A compendium of bacterial and archaeal single-cell amplified genomes from oxygen deficient marine waters

Oxygen-deficient marine waters referred to as oxygen minimum zones (OMZs) or anoxic marine zones (AMZs) are common oceanographic features. They host both cosmopolitan and endemic microorganisms adapted to low oxygen conditions. Microbial metabolic interactions within OMZs and AMZs drive coupled biogeochemical cycles resulting in nitrogen loss and climate active trace gas production and consumption. Global warming is causing oxygen-deficient waters to expand and intensify. Therefore, studies focused on microbial communities inhabiting oxygen-deficient regions are necessary to both monitor and model the impacts of climate change on marine ecosystem functions and services. Here we present a compendium of 5,129 single-cell amplified genomes (SAGs) from marine environments encompassing representative OMZ and AMZ geochemical profiles. Of these, 3,570 SAGs have been sequenced to different levels of completion, providing a strain-resolved perspective on the genomic content and potential metabolic interactions within OMZ and AMZ microbiomes. Hierarchical clustering confirmed that samples from similar oxygen concentrations and geographic regions also had analogous taxonomic compositions, providing a coherent framework for comparative community analysis.

Plankton respiration in the Atacama Trench region: Implications for particulate organic carbon flux into the hadal realm

Respiration is a key process in the cycling of particulate matter and, therefore, an important control mechanism of carbon export to the ocean's interior. Most of the fixed carbon is lost in the upper ocean, and only a minor amount of organic material sustains life in the deep-sea. Conditions are particularly extreme in hadal trenches, and yet they host active biological communities. The source of organic carbon that supports them and the contribution of these communities to the ocean carbon cycle, however, remain uncertain. Here we report on size-fractionated depth profiles of plankton respiration assessed from the activity of the electron transport system in the Atacama Trench region, and provide estimates of the minimum carbon flux (FC) needed to sustain the respiratory requirements from the ocean surface to hadal waters of the trench and shallower nearby sites. Plankton < 100 μm contributed about 90% to total community respiration, whose magnitude was highly correlated with surface productivity. Remineralization rates were highest in the euphotic zone and declined sharply within intermediate oxygen-depleted waters, remaining fairly constant toward the bottom. Integrated respiration in ultra-deep waters (> 1000 m) was comparable to that found in upper layers, with 1.3 ± 0.4 mmol C m^-2 d^-1 being respired in the hadopelagic. The comparison between our FC models and estimates of sinking particle flux revealed a carbon imbalance through the mesopelagic that was paradoxically reduced at greater depths. We argue that large fast-sinking particles originated in the overlying surface ocean may effectively sustain the respiratory carbon demands in this ultra-deep marine environment.

Eurythenes atacamensis sp. nov. (Crustacea: Amphipoda) exhibits ontogenetic vertical stratification across abyssal and hadal depths in the Atacama Trench, eastern South Pacific Ocean

Eurythenes S.I. Smith in Scudder, 1882 (Crustacea: Amphipoda) are prevalent scavengers of the benthopelagic community from bathyal to hadal depths. While a well-studied genus, molecular systematic studies have uncovered cryptic speciation and multiple undescribed lineages. Here, we apply an integrative taxonomic approach and describe the tenth species, Eurythenes atacamensis sp. nov., based on specimens from the 2018 Atacamex and RV Sonne SO261 Expeditions to the southern sector of the Peru-Chile Trench, the Atacama Trench (24-⁠21°S). Eurythenes atacamensis sp. nov. is a large species, max. observed length 83.2 mm, possesses diagnostic features, including a short gnathopod 1 palm and a chelate gnathopod 2 palm, and a distinct genetic lineage based on a 16S rRNA and COI phylogeny. This species is a dominant bait-attending fauna with an extensive bathymetric range, spanning from 4974 to 8081 m. The RV Sonne SO261 specimens were recovered along a 10-station transect from abyssal to hadal depths and further examined for demographic and bathymetric-related patterns. Ontogenetic vertical stratification was evident across the trench axis, with only juveniles present at abyssal depths (4974-6025 m). Total length-depth analysis revealed that the size of females was unrelated to depth, whereas juveniles followed a sigmoidal relationship with a step-up in size at depths >7200 m. Thus, these bathymetric trends suggest that juveniles and females employ differing ecological strategies in subduction trench environments. This study highlights that even dominant and ecologically important species are still being discovered within the abyssal and hadal environments. Continued systematic expeditions will lead to an improved understanding of the eco-evolutionary drivers of speciation in the world's largest ecosystem.

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters

Viruses play an important role in the ecology and biogeochemistry of marine ecosystems. Beyond mortality and gene transfer, viruses can reprogram microbial metabolism during infection by expressing auxiliary metabolic genes (AMGs) involved in photosynthesis, central carbon metabolism, and nutrient cycling. While previous studies have focused on AMG diversity in the sunlit and dark ocean, less is known about the role of viruses in shaping metabolic networks along redox gradients associated with marine oxygen minimum zones (OMZs). Here, we analyzed relatively quantitative viral metagenomic datasets that profiled the oxygen gradient across Eastern Tropical South Pacific (ETSP) OMZ waters, assessing whether OMZ viruses might impact nitrogen (N) cycling via AMGs. Identified viral genomes encoded six N-cycle AMGs associated with denitrification, nitrification, assimilatory nitrate reduction, and nitrite transport. The majority of these AMGs (80%) were identified in T4-like Myoviridae phages, predicted to infect Cyanobacteria and Proteobacteria, or in unclassified archaeal viruses predicted to infect Thaumarchaeota. Four AMGs were exclusive to anoxic waters and had distributions that paralleled homologous microbial genes. Together, these findings suggest viruses modulate N-cycling processes within the ETSP OMZ and may contribute to nitrogen loss throughout the global oceans thus providing a baseline for their inclusion in the ecosystem and geochemical models.

