,700 OTUs). Algal aggregate-associated bacterial communities were mainly recruited from the sea-ice community, and were transported to the seafloor with the sinking ice algae. The algal deposits at the seafloor had a unique community structure, with some shared sequences with both the original sea-ice community (22% OTU overlap), as well as with the deep-sea sediment community (17% OTU overlap). We conclude that ice-algal aggregate export does not only affect carbon export from the surface to the seafloor, but may change microbial community composition in central Arctic habitats with potential effects for benthic ecosystem functioning in the future.

Little is known about the distribution and dynamics of macrobenthic communities of the deep Arctic Ocean. The few previous studies report low standing stocks and confirm a gradient with declining biomass from the slopes down to the basins, as commonly reported for deep-sea benthos. In this study, we investigated regional differences of faunal abundance and biomass, and made for the first time ever estimates of deep Arctic community production by using a multi-parameter artificial neural network model. The underlying data set combines data from recent field studies with published and unpublished data from the past 20 years, to analyse the influence of water depth, geographical latitude and sea-ice concentration on Arctic benthic communities. We were able to confirm the previously described negative relationship of macrofauna standing stock with water depth in the Arctic deep sea, while also detecting substantial regional differences. Furthermore, abundance, biomass and production decreased significantly with increasing sea-ice extent (towards higher latitudes) down to values

Permanent sea-ice cover and low primary productivity in the mostly ice-covered Central Arctic ocean basins result in significantly lower biomass and density of macrobenthos in the abyssal plains compared to the continental slopes. However, little is known on bathymetric and regional effects on the macrobenthos diversity. This study synthesizes new and available macrobenthos data to provide a baseline for future studies of the effects of Arctic change on macrofauna community composition in the Arctic basins. Samples collected during three expeditions (in 1993, 2012 and 2015) at 37 stations on the slope of the Barents and Laptev Seas and in the abyssal of the Nansen and Amundsen Basins in the depth range from 38 m to 4381 m were used for a quantitative analysis of species composition, abundance and biomass. Benthic communities clustered in five depth ranges across the slope and basin. A parabolic pattern of species diversity change with depth was found, with the diversity maximum for macrofauna at the shelf edge at depths of 100-300 m. This deviates from the typical species richness peak at mid-slope depths of 1500-3000 m in temperate oceans. Due to the limited availability of standardized benthos data, it remains difficult to assess if and how the significant sea-ice loss observed in the past decade has affected benthic community composition. The polychaete Ymerana pteropoda and the bryozoan Nolella sp. were found for the first time in the deep Nansen and Amundsen Basins.

Sinking of large organic food falls i.e. kelp, wood and whale carcasses to the oligotrophic deep-sea floor promotes the establishment of locally highly productive and diverse ecosystems, often with specifically adapted benthic communities. However, the fragmented spatial distribution and small area poses challenges for the dispersal of their microbial and faunal communities. Our study focused on the temporal dynamics and spatial distributions of sunken wood bacterial communities, which were deployed in the vicinity of different cold seeps in the Eastern Mediterranean and the Norwegian deep-seas. By combining fingerprinting of bacterial communities by ARISA and 454 sequencing with in situ and ex situ biogeochemical measurements, we show that sunken wood logs have a locally confined long-term impact (> 3y) on the sediment geochemistry and community structure. We confirm previous hypotheses of different successional stages in wood degradation including a sulphophilic one, attracting chemosynthetic fauna from nearby seep systems. Wood experiments deployed at similar water depths (1100-1700 m), but in hydrographically different oceanic regions harbored different wood-boring bivalves, opportunistic faunal communities, and chemosynthetic species. Similarly, bacterial communities on sunken wood logs were more similar within one geographic region than between different seas. Diverse sulphate-reducing bacteria of the Deltaproteobacteria, the sulphide-oxidizing bacteria Sulfurovum as well as members of the Acidimicrobiia and Bacteroidia dominated the wood falls in the Eastern Mediterranean, while Alphaproteobacteria and Flavobacteriia colonized the Norwegian Sea wood logs. Fauna and bacterial wood-associated communities changed between 1 to 3 years of immersion, with sulphate-reducers and sulphide-oxidizers increasing in proportion, and putative cellulose degraders decreasing with time. Only 6% of all bacterial genera, comprising the core community, were found at any time on the Eastern Mediterranean sunken wooden logs. This study suggests that biogeography and succession play an important role for the composition of bacteria and fauna of wood-associated communities, and that wood can act as stepping-stones for seep biota.

