Biology subjects

Dekas, A. E.

Publications and source records attributed to Dekas, A. E..

12 recordsLinked to original sources

bioRxiv2026

Piezophilic activity dominates the Puerto Rico Trench deep subseafloor biosphere

Hydrostatic pressure is a defining feature of the deep ocean, yet how it structures microbial activity across the subseafloor biosphere is poorly understood. Here, we assess pressure effects on anabolic activity in seafloor and subseafloor communities across a margin-to-hadal-to-abyssal transect of the Puerto Rico Trench region (493-8,385 m water depth). Community-level responses to pressure reverse with burial, revealing a previously unrecognized shift toward piezophily in resident subseafloor communities down to 20 meters below seafloor (mbsf). In pressure-incubation experiments, atmospheric pressure yielded higher proportions of active cells in surficial sediments, whereas in situ pressure yielded higher proportions in the subseafloor. Pressure also structured active-community composition; in trench-axis sediments extending to 8.35 mbsf, JS1/Atribacterota populations belonging to geographically widespread hadal lineages exhibited a physiological response to in situ pressure, indicative of subseafloor piezophily. These findings suggest that hydrostatic pressure acts as an ecological filter after burial, favoring piezophilic traits that may support microbial persistence in the deep subseafloor biosphere.

microbiology↗

bioRxiv2026

Deeply-sequenced metagenomes and over 1000 draft genomes from the epipelagic to bathypelagic Northeast Pacific Ocean

The deep ocean water column (>200 meters depth) hosts diverse and active microbial communities that play critical roles in Earths biogeochemical cycles. However, this habitat has been massively undersampled compared to shallower depths where sunlight penetrates, as well as benthic features like hydrothermal vents and seeps. In particular, few existing deep-sea datasets provide adequate spatial resolution to study the impact of physical and geochemical gradients on marine microbial communities over both horizontal and vertical spatial scales. Here, we present a deeply-sequenced, spatially-resolved set of 28 water column metagenomes from a [~]300 km horizontal transect off the coast of central California, spanning 50 to 4000 meters depth. We estimate that the deepest portion of the resulting [~]1.5 terabases of sequencing data comprises nearly 9% of all shotgun metagenomic sequencing currently available from 1000 meters depth or below. Additionally, we generate over one thousand draft genomes describing the bacteria and archaea present in our bulk metagenomic data. These genomes frequently account for the majority of reads sequenced, and show discernable patterns of abundance with depth, underscoring the presence of distinct microbial cohorts inhabiting different ocean compartments. Additionally, the depth of sequencing performed (mean of [~]51.9 gigabases per sample) enables resolution of rare community members that are, on average, more phylogenetically novel than their abundant counterparts, forming an important contribution to genomic catalogues for this habitat. We anticipate that the combined datasets will enable diverse research questions concerning the adaptation, functional potential, and distribution of deep sea microbes as well as their genes and proteins.

microbiology↗

bioRxiv2026

Anaerobic methane oxidation by ANME-2a at two molar chloride in Orca Basin

Anaerobic methane oxidation, typically mediated by consortia of archaea and bacteria, is a key process in the global methane cycle, but little is known about its upper salinity limits. We characterized the microbial methane cycle in the anoxic, hypersaline Orca Basin using metagenomics, metatranscriptomics, fluorescence in situ hybridization, and geochemical measurements at sub-meter resolution. In the brine, we detected transcriptional activity of the halophilic methylotrophic methanogen Methanohalophilus, consistent with a biological source for Orca Basin methane. In the particle-rich halocline ([~]2 M Cl-; [~]2235 meters depth), high mcrA transcription by a novel ANME-2a species was co-located with a positive shift in {delta}13C-CH4 indicative of anaerobic oxidation of methane. ANME-2a also transcribed genes for biosynthesis of the osmolyte N({varepsilon})-acetyl-{beta}-L-lysine, supporting adaptation for hypersaline conditions. At the same depth, consortia of sarcina-like archaea, likely ANME-2a, were observed in association with vibrioid and filamentous bacteria, potentially members of a halotolerant genus in the order Desulfobulbales (family SURF-16, which includes the previously identified ANME partner Seep-DBB) that were active at the same depth. At and above the oxic-anoxic interface, aerobic methane oxidation appears to be mediated by three genera of uncultivated Methylococcales bacteria. Our results double the upper salinity range of ANME-2a to [~]2 M Cl- and reveal the key microbial players in the methane bio-filter between the Orca Basin brine and overlying seawater.