Genome-resolved viral ecology in a marine oxygen minimum zone

Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O₂ ) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10-fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral-encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico-chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.

Autotrophic carbon fixation pathways along the redox gradient in oxygen-depleted oceanic waters

Anoxic marine zones (AMZs), also known as 'oxygen-deficient zones', contribute to the loss of fixed nitrogen from the ocean by anaerobic microbial processes. While these microbial processes associated with the nitrogen cycle have been extensively studied, those linked to the carbon cycle in AMZs have received much less attention, particularly the autotrophic carbon fixation - a crucial component of the carbon cycle. Using metagenomic and metatranscriptomic data from major AMZs, we report an explicit partitioning of the marker genes associated with different autotrophic carbon fixation pathways along the redox gradient (from oxic to anoxic conditions) present in the water column of AMZs. Sequences related to the Calvin-Benson-Bassham cycle were found along the entire gradient, while those related to the reductive Acetyl-CoA pathway were restricted to suboxic and anoxic waters. Sequences putatively associated with the 3-hydroxypropionate/4-hydroxybutyrate cycle dominated in the upper and lower oxyclines. Genes related to the reductive tricarboxylic acid cycle were represented from dysoxic to anoxic waters. The taxonomic affiliation of the sequences is consistent with the presence of microorganisms involved in crucial steps of biogeochemical cycles in AMZs, such as the gamma-proteobacteria sulfur oxidisers, the anammox bacteria Candidatus Scalindua and the thaumarcheota ammonia oxidisers of the Marine Group I.

Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific

Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorly known Southeast Pacific region, with samples spanning an ocean gradient from coastal upwelling to the oligotrophic South Pacific Subtropical Gyre. We assessed variation in fragments of the mitochondrial (mt) genes cytochrome c oxidase subunit I (COI) and Cytochrome b as well as in the nuclear internal transcribed spacer (ITS) region and 28 S rRNA. Phylogenetic analyses revealed the presence of 8 divergent lineages occurring across the gradient with genetic distances in the range of 0.036 and 0.44 (mt genes), and GMYC species delimitation methods support their inference as distinct (undescribed) species. Genetic lineages occurring across the zonal gradient showed strong genetic structuring, with the presence of at least two new lineages within the coastal upwelling zone, revealing an unexpectedly high level of endemism within the Humboldt Current System. Multivariate analyses found strong correlation between genetic variation and surface chlorophyll-a and salinity, suggesting an important role for hydrographic gradients in maintaining genetic diversity. However, the presence of cryptic lineages within the upwelling zone cannot be easily accounted for by environmental heterogeneity and poses challenging questions for understanding the speciation process for oceanic zooplankton.

Distinctive Archaeal Composition of an Artisanal Crystallizer Pond and Functional Insights Into Salt-Saturated Hypersaline Environment Adaptation

Hypersaline environments represent some of the most challenging settings for life on Earth. Extremely halophilic microorganisms have been selected to colonize and thrive in these extreme environments by virtue of a broad spectrum of adaptations to counter high salinity and osmotic stress. Although there is substantial data on microbial taxonomic diversity in these challenging ecosystems and their primary osmoadaptation mechanisms, less is known about how hypersaline environments shape the genomes of microbial inhabitants at the functional level. In this study, we analyzed the microbial communities in five ponds along the discontinuous salinity gradient from brackish to salt-saturated environments and sequenced the metagenome of the salt (halite) precipitation pond in the artisanal Cáhuil Solar Saltern system. We combined field measurements with spectrophotometric pigment analysis and flow cytometry to characterize the microbial ecology of the pond ecosystems, including primary producers and applied metagenomic sequencing for analysis of archaeal and bacterial taxonomic diversity of the salt crystallizer harvest pond. Comparative metagenomic analysis of the Cáhuil salt crystallizer pond against microbial communities from other salt-saturated aquatic environments revealed a dominance of the archaeal genus Halorubrum and showed an unexpectedly low abundance of Haloquadratum in the Cáhuil system. Functional comparison of 26 hypersaline microbial metagenomes revealed a high proportion of sequences associated with nucleotide excision repair, helicases, replication and restriction-methylation systems in all of them. Moreover, we found distinctive functional signatures between the microbial communities from salt-saturated (>30% [w/v] total salinity) compared to sub-saturated hypersaline environments mainly due to a higher representation of sequences related to replication, recombination and DNA repair in the former. The current study expands our understanding of the diversity and distribution of halophilic microbial populations inhabiting salt-saturated habitats and the functional attributes that sustain them.

Single cell genomic and transcriptomic evidence for the use of alternative nitrogen substrates by anammox bacteria

Anaerobic ammonium oxidation (anammox) contributes substantially to ocean nitrogen loss, particularly in anoxic marine zones (AMZs). Ammonium is scarce in AMZs, raising the hypothesis that organic nitrogen compounds may be ammonium sources for anammox. Biochemical measurements suggest that the organic compounds urea and cyanate can support anammox in AMZs. However, it is unclear if anammox bacteria degrade these compounds to ammonium themselves, or rely on other organisms for this process. Genes for urea degradation have not been found in anammox bacteria, and genomic evidence for cyanate use for anammox is limited to a cyanase gene recovered from the sediment bacterium Candidatus Scalindua profunda. Here, analysis of Ca. Scalindua single amplified genomes from the Eastern Tropical North Pacific AMZ revealed genes for urea degradation and transport, as well as for cyanate degradation. Urease and cyanase genes were transcribed, along with anammox genes, in the AMZ core where anammox rates peaked. Homologs of these genes were also detected in meta-omic datasets from major AMZs in the Eastern Tropical South Pacific and Arabian Sea. These results suggest that anammox bacteria from different ocean regions can directly access organic nitrogen substrates. Future studies should assess if and under what environmental conditions these substrates contribute to the ammonium budget for anammox.