The Eurasian basin of the Central Arctic Ocean is nitrogen limited, but little is known about the presence and role of nitrogen-fixing bacteria. Recent studies have indicated the occurrence of diazotrophs in Arctic coastal waters potentially of riverine origin. Here, we investigated the presence of diazotrophs in ice and surface waters of the Central Arctic Ocean in the summer of 2012. We identified diverse communities of putative diazotrophs through targeted analysis of the nifH gene, which encodes the iron protein of the nitrogenase enzyme. We amplified 529 nifH sequences from 26 samples of Arctic melt ponds, sea ice and surface waters. These sequences resolved into 43 clusters at 92% amino acid sequence identity, most of which were non-cyanobacterial phylotypes from sea ice and water samples. One cyanobacterial phylotype related to Nodularia sp. was retrieved from sea ice, suggesting that this important functional group is rare in the Central Arctic Ocean. The diazotrophic community in sea-ice environments appear distinct from other cold-adapted diazotrophic communities, such as those present in the coastal Canadian Arctic, the Arctic tundra and glacial Antarctic lakes. Molecular fingerprinting of nifH and the intergenic spacer region of the rRNA operon revealed differences between the communities from river-influenced Laptev Sea waters and those from ice-related environments pointing towards a marine origin for sea-ice diazotrophs. Our results provide the first record of diazotrophs in the Central Arctic and suggest that microbial nitrogen fixation may occur north of 77ºN. To assess the significance of nitrogen fixation for the nitrogen budget of the Arctic Ocean and to identify the active nitrogen fixers, further biogeochemical and molecular biological studies are needed.

During the European Commission's Framework Six Programme, HERMES, we investigated three main areas along the European margin, each characterized by the presence of seep-related structures exhibiting different intensity of activity and biological diversity. These areas are: (1) the Nordic margin with the Håkon Mosby mud volcano and many pockmarks, (2) the Gulf of Cádiz, and (3) the eastern Mediterranean with its hundreds of mud volcanoes and brine pool structures. One of the main goals of the HERMES project was to unravel the biodiversity associated with these seep-associated ecosystems, and to understand their driving forces and functions, using an integrated approach. Several multidisciplinary research cruises to these three areas provided evidence of high variability in ecosystem processes and associated biodiversity at different spatial scales, illustrating the "hotspot" nature of these deep water systems.

This issue of Oceanography mainly describes results from the HERMES project, which comes to a close in spring 2009. Building on the success of HERMES, the European Commission has funded a new project that will begin as HERMES ends. This project, entitled HERMIONE (Hotspot Ecosystem Research and Man's Impact on European Seas), will have a greater focus on human impacts in the deep-sea environment and will place more emphasis on the translation of information into policy. It will have a wider public outreach program and will include new areas of research, such as seamounts and hydrothermal vents. The HERMIONE project will address issues raised in the EC foresight document, The Deep-Sea Frontier: Science Challenges for a Sustainable Future (Cochonat et al., 2007), and will focus on four key objectives. These follow a logical progression, from investigating the physical dimensions of ecosystems, to understanding how they function and interconnect, to studying how they are impacted by human activity, to ensuring that this project can contribute to their sustainable management and protection. The HERMIONE consortium comprises 38 partners, including four small businesses, from 13 countries across Europe.

Submarine hydrocarbon seeps are geologically driven "hotspots" of increased biological activity on the seabed. As part of the HERMES project, several sites of natural hydrocarbon seepage in the European seas were investigated in detail, including mud volcanoes and pockmarks, in study areas extending from the Nordic margin, to the Gulf of Cádiz, to the Mediterranean and Black seas. High-resolution seabed maps and the main properties of key seep sites are presented here. Individual seeps show ecosystem zonation related to the strength of the methane flux and distinct biogeochemical processes in surface sediments. A feature common to many seeps is the formation of authigenic carbonate constructions. These constructions exhibit various morphologies ranging from large pavements and fragmented slabs to chimneys and mushroom-shaped mounds, and they form hard substrates colonized by fixed fauna. Gas hydrate dissociation could contribute to sustain seep chemosynthetic communities over several thousand years following large gas-release events.

