Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank

The subseafloor crustal biosphere: Ocean's hidden biogeochemical reactor

Underlying the thick sediment layer in ocean basins, the flow of seawater through the cracked and porous upper igneous crust supports a previously hidden and largely unexplored active subsurface microbial biome. Subseafloor crustal systems offer an enlarged surface area for microbial habitats and prolonged cell residence times, promoting the evolution of novel microbial lineages in the presence of steep physical and thermochemical gradients. The substantial metabolic potential and dispersal capabilities of microbial communities within these systems underscore their crucial role in biogeochemical cycling. However, the intricate interplay between fluid chemistry, temperature variations, and microbial activity remains poorly understood. These complexities introduce significant challenges in unraveling the factors that regulate microbial distribution and function within these dynamic ecosystems. Using synthesized data from previous studies, this work describes how the ocean crustal biosphere functions as a continuous-flow biogechemical reactor. It simultaneously promotes the breakdown of surface-derived organic carbon and the creation of new, chemosynthetic material, thereby enhancing element recycling and ocean carbon productivity. Insights gained from the qualitative analysis of the extent of biogeochemical microbial activity and diversity across the temperature and chemical gradients that characterize these habitats, as reviewed herein, challenge traditional models of global ocean carbon productivity and provide the development of a new conceptual framework for understanding the quantitative metabolic potential and broad dispersal of the crustal microbial biome.

A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA

The deep terrestrial subsurface is a large and diverse microbial habitat and vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km into the crust. From eight geochemically and spatially distinct fluid samples we reconstructed ~600 partial to near-complete metagenome-assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include members of the candidate phyla radiation, two new MAGs from OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available, and new MAGs from the Eisenbacteria, Omnitrophota, and Edwardsbacteria. We find that microbes spanning this expansive phylogenetic diversity and physical subsurface space gain a competitive edge by maintaining a wide variety of functional pathways, are often capable of numerous dissimilatory energy metabolisms and poised to take advantage of nutrients as they become available in isolated fracture fluids. Our results support and expand on emerging themes of tight nutrient cycling and genomic plasticity in deep subsurface biosphere taxa.

Decorated Vesicles as Prebiont Systems (a Hypothesis)

Decorated vesicles in deep, seafloor basalts form abiotically, but show at least four life-analogous features, which makes them a candidate for origin of life research. These features are a physical enclosure, carbon-assimilatory catalysts, semi-permeable boundaries, and a source of usable energy. The nanometer-to-micron-sized spherules on the inner walls of decorated vesicles are proposed to function as mineral proto-enzymes. Chemically, these structures resemble synthetic FeS clusters shown to convert CO2, CO and H2 into methane, formate, and acetate. Secondary phyllosilicate minerals line the vesicles' inner walls and can span openings in the vesicles and thus can act as molecular sieves between the vesicles' interior and the surrounding aquifer. Lastly, basalt glass in the vesicle walls takes up protons, which replace cations in the silicate framework. This results in an inward proton flux, reciprocal outward flux of metal cations, more alkaline pH inside the vesicle than outside, and production of more phyllosilicates. Such life-like features could have been exploited to move decorated vesicles toward protolife systems. Decorated vesicles are proposed as study models of prebiotic systems that are expected to have existed on the early Earth and Earth-like exoplanets. Their analysis can lead to better understanding of changes in planetary geocycles during the origin of life.

First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones

The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In this study, we present the first shotgun metagenomics study of unamplified DNA from sediment samples from different depths in this stratified environment. Bioinformatic analyses showed a shift from a heterotrophic, Chloroflexota-dominated community above the upper SMTZ to a chemolithoautotrophic Proteobacteria-dominated community below the secondary SMTZ. The reintroduction of sulfate likely enables respiration and boosts active cells that oxidize acetate, iron, and complex carbohydrates to degrade dead biomass in this low-abundance, low-diversity environment. In addition, analyses showed many proteins of unknown function as well as novel metagenome-assembled genomes (MAGs). The study provides new insights into microbial communities in this habitat, enabled by an improved DNA extraction protocol that allows a less biased view of taxonomic composition and metabolic activities, as well as uncovering novel taxa. Our approach presents the first successful attempt at unamplified shotgun sequencing samples from beyond 50 meters below the seafloor and opens new ways for capturing the true diversity and functional potential of deep-sea sediments.