Hydrography shapes community composition and diversity of amoA-containing Thaumarchaeota in the coastal waters off central Chile

Thaumarchaea are often abundant in low oxygen marine environments, and recent kinetic studies indicate a capacity for aerobic ammonia oxidation at vanishingly low oxygen levels (nM). However, molecular diversity surveys targeting this group to high sequencing coverage are limited, and how these populations are coupled to changes in dissolved oxygen remains unknown. In this study, the ammonia monooxygenase subunit A (amoA) gene was sequenced from samples collected in the Chilean coast (36.5 °S), a system prone to recurrent seasonal hypoxia and anoxia, at several depths over one year, to read depths that saturated coverage statistics. Temperature, salinity and depth displayed a stronger impact on community composition than chemical and biological variables, such as dissolved oxygen. The Nitrosopumilus water-column A clade (WCA) displayed high proportional representation in all samples (42%-100% of all amoA OTUs). The two dominant WCA OTUs displayed differences in their distributions that were inversely correlated with one another, providing the first evidence for intra-subgroup specific differences in the distributions among closely related WCA Thaumarcheota. Nitrosopumilus water-column B (WCB) representatives displayed increased proportional abundances (42%) at deeper depths during the spring and summer, were highly coupled to decreased dissolved oxygen conditions and were non-detectable during the austral winter. The depth of sequencing also enabled observation of lower abundance taxa that are typically not observed in marine environments, such as members of the genus Nitrosotalea amid austral winter surface waters. This study highlights a strong coupling between Thaumarchaeal community diversity and hydrographic variables, is the first to highlight intra-subclade depth specific shifts in community diversity amongst members of the WCA clade, and links the WCB clade to upwelling conditions associated with seasonal oxygen depletion.

Cryptic oxygen cycling in anoxic marine zones

Oxygen availability drives changes in microbial diversity and biogeochemical cycling between the aerobic surface layer and the anaerobic core in nitrite-rich anoxic marine zones (AMZs), which constitute huge oxygen-depleted regions in the tropical oceans. The current paradigm is that primary production and nitrification within the oxic surface layer fuel anaerobic processes in the anoxic core of AMZs, where 30-50% of global marine nitrogen loss takes place. Here we demonstrate that oxygenic photosynthesis in the secondary chlorophyll maximum (SCM) releases significant amounts of O2 to the otherwise anoxic environment. The SCM, commonly found within AMZs, was dominated by the picocyanobacteria Prochlorococcus spp. Free O2 levels in this layer were, however, undetectable by conventional techniques, reflecting a tight coupling between O2 production and consumption by aerobic processes under apparent anoxic conditions. Transcriptomic analysis of the microbial community in the seemingly anoxic SCM revealed the enhanced expression of genes for aerobic processes, such as nitrite oxidation. The rates of gross O2 production and carbon fixation in the SCM were found to be similar to those reported for nitrite oxidation, as well as for anaerobic dissimilatory nitrate reduction and sulfate reduction, suggesting a significant effect of local oxygenic photosynthesis on Pacific AMZ biogeochemical cycling.

Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone

Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus.

The first report of a microdiverse anammox bacteria community in waters of Colombian Pacific, a transition area between prominent oxygen minimum zones of the eastern tropical Pacific

Anaerobic ammonium oxidizers contribute to the removal of fixed nitrogen in oxygen-deficient marine ecosystems such as oxygen minimum zones (OMZ). Here we surveyed for the first time the occurrence and diversity of anammox bacteria in the Colombian Pacific, a transition area between the prominent South and North Pacific OMZs. Anammox bacteria were detected in the coastal and oceanic areas of the Colombian Pacific in low oxygen (< 22 μM), high nitrate (25–35 μM) and low nitrite (< 0.07 μM), and ammonium (< 1 μM) waters. In these waters, anammox bacteria were rich [∼ 7 operational taxonomic units (OTUs), 98% cut-off) and microdiverse (Shannon index H′ < 1.24), in comparison with the observed at the prominent OMZ of the Eastern Tropical South Pacific, Arabian Sea and Black Sea. Anammox bacteria-like sequences from the Colombian Pacific were grouped together with sequences retrieved from the distinct OMZ's marine subclusters (Peru, Northern Chile and Arabian Sea) within Candidatus ‘Scalindua spp’. Moreover, some anammox bacteria OTUs shared a low similarity with environmental phylotypes (86–94%). Our results indicated that a microdiverse anammox community inhabits the Colombian Pacific, generating new questions about the ecological and biogeochemical differences influencing its community structure.

Metagenome sequencing of the microbial community of a solar saltern crystallizer pond at cáhuil lagoon, chile

Cáhuil Lagoon in central Chile harbors distinct microbial communities in various solar salterns that are arranged as interconnected ponds with increasing salt concentrations. Here, we report the metagenome of the 3.0- to 0.2-µm fraction of the microbial community present in a crystallizer pond with 34% salinity.

