Molecular hydrogen in seawater supports growth of diverse marine bacteria

Hydrogen gas oxidation-driven reductive mobilization of arsenic in solid phase contributing to arsenite contamination in groundwater: Insights from metagenomic and microcosm analyses

Hydrogen gas (H2) is naturally produced by biological and non-biological reactions in various environmental niches. However, the influence of H2 on microbial processes that cause the mobilization and release of arsenic from solid phase into groundwater remains to be resolved. Given that dissimilatory arsenate [As(V)]-respiring prokaryotes (DARPs) have been demonstrated to significantly contribute to the formation of As-contaminated groundwater, our study specifically examined the interactions between H2 and DARPs. We prepared an enriched DARP population from As-contaminated soils. Metagenomic analyses of the DARP population revealed that approximately 46.7 % of the qualified DARPs' MAGs contain at least one type I Ni-Fe hydrogenase. The Ni-Fe hydrogenase proteins in DARPs show unique diversity. Functional assays indicate that the DARP population exhibited notable activity in oxidizing H2 while concurrently reducing As(V) under strictly anaerobic conditions. Arsenic release assays indicate that the DARP population is highly proficient at catalyzing the reductive mobilization of arsenic in scorodite, using hydrogen as the electron donor. These findings offer the initial evidence that H2 can directly promote the formation of arsenic-contaminated groundwater mediated by DARPs, a biogeochemical process that has long been overlooked. Therefore, this study increases our insight into the microbial mechanisms involved in the formation of arsenic-contaminated groundwater.

Microbial hydrogen oxidation potential in seasonally hypoxic Baltic Sea sediments

The majority of the organic matter (OM) degradation on the seafloor occurs in coastal regions. Since oxygen (O2) becomes quickly depleted in the top sediments, most of the OM decomposition is driven by microbial sulfate reduction (SR) and fermentation, the latter generating molecular hydrogen (H2). If the H2 is not consumed by hydrogenotrophic microorganisms and accumulates in the sedimentary porewaters, OM degradation is hindered. Despite the importance of H2 scavenging microorganisms for OM mineralization, the knowledge on H2 oxidizers and their constraints in coastal marine sediments is still quite limited. Here we investigated the role of H2 oxidizers in top (2 to 5 cm, suboxic-sulfidic) and bottom (18 to 22 cm, sulfidic) coastal sediments from a location exposed to seasonal hypoxia in the SW Baltic Sea. We used sediments from April, May and August, representative of different seasons. We spiked respective sediment slurries with H2 and incubated them for up to 4 weeks under O2-free conditions. H2 consumption potential, methane production and shifts in bacterial and archaeal 16S rRNA gene amplicons (generated from RNA) were assessed over time. The seasonal variations in sedimentary community compositions and pore water geochemistry already gave distinct starting conditions for the H2 enrichments. Sediments exposed to near anoxic bottom water conditions favored a microbial starter community exhibiting the highest H2 oxidation potential. Most of the observed H2 oxidation potential appeared associated with hydrogenotrophic sulfate reducers. The putative involvement of massively enriched ANME in H2 cycling in May 18 to 22 cm sediment horizons is conspicuous. While the differences in the observed H2 oxidation potentials in the studied sediment slurries are likely related to the (season-depending) overall redox state of the sediments and interstitial waters, the influence of microbial interconnections could not be fully resolved and evaluated, demonstrating the need for further consumption- and community-based studies.

Temperature-dependent responses of the hard corals Acropora sp. and Pocillopora verrucosa to molecular hydrogen

Coral reefs are increasingly threatened by mass bleaching events due to global ocean warming. Novel management strategies are urgently needed to support coral survival until global efforts can mitigate ocean warming. Given the strong antioxidant, anti-inflammatory and anti-apoptotic properties of molecular hydrogen, our study explores its potential to alleviate the negative effects of heat stress on corals. We investigated the ecophysiological responses of two common hard corals (Acropora sp. and Pocillopora verrucosa) from the Central Red Sea under ambient (26 °C) and elevated seawater temperatures (32 °C), with and without hydrogen addition ( ~ 150 µ M H2) over 48 h. Our results showed that at 32 °C without hydrogen addition, P. verrucosa exhibited high temperature tolerance, whereas Acropora sp. showed significant reductions in photosynthetic efficiency and maximum electron transport rate compared to the ambient condition (26 °C). The addition of hydrogen at 32 °C increased the maximum electron transport rate of Acropora sp. by 28%, maintaining it at levels compared to those at 26 °C. In contrast, the addition of hydrogen at 26 °C caused a significant decrease in the photophysiology of both Acropora sp. and P. verrucosa. This suggests that the short-term response of the coral holobiont to molecular hydrogen is temperature-dependent, potentially benefiting the coral holobiont under heat stress, while impairing the photophysiology under ambient temperatures. Our findings therefore provide the foundation for future long-term studies uncovering the mechanisms behind molecular hydrogen, potentially informing the development of new management strategies to enhance coral resilience to ocean warming.