The deep ocean floor covers more than 60% of the Earth's surface, and hosts diverse bacterial communities with important functions in carbon and nutrient cycles. The identification of key bacterial members remains a challenge and their patterns of distribution in seafloor sediment yet remain poorly described. Previous studies were either regionally restricted or included few deep-sea sediments, and did not specifically test biogeographic patterns across the vast oligotrophic bathyal and abyssal seafloor. Here we define the composition of this deep seafloor microbiome by describing those bacterial operational taxonomic units (OTU) that are specifically associated with deep-sea surface sediments at water depths ranging from 1000-5300 m. We show that the microbiome of the surface seafloor is distinct from the subsurface seafloor. The cosmopolitan bacterial OTU were affiliated with the clades JTB255 (class Gammaproteobacteria, order Xanthomonadales) and OM1 (Actinobacteria, order Acidimicrobiales), comprising 21% and 7% of their respective clades, and about 1% of all sequences in the study. Overall, few sequence-abundant bacterial types were globally dispersed and displayed positive range-abundance relationships. Most bacterial populations were rare and exhibited a high degree of endemism, explaining the substantial differences in community composition observed over large spatial scales. Despite the relative physicochemical uniformity of deep-sea sediments, we identified indicators of productivity regimes, especially sediment organic matter content, as factors significantly associated with changes in bacterial community structure across the globe.

Sea-ice diatoms are known to accumulate in large aggregates in and under sea ice and in melt ponds. There is recent evidence from the Arctic that such aggregates can contribute substantially to particle export when sinking from the ice. The role and regulation of microbial aggregation in the highly seasonal, nutrient- and light-limited Arctic sea-ice ecosystem is not well understood. To elucidate the mechanisms controlling the formation and export of algal aggregates from sea ice, we investigated samples taken in late summer 2011 and 2012, during two cruises to the Eurasian Basin of the Central Arctic Ocean. Spherical aggregates densely packed with pennate diatoms, as well as filamentous aggregates formed by Melosira arctica showed sign of different stages of degradation and physiological stoichiometries, with carbon to chlorophyll a ratios ranging from 110 to 66700, and carbon to nitrogen molar ratios of 8-35 and 9-40, respectively. Sub-ice algal aggregate densities ranged between 1 and 17 aggregates m(-2), maintaining an estimated net primary production of 0.4-40 mg C m(-2) d(-1), and accounted for 3-80% of total phototrophic biomass and up to 94% of local net primary production. A potential factor controlling the buoyancy of the aggregates was light intensity, regulating photosynthetic oxygen production and the amount of gas bubbles trapped within the mucous matrix, even at low ambient nutrient concentrations. Our data-set was used to evaluate the distribution and importance of Arctic algal aggregates as carbon source for pelagic and benthic communities.

Large organic food falls to the deep sea--such as whale carcasses and wood logs--are known to serve as stepping stones for the dispersal of highly adapted chemosynthetic organisms inhabiting hot vents and cold seeps. Here we investigated the biogeochemical and microbiological processes leading to the development of sulfidic niches by deploying wood colonization experiments at a depth of 1690 m in the Eastern Mediterranean for one year. Wood-boring bivalves of the genus Xylophaga played a key role in the degradation of the wood logs, facilitating the development of anoxic zones and anaerobic microbial processes such as sulfate reduction. Fauna and bacteria associated with the wood included types reported from other deep-sea habitats including chemosynthetic ecosystems, confirming the potential role of large organic food falls as biodiversity hot spots and stepping stones for vent and seep communities. Specific bacterial communities developed on and around the wood falls within one year and were distinct from freshly submerged wood and background sediments. These included sulfate-reducing and cellulolytic bacterial taxa, which are likely to play an important role in the utilization of wood by chemosynthetic life and other deep-sea animals.

Cold-water coral reefs are known to locally enhance the diversity of deep-sea fauna as well as of microbes. Sponges are among the most diverse faunal groups in these ecosystems, and many of them host large abundances of microbes in their tissues. In this study, twelve sponge species from three cold-water coral reefs off Norway were investigated for the relationship between sponge phylogenetic classification (species and family level), as well as sponge type (high versus low microbial abundance), and the diversity of sponge-associated bacterial communities, taking also geographic location and water depth into account. Community analysis by Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that as many as 345 (79%) of the 437 different bacterial operational taxonomic units (OTUs) detected in the dataset were shared between sponges and sediments, while only 70 (16%) appeared purely sponge-associated. Furthermore, changes in bacterial community structure were significantly related to sponge species (63% of explained community variation), sponge family (52%) or sponge type (30%), whereas mesoscale geographic distances and water depth showed comparatively small effects (

