Background Oysters in coastal environments are subject to fluctuating environmental conditions that may impact the ecosystem services they provide. Oyster-associated microbiomes are responsible for some of these services, particularly nutrient cycling in benthic habitats. The effects of climate change on host-associated microbiome composition are well-known, but functional changes and how they may impact host physiology and ecosystem functioning are poorly characterized. We investigated how environmental parameters affect oyster-associated microbial community structure and function along a trophic gradient in Narragansett Bay, Rhode Island, USA. Adult eastern oyster, Crassostrea virginica, gut and seawater samples were collected at 5 sites along this estuarine nutrient gradient in August 2017. Samples were analyzed by 16S rRNA gene sequencing to characterize bacterial community structures and metatranscriptomes were sequenced to determine oyster gut microbiome responses to local environments. Results There were significant differences in bacterial community structure between the eastern oyster gut and water samples, suggesting selection of certain taxa by the oyster host. Increasing salinity, pH, and dissolved oxygen, and decreasing nitrate, nitrite and phosphate concentrations were observed along the North to South gradient. Transcriptionally active bacterial taxa were similar for the different sites, but expression of oyster-associated microbial genes involved in nutrient (nitrogen and phosphorus) cycling varied throughout the Bay, reflecting the local nutrient regimes and prevailing environmental conditions. Conclusions The observed shifts in microbial community composition and function inform how estuarine conditions affect host-associated microbiomes and their ecosystem services. As the effects of estuarine acidification are expected to increase due to the combined effects of eutrophication, coastal pollution, and climate change, it is important to determine relationships between host health, microbial community structure, and environmental conditions in benthic communities.

The secondary metabolites geosmin and 2-methylisoborneol (MIB) are known to taint fish with an undesirable, earthy-muddy taste and odor. In an earlier study on a zero-discharge recirculating aquaculture system (RAS), it was found that geosmin and MIB were removed by microbial communities residing in sludge from the digestion basin of the system. In the present study, 16S amplicon sequencing was used to identify changes in relative abundances of bacterial taxa in geosmin and MIB-enriched crude sludge. The removal of geosmin and MIB by the sludge was accompanied by increased abundances of 12 operational taxonomic units (OTUs). The most prominent increase in abundances was recorded for OTUs affiliated with bacterial genera known to harbor denitrifiers. Among these were the Betaproteobacteria genera Thauera , which utilizes terpenes to fuel denitrification, and Comamonas , which was previously isolated from the digestion basin of the same system and is capable of growth on geosmin and MIB as sole carbon and energy sources. Thus far, denitrification has been associated with bacteria capable of utilizing terpenes other than geosmin and MIB. The significant increase in the abundance of denitrifying bacterial genera in sludge in which geosmin and MIB comprised only 0.06% of the total carbon content might indicate that such bacteria play a major role in the removal of these compounds in anoxic environments.

Larval oysters in hatcheries are susceptible to diseases caused by bacterial pathogens, including Vibrio spp. Previous studies have shown that daily addition of the probiotic Bacillus pumilus RI06-95 to water in rearing tanks increases larval survival when challenged with the pathogen Vibrio coralliilyticus. We propose that the presence of probiotics causes shifts in bacterial community structure in rearing tanks, leading to a net decrease in the relative abundance of potential pathogens. During three trials spanning the 2012-2015 hatchery seasons, larvae, tank biofilm, and rearing water samples were collected from control and probiotic-treated tanks in an oyster hatchery over a 12-day period after spawning. Samples were analyzed by 16S rRNA sequencing of the V4 or V6 regions followed by taxonomic classification, in order to determine bacterial community structures. There were significant differences in bacterial composition over time and between sample types, but no major effect of probiotics on the structure and diversity of bacterial communities (phylum level, Bray-Curtis k = 2, 95% confidence). Probiotic treatment, however, led to a higher relative percent abundance of Oceanospirillales and Bacillus spp., in water and oyster larvae. In the water, an increase in Vibrio spp. diversity in the absence of a net increase in relative read abundance suggests a likely decrease in the abundance of specific pathogenic Vibrio spp., and therefore lower chances of a disease outbreak. Co-occurrence network analysis also suggests that probiotic treatment had a systemic effect on targeted members of the bacterial community, leading to a net decrease in potentially pathogenic species.