Oxygen at nanomolar levels reversibly suppresses process rates and gene expression in anammox and denitrification in the oxygen minimum zone off northern Chile

A major percentage (20 to 40%) of global marine fixed-nitrogen loss occurs in oxygen minimum zones (OMZs). Concentrations of O2 and the sensitivity of the anaerobic N2-producing processes of anammox and denitrification determine where this loss occurs. We studied experimentally how O2 at nanomolar levels affects anammox and denitrification rates and the transcription of nitrogen cycle genes in the anoxic OMZ off Chile. Rates of anammox and denitrification were reversibly suppressed, most likely at the enzyme level. Fifty percent inhibition of N2 and N2O production by denitrification was achieved at 205 and 297 nM O2, respectively, whereas anammox was 50% inhibited at 886 nM O2. Coupled metatranscriptomic analysis revealed that transcripts encoding nitrous oxide reductase (nosZ), nitrite reductase (nirS), and nitric oxide reductase (norB) decreased in relative abundance above 200 nM O2. This O2 concentration did not suppress the transcription of other dissimilatory nitrogen cycle genes, including nitrate reductase (narG), hydrazine oxidoreductase (hzo), and nitrite reductase (nirK). However, taxonomic characterization of transcripts suggested inhibition of narG transcription in gammaproteobacteria, whereas the transcription of anammox narG, whose gene product is likely used to oxidatively replenish electrons for carbon fixation, was not inhibited. The taxonomic composition of transcripts differed among denitrification enzymes, suggesting that distinct groups of microorganisms mediate different steps of denitrification. Sulfide addition (1 µM) did not affect anammox or O2 inhibition kinetics but strongly stimulated N2O production by denitrification. These results identify new O2 thresholds for delimiting marine nitrogen loss and highlight the utility of integrating biogeochemical and metatranscriptomic analyses.

IMPORTANCE

The removal of fixed nitrogen via anammox and denitrification associated with low O2 concentrations in oceanic oxygen minimum zones (OMZ) is a major sink in oceanic N budgets, yet the sensitivity and dynamics of these processes with respect to O2 are poorly known. The present study elucidated how nanomolar O2 concentrations affected nitrogen removal rates and expression of key nitrogen cycle genes in water from the eastern South Pacific OMZ, applying state-of-the-art (15)N techniques and metatranscriptomics. Rates of both denitrification and anammox responded rapidly and reversibly to changes in O2, but denitrification was more O2 sensitive than anammox. The transcription of key nitrogen cycle genes did not respond as clearly to O2, although expression of some of these genes decreased. Quantifying O2 sensitivity of these processes is essential for predicting through which pathways and in which environments, from wastewater treatment to the open oceans, nitrogen removal may occur.

Vertical partitioning of nitrogen-loss processes across the oxic-anoxic interface of an oceanic oxygen minimum zone

We investigated anammox, denitrification and dissimilatory reduction of nitrite to ammonium (DNRA) activity in the Eastern Tropical South Pacific oxygen minimum zone (OMZ) off northern Chile, at high-depth resolution through the oxycline into the anoxic OMZ core. This was accompanied by high-resolution nutrient and oxygen profiles to link changes in nitrogen transformation rates to physicochemical characteristics of the water column. Denitrification was detected at most depths, but anammox was the most active N2 -producing process, while DNRA was not detectable. Anammox and denitrification were mainly active in the anoxic OMZ core while activity was low to not detectable in the oxycline, except in association with an intrusion of OMZ core water. This indicates that continuous exposure to even submicromolar oxygen levels inhibits the processes either directly or through nitrite limitation. Anammox activity did not peak at the oxic-anoxic boundary but 20-50 m below matching the salinity maximum of the Equatorial Subsurface Water. This suggests that water history plays a major role for anammox activity possibly due to slow growth of anammox bacteria. Denitrification peaked deeper than anammox, likely reflecting a shift in the balance between this process and nitrate reduction to nitrite, governed by the relative availability of nitrate and nitrite.

Oxygen minimum zones harbour novel viral communities with low diversity

Oxygen minimum zones (OMZs) are oceanographic features that affect ocean productivity and biodiversity, and contribute to ocean nitrogen loss and greenhouse gas emissions. Here we describe the viral communities associated with the Eastern Tropical South Pacific (ETSP) OMZ off Iquique, Chile for the first time through abundance estimates and viral metagenomic analysis. The viral-to-microbial ratio (VMR) in the ETSP OMZ fluctuated in the oxycline and declined in the anoxic core to below one on several occasions. The number of viral genotypes (unique genomes as defined by sequence assembly) ranged from 2040 at the surface to 98 in the oxycline, which is the lowest viral diversity recorded to date in the ocean. Within the ETSP OMZ viromes, only 4.95% of genotypes were shared between surface and anoxic core viromes using reciprocal BLASTn sequence comparison. ETSP virome comparison with surface marine viromes (Sargasso Sea, Gulf of Mexico, Kingman Reef, Chesapeake Bay) revealed a dissimilarity of ETSP OMZ viruses to those from other oceanic regions. From the 1.4 million non-redundant DNA sequences sampled within the altered oxygen conditions of the ETSP OMZ, more than 97.8% were novel. Of the average 3.2% of sequences that showed similarity to the SEED non-redundant database, phage sequences dominated the surface viromes, eukaryotic virus sequences dominated the oxycline viromes, and phage sequences dominated the anoxic core viromes. The viral community of the ETSP OMZ was characterized by fluctuations in abundance, taxa and diversity across the oxygen gradient. The ecological significance of these changes was difficult to predict; however, it appears that the reduction in oxygen coincides with an increased shedding of eukaryotic viruses in the oxycline, and a shift to unique viral genotypes in the anoxic core.

Microbial oceanography of anoxic oxygen minimum zones

Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.

Metagenomes of the picoalga Bathycoccus from the Chile coastal upwelling

Among small photosynthetic eukaryotes that play a key role in oceanic food webs, picoplanktonic Mamiellophyceae such as Bathycoccus, Micromonas, and Ostreococcus are particularly important in coastal regions. By using a combination of cell sorting by flow cytometry, whole genome amplification (WGA), and 454 pyrosequencing, we obtained metagenomic data for two natural picophytoplankton populations from the coastal upwelling waters off central Chile. About 60% of the reads of each sample could be mapped to the genome of Bathycoccus strain from the Mediterranean Sea (RCC1105), representing a total of 9 Mbp (sample T142) and 13 Mbp (sample T149) of non-redundant Bathycoccus genome sequences. WGA did not amplify all regions uniformly, resulting in unequal coverage along a given chromosome and between chromosomes. The identity at the DNA level between the metagenomes and the cultured genome was very high (96.3% identical bases for the three larger chromosomes over a 360 kbp alignment). At least two to three different genotypes seemed to be present in each natural sample based on read mapping to Bathycoccus RCC1105 genome.