The methane-emitting cold seeps of Hikurangi margin (New Zealand) are among the few deep-sea chemosynthetic ecosystems of the Southern Hemisphere known to date. Here we compared the biogeochemistry and microbial communities of a variety of Hikurangi cold seep ecosystems. These included highly reduced seep habitats dominated by bacterial mats, partially oxidized habitats populated by heterotrophic ampharetid polychaetes and deeply oxidized habitats dominated by chemosynthetic frenulate tubeworms. The ampharetid habitats were characterized by a thick oxic sediment layer that hosted a diverse and biomass-rich community of aerobic methanotrophic Gammaproteobacteria. These bacteria consumed up to 25% of the emanating methane and clustered within three deep-branching groups named Marine Methylotrophic Group (MMG) 1-3. MMG1 and MMG2 methylotrophs belong to the order Methylococcales, whereas MMG3 methylotrophs are related to the Methylophaga. Organisms of the groups MMG1 and MMG3 are close relatives of chemosynthetic endosymbionts of marine invertebrates. The anoxic sediment layers of all investigated seeps were dominated by anaerobic methanotrophic archaea (ANME) of the ANME-2 clade and sulfate-reducing Deltaproteobacteria. Microbial community analysis using Automated Ribosomal Intergenic Spacer Analysis (ARISA) showed that the different seep habitats hosted distinct microbial communities, which were strongly influenced by the seep-associated fauna and the geographic location. Despite outstanding features of Hikurangi seep communities, the organisms responsible for key ecosystem functions were similar to those found at seeps worldwide. This suggests that similar types of biogeochemical settings select for similar community composition regardless of geographic distance. Because ampharetid polychaetes are widespread at cold seeps the role of aerobic methanotrophy may have been underestimated in seafloor methane budgets.

Cold seep ecosystems can support enormous biomasses of free-living and symbiotic chemoautotrophic organisms that get their energy from the oxidation of methane or sulfide. Most of this biomass derives from animals that are associated with bacterial symbionts, which are able to metabolize the chemical resources provided by the seeping fluids. Often these systems also harbor dense accumulations of non-symbiotic megafauna, which can be relevant in exporting chemosynthetically fixed carbon from seeps to the surrounding deep sea. Here we investigated the carbon sources of lithodid crabs (Paralomis sp.) feeding on thiotrophic bacterial mats at an active mud volcano at the Costa Rica subduction zone. To evaluate the dietary carbon source of the crabs, we compared the microbial community in stomach contents with surface sediments covered by microbial mats. The stomach content analyses revealed a dominance of epsilonproteobacterial 16S rRNA gene sequences related to the free-living and epibiotic sulfur oxidiser Sulfurovum sp. We also found Sulfurovum sp. as well as members of the genera Arcobacter and Sulfurimonas in mat-covered surface sediments where Epsilonproteobacteria were highly abundant constituting 10% of total cells. Furthermore, we detected substantial amounts of bacterial fatty acids such as i-C15∶0 and C17∶1ω6c with stable carbon isotope compositions as low as -53‰ in the stomach and muscle tissue. These results indicate that the white microbial mats at Mound 12 are comprised of Epsilonproteobacteria and that microbial mat-derived carbon provides an important contribution to the crab's nutrition. In addition, our lipid analyses also suggest that the crabs feed on other (13)C-depleted organic matter sources, possibly symbiotic megafauna as well as on photosynthetic carbon sources such as sedimentary detritus.

Knowledge on spatial scales of the distribution of deep-sea life is still sparse, but highly relevant to the understanding of dispersal, habitat ranges and ecological processes. We examined regional spatial distribution patterns of the benthic bacterial community and covarying environmental parameters such as water depth, biomass and energy availability at the Arctic Long-Term Ecological Research (LTER) site HAUSGARTEN (Eastern Fram Strait). Samples from 13 stations were retrieved from a bathymetric (1,284-3,535 m water depth, 54 km in length) and a latitudinal transect (∼ 2,500 m water depth; 123 km in length). 454 massively parallel tag sequencing (MPTS) and automated ribosomal intergenic spacer analysis (ARISA) were combined to describe both abundant and rare types shaping the bacterial community. This spatial sampling scheme allowed detection of up to 99% of the estimated richness on phylum and class levels. At the resolution of operational taxonomic units (97% sequence identity; OTU3%) only 36% of the Chao1 estimated richness was recovered, indicating a high diversity, mostly due to rare types (62% of all OTU3%). Accordingly, a high turnover of the bacterial community was also observed between any two sampling stations (average replacement of 79% of OTU3%), yet no direct correlation with spatial distance was observed within the region. Bacterial community composition and structure differed significantly with increasing water depth along the bathymetric transect. The relative sequence abundance of Verrucomicrobia and Planctomycetes decreased significantly with water depth, and that of Deferribacteres increased. Energy availability, estimated from phytodetrital pigment concentrations in the sediments, partly explained the variation in community structure. Overall, this study indicates a high proportion of unique bacterial types on relatively small spatial scales (tens of kilometers), and supports the sampling design of the LTER site HAUSGARTEN to study bacterial community shifts in this rapidly changing area of the world's oceans.