microbiology↗

bioRxiv2026

Substantial genetic potential for deep-sea chemoautotrophy extends beyond nitrifiers

I.Microbial chemoautotrophy in the deep sea has the potential to sustain ecosystems at depth, contribute to global carbon sequestration, and ameliorate the currently unbalanced deep-sea carbon budget. However, an understanding of its mechanisms and feasibility is still emerging, particularly beyond that fueled by nitrification. Here, we conduct both a gene-based and genome-resolved analysis of 28 metagenomes in the Northeast Pacific Ocean to investigate the prevalence, distribution, and phylogenetic and metabolic diversity of deep-sea chemoautotrophs. We find that organisms encoding marker genes for dissolved inorganic carbon (DIC) fixation are abundant and widespread at our study site, comprising 11-26% of microbial communities from 150-4000 m water depth. Marker genes for the Calvin cycle and 3-Hydroxypropionate (3HP) bi-cycles are more prevalent than those for the 3-Hydroxypropionate/4-Hydroxybutyrate (3HP/4HB) and reverse Tricarboxylic Acid (rTCA) cycles, the latter two of which are encoded by organisms conducting nitrification. We construct and identify 128 putatively chemoautotrophic metagenome-assembled genomes, spanning 14 phyla including the Proteobacteria, Actinobacteria, SAR324, and the Thermoproteota. They contained genes for the oxidation of carbon monoxide (77.3%), sulfur (68.8%), ammonia (5.5%), and/or methane (3.1%), suggesting diverse catabolisms fuel deep-sea DIC fixation and an underappreciated potential role for aerobic carbon monoxide oxidation. Fifty percent of these genomes encoded multiple inorganic catabolic pathways and 99% included genes for organic matter transport, suggesting catabolic flexibility and potentially facultative autotrophy, respectively. We create an inclusive inventory and map of potential chemoautotrophs at our study site, expanding their known phylogenetic breadth, metabolic repertoires, and potential to impact the carbon cycle. ImportanceThe deep-sea carbon cycle plays a central role regulating marine ecosystem productivity and the global climate. Chemoautotrophy, the microbial conversion of inorganic carbon (e.g., CO2 or HCO-3) into cellular biomass, is an understudied process with the potential to significantly shift models of the marine carbon budget. While some deep-sea chemoautotrophs are known, a wholistic analysis of organisms with the genetic potential for chemoautotrophy in the dark water column is lacking. Here, we find that microorganisms with the genetic potential for chemoautotrophy are widespread and abundant, and that they are more phylogenetically and metabolically diverse than previously appreciated. In particular, the prevalence of genes involved in CO oxidation suggests a currently unrecognized role in fueling deep-sea chemoautotrophy. By identifying the potential microbial mediators and coupled energy sources, our results allow for more accurate predictions of when, where, and how deep-sea chemoautotrophy occurs, and therefore its potential role in carbon cycling.

microbiology↗

bioRxiv2025

Microbial N2O reduction in sulfidic waters:Implications for Proterozoic oceans

Throughout Earths history, shifts in ocean redox influenced the bioavailability of trace metals, shaping the activity of microorganisms. In Proterozoic oceans, the precipitation of copper (Cu) with sulfide was hypothesized to limit the bioavailability of Cu. This limitation may have suppressed microbial reduction of nitrous oxide (N2O), due to the Cu dependency of nitrous oxide reductase (Nos). It is thought that without this critical microbial sink, Proterozoic oceans were a significant net source of N2O. Here, we revisit this paradigm in light of recently derived [~]20-fold lower estimates for sulfide in Proterozoic seawater and an empirical evaluation of the potential for microbial N2O reduction under sulfidic conditions. Leveraging publicly available environmental metatranscriptomes, we infer active N2O reduction from the detection of nosZ transcripts in multiple marine and lacustrine systems in which sulfide and Cu concentrations are analogous to those of the Proterozoic. In controlled culture experiments, we demonstrate that the purple non-sulfur bacterium Rhodopseudomonas palustris can reduce N2O at sulfide concentrations up to 100 {micro}M, well above levels predicted for Proterozoic oceans. Based on trace metal speciation modeling, we suggest that Cu remains bioavailable under Proterozoic-like conditions as a dissolved CuHS0 complex. Using phylogenetics, we infer that early N2O reducers were probably anoxygenic phototrophs and performed N2O reduction as dark metabolism. Collectively, these observations suggest microbial N2O reduction occurs under euxinic conditions, implying that Proterozoic marine N2O emissions were substantially lower than previously proposed. Our conclusions inform our understanding of the microbial ecology in sulfidic waters, the early climate, and the search for extraterrestrial life.

