Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

Seasonal and interannual variability of the free-living and particle-associated bacteria of a coastal microbiome

Marine microbial communities differ genetically, metabolically, and ecologically according to their lifestyle, and they may respond differently to environmental changes. In this study, we investigated the seasonal dynamics of bacterial assemblies in the free-living (FL) and particle-associated (PA) fractions across a span of 6 years in the Blanes Bay Microbial Observatory in the Northwestern Mediterranean. Both lifestyles showed marked seasonality. The trends in alpha diversity were similar, with lower values in spring-summer than in autumn-winter. Samples from both fractions were grouped seasonally and the percentage of community variability explained by the measured environmental variables was comparable (32% in FL and 31% in PA). Canonical analyses showed that biotic interactions were determinants of bacterioplankton dynamics and that their relevance varies depending on lifestyles. Time-decay curves confirmed a high degree of predictability in both fractions. Yet, 'seasonal' Amplicon Sequence Variants (ASVs) (as defined by Lomb Scargle time series analysis) in the PA communities represented 46% of the total relative abundance while these accounted for 30% in the FL fraction. These results demonstrate that bacteria inhabiting both fractions exhibit marked seasonality, highlighting the importance of accounting for both lifestyles to fully comprehend the dynamics of marine prokaryotic communities.

Comparative analysis of microbiome inhabiting oxygenated and deoxygenated habitats using V3 and V6 metabarcoding of 16S rRNA gene

We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.

Functional vertical connectivity of microbial communities in the ocean

Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16S rRNA amplicon sequencing approach. A clear compositional and functional vertical connectivity of microbial communities was observed throughout the water column with Oceanospirillales, Alteromonadales, and Rhodobacterales as key taxa. The surface-derived particle-associated microbes increased the expression of proteins involved in basic metabolism, organic matter processing, and environmental stress response in deep waters. This study highlights the functional vertical connectivity between surface and deep-sea microbial communities via sinking particles and reveals that a considerable proportion of the deep-sea microbes might originate from surface waters and have a major impact on the biogeochemical cycles in the deep sea.

Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone

Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase (nod) gene from Methylomirabilota has been reported in the anoxic core of ODZs. Here, we show that the most abundantly transcribed nod genes in the Eastern Tropical North Pacific ODZ belong to a new order (UBA11136) of Alphaproteobacteria, rather than Methylomirabilota as previously assumed. Gammaproteobacteria and Planctomycetia also transcribe nod, but at lower relative abundance than UBA11136 in the upper ODZ. The nod-transcribing Alphaproteobacteria likely use formaldehyde and formate as a source of electrons for aerobic respiration, with additional electrons possibly from sulfide oxidation. They also transcribe multiheme cytochrome (here named ptd) genes for a putative porin-cytochrome protein complex of unknown function, potentially involved in extracellular electron transfer. Molecular oxygen for aerobic respiration may originate from nitric oxide dismutation via cryptic oxygen cycling. Our results implicate Alphaproteobacteria order UBA11136 as a significant player in marine nitrogen loss and highlight their potential in one-carbon, nitrogen, and sulfur metabolism in ODZs.IMPORTANCEIn marine oxygen-deficient zones (ODZs), microbes transform bioavailable nitrogen to gaseous nitrogen, with nitric oxide as a key intermediate. The Eastern Tropical North Pacific contains the world's largest ODZ, but the identity of the microbes transforming nitric oxide remains unknown. Here, we show that highly transcribed nitric oxide dismutase (nod) genes belong to Alphaproteobacteria of the novel order UBA11136, which lacks cultivated isolates. These Alphaproteobacteria show evidence for aerobic respiration, using oxygen potentially sourced from nitric oxide dismutase, and possess a novel porin-cytochrome protein complex with unknown function. Gammaproteobacteria and Planctomycetia transcribe nod at lower levels. Our results pinpoint the microbes mediating a key step in marine nitrogen loss and reveal an unexpected predicted metabolism for marine Alphaproteobacteria.

Gradients of bacteria in the oceanic water column reveal finely-resolved vertical distributions

Bacterial communities directly influence ecological processes in the ocean, and depth has a major influence due to the changeover in primary energy sources between the sunlit photic zone and dark ocean. Here, we examine the abundance and diversity of bacteria in Monterey Bay depth profiles collected from the surface to just above the sediments (e.g., 2000 m). Bacterial abundance in these Pacific Ocean samples decreased by >1 order of magnitude, from 1.22 ±0.69 ×106 cells ml-1 in the variable photic zone to 1.44 ± 0.25 ×105 and 6.71 ± 1.23 ×104 cells ml-1 in the mesopelagic and bathypelagic, respectively. V1-V2 16S rRNA gene profiling showed diversity increased sharply between the photic and mesopelagic zones. Weighted Gene Correlation Network Analysis clustered co-occurring bacterial amplicon sequence variants (ASVs) into seven subnetwork modules, of which five strongly correlated with depth-related factors. Within surface-associated modules there was a clear distinction between a 'copiotrophic' module, correlating with chlorophyll and dominated by e.g., Flavobacteriales and Rhodobacteraceae, and an 'oligotrophic' module dominated by diverse Oceanospirillales (such as uncultured JL-ETNP-Y6, SAR86) and Pelagibacterales. Phylogenetic reconstructions of Pelagibacterales and SAR324 using full-length 16S rRNA gene data revealed several additional subclades, expanding known microdiversity within these abundant lineages, including new Pelagibacterales subclades Ia.B, Id, and IIc, which comprised 4-10% of amplicons depending on the subclade and depth zone. SAR324 and Oceanospirillales dominated in the mesopelagic, with SAR324 clade II exhibiting its highest relative abundances (17±4%) in the lower mesopelagic (300-750 m). The two newly-identified SAR324 clades showed highest relative abundances in the photic zone (clade III), while clade IV was extremely low in relative abundance, but present across dark ocean depths. Hierarchical clustering placed microbial communities from 900 m samples with those from the bathypelagic, where Marinimicrobia was distinctively relatively abundant. The patterns resolved herein, through high resolution and statistical replication, establish baselines for marine bacterial abundance and taxonomic distributions across the Monterey Bay water column, against which future change can be assessed.

Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle

Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

IMPORTANCE

Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.

Transfer, elimination and accumulation of antibiotic resistance genes in decentralized household wastewater treatment facility treating total wastewater from residential complex

The fate and behavior of antibiotic resistance genes (ARGs) in decentralized household wastewater treatment facilities (DHWWTFs) are unclear. In this study, targeting on a representative DHWWTF that receive all wastewater from a residential complex having 150 households, the transfer, elimination and accumulation of tetG, tetM, sul1, sul2 and intl1 were quantitively studied through real-time PCR-based quantification, mass balance evaluation and the existing state analysis based on size fractionation. Significant abundance changes of the genes were observed in involved biological reactions and the sedimentation process due to microbial growth and decomposition as well as the accumulation of the genes to sludge. tetG and sul1 increased in their fluxes against respective input in the influent. Although substantial portions of the increased genes were found in excess sludge compared to the flux of genes in the influent, those remaining in the discharge were still high, with an average about 3.4 × 1014 copies/d. The abundance of all four genes (tetG, tetM, sul1and sul2) in both water and sludge phases showed a general trend of reduction as sludge accumulated gradually in its storage tank within two months after desludging. Classification of ARGs based on particle sizes (>250 μm, 125-250 μm, 75-125 μm, 25-75 μm, 3-25 μm, <3 μm) indicated that while the major part of ARGs were distributed in particles with larger sizes (125-250 μm), ARGs in smaller particles (3-25 μm) and free ARGs (<3 μm) still existed, which may pose a greater threat to water environment due to their poor settleability. The results of this study can benefit the optimization of on-site maintenance and operation of decentralized wastewater treatment facility for elimination of the transfer of ARGs.