Insights into the hydrogen-fueled bioreduction of vanadium(V) by marine Shewanella sp. FDA-1: Process and mechanism

Microbial-driven V(V) reduction plays a crucial role in its biogeochemical cycle, yet the mechanisms underlying this bioreduction remain inadequately understood. While the effectiveness of organic compounds as electron donors in facilitating bacterial reduction of V(V) has been established, the role of inorganic electron donors in initiating this process at the level of pure cultured bacteria has not been explored. In this study, we report on a marine Shewanella sp. FDA-1 that utilizes hydrogen (H2) as an energy source to reduce V(V). In addition, the reduction mechanism was investigated through a combination of genomics, RT-qPCR, heterologous expression of key proteins, extracellular secretion analyses, and electron transfer activity assays. Our results demonstrate that H2 serves as an effective electron donor, enabling Shewanella sp. FDA-1 to reduce V(V) across various salinities (2-7 %) and pH values (5-9). When exposed to 5 mM V(V), the presence of 1-20 mL of H2 resulted in V(V) bioreduction rates ranging from 0.039 to 0.11 h-1 (R2 > 0.73). Amorphous V(IV) compounds were characterized as reduction products using XRD, XPS, FTIR, and SEM. Mechanistic studies indicate that the glutathione system, cytochromes, and extracellular substances such as riboflavin play important roles in V(V) reduction (p < 0.05). Furthermore, our findings reveal that the addition of H2 and lactate triggers different response sequences among these three reduction pathways, suggesting distinct reduction mechanisms between organic and inorganic electron donors. These insights enhance our understanding of microbial vanadium transformation and provide valuable guidance for developing novel H2-based remediation technologies for vanadium-contaminated environments.

Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria

Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring the obtained electrons to the aerobic respiratory chain. However, it is unknown how these enzymes oxidize CO at low concentrations and interact with the respiratory chain. Here, we use cryo-electron microscopy and structural modeling to show how Mo-CODHMs (CoxSML) from Mycobacterium smegmatis interacts with its partner, the membrane-bound menaquinone-binding protein CoxG. We provide electrochemical, biochemical and genetic evidence that Mo-CODH transfers CO-derived electrons to the aerobic respiratory chain through CoxG. Lastly, we show that Mo-CODH and CoxG genetically and structurally associate in diverse bacteria and archaea. These findings reveal the basis of the biogeochemically and ecologically important process of atmospheric CO oxidation, while demonstrating that long-range quinone transport is a general mechanism of energy conservation, which convergently evolved on multiple occasions.

Metabolism of CO and H2 by pioneer bacteria in volcanic soils and the phyllosphere

Trace gas degradation is a widespread metabolic adaptation in microbial communities, driving chemosynthesis and providing auxiliary energy that enhances persistence during nutrient starvation. In particular, carbon monoxide and hydrogen degradation can be of crucial importance for pioneering microbial communities colonising new, oligotrophic environmental niches, such as fresh volcanic deposits or the aerial interface of the phyllosphere. After volcanic eruptions, trace gas metabolism helps pioneer colonisers to initiate soil formation in ash deposits and on recently solidified lava, a vital ecosystem service. Similarly, in the phyllosphere, bacteria colonising newly emerging leaves and shoots, and/or persisting on the oligotrophic surface of plants, also benefit from trace gas oxidation and, given the global size of this habitat, likely constitute a significant sink for these trace gases affecting atmospheric chemistry. Herein, we review the current state of knowledge surrounding microbial oxidation of carbon monoxide and hydrogen and discuss how this may contribute to niche colonisation in oligotrophic ecosystems.