ecology↗

bioRxiv2024

Cyanobacteria from marine oxygen deficient zones encode both form I and form II rubiscos

Cyanobacteria are highly abundant in the marine photic zone and primary drivers of the conversion of inorganic carbon to biomass. To date, all studied Cyanobacterial lineages encode carbon fixation machinery hinged upon form I rubisco enzymes within a CO2-concentrating carboxysome. Here, we report that the AMZ IB lineage of Prochlorococcus from global oxygen deficient zones (ODZs) harbor both form I and form II rubisco enzymes, the latter of which are typically non-carboxysomal and possess biochemical properties tuned towards low oxygen environments. Our analyses reveal that these cyanobacterial form II enzymes are functional in vitro and were likely acquired via lateral gene transfer from proteobacteria. Global metagenomic read recruitment demonstrates that Prochlorococcus with form II rubisco are essentially restricted to ODZs in the Eastern Tropical Pacific, suggesting that acquisition may confer an advantage specifically under low-O2 conditions. Populations of AMZ IB Prochlorococcus express both forms of rubisco in situ, with the highest form II rubisco expression at depths where both oxygen and light are particularly low, possibly as a mechanism to increase the efficiency of photoautotrophy under energy limitation. Our findings expand the diversity of carbon fixation configurations in the microbial world and may have implications for the overall capacity of ODZs to sequester carbon.

microbiology↗

bioRxiv2024

Abundance, identity, and potential diazotrophic activity of nifH-containing organisms at marine cold seeps

Diazotrophic microorganisms alleviate nitrogen limitation at marine cold seeps using nitrogenase, encoded in part by the gene nifH. Here, we investigated nifH-containing organisms (NCOs) inside and outside six biogeochemically heterogeneous seeps using amplicon sequencing and quantitative real-time PCR (qPCR) of nifH genes and transcripts. We detected nifH genes affiliated with anaerobic methane-oxidizing ANME-2 archaea and sulfate-reducing Desulfobacteraceae, consistent with previous studies, but also phylogenetically and likely metabolically diverse organisms, including Desulfoglaeba, Candidatus Methanoliparia, and Desulfuromonadales. In total, we recovered 10,734 bona fide nifH sequence variants affiliated with 18 bacterial and archaeal phyla (17 within seeps), a subset of which were transcribed at nearly all seeps investigated. We corrected our qPCR data based on our amplicon results, which found that 71% of recovered sequences were not bona fide nifH, and we recommend a similar correction in future qPCR studies that use broad nifH primers. NifH abundance was up to three orders of magnitude higher within seeps, was highly correlated with mcrA gene abundance, and, when corrected, was negatively correlated with porewater ammonium <25 uM, consistent with the inhibition of diazotrophy by ammonium. Our findings significantly expand the known diversity of NCOs at seeps and emphasize seeps as hotspots for deep-sea diazotrophy.

microbiology↗

bioRxiv2024

Urea assimilation and oxidation supports the activity of a phylogenetically diverse microbial community in the dark ocean