Distinct Assembly Processes Structure Planktonic Bacterial Communities Among Near- and Offshore Ecosystems in the Yangtze River Estuary

The estuarine system functions as natural filters due to its ability to facilitate material transformation, planktonic bacteria play a crucial role in the cycling of complex nutrients and pollutants within estuaries, and understanding the community composition and assembly therein is crucial for comprehending bacterial ecology within estuaries. Despite extensive investigations into the composition and community assembly of two bacterial fractions (free-living, FLB; particle-attached, PAB), the process by which bacterioplankton communities in these two habitats assemble in the nearshore and offshore zones of estuarine ecosystems remains poorly understood. In this study, we conducted sampling in the Yangtze River Estuary (YRE) to investigate potential variations in the composition and community assembly of FLB and PAB in nearshore and offshore regions. We collected 90 samples of surface, middle, and bottom water from 16 sampling stations and performed 16S rRNA gene amplicon analysis along with environmental factor measurements. The results unveiled that the nearshore communities demonstrated significantly greater species richness and Chao1 indices compared to the offshore communities. In contrast, the nearshore communities had lower values of Shannon and Simpson indices. When compared to the FLB, the PAB exhibit a higher level of biodiversity and abundance. However, no distinct alpha and beta diversity differences were observed between the bottom, middle, and surface water layers. The community assembly analysis indicated that nearshore communities are predominantly shaped by deterministic processes, particularly due to heterogeneous selection of PAB; In contrast, offshore communities are governed more by stochastic processes, largely due to homogenizing dispersal of FLB. Consequently, the findings of this study demonstrate that nearshore and PAB communities exhibit higher levels of species diversity, while stochastic and deterministic processes exert distinct influences on communities among near- and offshore regions. This study further sheds new light on our understanding of the mechanisms governing bacterial communities in estuarine ecosystems.

Archaeal blooms and busts in an estuarine time series

Coastal bays, such as Delaware Bay, are highly productive, ecologically important transitions between rivers and the coastal ocean. They offer opportunities to investigate archaeal assemblages across seasons, with the exchange of water masses that occurs with tidal cycles, and in the context of variable organic matter quality. For a year-long estuarine, size-fractionated time series, we used amplicon sequencing, chemical measurements, and qPCR to follow archaeal groups through the seasons. We detected seasonally high abundances of Marine Group II archaea in summer months which correlate with indicators of phytoplankton production, although not phytoplankton biomass. Although previous studies have reported associations between Marine Group II archaea and particles, here they are almost entirely found in very small particles (0.22-0.7 μm), suggesting they are free-living cells. Populations of Nitrososphaeria did not vary with particle size or environmental conditions. Methanogens were significant fractions of archaeal sequences in large particles at low tide during winter months. Contrary to expectations, Nanoarchaeia were found predominantly in the free-living fraction despite the previous observation that they require an association with hosts. These results underscore the utility of time series studies in shallow, tidally mixed estuarine environments that capture variable conditions for understanding the ecology and biogeochemistry of planktic archaea.

Direct observations of microbial community succession on sinking marine particles

Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.

Spatio-temporal distribution characteristics and influencing factors of protoporphyrin IX in the estuarine-coastal ecosystems

Protoporphyrin IX (PPIX), a key precursor for the synthesis of chlorophyll and heme, is fundamental to photosynthetic eukaryotic cells and participates in light absorption, energy transduction, and numerous other cellular metabolic activities. Along with the application of genetic and biochemical techniques over the past few years, our understanding of the formation of PPIX has been largely advanced, especially regarding possible metabolic pathways. However, the ecological role and function of PPIX in natural ecosystems remains unclear. We have previously established a method for quantifying PPIX in marine ecosystems. Here, our results provide evidence that PPIX is not only subtly linked to nutrient uptake but also triggers phytoplankton productivity. PPIX and its derivatives are dynamic spatiotemporally in direct response to increased nutrient availability. Using 16 S rRNA gene amplicon sequencing, PPIX was revealed to interact strongly with many microorganisms, indicating that PPIX serves as a critical metabolite in maintaining microbial metabolism and community development. In summary, we observed that PPIX is linearly related to nutrient availability and microbial diversity. The levels of microbial PPIX reflect ecological health, and the availability of PPIX and nutrients jointly affect microbial community composition.

Microbial diversity and abundance vary along salinity, oxygen, and particle size gradients in the Chesapeake Bay

Marine snow and other particles are abundant in estuaries, where they drive biogeochemical transformations and elemental transport. Particles range in size, thereby providing a corresponding gradient of habitats for marine microorganisms. We used standard normalized amplicon sequencing, verified with microscopy, to characterize taxon-specific microbial abundances, (cells per litre of water and per milligrams of particles), across six particle size classes, ranging from 0.2 to 500 μm, along the main stem of the Chesapeake Bay estuary. Microbial communities varied in salinity, oxygen concentrations, and particle size. Many taxonomic groups were most densely packed on large particles (in cells/mg particles), yet were primarily associated with the smallest particle size class, because small particles made up a substantially larger portion of total particle mass. However, organisms potentially involved in methanotrophy, nitrite oxidation, and sulphate reduction were found primarily on intermediately sized (5-180 μm) particles, where species richness was also highest. All abundant ostensibly free-living organisms, including SAR11 and Synecococcus, appeared on particles, albeit at lower abundance than in the free-living fraction, suggesting that aggregation processes may incorporate them into particles. Our approach opens the door to a more quantitative understanding of the microscale and macroscale biogeography of marine microorganisms.

Influences of hydrodynamics on microbial community assembly and organic carbon composition of resuspended sediments in shallow marginal seas

Hydrodynamic processes play a crucial role in driving the transmission of sediments, likely harboring diverse microbes and heterogeneous organic carbon (OC) in the ocean. Here we conducted continuous micro-erosion experiments on surface sediments retrieved from shallow marginal seas, and analyzed the microbial community structures, OC content, and isotope compositions (δ13C and Δ14C) of resuspended sediments to investigate the effects of hydrodynamics on microbial assembly and OC composition in marginal seas. Our results showed that gene abundance and major microbial compositions in resuspended sediments changed with varying benthic shear stresses, which evolved towards diversification after continuous hydrodynamic erosion. Aerobic bacteria were more likely to be eroded out from sediments under lower shear stresses compared with anaerobic bacteria. Our study provides evidence that hydrodynamic disturbances shape the assembly of microbial communities with different metabolic functions, especially for bacteria, which may spatially influence the microbial-mediated biogeochemical transformation in marginal seas. Isotopic results revealed that more terrestrial OC was resuspended under initial erosion, while more marine OC was eroded out with increasing shear stresses, suggesting that hydrodynamics may control the redistribution of different sourced OC and contribute to the dispersion and degradation of terrestrial OC during transport process. Our findings further suggest that the nature of resuspended OC may influence the assembly of sediment-attached microbes due to their metabolic preference for carbon sources, as evidenced by correlations between OC compositions and microbial diversity and abundance. We thus suggest that hydrodynamic disturbance is an extrinsic physical driver of OC redistribution and microbial reassembly, whereas OC may be an intrinsic factor influencing microbial colonization, helping to interpret the spatial heterogeneity of microbes and OC compositions observed in marginal sea sediments. Our study underscores the significant roles of hydrodynamic-driven sediment resuspension in shaping diverse microbial communities and redistributing OC in aquatic systems, and highlights the importance of this process in biogeochemical cycles and ecological environment evolution in shallow marginal sea systems.

Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones

Anammox bacteria inhabiting oxygen-deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss in the global ocean. However, many basic questions regarding the diversity, broad metabolisms, origin, and adaptive mechanisms of ODZ anammox bacteria remain unaddressed. Here we report two novel metagenome-assembled genomes of anammox bacteria affiliated with the Scalindua genus, which represent most, if not all, of the anammox bacteria in the global ODZs. Metagenomic read-recruiting and comparison with historical data show that they are ubiquitously present in all three major ODZs. Beyond the core anammox metabolism, both organisms contain cyanase, and the more dominant one encodes a urease, indicating most ODZ anammox bacteria can utilize cyanate and urea in addition to ammonium. Molecular clock analysis suggests that the evolutionary radiation of these bacteria into ODZs occurred no earlier than 310 million years ago, ~1 billion years after the emergence of the earliest modern-type ODZs. Different strains of the ODZ Scalindua species are also found in benthic sediments, and the first ODZ Scalindua is likely derived from the benthos. Compared to benthic strains of the same clade, ODZ Scalindua uniquely encodes genes for urea utilization but has lost genes related to growth arrest, flagellum synthesis, and chemotaxis, presumably for adaptation to thrive in the global ODZ waters. Our findings expand the known metabolisms and evolutionary history of the bacteria controlling the global nitrogen budget.

Increased cyanophage infection at the bottom of the euphotic zone, especially in the fall

Picocyanobacteria contribute greatly to offshore primary production with cells extending through the deep euphotic zone. Literature indicates high viral infection of cyanobacteria in ocean transition zones. We postulate that the bottom of the euphotic zone is a transition zone, where communities transition from phototrophic to aphotic processes. We use single-copy core genes to examine cyanophage to cyanobacteria ratios in cellular metagenomes in the subtropical North Atlantic and Pacific. Cyanophage to cyanobacteria terL/rpoB ratios generally increase to >10 in the deep euphotic zone. As light levels decrease in the fall, Prochlorococcus in the deep euphotic zone experience reduced light levels. We find clear differences between spring (Geotraces GA02) and fall (GA03) in the North Atlantic, with terL/rpoB ratios increasing to >40 in the fall. When examining 23 months of the North Pacific Hawaii Ocean Timeseries, the depth of elevated cyanophage to cyanobacteria ratios in cellular metagenomes negatively correlated with surface photosynthetic radiation (PAR), particularly with the change in PAR, which reflected the season. In fall, all picocyanobacteria ecotypes were found at depths enriched with viruses, while in summer, only low light ecotypes were affected. Thus, we find high cyanophage infection both in the deep euphotic zone and during seasonal transitions.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential

Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.

Reductions in abundances of intracellular and extracellular antibiotic resistance genes by SiO2 nanoparticles during composting driven by mobile genetic elements

Applying exogenous additives during the aerobic composting of livestock manure is effective for slowing down the spread of antibiotic resistance genes (ARGs) in the environment. Nanomaterials have received much attention because only low amounts need to be added and they have a high capacity for adsorbing pollutants. Intracellular ARGs (i-ARGs) and extracellular ARGs (e-ARGs) comprise the resistome in livestock manure but the effects of nanomaterials on the fates of these different fractions during composting are still unclear. Thus, we investigated the effects of adding SiO₂ nanoparticles (SiO₂NPs) at four levels (0 (CK), 0.5 (L), 1 (M), and 2 g/kg (H)) on i-ARGs, e-ARGs, and the bacterial community during composting. The results showed that i-ARGs represented the main fraction of ARGs during aerobic composting of swine manure, and their abundance was lowest under M. Compared with CK, M increased the removal rates of i-ARGs and e-ARGs by 17.9% and 100%, respectively. SiO₂NPs enhanced the competition between ARGs hosts and non-hosts. M optimized the bacterial community by reducing the abundances of co-hosts (Clostridium_sensu_stricto_1, Terrisporobacter, and Turicibacter) of i-ARGs and e-ARGs (by 96.0% and 99.3%, respectively) and killing 49.9% of antibiotic-resistant bacteria. Horizontal gene transfer dominated by mobile genetic elements (MGEs) played a key role in the changes in the abundances of ARGs. i-intI1 and e-Tn916/1545 were key MGEs related closely to ARGs, and the maximum decreases of 52.8% and 100%, respectively, occurred under M, which mainly explained the decreased abundances of i-ARGs and e-ARGs. Our findings provide new insights into the distribution and main drivers of i-ARGs and e-ARGs, as well as demonstrating the possibility of adding 1 g/kg SiO₂NPs to reduce the propagation of ARGs.

Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia

Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.

Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin

Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.

Capturing marine microbiomes and environmental DNA: A field sampling guide

The expanding interest in marine microbiome and eDNA sequence data has led to a demand for sample collection and preservation standard practices to enable comparative assessments of results across studies and facilitate meta-analyses. We support this effort by providing guidelines based on a review of published methods and field sampling experiences. The major components considered here are environmental and resource considerations, sample processing strategies, sample storage options, and eDNA extraction protocols. It is impossible to provide universal recommendations considering the wide range of eDNA applications; rather, we provide information to design fit-for-purpose protocols. To manage scope, the focus here is on sampling collection and preservation of prokaryotic and microeukaryotic eDNA. Even with a focused view, the practical utility of any approach depends on multiple factors, including habitat type, available resources, and experimental goals. We broadly recommend enacting rigorous decontamination protocols, pilot studies to guide the filtration volume needed to characterize the target(s) of interest and minimize PCR inhibitor collection, and prioritizing sample freezing over (only) the addition of preservation buffer. An annotated list of studies that test these parameters is included for more detailed investigation on specific steps. To illustrate an approach that demonstrates fit-for-purpose methodologies, we provide a protocol for eDNA sampling aboard an oceanographic vessel. These guidelines can aid the decision-making process for scientists interested in sampling and sequencing marine microbiomes and/or eDNA.