Life strategies for Aminicenantia in subseafloor oceanic crust

After decades studying the microbial "deep biosphere" in subseafloor oceanic crust, the growth and life strategies in this anoxic, low energy habitat remain poorly described. Using both single cell genomics and metagenomics, we reveal the life strategies of two distinct lineages of uncultivated Aminicenantia bacteria from the basaltic subseafloor oceanic crust of the eastern flank of the Juan de Fuca Ridge. Both lineages appear adapted to scavenge organic carbon, as each have genetic potential to catabolize amino acids and fatty acids, aligning with previous Aminicenantia reports. Given the organic carbon limitation in this habitat, seawater recharge and necromass may be important carbon sources for heterotrophic microorganisms inhabiting the ocean crust. Both lineages generate ATP via several mechanisms including substrate-level phosphorylation, anaerobic respiration, and electron bifurcation driving an Rnf ion translocation membrane complex. Genomic comparisons suggest these Aminicenantia transfer electrons extracellularly, perhaps to iron or sulfur oxides consistent with mineralogy of this site. One lineage, called JdFR-78, has small genomes that are basal to the Aminicenantia class and potentially use "primordial" siroheme biosynthetic intermediates for heme synthesis, suggesting this lineage retain characteristics of early evolved life. Lineage JdFR-78 contains CRISPR-Cas defenses to evade viruses, while other lineages contain prophage that may help prevent super-infection or no detectable viral defenses. Overall, genomic evidence points to Aminicenantia being well adapted to oceanic crust environments by taking advantage of simple organic molecules and extracellular electron transport.

Genomics discovery of giant fungal viruses from subsurface oceanic crustal fluids

The oceanic igneous crust is a vast reservoir for microbial life, dominated by diverse and active bacteria, archaea, and fungi. Archaeal and bacterial viruses were previously detected in oceanic crustal fluids at the Juan de Fuca Ridge (JdFR). Here we report the discovery of two eukaryotic Nucleocytoviricota genomes from the same crustal fluids by sorting and sequencing single virions. Both genomes have a tRNA^Tyr gene with an intron (20 bps) at the canonical position between nucleotide 37 and 38, a common feature in eukaryotic and archaeal tRNA genes with short introns (<100 bps), and fungal genes acquired through horizontal gene transfer (HGT) events. The dominance of Ascomycota fungi as the main eukaryotes in crustal fluids and the evidence for HGT point to these fungi as the putative hosts, making these the first putative fungi-Nucleocytoviricota specific association. Our study suggests active host-viral dynamics for the only eukaryotic group found in the subsurface oceanic crust and raises important questions about the impact of viral infection on the productivity and biogeochemical cycling in this ecosystem.

Culturable Bacterial Diversity from the Basaltic Subsurface of the Young Volcanic Island of Surtsey, Iceland

The oceanic crust is the world's largest and least explored biosphere on Earth. The basaltic subsurface of Surtsey island in Iceland represents an analog of the warm and newly formed-oceanic crust and offers a great opportunity for discovering novel microorganisms. In this study, we collected borehole fluids, drill cores, and fumarole samples to evaluate the culturable bacterial diversity from the subsurface of the island. Enrichment cultures were performed using different conditions, media and temperatures. A total of 195 bacterial isolates were successfully cultivated, purified, and identified based on MALDI-TOF MS analysis and by 16S rRNA gene sequencing. Six different clades belonging to Firmicutes (40%), Gammaproteobacteria (28.7%), Actinobacteriota (22%), Bacteroidota (4.1%), Alphaproteobacteria (3%), and Deinococcota (2%) were identified. Bacillus (13.3%) was the major genus, followed by Geobacillus (12.33%), Enterobacter (9.23%), Pseudomonas (6.15%), and Halomonas (5.64%). More than 13% of the cultured strains potentially represent novel species based on partial 16S rRNA gene sequences. Phylogenetic analyses revealed that the isolated strains were closely related to species previously detected in soil, seawater, and hydrothermal active sites. The 16S rRNA gene sequences of the strains were aligned against Amplicon Sequence Variants (ASVs) from the previously published 16S rRNA gene amplicon sequence datasets obtained from the same samples. Compared with the culture-independent community composition, only 5 out of 49 phyla were cultivated. However, those five phyla accounted for more than 80% of the ASVs. Only 121 out of a total of 5642 distinct ASVs were culturable (≥98.65% sequence similarity), representing less than 2.15% of the ASVs detected in the amplicon dataset. Here, we support that the subsurface of Surtsey volcano hosts diverse and active microbial communities and that both culture-dependent and -independent methods are essential to improving our insight into such an extreme and complex volcanic environment.

Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume

Fluids circulating through oceanic crust play important roles in global biogeochemical cycling mediated by their microbial inhabitants, but studying these sites is challenged by sampling logistics and low biomass. Borehole observatories installed at the North Pond study site on the western flank of the Mid-Atlantic Ridge have enabled investigation of the microbial biosphere in cold, oxygenated basaltic oceanic crust. Here we test a methodology that applies redox-sensitive fluorescent molecules for flow cytometric sorting of cells for single cell genomic sequencing from small volumes of low biomass (approximately 103 cells ml-1) crustal fluid. We compare the resulting genomic data to a recently published paired metagenomic and metatranscriptomic analysis from the same site. Even with low coverage genome sequencing, sorting cells from less than one milliliter of crustal fluid results in similar interpretation of dominant taxa and functional profiles as compared to 'omics analysis that typically filter orders of magnitude more fluid volume. The diverse community dominated by Gammaproteobacteria, Bacteroidetes, Desulfobacterota, Alphaproteobacteria, and Zetaproteobacteria, had evidence of autotrophy and heterotrophy, a variety of nitrogen and sulfur cycling metabolisms, and motility. Together, results indicate fluorescence activated cell sorting methodology is a powerful addition to the toolbox for the study of low biomass systems or at sites where only small sample volumes are available for analysis.