Experimental incubations elicit profound changes in community transcription in OMZ bacterioplankton

Sequencing of microbial community RNA (metatranscriptome) is a useful approach for assessing gene expression in microorganisms from the natural environment. This method has revealed transcriptional patterns in situ, but can also be used to detect transcriptional cascades in microcosms following experimental perturbation. Unambiguously identifying differential transcription between control and experimental treatments requires constraining effects that are simply due to sampling and bottle enclosure. These effects remain largely uncharacterized for "challenging" microbial samples, such as those from anoxic regions that require special handling to maintain in situ conditions. Here, we demonstrate substantial changes in microbial transcription induced by sample collection and incubation in experimental bioreactors. Microbial communities were sampled from the water column of a marine oxygen minimum zone by a pump system that introduced minimal oxygen contamination and subsequently incubated in bioreactors under near in situ oxygen and temperature conditions. Relative to the source water, experimental samples became dominated by transcripts suggestive of cell stress, including chaperone, protease, and RNA degradation genes from diverse taxa, with strong representation from SAR11-like alphaproteobacteria. In tandem, transcripts matching facultative anaerobic gammaproteobacteria of the Alteromonadales (e.g., Colwellia) increased 4-13 fold up to 43% of coding transcripts, and encoded a diverse gene set suggestive of protein synthesis and cell growth. We interpret these patterns as taxon-specific responses to combined environmental changes in the bioreactors, including shifts in substrate or oxygen availability, and minor temperature and pressure changes during sampling with the pump system. Whether such changes confound analysis of transcriptional patterns may vary based on the design of the experiment, the taxonomic composition of the source community, and on the metabolic linkages between community members. These data highlight the impressive capacity for transcriptional changes within complex microbial communities, underscoring the need for caution when inferring in situ metabolism based on transcript abundances in experimental incubations.

Water-column stratification governs the community structure of subtropical marine picophytoplankton

The increase in the areal extent of the subtropical gyres over the past decade has been attributed to a global tendency towards increased water-column stratification. Here, we examine how vertical stratification governs the community structure of the picophytoplankton that dominate these vast marine ecosystems. We analysed phytoplankton community composition in the three Southern Subtropical basins of the Pacific, Indian and Atlantic Oceans using a variety of methods and show that the distributions of picocyanobacteria and photosynthetic picoeukaryotes (PPEs) are strongly correlated with depth and strength of vertical mixing: the changes in community structure occur at various taxonomic levels. In well-mixed waters, PPEs, in particular haptophytes, dominate, whereas in strongly stratified waters, picocyanobacteria of the genus Prochlorococcus are prevalent, regardless of whether the relative contributions to total biomass are assessed in terms of pigment or of carbon. This ecological diochotomy within the picophytoplankton supports the hypothesis that genomic streamlining provides a selective advantage for Prochlorococcus in highly stable, oligotrophic systems, but may restrict their ability to dominate in regions subject to dynamic mixing.

Abundance and phylogenetic identity of archaeoplankton in the permanent oxygen minimum zone of the eastern tropical South Pacific

We assessed the abundance and molecular phylogeny of archaeoplankton in the oxygen minimum zone (OMZ) of the eastern tropical South Pacific, using specific-probe hybridization and phylogenetic analysis of the SSU-rRNA gene. Euryarchaea from Marine Group-II (MG-II) were most abundant in the surface oxic layer, representing 4.0±2.0% of the total picoplankton, while crenarchaea from Group I.1a (G-I.1a) peaked at the oxyclines, with a relative abundance of 8.1±4.3% (upper oxycline). In most of the stations, the abundance of both the groups decreased at the core of the OMZ, where a secondary maximum in cell density is commonly observed. The majority of the phylotypes affiliated with one of three groups: MG-II, euryarchaeal Marine Group-III (MG-III) and G-I.1a (75.9%, 12.8% and 10.3%, respectively). While MG-II phylotypes were found throughout the water column and G-I.1a ones were predominantly found within the oxyclines, MG-III phylotypes came almost exclusively from the OMZ core. Higher archaeal richness was found within the OMZ, with some of the exclusive lineages grouping with sequences from the deep ocean and hydrothermal vents. Moreover, G-I.1a sequences from the OMZ grouped into a different subcluster from the aerobic ammonium-oxidizer Nitrosopumilus maritimus. Thus, the community structure of archaeoplankton in OMZs is rich and distinct, with G-I.1a members particularly prominent at the oxyclines.

Nitrogen fixation in denitrified marine waters

Nitrogen fixation is an essential process that biologically transforms atmospheric dinitrogen gas to ammonia, therefore compensating for nitrogen losses occurring via denitrification and anammox. Currently, inputs and losses of nitrogen to the ocean resulting from these processes are thought to be spatially separated: nitrogen fixation takes place primarily in open ocean environments (mainly through diazotrophic cyanobacteria), whereas nitrogen losses occur in oxygen-depleted intermediate waters and sediments (mostly via denitrifying and anammox bacteria). Here we report on rates of nitrogen fixation obtained during two oceanographic cruises in 2005 and 2007 in the eastern tropical South Pacific (ETSP), a region characterized by the presence of coastal upwelling and a major permanent oxygen minimum zone (OMZ). Our results show significant rates of nitrogen fixation in the water column; however, integrated rates from the surface down to 120 m varied by ∼30 fold between cruises (7.5±4.6 versus 190±82.3 µmol m⁻² d⁻¹). Moreover, rates were measured down to 400 m depth in 2007, indicating that the contribution to the integrated rates of the subsurface oxygen-deficient layer was ∼5 times higher (574±294 µmol m⁻² d⁻¹) than the oxic euphotic layer (48±68 µmol m⁻² d⁻¹). Concurrent molecular measurements detected the dinitrogenase reductase gene nifH in surface and subsurface waters. Phylogenetic analysis of the nifH sequences showed the presence of a diverse diazotrophic community at the time of the highest measured nitrogen fixation rates. Our results thus demonstrate the occurrence of nitrogen fixation in nutrient-rich coastal upwelling systems and, importantly, within the underlying OMZ. They also suggest that nitrogen fixation is a widespread process that can sporadically provide a supplementary source of fixed nitrogen in these regions.