Seasonal hydrological dynamics govern lifestyle preference of aquatic antibiotic resistome

Antibiotic resistance genes (ARGs) are a well-known environmental concern. Yet, limited knowledge exists on the fate and transport of ARGs in deep freshwater reservoirs experiencing seasonal hydrological changes, especially in the context of particle-attached (PA) and free-living (FL) lifestyles. Here, the ARG profiles were examined using high-throughput quantitative PCR in PA and FL lifestyles during four seasons representing two hydrological phenomena (vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing the ARGs in PA and FL and the transition of ARGs between the two lifestyles. ARG profiles both in PA and FL were likely to be shaped by horizontal gene transfer. However, they exhibited distinct responses to the physicochemical (e.g., nutrients and dissolved oxygen) changes under seasonal hydrological dynamics. The particle-association niche (PAN) index revealed 94 non-conservative ARGs (i.e., no preferences for PA and FL) and 23 and 16 conservative ARGs preferring PA and FL lifestyles, respectively. A sharp decline in conservative ARGs under stratified hydrologic suggested seasonal influence on the ARGs transition between PA and FL lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle than their counterparts, indicating lifestyle-dependent ARG enrichment. Altogether, these findings enhanced our understanding of the ARG lifestyles and the role of seasonal hydrological changes in governing the ARG transition between the lifestyles in a typical deep freshwater ecosystem.

Composition and assembly of the bacterial community in the overlying waters of the coral reef of China's Xisha Islands

Coral reef ecosystems are one of the most diverse and productive habitats on Earth. Microbes in the reef-overlying waters are key players in maintaining this ecosystem through regulating biogeochemical and ecological processes. However, the composition structure and assembly mechanism of microbial community in the reef-overlying waters remain largely unknown. In the present study, the bacterial communities from the overlying waters of atolls and fringing reefs as well as the surface waters of the adjacent open ocean of the Xisha Islands in the South China Sea were investigated using 16S rRNA high-throughput sequencing combined with a size-fractionation strategy. The results showed that environments of all sampling stations were similar, characterized by an almost complete lack of inorganic nutrients such as nitrogen and phosphorus. Proteobacteria, Cyanobacteria and Bacteroidetes were the dominant phyla, and Synechococcus was most abundant at the genus level in both large fraction (LF; 1.6-200 μm) and small fraction (SF; 0.2-1.6 μm) communities. Only a slight difference in community composition between LF and SF samples was observed. The bacterial communities among the three habitat types showed noticeable differences, and the bacterial composition among the atoll reefs was more varied than that among the fringing reefs. The similarity of bacterial communities significantly declined with the increasing geographic distance, and stochastic processes were more important than deterministic processes in bacterial community assembly. This study sheds lights on the bacterial biodiversity of coral reefs and the importance of stochastic process in structuring bacterial communities.

Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study

The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.

Physical-chemical factors influencing the vertical distribution of phototrophic pico-nanoplankton in the Oxygen Minimum Zone (OMZ) off Northern Chile: The relative influence of low pH/low O2 conditions

The vertical distribution of phytoplankton is of fundamental importance in the structure, dynamic, and biogeochemical pathways in marine ecosystems. Nevertheless, what are the main factors determining this distribution remains as an open question. Here, we evaluated the relative influence of environmental factors that might control the coexistence and vertical distribution of pico-nanoplankton associated with the OMZ off northern Chile. Our results showed that in the upper layer Synechococcus-like cells were numerically important at all sampling stations. Pico-nano eukaryotes and phototrophic nanoflagellates (PNF) also showed high abundances in the upper layer decreasing in abundance down to the upper oxycline, while only Prochlorococcus showed high abundances under oxycline and within the oxygen-depleted layer. Statistical analyses evidenced that temperature, oxygen, and carbonate chemistry parameters (pH and dissolved inorganic carbon, DIC) influenced significantly the vertical distribution of phototrophic pico-nanoplankton. Additionally, we experimentally-evaluated the combined effect of low pH/low O₂ conditions on a nanophytoplankton species, the haptophyte Imantonia sp. Under control conditions (pH = 8.1; O₂ = 287.5 μM, light = 169.6 μEm^-2s^-1), Imantonia sp. in vivo fluorescence increased over fifty times, inducing supersaturated O₂ conditions (900 μM) and an increasing pH (8.5), whereas upon an experimental treatment mimicking OMZ conditions (pH = 7.5; O₂ = 55.6 μM; light = 169.6 μEm^-2s^-1), in vivo fluorescence declined dramatically, suggesting that Imantonia sp. did not survive. Although preliminary, our study provides evidence about the role of low pH/low O₂ conditions on the vertical distribution of nanophytoplankton, which deserve future attention through both fieldwork and more extended experimental experiences.

Habitat-dependent prokaryotic microbial community, potential keystone species, and network complexity in a subtropical estuary

Microbes (e.g., bacteria and archaea) are indispensable components for the key biological processes of estuarine ecosystems and three main habitats (sediment, particle, and water) are harboring diverse estuarine microbes. However, we still know little about how the microbial community structures, potential keystone species, and network properties change among these three habitats in estuarine ecosystems. In this study, we collected size-fractioned water and sediment samples from the Pearl River Estuary to reveal their microbial diversity, community structures, network properties, and potential keystone taxa. We found that the sediment microbial community was remarkably more diverse than particle-attached (PA) and free-living (FL) communities, whereas its ecological network was less complex in terms of node distance and connectivity. TOC was determined as the main driver of sediment community, while the PA and FL communities were predominantly shaped by NO₂^-, non-ionic ammonia (NH) and pH. Among the bulk water, there were no significant differences between PA and FL communities in diversity, community structure, and network complexity. However, the PA community was more susceptible to metal elements, suggesting their higher level of involvement in physiological metabolism. Potential keystone taxa among community networks were taxonomically divergent in three habitats. Specifically, Synechococcales (Cyanobacteria) and Actinomarinales (Actinobacteria) exclusively served as the module-hubs in FL network, while members from phylum Proteobacteria and Bacteroidetes were the module-hubs and connectors in PA network. Potential keystone taxa in sediment network were more diverse and covered 9 phyla, including the only archaeal lineage Bathyarchaeia (Crenarchaeota). Overall, our study provided more detailed information about estuarine microbial communities in three habitats, especially the potential keystone species, which provided new perspectives on evaluating further effects of anthropogenic disturbances on estuarine microbes and facilitated the environment monitoring based on microbial community.

Genomic insights into versatile lifestyle of three new bacterial candidate phyla

Metagenomic explorations of the Earth's biosphere enable the discovery of previously unknown bacterial lineages of phylogenetic and ecological significance. Here, we retrieved 11 metagenomic-assembled genomes (MAGs) affiliated to three new monophyletic bacterial lineages from the seawater of the Yap Trench. Phylogenomic analysis revealed that each lineage is a new bacterial candidate phylum, subsequently named Candidatus Qinglongiota, Candidatus Heilongiota, and Candidatus Canglongiota. Metabolic reconstruction of genomes from the three phyla suggested that they adopt a versatile lifestyle, with the potential to utilize various types of sugars, proteins, and/or short-chain fatty acids through anaerobic pathways. This was further confirmed by a global distribution map of the three phyla, indicating a preference for oxygen-limited or particle-attached niches, such as anoxic sedimentary environments. Of note, Candidatus Canglongiota genomes harbor genes for the complete Wood- Ljungdahl pathway and sulfate reduction that are similar to those identified in some sulfate-reducing bacteria. Evolutionary analysis indicated that gene gain and loss events, and horizontal gene transfer (HGT) play important roles in shaping the genomic and metabolic features of the three new phyla. This study presents the genomic insight into the ecology, metabolism, and evolution of three new phyla, which broadens the phylum-level diversity within the domain Bacteria.