Agro-industrial Waste Utilization, Medium Optimization, and Immobilization of Economically Feasible Halo-Alkaline Protease Produced by Nocardiopsis dassonvillei Strain VCS-4

The oceanic actinobacteria have strong potential to secrete novel enzymes with unique properties useful for biotechnological applications. The Nocardiopsis dassonvillei strain VCS-4, associated with seaweed Caulerpa scalpeliformis, was a halo-alkaline protease producer. Further investigation focuses on medium optimization and the use of agro-industrial waste for economically feasible, high-yield protease production. A total of 12 experimental runs were designed using Minitab-20 software and Placket-Burman design. Among the 7 physicochemical parameters analyzed, incubation time and gelatin were detected as significant factors responsible for higher protease production. Incubation time and gelatin were further analyzed using OVATs. Optimal protease production was achieved with 2% gelatin, 0.1% yeast extract, 0.1% bacteriological peptone, 7% NaCl, pH 8, 5% inoculum, and a 7-day incubation period, resulting in a maximum protease activity (Pmax) of 363.97 U/mL, generation time of 11.9 h, specific growth rate of 0.161 g/mL/h, and protease productivity (Qp) of 61.65 U/mL/h. Moreover, utilizing groundnut cake as an agro-industrial waste led to enhanced production parameters: Pmax of 408.42 U/mL, generation time of 9.74 h, specific growth rate of 0.361 g/mL/h, and Qp of 68.07 U/mL/h. The immobilization of crude protease was achieved using Seralite SRC 120 as a support matrix resulting in 470.38 U/g immobilization, 88.20% immobilization yield, and 28.90% recovery activity. Characterization of both crude and immobilized proteases revealed optimal activity at pH 10 and 70 °C. Immobilization enhanced the shelf-life, reusability, and stability of VCS-4 protease under extreme conditions.

Hydrothermal vents supporting persistent plumes and microbial chemoautotrophy at Gakkel Ridge (Arctic Ocean)

Hydrothermal vents emit hot fluids enriched in energy sources for microbial life. Here, we compare the ecological and biogeochemical effects of hydrothermal venting of two recently discovered volcanic seamounts, Polaris and Aurora of the Gakkel Ridge, in the ice-covered Central Arctic Ocean. At both sites, persistent hydrothermal plumes increased up to 800 m into the deep Arctic Ocean. In the two non-buoyant plumes, rates of microbial carbon fixation were strongly elevated compared to background values of 0.5-1 μmol m-3 day-1 in the Arctic deep water, which suggests increased chemoautotrophy on vent-derived energy sources. In the Polaris plume, free sulfide and up to 360 nM hydrogen enabled microorganisms to fix up to 46 μmol inorganic carbon (IC) m-3 day-1. This energy pulse resulted in a strong increase in the relative abundance of SUP05 by 25% and Candidatus Sulfurimonas pluma by 7% of all bacteria. At Aurora, microorganisms fixed up to 35 μmol IC m-3 day-1. Here, metal sulfides limited the bioavailability of reduced sulfur species, and the putative hydrogen oxidizer Ca. S. pluma constituted 35% and SUP05 10% of all bacteria. In accordance with this data, transcriptomic analysis showed a high enrichment of hydrogenase-coding transcripts in Aurora and an enrichment of transcripts coding for sulfur oxidation in Polaris. There was neither evidence for methane consumption nor a substantial increase in the abundance of putative methanotrophs or their transcripts in either plume. Together, our results demonstrate the dominance of hydrogen and sulfide as energy sources in Arctic hydrothermal vent plumes.

Marine sponge microbe provides insights into evolution and virulence of the tubercle bacillus

Reconstructing the evolutionary origins of Mycobacterium tuberculosis, the causative agent of human tuberculosis, has helped identify bacterial factors that have led to the tubercle bacillus becoming such a formidable human pathogen. Here we report the discovery and detailed characterization of an exceedingly slow growing mycobacterium that is closely related to M. tuberculosis for which we have proposed the species name Mycobacterium spongiae sp. nov., (strain ID: FSD4b-SM). The bacterium was isolated from a marine sponge, taken from the waters of the Great Barrier Reef in Queensland, Australia. Comparative genomics revealed that, after the opportunistic human pathogen Mycobacterium decipiens, M. spongiae is the most closely related species to the M. tuberculosis complex reported to date, with 80% shared average nucleotide identity and extensive conservation of key M. tuberculosis virulence factors, including intact ESX secretion systems and associated effectors. Proteomic and lipidomic analyses showed that these conserved systems are functional in FSD4b-SM, but that it also produces cell wall lipids not previously reported in mycobacteria. We investigated the virulence potential of FSD4b-SM in mice and found that, while the bacteria persist in lungs for 56 days after intranasal infection, no overt pathology was detected. The similarities with M. tuberculosis, together with its lack of virulence, motivated us to investigate the potential of FSD4b-SM as a vaccine strain and as a genetic donor of the ESX-1 genetic locus to improve BCG immunogenicity. However, neither of these approaches resulted in superior protection against M. tuberculosis challenge compared to BCG vaccination alone. The discovery of M. spongiae adds to our understanding of the emergence of the M. tuberculosis complex and it will be another useful resource to refine our understanding of the factors that shaped the evolution and pathogenesis of M. tuberculosis.