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycline and into the upper OMZ. Shotgun pyrosequencing of cDNA yielded 180,000 to 550,000 transcript sequences per depth. Based on functional gene representation, transcriptome samples clustered apart from corresponding metagenome samples from the same depth, highlighting the discrepancies between metabolic potential and actual transcription. BLAST-based characterizations of non-ribosomal RNA sequences revealed a dominance of genes involved with both oxidative (nitrification) and reductive (anammox, denitrification) components of the marine nitrogen cycle. Using annotations of protein-coding genes as proxies for taxonomic affiliation, we observed depth-specific changes in gene expression by key functional taxonomic groups. Notably, transcripts most closely matching the genome of the ammonia-oxidizing archaeon Nitrosopumilus maritimus dominated the transcriptome in the upper three depths, representing one in five protein-coding transcripts at 85 m. In contrast, transcripts matching the anammox bacterium Kuenenia stuttgartiensis dominated at the core of the OMZ (200 m; 1 in 12 protein-coding transcripts). The distribution of N. maritimus-like transcripts paralleled that of transcripts matching ammonia monooxygenase genes, which, despite being represented by both bacterial and archaeal sequences in the community DNA, were dominated (> 99%) by archaeal sequences in the RNA, suggesting a substantial role for archaeal nitrification in the upper OMZ. These data, as well as those describing other key OMZ metabolic processes (e.g. sulfur oxidation), highlight gene-specific expression patterns in the context of the entire community transcriptome, as well as identify key functional groups for taxon-specific genomic profiling.

Novel lineages of Prochlorococcus thrive within the oxygen minimum zone of the eastern tropical South Pacific

The eastern tropical Pacific Ocean holds two of the main oceanic oxygen minimum zones of the global ocean. The presence of an oxygen-depleted layer at intermediate depths, which also impinges on the seafloor and in some cases the euphotic zone, plays a significant role in structuring both pelagic and benthic communities, and also in the vertical partitioning of microbial assemblages. Here, we assessed the genetic diversity and distribution of natural populations of the cyanobacteria Prochlorococcus and Synechococcus within oxic and suboxic waters of the eastern tropical Pacific using cloning and sequencing, and terminal restriction fragment length polymorphism (T-RFLP) analyses applied to the 16S-23S rRNA internal transcribed spacer region. With the T-RFLP approach we could discriminate 19 cyanobacterial clades, of which 18 were present in the study region. Synechococcus was more abundant in the surface oxic waters of the eastern South Pacific, while Prochlorococcus dominated the subsurface low-oxygen waters. Two of the dominant clades in the oxygen-deficient waters belong to novel and yet uncultivated lineages of low-light adapted Prochlorococcus.

High diversity of ammonia-oxidizing archaea in permanent and seasonal oxygen-deficient waters of the eastern South Pacific

The community structure of putative aerobic ammonia-oxidizing archaea (AOA) was explored in two oxygen-deficient ecosystems of the eastern South Pacific: the oxygen minimum zone off Peru and northern Chile (11°S-20°S), where permanent suboxic and low-ammonium conditions are found at intermediate depths, and the continental shelf off central Chile (36°S), where seasonal oxygen-deficient and relatively high-ammonium conditions develop in the water column, particularly during the upwelling season. The AOA community composition based on the ammonia monooxygenase subunit A (amoA) genes changed according to the oxygen concentration in the water column and the ecosystem studied, showing a higher diversity in the seasonal low-oxygen waters. The majority of the archaeal amoA genotypes was affiliated to the uncultured clusters A (64%) and B (35%), with Cluster A AOA being mainly associated with higher oxygen and ammonium concentrations and Cluster B AOA with permanent oxygen- and ammonium-poor waters. Q-PCR assays revealed that AOA are an abundant community (up to 10(5) amoA copies ml(-1) ), while bacterial amoA genes from β proteobacteria were undetected. Our results thus suggest that a diverse uncultured AOA community, for which, therefore, we do not have any physiological information, to date, is an important component of the nitrifying community in oxygen-deficient marine ecosystems, and particularly in rich coastal upwelling ones.

Autonomous observations of in vivo fluorescence and particle backscatteringin an oceanic oxygen minimum zone

The eastern South Pacific (ESP) oxygen minimum zone (OMZ) is a permanent hydrographic feature located directly off the coasts of northern Chile and Peru. The ESP OMZ reaches from coastal waters out to thousands of kilometers offshore, and can extend from the near surface to depths greater than 700 m. Oxygen minimum zones support unique microbial assemblages and play an important role in marine elemental cycles. We present results from two autonomous profiling floats that provide nine months of time-series data on temperature, salinity, dissolved oxygen, chlorophyll a, and particulate backscattering in the ESP OMZ. We observed consistently elevated backscattering signals within low-oxygen waters, which appear to be the result of enhanced microbial biomass in the OMZ intermediate waters. We also observed secondary chlorophyll a fluorescence maxima within low-oxygen waters when the upper limit of the OMZ penetrated the base of the photic zone. We suggest that autonomous profiling floats are useful tools for monitoring physical dynamics of OMZs and the microbial response to perturbations in these areas.