Nitrous oxide (N2O) is a climate-relevant atmospheric trace gas. It is produced as an intermediate of the nitrogen cycle. The open and coastal oceans are major sources of atmospheric N2O. However, its oceanic distribution is still largely unknown. Here we present the first measurements of the water column distribution of N2O in the Gulf of Aqaba and the Red Sea. Samples for N2O depth profiles were collected at the time-series site Station A in the northern Gulf of Aqaba (June and September 2003, and February 2004) and at several stations in the central Red Sea (October 2014, January and August 2016). Additionally, we measured N2O concentrations in brine pool samples collected in the northern and central Red Sea (January 2005 and August 2016). In the Gulf of Aqaba, N2O surface concentrations ranged from 6 to 8 nmol L-1 (97-111% saturation) and were close to the equilibrium with the overlying atmosphere. A pronounced temporal variability of the N2O water column distribution was observed. We suggest that this variability is a reflection of the interplay between N2O production by nitrification and its consumption by N-2 fixation in the layers below 150 m during summer. N2O surface concentrations and saturations in the central Red Sea basin ranged from 2 to 9 nmol L-1 (43-155% saturation). A pronounced temporal variability with significant supersaturation in October 2014 and undersaturation in January and August 2016 was observed in the surface layer. In October 2014, N2O in the water column seemed to result from production via nitrification. Low N2O water column concentrations in January and August 2016 indicated a significant removal of N2O. We speculate that either in-situ consumption or remote loss processes of N2O such as denitrification in coastal regions were responsible for this difference. Strong meso- and submesoscale processes might have transported the coastal signals across the Red Sea. In addition, enhanced N2O concentrations of up to 39 nmol L-1 were found at the seawater-brine pool interfaces which point to an N2O production via nitrification and/or denitrification at low O-2 concentrations. Our results indicate that the Red Sea and the Gulf of Aqaba are unique natural laboratories for the study of N2O production and consumption pathways under extreme conditions in one of the warmest and most saline region of the global oceans.

SummaryMarine Synechococcus thrive over a range of light regimes in the ocean. We examined the proteomic, genomic and physiological responses of seven Synechococcus isolates to moderate irradiances (5–80 μE m−2 s−1), and show that Synechococcus spans a continuum of light responses ranging from low light optimized (LLO) to high light optimized (HLO). These light responses are linked to phylogeny and pigmentation. Marine sub‐cluster 5.1A isolates with higher phycouribilin: phycoerythrobilin ratios fell toward the LLO end of the continuum, while sub‐cluster 5.1B, 5.2 and estuarine Synechococcus with less phycouribilin fell toward the HLO end of the continuum. Global proteomes were highly responsive to light, with > 50% of abundant proteins varying more than twofold between the lowest and highest irradiance. All strains downregulated phycobilisome proteins with increasing irradiance. Regulation of proteins involved in photosynthetic electron transport, carbon fixation, oxidative stress protection (superoxide dismutases) and iron and nitrogen metabolism varied among strains, as did the number of high light inducible protein (Hlip) and DNA photolyase genes in their genomes. All but one LLO strain possessed the photoprotective orange carotenoid protein (OCP). The unique combinations of light responses in each strain gives rise to distinct photophysiological phenotypes that may affect Synechococcus distributions in the ocean.