Oxygen availability driven trends in DOM molecular composition and reactivity in a seasonally stratified fjord

Ocean deoxygenation could potentially trigger substantial changes in the composition and reactivity of dissolved organic matter (DOM) pool, which plays an important role in the global carbon cycle. To evaluate links between DOM dynamics and oxygen availability, we investigated the DOM composition under varying levels of oxygen in a seasonally hypoxic fjord through a monthly time-series over two years. We used ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) to characterize DOM on a molecular level. We find a clear trend both in diversity and molecular composition of the DOM along the oxygen gradient. As oxygen decreased, the chemodiversity was significantly increased, along with accumulation of relatively high-molecular-weight, reduced and unsaturated compounds enriched with carboxyl-group structures, which were also thermodynamically less favorable to biodegradation. Our results suggested that oxygen depletion selectively protected otherwise bioavailable compounds from decomposition and may promote the accumulation of a larger recalcitrant DOM pool in the global ocean, which could provide negative feedback to the ocean carbon sequestration and climate change.

Stochastic processes shape the aggregation of free-living and particle-attached bacterial communities in the Yangtze River Estuary, China

An estuary plays an important role in material and energy exchange between the land and sea, where complex physical, chemical, and biological processes occur. Here, we investigated the assembly processes of free-living (FL) and particle-associated (PA) bacterial communities in two seawater layers at five stations in the Yangtze River Estuary (YRE) by using 16S rRNA sequencing methods. The results indicated that Proteobacteria was the most abundant phylum in the YRE. The α-diversity of PA community was significantly higher than FL community, and analysis of similarity showed significantly different (Global R = 0.2809, p < 0.005). RDA revealed that phosphate (PO₄ ^3- ) was significantly correlated with PA bacterial community abundance (p < 0.05). An ecological null model showed that both PA and FL bacterial communities were mainly influenced by stochastic processes (PA: 100%, FL: 70%), which PA attached to nutrient particles and are less affected by environmental filtration. Dispersal limitation (50%) was the main assembly process of the PA community, while homogeneous selection (30%) and drift (30%) were important processes in the FL community assembly. The available substrate for colonization limits the transformation from FL to PA bacteria. This study would improve our understanding of FL and PA bacterial community structure and factors affecting assembly process in estuarine environments.

Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column

Bacteria and archaea are central to the production, consumption, and remineralization of dissolved and particulate organic matter and contribute critically to carbon delivery, nutrient availability, and energy transformations in the deep ocean. To explore environmentally relevant genomic traits of sinking-particle-associated versus free-living microbes, we compared habitat-specific metagenome-assembled genomes recovered throughout the water column in the North Pacific Subtropical Gyre. The genomic traits of sinking-particle-associated versus free-living prokaryotes were compositionally, functionally, and phylogenetically distinct. Substrate-specific transporters and extracellular peptidases and carbohydrate-active enzymes were more enriched and diverse in particle-associated microbes at all depths than in free-living counterparts. These data indicate specific roles for particle-attached microbes in particle substrate hydrolysis, uptake, and remineralization. Shallow-water particle-associated microbes had elevated genomic GC content and proteome nitrogen content and reduced proteome carbon content in comparison to abyssal particle-associated microbes. An inverse trend was observed for their sympatric free-living counterparts. These different properties of attached microbes are postulated to arise in part due to elevated organic and inorganic nitrogen availability inside sinking particles. Particle-attached microbes also were enriched in genes for environmental sensing via two-component regulatory systems, and cell-cell interactions via extracellular secretion systems, reflecting their surface-adapted lifestyles. Finally, particle-attached bacteria had greater predicted maximal growth efficiencies than free-living bacterioplankton at all depths. All of these particle-associated specific genomic and proteomic features appear to be driven by microhabitat-specific elevated nutrient and energy availability as well as surface-associated competitive and synergistic ecological interactions. Although some of these characteristics have been previously postulated or observed individually, we report them together here in aggregate via direct comparisons of cooccurring free-living and sinking-particle-attached microbial genomes from the open ocean.

Microbial production of toluene in oxygen minimum zone waters in the Humboldt Current System off Chile

Expansion of oxygen minimum zones in the world's oceans is likely to enhance the production of anaerobic metabolites by marine microorganisms. Here we show that toluene is present throughout the year in shelf waters of the upwelling ecosystem off Concepción (36° S), Chile, and it is a product of microbial anaerobic metabolism. The intra-annual variability in toluene concentrations is consistent with seasonal variability in the strengths of suboxic equatorial and oxygenated subantarctic water masses. Laboratory incubations of oxygen minimum zone water showed microbial production of toluene in the absence of O₂. Toluene concentrations were elevated (up to 96 nM) in deeper O₂-depleted waters and followed a seasonal pattern in oceanographic conditions. There is evidence to hypothesize that microbial production of toluene could be a homeostatic biochemical mechanism to thrive in the more acidic oxygen minimum zone waters. On the other hand, evidence indicates that microbial anaerobic degradation of toluene may be a source of NO₂⁻ by partial denitrification, as shown for aquifer sediments. Since toluene production was not detected in incubations under aerobic conditions, we hypothesize that oxygen minimum zone waters export toluene to surrounding oxygenated waters. Expansion of hypoxia in the ocean will certainly enhance the production and export of anaerobic metabolites by marine microorganisms.

Insights into Prokaryotic Community and Its Potential Functions in Nitrogen Metabolism in the Bay of Bengal, a Pronounced Oxygen Minimum Zone

Ocean oxygen minimum zones (OMZs) around the global ocean are expanding both horizontally and vertically. Multiple studies have identified the significant influence of anoxic conditions (≤1 μM O₂) on marine prokaryotic communities and biogeochemical cycling of elements. However, little attention has been paid to the expanding low-oxygen zones where the oxygen level is still above the anoxic level. Here, we studied the abundance and taxonomic and functional profiles of prokaryotic communities in the Bay of Bengal (BoB), where the oxygen concentration is barely above suboxic level (5 μM O₂). We found the sinking of Trichodesmium into deep water was far more efficient than that of Prochlorococcus, suggesting Trichodesmium blooms might be an essential carbon and nitrogen source for the maintenance of the BoB OMZ. In addition to the shift in the prokaryotic community composition, the abundance of some functional genes also changed with the change of oxygen concentration. Compared to oxic (>60 μM O₂) Tara Ocean and high-hypoxic (>20 to ≤60 μM O₂) BoB samples, we found more SAR11-nar sequences (responsible for reducing nitrate to nitrite) in low-hypoxic (>5 to ≤20 μM O₂) BoB waters. This suggested SAR11-nar genes would be more widespread due to the expansion of OMZs. It seems that the nitrite-N was not further reduced to nitrogen through denitrification but likely oxidized to nitrate by Nitrospinae in the BoB OMZ and then accumulated in the form of nitrate-N. However, the lack of N₂ production in the BoB would change if the BoB OMZ became anoxic. Together, these results suggested that reduction of oxygen concentration and OMZ expansion may increase the use of nitrate by SAR11 and N₂ production in the BoB.