Bosque: integrated phylogenetic analysis software

Phylogenetic analyses today involve dealing with computer files in different formats and often several computer programs. Although some widely used applications have integrated important functionalities for such analyses, they still work with local resources only: input/output files (users have to manage them) and local computing (users have sometimes to leave their programs, on their desktop computers, running for extended periods of time). To address these problems we have developed 'Bosque', a multi-platform client-server software that performs standard phylogenetic tasks either locally or remotely on servers, and integrates the results on a local relational database. Bosque performs sequence alignments and graphical visualization and editing of trees, thus providing a powerful environment that integrates all the steps of phylogenetic analyses.

AVAILABILITY

http://bosque.udec.cl

Impacts of atmospheric anthropogenic nitrogen on the open ocean

Increasing quantities of atmospheric anthropogenic fixed nitrogen entering the open ocean could account for up to about a third of the ocean's external (nonrecycled) nitrogen supply and up to approximately 3% of the annual new marine biological production, approximately 0.3 petagram of carbon per year. This input could account for the production of up to approximately 1.6 teragrams of nitrous oxide (N2O) per year. Although approximately 10% of the ocean's drawdown of atmospheric anthropogenic carbon dioxide may result from this atmospheric nitrogen fertilization, leading to a decrease in radiative forcing, up to about two-thirds of this amount may be offset by the increase in N2O emissions. The effects of increasing atmospheric nitrogen deposition are expected to continue to grow in the future.

Bacterial diversity in the oxygen minimum zone of the eastern tropical South Pacific

The structure and diversity of bacterial communities associated with the oxygen minimum zone (OMZ) of the eastern tropical South Pacific was studied through phylogenetic analysis. Clone libraries of 16S rRNA gene fragments were constructed using environmental DNA collected from the OMZ (60 m and 200 m), the sea surface (10 m), and the deep oxycline (450 m). At the class level, the majority of sequences affiliated to the gamma- (53.7%) and alpha-Proteobacteria (19.7%), and to the Bacteroidetes (11.2%). A vertical partitioning of the bacterial communities was observed, with main differences between the suboxic OMZ and the more oxygenated surface and deep oxycline waters. At the surface, the microbial community was predominantly characterized by SAR86, Loktanella and unclassified Flavobacteriaceae, whereas the deeper layer was dominated by Sulfitobacter and unclassified Alteromonadaceae. In the OMZ, major constituents affiliated to the marine SAR11 clade and to thiotrophic gamma-symbionts (25% of all sequences), a group not commonly found in pelagic waters. Sequences affiliating to the phylum Chloroflexi, to the AGG47 and SAR202 clades, to the delta-Proteobacteria, to the Acidobacteria, and to the 'anammox group' of the Planctomycetes were found exclusively in the OMZ. The bacterial richness in the OMZ was higher than in the oxic surface and deeper oxycline, as revealed by rarefaction analysis and the Chao1 richness estimator (surface: 45 +/- 8, deeper oxycline: 76 +/- 26; OMZ (60 m): 97 +/- 33, OMZ (200 m): 109 +/- 31). OMZ bacterial diversity indices (Fisher's: approximately 30 +/- 5, Shannon's: approximately 3.31, inverse Simpson's: approximately 20) were similar to those found in other pelagic marine environments. Thus, our results indicate a distinct and diverse bacterial community within the OMZ, with presumably novel and yet uncultivated bacterial lineages.

Global phylogeography of marine Synechococcus and Prochlorococcus reveals a distinct partitioning of lineages among oceanic biomes

Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are important contributors to global primary production occupying a key position at the base of marine food webs. The genetically diverse nature of each genus is likely an important reason for their successful colonization of vast tracts of the world's oceans, a feature that has led to detailed analysis of the distribution of these genetic lineages at the local and ocean basin scale. Here, we extend these analyses to the global dimension, using new data from cruises in the Pacific, Indian and Arctic Oceans in combination with data from previous studies in the Atlantic Ocean, Arabian Sea, Red Sea and a circumnavigation of the southern hemisphere to form a data set which comprises most of the world's major ocean systems. We show that the distribution patterns of Prochlorococcus and Synechococcus lineages are remarkably similar in different ocean systems with comparable environmental conditions, but producing a strikingly different 'signature' in the four major ocean domains or biomes (the Polar Domain, Coastal Boundary Domain, Trade Winds Domain and Westerly Winds Domain). This clearly reiterates the idea of spatial partitioning of individual cyanobacterial lineages, but at the global scale.

High abundances of aerobic anoxygenic photosynthetic bacteria in the South Pacific Ocean

Little is known about the abundance, distribution, and ecology of aerobic anoxygenic phototrophic (AAP) bacteria, particularly in oligotrophic environments, which represent 60% of the ocean. We investigated the abundance of AAP bacteria across the South Pacific Ocean, including the center of the gyre, the most oligotrophic water body of the world ocean. AAP bacteria, Prochlorococcus, and total prokaryotic abundances, as well as bacteriochlorophyll a (BChl a) and divinyl-chlorophyll a concentrations, were measured at several depths in the photic zone along a gradient of oligotrophic conditions. The abundances of AAP bacteria and Prochlorococcus were high, together accounting for up to 58% of the total prokaryotic community. The abundance of AAP bacteria alone was up to 1.94 x 10(5) cells ml(-1) and as high as 24% of the overall community. These measurements were consistent with the high BChl a concentrations (up to 3.32 x 10(-3) microg liter(-1)) found at all stations. However, the BChl a content per AAP bacterial cell was low, suggesting that AAP bacteria are mostly heterotrophic organisms. Interestingly, the biovolume and therefore biomass of AAP bacteria was on average twofold higher than that of other prokaryotic cells. This study demonstrates that AAP bacteria can be abundant in various oligotrophic conditions, including the most oligotrophic regime of the world ocean, and can account for a large part of the bacterioplanktonic carbon stock.