ABSTRACT The leaves of Tamarix aphylla, a globally distributed, salt-secreting desert tree, are dotted with alkaline droplets of high salinity. To successfully inhabit these organic carbon-rich droplets, bacteria need to be adapted to multiple stress factors, including high salinity, high alkalinity, high UV radiation, and periodic desiccation. To identify genes that are important for survival in this harsh habitat, microbial community DNA was extracted from the leaf surfaces of 10 Tamarix aphylla trees along a 350-km longitudinal gradient. Shotgun metagenomic sequencing, contig assembly, and binning yielded 17 genome bins, six of which were >80% complete. These genomic bins, representing three phyla (Proteobacteria, Bacteroidetes, and Firmicutes), were closely related to halophilic and alkaliphilic taxa isolated from aquatic and soil environments. Comparison of these genomic bins to the genomes of their closest relatives revealed functional traits characteristic of bacterial populations inhabiting the Tamarix phyllosphere, independent of their taxonomic affiliation. These functions, most notably light-sensing genes, are postulated to represent important adaptations toward colonization of this habitat. IMPORTANCE Plant leaves are an extensive and diverse microbial habitat, forming the main interface between solar energy and the terrestrial biosphere. There are hundreds of thousands of plant species in the world, exhibiting a wide range of morphologies, leaf surface chemistries, and ecological ranges. In order to understand the core adaptations of microorganisms to this habitat, it is important to diversify the type of leaves that are studied. This study provides an analysis of the genomic content of the most abundant bacterial inhabitants of the globally distributed, salt-secreting desert tree Tamarix aphylla. Draft genomes of these bacteria were assembled, using the culture-independent technique of assembly and binning of metagenomic data. Analysis of the genomes reveals traits that are important for survival in this habitat, most notably, light-sensing and light utilization genes.

The vast majority of the phytoplankton communities in surface mixed layer of the oligotrophic ocean are numerically dominated by one of two ecotypes of Prochlorococcus, eMIT9312 or eMED4. In this study, we surveyed large latitudinal transects in the Atlantic and Pacific Ocean to determine if these ecotypes discretely partition the surface mixed layer niche, or if populations exist as a continuum along key environmental gradients, particularly temperature. Transitions of dominance occurred at approximately 19-21°C, with the eMED4 ecotype dominating the colder, and eMIT9312 ecotype dominating the warmer regions. Within these zones of regional dominance, however, the minority ecotype was not competed to extinction. Rather, a robust log-linear relationship between ecotype ratio and temperature characterized this stabilized coexistence: for every 2.5°C increase in temperature, the eMIT9312:eMED4 ratio increased by an order of magnitude. This relationship was observed in both quantitative polymerase chain reaction and in pyrosequencing assays. Water column stratification also contributed to the ecotype ratio along the basin-scale transects, but to a lesser extent. Finally, instances where the ratio of the eMED4 and eMIT9312 abundances did not correlate well with temperature were identified. Such occurrences are likely due to changes in water temperatures outpacing changes in community structure.

Oligotrophic Lake Superior and mesotrophic Lake Erie are trophic end members of the hydrologically connected Laurentian Great Lakes system, and as such exhibit different profiles of dissolved nitrogen species. Nitrification in Lake Superior has led to increasing nitrate concentrations over the past century, as opposed to Erie, where nitrate inventories have declined due to denitrification. In this study, we examined the abundance and diversity of nitrifying microbes involved in the oxidation of ammonia to nitrite, and nitrite to nitrate. By in situ hybridization methods, we enumerated the major planktonic ammonia oxidizing bacteria (AOB) and archaea (AOA) during a July 2011 cruise from Lake Superior to Lake Erie. In Lake Superior, AOA dominated compared to AOB, typically exceeding 5×103mL−1, whereas in Erie, AOB were more abundant than AOA. These data parallel prior work on Lake Superior and Lake Erie sediments, in which AOA are far more abundant in Superior, but AOB dominate in Erie. The lakes were sampled during stratification, and AOA and AOB were largely restricted to the hypolimnion, consistent with the observation that ammonia oxidizers are photoinhibited in surface waters. In Lakes Superior and Erie, we also detected nitrite oxidizing bacteria (NOB) in a pattern paralleling AOA/AOB abundance. Phylogenetic analysis of archaeal 16S rRNA revealed that the planktonic archaea of Lake Superior are members of the ammonia oxidizing Group I.1a Thaumarchaeota most closely related to Nitrosoarchaeum limnia. These AOA are distinct from the Group I.1a AOA in Lake Superior sediments. The major AOB of Lake Erie form a subcluster within the genus Nitrosospira.

