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.

The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean.

Marine picocyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean, where they exert a profound influence on elemental cycling and energy flow. The use of transmembrane chlorophyll complexes instead of phycobilisomes as light-harvesting antennae is considered a defining attribute of Prochlorococcus Its ecology and evolution are understood in terms of light, temperature, and nutrients. Here, we report single-cell genomic information on previously uncharacterized phylogenetic lineages of this genus from nutrient-rich anoxic waters of the eastern tropical North and South Pacific Ocean. The most basal lineages exhibit optical and genotypic properties of phycobilisome-containing cyanobacteria, indicating that the characteristic light-harvesting antenna of the group is not an ancestral attribute. Additionally, we found that all the indigenous lineages analyzed encode genes for pigment biosynthesis under oxygen-limited conditions, a trait shared with other freshwater and coastal marine cyanobacteria. Our findings thus suggest that Prochlorococcus diverged from other cyanobacteria under low-oxygen conditions before transitioning from phycobilisomes to transmembrane chlorophyll complexes and may have contributed to the oxidation of the ancient ocean.

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.

The Influence of pCO2-Driven Ocean Acidification on Open Ocean Bacterial Communities during A Short-Term Microcosm Experiment in the Eastern Tropical South Pacific (ETSP) off Northern Chile.

Due to the increasing anthropogenic CO2 emissions, Ocean Acidification (OA) is progressing rapidly around the world. Despite the major role that microorganisms play on the marine biogeochemical cycling and ecosystem functioning, the response of bacterial communities upon OA scenarios is still not well understood. Here, we have conducted a detailed characterization of the composition and relative abundance of bacterial communities in the water column of an open-ocean station in the Eastern Tropical South Pacific (ETSP) off northern Chile and their interactions with environmental factors. In addition, through a short-term microcosm experiment, we have assessed the effect of low pH/high pCO2 conditions over the abundance and genetic diversity of bacterial communities. Our results evidence a clear partitioning of community composition that could be attributed mostly to dissolved oxygen. However, our experimental approach demonstrated that low pH/high pCO2 conditions might modify the structure of the bacterial community, evidencing that small changes in pH may impact significantly the abundance and diversity of key microorganisms. This study constitutes a first step aiming to provide insight about the influence of changing carbonate chemistry conditions on natural bacterial communities and to shed light on the potential impact of OA in biogeochemical cycles on the ETSP region.

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.

Redox traits characterize the organization of global microbial communities.

The structure of biological communities is conventionally described as profiles of taxonomic units, whose ecological functions are assumed to be known or, at least, predictable. In environmental microbiology, however, the functions of a majority of microorganisms are unknown and expected to be highly dynamic and collectively redundant, obscuring the link between taxonomic structure and ecosystem functioning. Although genetic trait-based approaches at the community level might overcome this problem, no obvious choice of gene categories can be identified as appropriate descriptive units in a general ecological context. We used 247 microbial metagenomes from 18 biomes to determine which set of genes better characterizes the differences among biomes on the global scale. We show that profiles of oxidoreductase genes support the highest biome differentiation compared with profiles of other categories of enzymes, general protein-coding genes, transporter genes, and taxonomic gene markers. Based on oxidoreductases' description of microbial communities, the role of energetics in differentiation and particular ecosystem function of different biomes become readily apparent. We also show that taxonomic diversity is decoupled from functional diversity, e.g., grasslands and rhizospheres were the most diverse biomes in oxidoreductases but not in taxonomy. Considering that microbes underpin biogeochemical processes and nutrient recycling through oxidoreductases, this functional diversity should be relevant for a better understanding of the stability and conservation of biomes. Consequently, this approach might help to quantify the impact of environmental stressors on microbial ecosystems in the context of the global-scale biome crisis that our planet currently faces.

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.

Metabolic potential and in situ transcriptomic profiles of previously uncharacterized key microbial groups involved in coupled carbon, nitrogen and sulfur cycling in anoxic marine zones.

Anoxic marine zones (AMZs) impact biogeochemical cycles at the global scale, particularly the nitrogen cycle. Key microbial players from AMZs have been identified, but the majority remains unrecognized or uncharacterized. Thirty-one single-cell amplified genomes (SAGs) from the eastern tropical North and South Pacific AMZs were sequenced to gain insight into the distribution, metabolic potential and contribution to the community transcriptional profile of these uncharacterized bacterial and archaeal groups. Detailed analyses focused on SAG-bins assigned to three of these groups that presented 79%-100% estimated genome completeness: the putative sulphur-oxidizing Gamaproteobacteria EOSA II clade, a Marinimicrobia member of the recently recognized PN262000N21 clade found to be abundant in AMZ anoxic cores, and a representative of the Marine Benthic Group A Thaumarchaeota. Community-based analyses revealed that these three groups are significantly more abundant and transcriptionally more active in the AMZ microbial communities than previously described phylogenetically related microbial groups. Collectively, these groups have the potential to link biogeochemically relevant processes by coupling the carbon, nitrogen and sulfur cycles. Together, these results increase our understanding of key microbial components inhabiting AMZs and other oxygen-deficient marine environments, enhancing our capacity to predict the impact of the expansion of these ecosystems due to climate change.

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.

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters.

A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (<10 nmol⋅L(-1)) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O2 levels between 5 nmol⋅L(-1) and 20 µmol⋅L(-1) Rates of both processes were detectable in the low nanomolar range (5-33 nmol⋅L(-1) O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L(-1) O2 for ammonium oxidation and 778 ± 168 nmol⋅L(-1) O2 for nitrite oxidation assuming one-component Michaelis-Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis-Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.

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.

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.