Ammonia-oxidizing beta-proteobacteria from the oxygen minimum zone off northern Chile

The composition of ammonia-oxidizing bacteria from the beta-Proteobacteria subclass (betaAOB) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, approximately 200 to 44 microM O(2)) and within the oxygen minimum zone (OMZ) suboxic waters (50- to 400-m depth, < or =10 microM O(2)) of the eastern South Pacific off northern Chile. This study was carried out through cloning and sequencing of genes coding for 16S rRNA and the ammonia monooxygenase enzyme active subunit (amoA). Sequences affiliated with Nitrosospira-like cluster 1 dominated the 16S rRNA gene clone libraries constructed from both oxic and suboxic waters. Cluster 1 consists exclusively of yet-uncultivated betaAOB from marine environments. However, a single clone, out of 224 obtained from the OMZ, was found to belong to Nitrosospira lineage cluster 0. To our knowledge, cluster 0 sequences have been derived from betaAOB isolated only from sand, soil, and freshwater environments. Sequences in clone libraries of the amoA gene from the surface and upper oxycline could be grouped in a marine subcluster, also containing no cultured representatives. In contrast, all 74 amoA sequences originating from the OMZ were either closely affiliated with cultured Nitrosospira spp. from clusters 0 and 2 or with other yet-uncultured betaAOB from soil and an aerated-anoxic Orbal process waste treatment plant. Our results reveal the presence of Nitrosospira-like betaAOB in both oxic and suboxic waters associated with the OMZ but with a clear community shift at the functional level (amoA) along the strong oxygen gradient.

Oceanographic Basis of the Global Surface Distribution of Prochlorococcus Ecotypes

By using data collected during a continuous circumnavigation of the Southern Hemisphere, we observed clear patterns in the population-genetic structure of Prochlorococcus, the most abundant photosynthetic organism on Earth, between and within the three Southern Subtropical Gyres. The same mechanisms that were previously invoked to account for the vertical distribution of ecotypes at local scales accounted for the global (horizontal) patterns we observed. Basin-scale and seasonal variations in the structure and strength of vertical stratification provide a basis for understanding large-scale horizontal distribution in genetic and physiological traits of Prochlorococcus, and perhaps of marine microbial communities in general.

Communities of nirS-type denitrifiers in the water column of the oxygen minimum zone in the eastern South Pacific

The major sites of water column denitrification in the ocean are oxygen minimum zones (OMZ), such as one in the eastern South Pacific (ESP). To understand the structure of denitrifying communities in the OMZ off Chile, denitrifier communities at two sites in the Chilean OMZ (Antofagasta and Iquique) and at different water depths were explored by terminal restriction fragment length polymorphism analysis and cloning of polymerase chain reaction (PCR)-amplified nirS genes. NirS is a functional marker gene for denitrification encoding cytochrome cd1-containing nitrite reductase, which catalyses the reduction of nitrite to nitric oxide, the key step in denitrification. Major differences were found between communities from the two geographic locations. Shifts in community structure occurred along a biogeochemical gradient at Antofagasta. Canonical correspondence analysis indicated that O2, NO3-, NO2- and depth were important environmental factors governing these communities along the biogeochemical gradient in the water column. Phylogenetic analysis grouped the majority of clones from the ESP in distinct clusters of genes from presumably novel and yet uncultivated denitrifers. These nirS clusters were distantly related to those found in the water column of the Arabian Sea but the phylogenetic distance was even higher compared with environmental sequences from marine sediments or any other habitat. This finding suggests similar environmental conditions trigger the development of denitrifiers with related nirS genotypes despite large geographic distances.

Effect of the particle-size distribution on the backscattering ratio in seawater

Mie theory is used to model the backscattering ratio (the ratio of the backscattering coefficient to the total scattering coefficient) of marine particles with the assumption that they follow a Junge-type size distribution. Results show that the backscattering ratio is very sensitive to the presence of submicrometer particles and depends strongly on the shape of the size distribution. However, it is not affected significantly by absorption and does not vary with wavelength over the visible range. The implications for modeling of backscattering and ocean color in terms of phytoplankton pigment concentration are discussed.

Photoacclimation of Prochlorococcus sp. (Prochlorophyta) Strains Isolated from the North Atlantic and the Mediterranean Sea

Two Atlantic (SARG and NATL1) strains and one Mediterranean (MED) strain of Prochlorococcus sp., a recently discovered marine, free-living prochlorophyte, were grown over a range of "white" irradiances (lg) and under low blue light to examine their photoacclimation capacity. All three strains contained divinyl (DV) chlorophylls (Chl) a and b, both distinguishable from "normal" Chls by their red-shifted blue absorption maximum, a Chl c-like pigment at low concentration, zeaxanthin, and [alpha]-carotene. The presence of two phaeophytin b peaks in acidified extracts from both Atlantic strains grown at high lg suggests that these strains also had a normal Chl b-like pigment. In these strains, the total Chl b to DV-Chl a molar ratio decreased from about 1 at 7.5 [mu]mol quanta m-2 s-1 to 0.4 to 0.5 at 133 [mu]mol quanta m-2 s-1. In contrast, the MED strain always had a low DV-Chl b to DV-Chl a molar ratio, ranging between 0.13 at low lg and 0.08 at high lg. The discrepancies between the Atlantic and MED strains could result from differences either in the number of light-harvesting complexes (LHC) II per photosystem II or in the Chl b-binding capacity of the apoproteins constituting LHC II. Photosynthesis was saturated at approximately 5 fg C(fg Chl)-1 h-1 or 6 fg C cell-1 h-1, and growth was saturated at approximately 0.45 d-1 for both MED and SARG strains at 18[deg]C, but saturating irradiances differed between strains. Atlantic strains exhibited increased light-saturated rates and quantum yield for carbon fixation under blue light.