Abstract Polynyas, or recurring areas of seasonally open water surrounded by sea ice, are foci for energy and material transfer between the atmosphere and the polar ocean. They are also climate sensitive, with both sea ice extent and glacial melt influencing their productivity. The Amundsen Sea Polynya (ASP) is the greenest polynya in the Southern Ocean, with summertime chlorophyll a concentrations exceeding 20 µg L−1. During the Amundsen Sea Polynya International Research Expedition (ASPIRE) in austral summer 2010–11, we aimed to determine the fate of this high algal productivity. We collected water column profiles for total dissolved inorganic carbon (DIC) and nutrients, particulate and dissolved organic matter, chlorophyll a, mesozooplankton, and microbial biomass to make a carbon budget for this ecosystem. We also measured primary and secondary production, community respiration rates, vertical particle flux and fecal pellet production and grazing. With observations arranged along a gradient of increasing integrated dissolved inorganic nitrogen drawdown (ΔDIN; 0.027–0.74 mol N m−2), changes in DIC in the upper water column (ranging from 0.2 to 4.7 mol C m−2) and gas exchange (0–1.7 mol C m−2) were combined to estimate early season net community production (sNCP; 0.2–5.9 mol C m−2) and then compared to organic matter inventories to estimate export. From a phytoplankton bloom dominated by Phaeocystis antarctica, a high fraction (up to ∼60%) of sNCP was exported to sub-euphotic depths. Microbial respiration remineralized much of this export in the mid waters. Comparisons to short-term (2–3 days) drifting traps and a year-long moored sediment trap capturing the downward flux confirmed that a relatively high fraction (3–6%) of the export from ∼100 m made it through the mid waters to depth. We discuss the climate-sensitive nature of these carbon fluxes, in light of the changing sea ice cover and melting ice sheets in the region.

The cyanobacterium Synechococcus is a ubiquitous, important phytoplankter across the world's oceans. A high degree of genetic diversity exists within the marine group, which likely contributes to its global success. Over 20 clades with different distribution patterns have been identified. However, we do not fully understand the environmental factors that control clade distributions. These factors are likely to change seasonally, especially in dynamic coastal systems. To investigate how coastal Synechococcus assemblages change temporally, we assessed the diversity of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) over three annual cycles with culture-dependent and independent approaches. We further investigated the abundance of both phycoerythrin (PE)-containing and phycocyanin (PC)-only Synechococcus with a flow cytometric setup that distinguishes PC-only Synechococcus from picoeukaryotes. We found that the Synechococcus assemblage at MVCO is diverse (13 different clades identified), but dominated by clade I representatives. Many clades were only isolated during late summer and fall, suggesting more favorable conditions for isolation at this time. PC-only strains from four different clades were isolated, but these cells were only detected by flow cytometry in a few samples over the time series, suggesting they are rare at this site. Within clade I, we identified four distinct subclades. The relative abundances of each subclade varied over the seasonal cycle, and the high Synechococcus cell concentration at MVCO may be maintained by the diversity found within this clade. This study highlights the need to understand how temporal aspects of the environment affect Synechococcus community structure and cell abundance.