Chemosynthesis: a neglected foundation of marine ecology and biogeochemistry

Chemosynthesis is a metabolic process that transfers carbon to the biosphere using reduced compounds. It is well recognised that chemosynthesis occurs in much of the ocean, but it is often thought to be a negligible process compared to photosynthesis. Here we propose that chemosynthesis is the underlying process governing primary production in much of the ocean and suggest that it extends to a much wider range of compounds, microorganisms, and ecosystems than previously thought. In turn, this process has had a central role in controlling marine biogeochemistry, ecology, and carbon budgets across the vast realms of the ocean, from the dawn of life to contemporary times.

Genomic and phenotypic characterization of 26 novel marine bacterial strains with relevant biogeochemical roles and widespread presence across the global ocean

Prokaryotes dominate global oceans and shape biogeochemical cycles, yet most taxa remain uncultured and uncharacterized as of today. Here we present the characterization of 26 novel marine bacterial strains from a large isolate collection obtained from Blanes Bay (NW Mediterranean) microcosm experiments made in the four seasons. Morphological, cultural, biochemical, physiological, nutritional, genomic, and phylogenomic analyses were used to characterize and phylogenetically place the novel isolates. The strains represent 23 novel bacterial species and six novel genera: three novel species pertaining to class Alphaproteobacteria (families Rhodobacteraceae and Sphingomonadaceae), six novel species and three new genera from class Gammaproteobacteria (families Algiphilaceae, Salinispheraceae, and Alteromonadaceae), 13 novel species and three novel genera from class Bacteroidia (family Flavobacteriaceae), and one new species from class Rhodothermia (family Rubricoccaceae). The bacteria described here have potentially relevant roles in the cycles of carbon (e.g., carbon fixation or energy production via proteorhodopsin), nitrogen (e.g., denitrification or use of urea), sulfur (oxidation of sulfur compounds), phosphorus (acquisition and use of different forms of phosphorus and remodeling of membrane phospholipids), and hydrogen (oxidation of hydrogen to obtain energy). We mapped the genomes of the presented strains to the Tara Oceans metagenomes to reveal that these strains were globally distributed, with those of the family Flavobacteriaceae being the most widespread and abundant, while Rhodothermia being the rarest and most localized. While molecular-only approaches are also important, our study stresses the importance of culturing as a powerful tool to further understand the functioning of marine bacterial communities.

Trace gas oxidation sustains energy needs of a thermophilic archaeon at suboptimal temperatures

Diverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Such trace gas oxidation is recognised as a globally significant process that serves as the main sink in the biogeochemical H2 cycle and sustains microbial biodiversity in oligotrophic ecosystems. However, it is unclear whether archaea can also use atmospheric H2. Here we show that a thermoacidophilic archaeon, Acidianus brierleyi (Thermoproteota), constitutively consumes H2 and CO to sub-atmospheric levels. Oxidation occurs across a wide range of temperatures (10 to 70 °C) and enhances ATP production during starvation-induced persistence under temperate conditions. The genome of A. brierleyi encodes a canonical CO dehydrogenase and four distinct [NiFe]-hydrogenases, which are differentially produced in response to electron donor and acceptor availability. Another archaeon, Metallosphaera sedula, can also oxidize atmospheric H2. Our results suggest that trace gas oxidation is a common trait of Sulfolobales archaea and may play a role in their survival and niche expansion, including during dispersal through temperate environments.

How to identify cell material in a single ice grain emitted from Enceladus or Europa

Icy moons like Enceladus, and perhaps Europa, emit material sourced from their subsurface oceans into space via plumes of ice grains and gas. Both moons are prime targets for astrobiology investigations. Cassini measurements revealed a large compositional diversity of emitted ice grains with only 1 to 4% of Enceladus's plume ice grains containing organic material in high concentrations. Here, we report experiments simulating mass spectra of ice grains containing one bacterial cell, or fractions thereof, as encountered by advanced instruments on board future space missions to Enceladus or Europa, such as the SUrface Dust Analyzer onboard NASA's upcoming Europa Clipper mission at flyby speeds of 4 to 6 kilometers per second. Mass spectral signals characteristic of the bacteria are shown to be clearly identifiable by future missions, even if an ice grain contains much less than one cell. Our results demonstrate the advantage of analyses of individual ice grains compared to a diluted bulk sample in a heterogeneous plume.

Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability

Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3 % of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.

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

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

IMPORTANCE

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

Bacterial chemolithoautotrophy in ultramafic plumes along the Mid-Atlantic Ridge

Hydrothermal vent systems release reduced chemical compounds that act as an important energy source in the deep sea. Chemolithoautotrophic microbes inhabiting hydrothermal plumes oxidize these compounds, in particular, hydrogen and reduced sulfur, to obtain the energy required for CO2 fixation. Here, we analysed the planktonic communities of four hydrothermal systems located along the Mid-Atlantic Ridge: Irinovskoe, Semenov-2, Logatchev-1, and Ashadze-2, by combining long-read 16S rRNA gene analysis, fluorescence in situ hybridization, meta-omics, and thermodynamic calculations. Sulfurimonas and SUP05 dominated the microbial communities in these hydrothermal plumes. Investigation of Sulfurimonas and SUP05 MAGs, and their gene transcription in plumes indicated a niche partitioning driven by hydrogen and sulfur. In addition to sulfur and hydrogen oxidation, a novel SAR202 clade inhabiting the plume, here referred to as genus Carboxydicoccus, harbours the capability for CO oxidation and CO2 fixation via reverse TCA cycle. Both pathways were also highly transcribed in other hydrogen-rich plumes, including the Von Damm vent field. Carboxydicoccus profundi reached up to 4% relative abundance (1.0 x 103 cell ml- 1) in Irinovskoe non-buoyant plume and was also abundant in non-hydrothermally influenced deep-sea metagenomes (up to 5 RPKM). Therefore, CO, which is probably not sourced from the hydrothermal fluids (1.9-5.8 μM), but rather from biological activities within the rising fluid, may serve as a significant energy source in hydrothermal plumes. Taken together, this study sheds light on the chemolithoautotrophic potential of the bacterial community in Mid-Atlantic Ridge plumes.

High diversity, abundance, and expression of hydrogenases in groundwater

Hydrogen may be the most important electron donor available in the subsurface. Here we analyse the diversity, abundance and expression of hydrogenases in 5 proteomes, 25 metagenomes, and 265 amplicon datasets of groundwaters with diverse geochemistry. A total of 1545 new [NiFe]-hydrogenase gene sequences were recovered, which considerably increased the number of sequences (1999) in a widely used database. [NiFe]-hydrogenases were highly abundant, as abundant as the DNA-directed RNA polymerase. The abundance of hydrogenase genes increased with depth from 0 to 129 m. Hydrogenases were present in 481 out of 1245 metagenome-assembled genomes. The relative abundance of microbes with hydrogenases accounted for ~50% of the entire community. Hydrogenases were actively expressed, making up as much as 5.9% of methanogen proteomes. Most of the newly discovered diversity of hydrogenases was in "Group 3b", which has been associated with sulfur metabolism. "Group 3d", facilitating the interconversion of electrons between hydrogen and NAD, was the most abundant and mainly observed in methanotrophs and chemoautotrophs. "Group 3a", associated with methanogenesis, was the most abundant in proteomes. Two newly discovered groups of [NiFe]-hydrogenases, observed in Methanobacteriaceae and Anaerolineaceae, further expanded diversity. Our results highlight the vast diversity, abundance and expression of hydrogenases in groundwaters, suggesting a high potential for hydrogen oxidation in subsurface habitats.

Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition

High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.

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

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

Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC

Introduction

Anaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate.

Methods

16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina.

Results

We found that methane began to accumulate while sulfate is still abundant (6-8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES).

Discussion

We conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the co-occurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations.

Depth drives the distribution of microbial ecological functions in the coastal western Antarctic Peninsula

The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research.

Aerobic marine bacteria can use H2 for growth

Molecular hydrogen (H₂) and carbon monoxide (CO) are ubiquitously available in the Earth's oceans, yet their low dissolved concentrations seemed unlikely to support microbial growth. Lappan, Shelley, Islam et al. now report that dissolved H₂ supports the growth of diverse aerobic marine bacteria in the oceans.