IMPORTANCE Recognizing the prokaryotic community and its functions in hypoxic (>5 to ≤60 μM O₂) environments before further expansion of OMZs is critical. We demonstrate the prokaryotic community and its potential functions in nitrogen metabolism in the Bay of Bengal (BoB), where oxygen concentration is barely above suboxic level. This study highlighted that Trichodesmium might be an essential carbon and nitrogen source in the maintenance of the BoB OMZ. Additionally, we suggest that the lack of N₂ production in the BoB would change if the BoB OMZ became anoxic, and the expansion of OMZs in the global ocean may potentially increase the use of nitrate by SAR11.

Microbial Activities and Selection from Surface Ocean to Subseafloor on the Namibian Continental Shelf

Oxygen minimum zones (OMZs) are hot spots for redox-sensitive nitrogen transformations fueled by sinking organic matter. In comparison, the regulating role of sulfur-cycling microbes in marine OMZs, their impact on carbon cycling in pelagic and benthic habitats, and activities below the seafloor remain poorly understood. Using ¹³C DNA stable isotope probing (SIP) and metatranscriptomics, we explored microbial guilds involved in sulfur and carbon cycling from the ocean surface to the subseafloor on the Namibian shelf. There was a clear separation in microbial community structure across the seawater-seafloor boundary, which coincided with a 100-fold-increased concentration of microbial biomass and unique gene expression profiles of the benthic communities. ¹³C-labeled 16S rRNA genes in SIP experiments revealed carbon-assimilating taxa and their distribution across the sediment-water interface. Most of the transcriptionally active taxa among water column communities that assimilated ¹³C from diatom exopolysaccharides (mostly Bacteroidetes, Actinobacteria, Alphaproteobacteria, and Planctomycetes) also assimilated ¹³C-bicarbonate under anoxic conditions in sediment incubations. Moreover, many transcriptionally active taxa from the seafloor community (mostly sulfate-reducing Deltaproteobacteria and sulfide-oxidizing Gammaproteobacteria) that assimilated ¹³C-bicarbonate under sediment anoxic conditions also assimilated ¹³C from diatom exopolysaccharides in the surface ocean and OMZ waters. Despite strong selection at the sediment-water interface, many taxa related to either planktonic or benthic communities were found to be present at low abundance and actively assimilating carbon under both sediment and water column conditions. In austral winter, mixing of shelf waters reduces stratification and suspends sediments from the seafloor into the water column, potentially spreading metabolically versatile microbes across niches.

IMPORTANCE Microbial activities in oxygen minimum zones (OMZs) transform inorganic fixed nitrogen into greenhouse gases, impacting the Earth’s climate and nutrient equilibrium. Coastal OMZs are predicted to expand with global change and increase carbon sedimentation to the seafloor. However, the role of sulfur-cycling microbes in assimilating carbon in marine OMZs and related seabed habitats remain poorly understood. Using ¹³C DNA stable isotope probing and metatranscriptomics, we explore microbial guilds involved in sulfur and carbon cycling from ocean surface to subseafloor on the Namibian shelf. Despite strong selection and differential activities across the sediment-water interface, many active taxa were identified in both planktonic and benthic communities, either fixing inorganic carbon or assimilating organic carbon from algal biomass. Our data show that many planktonic and benthic microbes linked to the sulfur cycle can cross redox boundaries when mixing of the shelf waters reduces stratification and suspends seafloor sediment particles into the water column.

Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series

Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.

Microbial Community Structure and Ecological Networks during Simulation of Diatom Sinking

Microbial-mediated utilization of particulate organic matter (POM) during its downward transport from the surface to the deep ocean constitutes a critical component of the global ocean carbon cycle. However, it remains unclear as to how high hydrostatic pressure (HHP) and low temperature (LT) with the sinking particles affects community structure and network interactions of the particle-attached microorganisms (PAM) and those free-living microorganisms (FLM) in the surrounding water. In this study, we investigated microbial succession and network interactions in experiments simulating POM sinking in the ocean. Diatom-derived ¹³C- and ¹²C-labeled POM were used to incubate surface water microbial communities from the East China Sea (ECS) under pressure (temperature) of 0.1 (25 °C), 20 (4 °C), and 40 (4 °C) MPa (megapascal). Our results show that the diversity and species richness of the PAM and FLM communities decreased significantly with HHP and LT. Microbial community analysis indicated an increase in the relative abundance of Bacteroidetes at high pressure (40 MPa), mostly at the expense of Gammaproteobacteria, Alphaproteobacteria, and Gracilibacteria at atmospheric pressure. Hydrostatic pressure and temperature affected lifestyle preferences between particle-attached (PA) and free-living (FL) microbes. Ecological network analysis showed that HHP and LT enhanced microbial network interactions and resulted in higher vulnerability to networks of the PAM communities and more resilience of those of the FLM communities. Most interestingly, the PAM communities occupied most of the module hubs of the networks, whereas the FLM communities mainly served as connectors of the modules, suggesting their different ecological roles of the two groups of microbes. These results provided novel insights into how HHP and LT affected microbial community dynamics, ecological networks during POM sinking, and the implications for carbon cycling in the ocean.

Particle foraging strategies promote microbial diversity in marine environments

Microbial foraging in patchy environments, where resources are fragmented into particles or pockets embedded in a large matrix, plays a key role in natural environments. In the oceans and freshwater systems, particle-associated bacteria can interact with particle surfaces in different ways: some colonize only during short transients, while others form long-lived, stable colonies. We do not yet understand the ecological mechanisms by which both short- and long-term colonizers can coexist. Here, we address this problem with a mathematical model that explains how marine populations with different detachment rates from particles can stably coexist. In our model, populations grow only while on particles, but also face the increased risk of mortality by predation and sinking. Key to coexistence is the idea that detachment from particles modulates both net growth and mortality, but in opposite directions, creating a trade-off between them. While slow-detaching populations show the highest growth return (i.e., produce more net offspring), they are more susceptible to suffer higher rates of mortality than fast-detaching populations. Surprisingly, fluctuating environments, manifesting as blooms of particles (favoring growth) and predators (favoring mortality) significantly expand the likelihood that populations with different detachment rates can coexist. Our study shows how the spatial ecology of microbes in the ocean can lead to a predictable diversification of foraging strategies and the coexistence of multiple taxa on a single growth-limiting resource.

Eukaryotic Parasites Are Integral to a Productive Microbial Food Web in Oxygen-Depleted Waters

Oxygen-depleted water columns (ODWCs) host a diverse community of eukaryotic protists that change dramatically in composition over the oxic-anoxic gradient. In the permanently anoxic Cariaco Basin, peaks in eukaryotic diversity occurred in layers where dark microbial activity (chemoautotrophy and heterotrophy) were highest, suggesting a link between prokaryotic activity and trophic associations with protists. Using 18S rRNA gene sequencing, parasites and especially the obligate parasitic clade, Syndiniales, appear to be particularly abundant, suggesting parasitism is an important, but overlooked interaction in ODWC food webs. Syndiniales were also associated with certain prokaryotic groups that are often found in ODWCs, including Marinimicrobia and Marine Group II archaea, evocative of feedbacks between parasitic infection events, release of organic matter, and prokaryotic assimilative activity. In a network analysis that included all three domains of life, bacterial and archaeal taxa were putative bottleneck and hub species, while a large proportion of edges were connected to eukaryotic nodes. Inclusion of parasites resulted in a more complex network with longer path lengths between members. Together, these results suggest that protists, and especially protistan parasites, play an important role in maintaining microbial food web complexity, particularly in ODWCs, where protist diversity and microbial productivity are high, but energy resources are limited relative to euphotic waters.