Abstract Heterotrophic bacteria play a key role in marine carbon cycling, and understanding their activities in polar systems is important for considering climate change impacts there. One goal of the ASPIRE project was to examine the relationship between the phytoplankton bloom and bacterial heterotrophy in the Amundsen Sea Polynya (ASP). Bacterial abundance, production (BP), respiration, growth efficiency, and extracellular enzyme activity (EEA) were compared to nutrient and organic matter inventories, chlorophyll a (Chl a), viral and microzooplankton abundance, and net primary production (NPP). Bacterial production and respiration clearly responded (0.04–4.0 and 10–53 µg C L−1 d−1, respectively) to the buildup of a massive Phaeocystis antarctica bloom (Chl a: 0.2–22 µg L−1), with highest rates observed in the central polynya where Chl a and particulate organic carbon (POC) were greatest. The highest BP rates exceeded those reported for the Ross Sea or any other Antarctic coastal system, yet the BP:NPP ratio (2.1–9.4%) was relatively low. Bacterial respiration was also high, and growth efficiency (2–27%; median = 10%) was similar to oligotrophic systems. Thus, the integrated bacterial carbon demand (0.8–2.8 g C m−2 d−1) was a high fraction (25–128%; median = 43%) of NPP during bloom development. During peak bloom, activity was particle-associated: BP and EEA correlated well with POC, and size fractionation experiments showed that the larger size fraction (> 3 µm) accounted for a majority (∼ 75%) of the BP. The community was psychrophilic, with a 5x reduction in BP when warmed to 20°C. In deeper waters, respiration remained relatively high, likely fueled by the significant downward particle flux in the region. A highly active, particle-associated, heterotrophic microbial community clearly responded to the extraordinary phytoplankton bloom in the ASP, likely limiting biological pump efficiency during the early season.

Southern Ocean primary productivity plays a key role in global ocean biogeochemistry and climate. At the Southern Ocean sea ice edge in coastal McMurdo Sound, we observed simultaneous cobalamin and iron limitation of surface water phytoplankton communities in late Austral summer. Cobalamin is produced only by bacteria and archaea, suggesting phytoplankton-bacterial interactions must play a role in this limitation. To characterize these interactions and investigate the molecular basis of multiple nutrient limitation, we examined transitions in global gene expression over short time scales, induced by shifts in micronutrient availability. Diatoms, the dominant primary producers, exhibited transcriptional patterns indicative of co-occurring iron and cobalamin deprivation. The major contributor to cobalamin biosynthesis gene expression was a gammaproteobacterial population, Oceanospirillaceae ASP10-02a. This group also contributed significantly to metagenomic cobalamin biosynthesis gene abundance throughout Southern Ocean surface waters. Oceanospirillaceae ASP10-02a displayed elevated expression of organic matter acquisition and cell surface attachment-related genes, consistent with a mutualistic relationship in which they are dependent on phytoplankton growth to fuel cobalamin production. Separate bacterial groups, including Methylophaga, appeared to rely on phytoplankton for carbon and energy sources, but displayed gene expression patterns consistent with iron and cobalamin deprivation. This suggests they also compete with phytoplankton and are important cobalamin consumers. Expression patterns of siderophore- related genes offer evidence for bacterial influences on iron availability as well. The nature and degree of this episodic colimitation appear to be mediated by a series of phytoplankton-bacterial interactions in both positive and negative feedback loops.

Abstract We report results from a yearlong, moored sediment trap in the Amundsen Sea Polynya (ASP), the first such time series in this remote and productive ecosystem. Results are compared to a long-term (1992–2013) time series from the western Antarctic Peninsula (WAP). The ASP trap was deployed from December 2010 to December 2011 at 350 m depth. We observed two brief, but high flux events, peaking at 8 and 5 mmol C m−2 d−1 in January and December 2011, respectively, with a total annual capture of 315 mmol C m−2. Both peak fluxes and annual capture exceeded the comparable WAP observations. Like the overlying phytoplankton bloom observed during the cruise in the ASP (December 2010 to January 2011), particle flux was dominated by Phaeocystis antarctica, which produced phytodetrital aggregates. Particles at the start of the bloom were highly depleted in 13C, indicating their origin in the cold, CO2-rich winter waters exposed by retreating sea ice. As the bloom progressed, microscope visualization and stable isotopic composition provided evidence for an increasing contribution by zooplankton fecal material. Incubation experiments and zooplankton observations suggested that fecal pellet production likely contributed 10–40% of the total flux during the first flux event, and could be very high during episodic krill swarms. Independent estimates of export from the surface (100 m) were about 5–10 times that captured in the trap at 350 m. Estimated bacterial respiration was sufficient to account for much of the decline in the flux between 50 and 350 m, whereas zooplankton respiration was much lower. The ASP system appears to export only a small fraction of its production deeper than 350 m within the polynya region. The export efficiency was comparable to other polar regions where phytoplankton blooms were not dominated by diatoms.