Urea is hypothesized to be an important source of nitrogen and chemical energy to microorganisms in the deep sea; however, direct evidence for urea use below the epipelagic ocean is lacking. Here, we explore urea utilization from 50 to 4000 meters depth in the northeastern Pacific Ocean using metagenomics, nitrification rates, and single-cell stable-isotope-uptake measurements with nanoscale secondary ion mass spectrometry (nanoSIMS). We find that the majority (>60%) of active cells across all samples assimilated urea-derived N, and that cell-specific nitrogen-incorporation rates from urea were higher than that from ammonium. Both urea concentrations and assimilation rates relative to ammonium generally increased below the euphotic zone. We detected ammonia- and urea-based nitrification at all depths at one of two sites analyzed, demonstrating their potential to support chemoautotrophy in the mesopelagic and bathypelagic regions. Using newly generated metagenomes we find that the ureC gene, encoding the catalytic subunit of urease, is found within 39% of deep-sea cells in this region, including the Nitrosophaerota (likely for nitrification) as well as thirteen other phyla such as Proteobacteria, Verrucomicrobia, Plantomycetota, Nitrospinota, and Chloroflexota (likely for assimilation). Analysis of public metagenomes revealed ureC within 10-46% of deep-sea cells around the world, with higher prevalance below the photic zone, suggesting urea is widely available to the deep-sea microbiome globally. Our results demonstrate that urea is a nitrogen source to abundant and diverse microorganisms in the dark ocean, as well as a significant contributor to deep-sea nitrification and therefore fuel for chemoautotrophy.

microbiology↗

bioRxiv2024

Abundant and metabolically flexible lineages within the SAR324 and gammaproteobacteria dominate the potential for rubisco-mediated carbon fixation in the dark ocean

BackgroundRubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of organisms that employ it for carbon fixation are still emerging, particularly in unlit ecosystems like the deep sea. ResultsHere, we generate fifteen deeply-sequenced metagenomes along a spatially-resolved transect off the California coast, and combine them with globally-distributed public data to examine the diversity, distribution, and metabolic features of rubisco-encoding organisms from the dark water column. Organisms with rubisco were detected in the vast majority of all samples, spanning over 1,000 species groups and together comprising up to [~]20% of the total microbial community. At 150 meters and below, potential for carbon fixation via rubisco was dominated by just two orders of gammaproteobacteria and SAR324, encoding either the form I or II rubisco. Many of these organisms also possessed genes for the oxidation of reduced sulfur compounds, which may energetically support carbon fixation. Transcriptomic profiling in the epi- and mesopelagic suggested that all major forms of rubisco can be highly expressed in the deep water column, but are not done so constitutively, consistent with metabolic flexibility. ConclusionOur results demonstrate that the genetic potential to fix carbon via rubisco is significant and spatially widespread in the dark ocean. We identify several rubisco-encoding species groups that are particularly abundant and cosmopolitan, highlighting the key role they may play in deep-sea chemoautotrophy and the global marine carbon cycle.

microbiology↗

bioRxiv2023

Single-cell analysis reveals an active and heterotrophic microbiome in the Guaymas Basin deep subsurface with significant heterotrophic inorganic carbon fixation

The marine subsurface is a long-term sink of atmospheric carbon dioxide with significant implications for climate on geologic timescales. Subsurface microbial cells can either enhance or reduce the potential for the subsurface to sequester carbon, depending on their metabolic activity. However, the activity of subsurface microbes is rarely measured, leaving their role in biogeochemical cycling poorly characterized. Here, we used nanoscale secondary ion mass spectrometry to quantify anabolic activity in 3,203 individual cells from the thermally altered deep subsurface in the Guaymas Basin, Mexico (3-75 m below the seafloor, 0-14 C). We observed that a large majority of cells were active (83-100%), although rates of biomass generation were low, suggesting cellular maintenance rather than doubling. Mean single-cell activity decreased with increasing sediment depth and temperature, and was most strongly correlated with porewater sulfate concentrations. Intracommunity heterogeneity in cell-specific activity decreased with increasing sediment depth and age. Using a dual-isotope labelling approach we determined that all active cells analyzed at all depths were heterotrophic. We detected and quantified inorganic carbon assimilation by heterotrophs and found that it contributes on average at least 5% of total heterotrophic biomass carbon in this community. Our results therefore suggest that the deep marine biosphere at Guaymas Basin is largely active and contributes to subsurface carbon cycling primarily by assimilating organic carbon but also by mediating heterotrophic inorganic carbon fixation. Heterotrophic assimilation of inorganic carbon may be a small yet significant and widespread underappreciated source of labile carbon in the global subsurface. ImportanceThe global subsurface is the largest reservoir of microbial life on the planet yet remains poorly characterized. The activity of life in this realm has implications for long-term elemental cycling, particularly of carbon, as well as how life survives in extreme environments. Here, we recovered cells from the deep subsurface of the Guaymas Basin and investigated the level and distribution of activity, the physicochemical drivers of activity, and the relative significance of organic versus inorganic carbon to subsurface biomass. Using a sensitive single-cell assay we find that the majority of cells are active, that activity is likely driven by availability of energy, and that while organic carbon supplies most cellular carbon, inorganic carbon also contributes. We additionally find that the inorganic carbon assimilation observed was mediated by heterotrophs, not autotrophs, highlighting the importance of this often overlooked mode of carbon assimilation in the subsurface and beyond.