Size-Fractionated Filtration Combined with Molecular Methods Reveals the Size and Diversity of Picophytoplankton

In this study, flow cytometry (FCM) and size-fractionated filtration, together with high-throughput molecular sequencing methods (SM), were used to investigate picophytoplankton. A particle separation filter and a higher-throughput sequencing method were used to evaluate the composition of a euphotic zone of picophytoplankton-especially picoeukaryotic phytoplankton-in the Western Pacific, and the results of flow cytometry, which is a classic way to detect picophytoplankton, were used as a standard to evaluate the reliability of the results of the SMs. Within a water column of 200 m, six water depths (5, 25, 50, 113 (DCM), 150, and 200 m) were established. In order to further study the particle size spectra of the picophytoplankton, size-fractionated filtration was used to separate water samples from each water depth into three particle size ranges: 0.2-0.6, 0.6-1.2, and 1.2-2 μm. A total of 36 (6 × 3 × 2) samples were obtained through PCR amplification of the 18S rRNA V4 hypervariable region and 16S rRNA, which were biased toward phytoplankton plastids, and then high-throughput sequencing was performed. The estimation of the picophytoplankton diameter relied on forward scattering (FSC) through FCM. The estimation of the vertical distribution and diameter of the picophytoplankton using the SM was consistent with the results with FCM; thus, we believe that the estimation of picophytoplankton composition with the SM has value as a reference, although the size-fractionated filtration seemed to cause some deviations. In addition to Prochlorococcus and Synechococcus, the SM was used to evaluate the composition of picoeukaryotic phytoplankton, which mainly included Prymnesiophycea (Haptophyta) (38.15%), Cryptophyceae (Cryptophyta) (22.36%), Dictyochophyceae (Chrysophyta) (12.22%), and Mamiellophyceae (Chlorophyta) (3.31%). In addition, the SM also detected Dinophyceae (Dinoflagellata) (11.69%) sequences and a small number of Bacillariophyceae (Diatom) (1.64%) sequences, which are generally considered to have large particle sizes. The results of the SM also showed that the picoeukaryotic phytoplankton were not evenly distributed in the euphotic layer, and the vertical distributions of the different picoeukaryotic phytoplankton were different. An analysis of correlations with environmental factors showed that temperature was the main environmental factor controlling the vertical distribution of picophytoplankton.

Diversity Distribution, Driving Factors and Assembly Mechanisms of Free-Living and Particle-Associated Bacterial Communities at a Subtropical Marginal Sea

Free-living (FL) and particle-associated (PA) bacterioplankton communities play critical roles in biogeochemical cycles in the ocean. However, their community composition, assembly process and functions in the continental shelf and slope regions are poorly understood. Based on 16S rRNA gene amplicon sequencing, we investigated bacterial communities’ driving factors, assembly processes and functional potentials at a subtropical marginal sea. The bacterioplankton community showed specific distribution patterns with respect to lifestyle (free living vs. particle associated), habitat (slope vs. shelf) and depth (surface vs. DCM and Bottom). Salinity and water temperature were the key factors modulating turnover in the FL community, whereas nitrite, silicate and phosphate were the key factors for the PA community. Model analyses revealed that stochastic processes outweighed deterministic processes and had stronger influences on PA than FL. Homogeneous selection (Hos) was more responsible for the assembly and turnover of FL, while drift and dispersal limitation contributed more to the assembly of PA. Importantly, the primary contributor to Hos in PA was Gammaproteobacteria:Others, whereas that in FL was Cyanobacteria:Bin6. Finally, the PICRUSt2 analysis indicated that the potential metabolisms of carbohydrates, cofactors, amino acids, terpenoids, polyketides, lipids and antibiotic resistance were markedly enriched in PA than FL.

Metagenomic prediction analysis of microbial aggregation in anammox-dominated community

Aggregation of anammox bacteria is essential to maintain high biomass concentrations and prevent the loss of biomass in anammox processes. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used in this study to predict the metagenomic potentials and characterize the microbial community structure and functional features in anammox aggregates (e.g., sludge flocs, biofilms, and granules). The results showed that Candidatus Brocadia was the most dominant anammox genera in all aggregates (38.0% in flocs, 69.4% in biofilm, and 52.0% in granules) and the functional gene involved in the anammox process was detected in the highest amount in biofilms, followed by granules and flocs. Furthermore, the anammox microbial aggregation pathway was explored that anammox bacteria have strong motility and high capability for early attachment. Anammox bacteria could produce large amounts of EPS (extracellular polymeric substances) regulated by quinolone and transport to extracellular environment through type II secretion system. The strong ability of c-di-GMP (bis-(3'-5')-cyclic dimeric guanosine monophosphate) synthesis enabled a stable architectural structure of aggregation. This study elucidated the aggregation mechanism of anammox microorganisms at the genetic level to enhance the stability of anammox processes. PRACTITIONER POINTS: Candidatus Brocadia was the most dominant anammox genera in aggregates. Anammox bacteria have strong motility and high attachment capability. Anammox bacteria possess strong EPS synthesis regulated by quinolone. c-di-GMP synthesis enables a stable structure of aggregation.

Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters

The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.

Seasonal succession of microbes in different size-fractions and their modular structures determined by both macro- and micro-environmental filtering in dynamic coastal waters

Microbes interact with each other in response to various environmental changes in coastal marine ecosystems. To explore how the macroenvironment (environmental filtering) and species-engineered microenvironment (niche construction) affect the ecological network of the marine microbiome in the highly dynamic coastal waters of Korea, we analyzed the modular structures of the microbial community and identified microbial interconnections in different size fractions for a year. Fluctuations in the macroenvironment, such as temperature and nutrient concentrations driven by seasonal changes, are the major factors in determining successive microbial modules. Compared to particle-associated (PA) microbes, free-living (FL) microbes seemed to be more affected by macroenvironmental filtering. Modules related to nutrients were further divided into various modules according to different lifestyles. In addition, a large transient discharge of the Changjiang (Yangtze River) in summer also formed a distinct microbial module, which was related to the high ammonia concentration arising from phytoplankton degradation. Microbes belonging to the SAR11, SAR86, and SAR116 clades, Flavobacteriaceae, and MG IIa-L showed repeated interconnections in temperature-related modules, while the SAR202 clade, Marinimicrobia, DEV007 clade, and Arctic97B-4 and Sva0996 marine groups displayed repeated connections in nutrient-related modules. These 'skeleton'-forming microbes created species-engineered microenvironments, further fine-tuning microbial modular structures. Furthermore, they serve as keystone species for module stability by linking interdependent microbial partners within their own modules through universally beneficial metabolic activities. Therefore, they could reinforce the ecological resilience of microbial communities under abiotic and biotic perturbations in dynamic coastal waters. In conclusion, both macro- and micro-environmental filtering were important for determining the seasonal succession of microbial community structures.

DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data

Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.

Exploring the genes involved in biosynthesis of dihydroquercetin and dihydromyricetin in Ampelopsis grossedentata

Dihydroquercetin (DHQ), an extremely low content compound (less than 3%) in plants, is an important component of dietary supplements and used as functional food for its antioxidant activity. Moreover, as downstream metabolites of DHQ, an extremely high content of dihydromyricetin (DHM) is up to 38.5% in Ampelopsis grossedentata. However, the mechanisms involved in the biosynthesis and regulation from DHQ to DHM in A. grossedentata remain unclear. In this study, a comparative transcriptome analysis of A. grossedentata containing extreme amounts of DHM was performed on the Illumina HiSeq 2000 sequencing platform. A total of 167,415,597 high-quality clean reads were obtained and assembled into 100,584 unigenes having an N50 value of 1489. Among these contigs, 57,016 (56.68%) were successfully annotated in seven public protein databases. From the differentially expressed gene (DEG) analysis, 926 DEGs were identified between the B group (low DHM: 210.31 mg/g) and D group (high DHM: 359.12 mg/g) libraries, including 446 up-regulated genes and 480 down-regulated genes (B vs. D). Flavonoids (DHQ, DHM)-related DEGs of ten structural enzyme genes, three myeloblastosis transcription factors (MYB TFs), one basic helix-loop-helix (bHLH) TF, and one WD40 domain-containing protein were obtained. The enzyme genes comprised three PALs, two CLs, two CHSs, one F3'H, one F3'5'H (directly converts DHQ to DHM), and one ANS. The expression profiles of randomly selected genes were consistent with the RNA-seq results. Our findings thus provide comprehensive gene expression resources for revealing the molecular mechanism from DHQ to DHM in A. grossedentata. Importantly, this work will spur further genetic studies about A. grossedentata and may eventually lead to genetic improvements of the DHQ content in this plant.

Illuminating key microbial players and metabolic processes involved in the remineralization of particulate organic carbon in the ocean's twilight zone by metaproteomics

The twilight zone (from the base of the euphotic zone to the depth of 1000 m) is the major area of particulate organic carbon (POC) remineralization in the ocean, and heterotrophic microbes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity directly associated with POC remineralization in this chronically understudied realm. Here, we characterized the microbial community proteomes of POCs collected from the twilight zone of three contrasting sites in the Northwest Pacific Ocean using a metaproteomic approach. The particle-attached bacteria from Alteromonadales, Rhodobacterales, and Enterobacteriales were the primary POC remineralizers. Hydrolytic enzymes, including proteases and hydrolases, that degrade proteinaceous components and polysaccharides, the main constituents of POC, were abundant and taxonomically associated with these bacterial groups. Furthermore, identification of diverse species-specific transporters and metabolic enzymes implied niche specialization for nutrient acquisition among these bacterial groups. Temperature was the main environmental factor driven the active bacterial groups and metabolic processes, and Enterobacteriales replaced Alteromonadales as the predominant group under low temperature. This study provides insight into the key bacteria and metabolic processes involved in POC remineralization, and niche complementarity and species substitution among bacterial groups are critical for efficient POC remineralization in the twilight zone. IMPORTANCE The Ocean's twilight zone is a critical zone where more than 70% of the sinking particulate organic carbon (POC) are remineralized. Therefore, the twilight zone determines the size of biological carbon storage in the ocean, and regulates the global climate. Prokaryotes are major players that govern remineralization of POC in this region. However, knowledge of microbial community structure and metabolic activity is still lacking. This study unveiled microbial communities and metabolic activities of POCs collected from the twilight zone of three contrasting environments in the Northwest Pacific Ocean using a metaproteomic approach. Alteromonadales, Rhodobacterales and Enterobacteriales were the major remineralizers of POC. They excreted diverse species-specific hydrolytic enzymes to split POC to solubilized POC or dissolved organic carbon. Temperature played a crucial role in regulating the community composition and metabolism. Furthermore, niche complementarity or species substitution among bacterial groups guaranteed the efficient remineralization of POC in the twilight zone.

Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines

Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼10⁵ cells mL^–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼10⁸ cells mL^–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.

The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters

Dysoxic marine waters (DMW, < 1 μM oxygen) are currently expanding in volume in the oceans, which has biogeochemical, ecological and societal consequences on a global scale. In these environments, distinct bacteria drive an active sulfur cycle, which has only recently been recognized for open-ocean DMW. This review summarizes the current knowledge on these sulfur-cycling bacteria. Critical bottlenecks and questions for future research are specifically addressed. Sulfate-reducing bacteria (SRB) are core members of DMW. However, their roles are not entirely clear, and they remain largely uncultured. We found support for their remarkable diversity and taxonomic novelty by mining metagenome-assembled genomes from the Black Sea as model ecosystem. We highlight recent insights into the metabolism of key sulfur-oxidizing SUP05 and Sulfurimonas bacteria, and discuss the probable involvement of uncultivated SAR324 and BS-GSO2 bacteria in sulfur oxidation. Uncultivated Marinimicrobia bacteria with a presumed organoheterotrophic metabolism are abundant in DMW. Like SRB, they may use specific molybdoenzymes to conserve energy from the oxidation, reduction or disproportionation of sulfur cycle intermediates such as S0 and thiosulfate, produced from the oxidation of sulfide. We expect that tailored sampling methods and a renewed focus on cultivation will yield deeper insight into sulfur-cycling bacteria in DMW.

Microbial community development on model particles in the deep sulfidic waters of the Black Sea

Microorganisms attached to particles have been shown to be different from free-living microbes and to display diverse metabolic activities. However, little is known about the ecotypes associated with particles and their substrate preference in anoxic marine waters. Here, we investigate the microbial community colonizing particles in the anoxic and sulfide-rich waters of the Black Sea. We incubated beads coated with different substrates in situ at 1000 and 2000 m depth. After 6 h, the particle-attached microbes were dominated by Gamma- and Alpha-proteobacteria, and groups related to the phyla Latescibacteria, Bacteroidetes, Planctomycetes and Firmicutes, with substantial variation across the bead types, indicating that the attaching communities were selected by the substrate. Further laboratory incubations for 7 days suggested the presence of a community of highly specialized taxa. After incubation for 35 days, the microbial composition across all beads and depths was similar and primarily composed of putative sulfur cycling microbes. In addition to the major shared microbial groups, subdominant taxa on chitin and protein-coated beads were detected pointing to specialized microbial degraders. These results highlight the role of particles as sites for attachment and biofilm formation, while the composition of organic matter defined a secondary part of the microbial community.

Small sinking particles control anammox rates in the Peruvian oxygen minimum zone

Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas.

Up to 40% of the ocean’s fixed nitrogen is lost in oxygen minimum zones (OMZs) by anammox, but despite the importance of this process, nitrogen loss patterns in OMZs are difficult to predict. Here the authors show that ammonium release from small particles is a major control of anammox in the Peruvian OMZ.