Marine Synechococcus are some of the most diverse and ubiquitous phytoplankton, and iron (Fe) is an essential micronutrient that limits productivity in many parts of the ocean. To investigate how coastal and oceanic Atlantic Synechococcus strains acclimate to Fe availability, we compared the growth, photophysiology, and quantitative proteomics of two Synechococcus strains from different Fe regimes. Synechococcus strain WH8102, from a region in the southern Sargasso Sea that receives substantial dust deposition, showed impaired growth and photophysiology as Fe declined, yet used few acclimation responses. Coastal WH8020, from the dynamic, seasonally variable New England shelf, displayed a multitiered, hierarchical cascade of acclimation responses with different Fe thresholds. The multitiered response included changes in Fe acquisition, storage, and photosynthetic proteins, substitution of flavodoxin for ferredoxin, and modified photophysiology, all while maintaining remarkably stable growth rates over a range of Fe concentrations. Modulation of two distinct ferric uptake regulator (Fur) proteins that coincided with the multitiered proteome response was found, implying the coastal strain has different regulatory threshold responses to low Fe availability. Low nitrogen (N) and phosphorus (P) availability in the open ocean may favor the loss of Fe response genes when Fe availability is consistent over time, whereas these genes are retained in dynamic environments where Fe availability fluctuates and N and P are more abundant.

Atmospheric deposition is a major source of trace metals in marine surface waters and supplies vital micronutrients to phytoplankton, yet measured aerosol trace metal solubility values are operationally defined, and there are relatively few multi-element studies on aerosol-metal solubility in seawater. Here we measure the solubility of aluminum (Al), cadmium (Cd), cobalt (Co), copper (Cu), iron (Fe), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) from natural aerosol samples in seawater over a 7 days period to (1) evaluate the role of extraction time in trace metal dissolution behavior and (2) explore how the individual dissolution patterns could influence biota. Dissolution behavior occurs over a continuum ranging from rapid dissolution, in which the majority of soluble metal dissolved immediately upon seawater exposure (Cd and Co in our samples), to gradual dissolution, where metals dissolved slowly over time (Zn, Mn, Cu, and Al in our samples). Additionally, dissolution affected by interactions with particles was observed in which a decline in soluble metal concentration over time occurred (Fe and Pb in our samples). Natural variability in aerosol chemistry between samples can cause metals to display different dissolution kinetics in different samples, and this was particularly evident for Ni, for which samples showed a broad range of dissolution rates. The elemental molar ratio of metals in the bulk aerosols was 23,189Fe: 22,651Al: 445Mn: 348Zn: 71Cu: 48Ni: 23Pb: 9Co: 1Cd, whereas the seawater soluble molar ratio after 7 days of leaching was 11Fe: 620Al: 205Mn: 240Zn: 20Cu: 14Ni: 9Pb: 2Co: 1Cd. The different kinetics and ratios of aerosol metal dissolution have implications for phytoplankton nutrition, and highlight the need for unified extraction protocols that simulate aerosol metal dissolution in the surface ocean.