microbiology↗

bioRxiv2022

Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring

The preeminent source of biological methane on Earth is methyl coenzyme M reductase (Mcr)-dependent archaeal methanogenesis. A growing body of evidence suggests a diversity of archaea possess Mcr, however, experimental validation of hypothesized methane metabolisms has been missing. Here, we provide evidence of a functional Mcr-based methanogenesis pathway in a novel member of the family Archaeoglobaceae, designated Methanoproducendum nevadense, which we enriched from a terrestrial hot spring on the polysaccharide xyloglucan. Our incubation assays demonstrate methane production that is highly sensitive to the Mcr-inhibitor bromoethanesulfonate, stimulated by xyloglucan and xyloglucan-derived sugars, concomitant with the consumption of molecular hydrogen, and causing a deuterium fractionation in methane characteristic of hydrogenotrophic and methylotrophic methanogens. Combined with the recovery and analysis of a high-quality M. nevadense metagenome-assembled genome encoding a divergent Mcr and diverse potential electron and carbon transfer pathways, our observations suggest methanogenesis in M. nevadense occurs via Mcr and is fueled by the consumption of cross-fed byproducts of xyloglucan fermentation mediated by other community members. Phylogenetic analysis shows close affiliation of the M. nevadense Mcr with those from Korarchaeota, Nezhaarchaeota, Verstraetearchaeota, and other Archaeoglobales that are divergent from well-characterized Mcrs. We propose these archaea likely also use functional Mcr complexes to generate methane on the basis of our experimental validation in M. nevadense. Although our stable isotope approach reveals that microbial methanogenesis contributes only a small proportion of the overall methane abundance in the native habitat, divergent Mcr-encoding archaea may be underestimated sources of biological methane in terrestrial and marine hydrothermal environments.

microbiology↗

bioRxiv2018

Culture-free generation of microbial genomes from human and marine microbiomes

Our understanding of natural microbial communities is shaped by the careful investigation of a relatively small number of isolated and cultured organisms, and by analysis of genomic sequences obtained by culture-free metagenomic sequencing approaches. Metagenomic shotgun sequencing has facilitated partial reconstruction of strain-level community structure and functional repertoire. Unfortunately, it remains difficult to cost-effectively produce high quality genome drafts for individual microbes without isolation and culture. Recent molecular techniques that partition long DNA fragments and then barcode short fragments derived from them produce \"read clouds\", which are short-read sequences containing long-range information. Here, we present a novel application of a read cloud technique to microbiome samples, as well as Athena, a de novo assembler that uses these barcodes to produce improved metagenomic assemblies. We apply our approach to sequence human stool samples from two healthy individuals, and compare it to existing short read and synthetic long read metagenomic sequencing approaches. We find that read cloud metagenomic sequencing and Athena assembly produce the most complete individual genome drafts. These genome drafts are also highly contiguous (>200kb N50, <10 contigs), even for bacteria that have relatively low (20x) raw short read sequence coverage. We also apply this approach to a significantly more complex marine sediment sample and obtain 23 genome drafts with valuable 16S ribosomal RNA taxonomic marker sequences, nine of which are complete genome drafts. Read cloud metagenomic sequencing allows culture-free generation of high quality microbial genome drafts using only a single shotgun experiment.

genomics↗