BACKGROUND: Cold-water coral reef ecosystems are recognized as biodiversity hotspots in the deep sea, but insights into their associated bacterial communities are still limited. Deciphering principle patterns of bacterial community variation over multiple spatial scales may however prove critical for a better understanding of factors contributing to cold-water coral reef stability and functioning. METHODOLOGY/PRINCIPAL FINDINGS: Bacterial community structure, as determined by Automated Ribosomal Intergenic Spacer Analysis (ARISA), was investigated with respect to (i) microbial habitat type and (ii) coral species and color, as well as the three spatial components (iii) geomorphologic reef zoning, (iv) reef boundary, and (v) reef location. Communities revealed fundamental differences between coral-generated (branch surface, mucus) and ambient microbial habitats (seawater, sediments). This habitat specificity appeared pivotal for determining bacterial community shifts over all other study levels investigated. Coral-derived surfaces showed species-specific patterns, differing significantly between Lophelia pertusa and Madrepora oculata, but not between L. pertusa color types. Within the reef center, no community distinction corresponded to geomorphologic reef zoning for both coral-generated and ambient microbial habitats. Beyond the reef center, however, bacterial communities varied considerably from local to regional scales, with marked shifts toward the reef periphery as well as between different in- and offshore reef sites, suggesting significant biogeographic imprinting but weak microbe-host specificity. CONCLUSIONS/SIGNIFICANCE: This study presents the first multi-scale survey of bacterial diversity in cold-water coral reefs, spanning a total of five observational levels including three spatial scales. It demonstrates that bacterial communities in cold-water coral reefs are structured by multiple factors acting at different spatial scales, which has fundamental implications for the monitoring of microbial diversity and function in those ecosystems.

BackgroundMarine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems.Methodology/principal findingsThe synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share Conclusions/significanceThis first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed.

A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects. The machine-learning algorithm, Random Forests, was employed to model and predict seafloor standing stocks from surface primary production, water-column integrated and export particulate organic matter (POM), seafloor relief, and bottom water properties. The predictive models explain 63% to 88% of stock variance among the major size groups. Individual and composite maps of predicted global seafloor biomass and abundance are generated for bacteria, meiofauna, macrofauna, and megafauna (invertebrates and fishes). Patterns of benthic standing stocks were positive functions of surface primary production and delivery of the particulate organic carbon (POC) flux to the seafloor. At a regional scale, the census maps illustrate that integrated biomass is highest at the poles, on continental margins associated with coastal upwelling and with broad zones associated with equatorial divergence. Lowest values are consistently encountered on the central abyssal plains of major ocean basins The shift of biomass dominance groups with depth is shown to be affected by the decrease in average body size rather than abundance, presumably due to decrease in quantity and quality of food supply. This biomass census and associated maps are vital components of mechanistic deep-sea food web models and global carbon cycling, and as such provide fundamental information that can be incorporated into evidence-based management.

Cold seeps, hydrothermal vents, deep water coral reefs, and submarine canyon systems are hotspot habitats characterized by intermediate to high fluid advection. They are shaped by a complex interplay of physical, biological, geochemical, and geological processes. Biogeochemical and physicochemical gradients in these ecosystems are frequently extremely steep and temporally and spatially variable. Zones of elevated microbial activity, such as the methane-sulfate interface at cold-seep sites, usually encompass no more than a few millimeters. Recovery of samples for further shipboard analysis from such hotspot zones generally causes severe artifacts in the biogeochemical gradients. Hence, to quantify chemical gradients, microbial processes, and transport rates in deep-sea hotspot ecosystems, we have developed and operated a variety of specialized in situ instruments (Figure 1).