Proteomics has great potential for studies of marine microbial biogeochemistry, yet high microbial diversity in many locales presents us with unique challenges. We addressed this challenge with a targeted metaproteomics workflow for NtcA and P‐II, two nitrogen regulatory proteins, and demonstrated its application for cyanobacterial taxa within microbial samples from the Central Pacific Ocean. Using METATRYP, an open‐source Python toolkit, we examined the number of shared (redundant) tryptic peptides in representative marine microbes, with the number of tryptic peptides shared between different species typically being 1% or less. The related cyanobacteria Prochlorococcus and Synechococcus shared an average of 4.8 ± 1.9% of their tryptic peptides, while shared intraspecies peptides were higher, 13 ± 15% shared peptides between 12 Prochlorococcus genomes. An NtcA peptide was found to target multiple cyanobacteria species, whereas a P‐II peptide showed specificity to the high‐light Prochlorococcus ecotype. Distributions of NtcA and P‐II in the Central Pacific Ocean were similar except at the Equator likely due to differential nitrogen stress responses between Prochlorococcus and Synechococcus. The number of unique tryptic peptides coded for within three combined oceanic microbial metagenomes was estimated to be ∼4 × 107, 1000‐fold larger than an individual microbial proteome and 27‐fold larger than the human proteome, yet still 20 orders of magnitude lower than the peptide diversity possible in all protein space, implying that peptide mapping algorithms should be able to withstand the added level of complexity in metaproteomic samples.

Phytoplankton blooms are an ecologically important yet not entirely understood phenomenon. This is certainly the case for the massive Phaeocystis blooms in climate-sensitive Antarctic polynyas. They interact with the atmosphere through the exchange of carbon dioxide and dimethylsulfide. They also sustain a distinct bacterial community that might play a role in bloom duration and intensity. Here we deeply sequenced a metagenome from an Amundsen Sea polynya bloom event and determined the genomic content of bacterial populations surrounding Phaeocystis. A pico-eukaryote genome (19.6 Mb) was also recovered. The identification of functional complementarities between P. antarctica and bacterial taxa organized in close association with Phaeocystis colonies makes a contribution to our understanding of bloom functioning in the Southern Ocean.

Cobalt-rich ferromanganese is an important seafloor mineral and is abundantly present in the seamount crusts.Such crusts form potential hotspots for biogeochemical activity and microbial diversity, yet our understanding of their microbial communities is lacking. In this study, a cultivation-independent approach was used to recover genomic information and derive ecological functions of the microbes in a sediment sample collected from the cobalt-rich ferromanganese crust of a seamount region in the central Pacific. A total of 78 distinct clones were obtained by fosmid library screening with a 16 SrRNA based PCR method. Proteobacteria and MGI Thaumarchaeota dominated the bacterial and archaeal 16 SrRNA gene sequence results in the microbial community. Nine fosmid clones were sequenced and annotated. Numerous genes encoding proteins involved in metabolic functions and heavy metal resistance were identified, suggesting alternative metabolic pathways and stress responses that are essential for microbial survival in the cobalt-rich ferromanganese crust. In addition, genes that participate in the synthesis of organic acids and exoploymers were discovered. Reconstruction of the metabolic pathways revealed that the nitrogen cycle is an important biogeochemical process in the cobalt-rich ferromanganese crust. In addition, horizontal gene transfer（HGT） events have been observed, and most of them came from bacteria, with some occurring in archaea and plants. Clone W4-93 a, belonging to MGI Thaumarchaeota, contained a region of gene synteny. Comparative analyses suggested that a high frequency of HGT events as well as genomic divergence play important roles in the microbial adaption to the deep-sea environment.

Marine primary productivity is strongly influenced by the scarcity of required nutrients, yet our understanding of these nutrient limitations is informed by experimental observations with sparse geographical coverage and methodological limitations. We developed a quantitative proteomic method to directly assess nutrient stress in high-light ecotypes of the abundant cyanobacterium Prochlorococcus across a meridional transect in the central Pacific Ocean. Multiple peptide biomarkers detected widespread and overlapping regions of nutritional stress for nitrogen and phosphorus in the North Pacific Subtropical Gyre and iron in the equatorial Pacific. Quantitative protein analyses demonstrated simultaneous stress for these nutrients at biome interfaces. This application of proteomic biomarkers to diagnose ocean metabolism demonstrated Prochlorococcus actively and simultaneously deploying multiple biochemical strategies for low-nutrient conditions in the oceans.