Microbial Abundance and Diversity in Subsurface Lower Oceanic Crust at Atlantis Bank, Southwest Indian Ridge

International Ocean Discovery Program Expedition 360 drilled Hole U1473A at Atlantis Bank, an oceanic core complex on the Southwest Indian Ridge, with the aim of recovering representative samples of the lower oceanic crust. Recovered cores were primarily gabbro and olivine gabbro. These mineralogies may host serpentinization reactions that have the potential to support microbial life within the recovered rocks or at greater depths beneath Atlantis Bank. We quantified prokaryotic cells and analyzed microbial community composition for rock samples obtained from Hole U1473A and conducted nutrient addition experiments to assess if nutrient supply influences the composition of microbial communities. Microbial abundance was low (≤10⁴ cells cm^-3) but positively correlated with the presence of veins in rocks within some depth ranges. Due to the heterogeneous nature of the rocks downhole (alternating stretches of relatively unaltered gabbros and more significantly altered and fractured rocks), the strength of the positive correlations between rock characteristics and microbial abundances was weaker when all depths were considered. Microbial community diversity varied at each depth analyzed. Surprisingly, addition of simple organic acids, ammonium, phosphate, or ammonium plus phosphate in nutrient addition experiments did not affect microbial diversity or methane production in nutrient addition incubation cultures over 60 weeks. The work presented here from Site U1473A, which is representative of basement rock samples at ultraslow spreading ridges and the usually inaccessible lower oceanic crust, increases our understanding of microbial life present in this rarely studied environment and provides an analog for basement below ocean world systems such as Enceladus. IMPORTANCE The lower oceanic crust below the seafloor is one of the most poorly explored habitats on Earth. The rocks from the Southwest Indian Ridge (SWIR) are similar to rock environments on other ocean-bearing planets and moons. Studying this environment helps us increase our understanding of life in other subsurface rocky environments in our solar system that we do not yet have the capability to access. During an expedition to the SWIR, we drilled 780 m into lower oceanic crust and collected over 50 rock samples to count the number of resident microbes and determine who they are. We also selected some of these rocks for an experiment where we provided them with different nutrients to explore energy and carbon sources preferred for growth. We found that the number of resident microbes and community structure varied with depth. Additionally, added nutrients did not shape the microbial diversity in a predictable manner.

Basalt-Hosted Microbial Communities in the Subsurface of the Young Volcanic Island of Surtsey, Iceland

The island of Surtsey was formed in 1963–1967 on the offshore Icelandic volcanic rift zone. It offers a unique opportunity to study the subsurface biosphere in newly formed oceanic crust and an associated hydrothermal-seawater system, whose maximum temperature is currently above 120°C at about 100m below surface. Here, we present new insights into the diversity, distribution, and abundance of microorganisms in the subsurface of the island, 50years after its creation. Samples, including basaltic tuff drill cores and associated fluids acquired at successive depths as well as surface fumes from fumaroles, were collected during expedition 5059 of the International Continental Scientific Drilling Program specifically designed to collect microbiological samples. Results of this microbial survey are investigated with 16S rRNA gene amplicon sequencing and scanning electron microscopy. To distinguish endemic microbial taxa of subsurface rocks from potential contaminants present in the drilling fluid, we use both methodological and computational strategies. Our 16S rRNA gene analysis results expose diverse and distinct microbial communities in the drill cores and the borehole fluid samples, which harbor thermophiles in high abundance. Whereas some taxonomic lineages detected across these habitats remain uncharacterized (e.g., Acetothermiia, Ammonifexales), our results highlight potential residents of the subsurface that could be identified at lower taxonomic rank such as Thermaerobacter, BRH-c8a (Desulfallas-Sporotomaculum), Thioalkalimicrobium, and Sulfurospirillum. Microscopy images reveal possible biotic structures attached to the basaltic substrate. Finally, microbial colonization of the newly formed basaltic crust and the metabolic potential are discussed on the basis of the data.

Microbial Diversity and Function in Shallow Subsurface Sediment and Oceanic Lithosphere of the Atlantis Massif

The marine lithospheric subsurface is one of the largest biospheres on Earth; however, little is known about the identity and ecological function of microorganisms found in low abundance in this habitat, though these organisms impact global-scale biogeochemical cycling. Here, we describe the diversity and metabolic potential of sediment and endolithic (within rock) microbial communities found in ultrasmall amounts (10¹ to 10⁴ cells cm⁻³) in the subsurface of the Atlantis Massif, an oceanic core complex on the Mid-Atlantic Ridge that was sampled on International Ocean Discovery Program (IODP) Expedition 357. This study used fluorescence-activated cell sorting (FACS) to enable the first amplicon, metagenomic, and single-cell genomic study of the shallow (<20 m below seafloor) subsurface of an actively serpentinizing marine system. The shallow subsurface biosphere of the Atlantis Massif was found to be distinct from communities observed in the nearby Lost City alkaline hydrothermal fluids and chimneys, yet similar to other low-temperature, aerobic subsurface settings. Genes associated with autotrophy were rare, although heterotrophy and aerobic carbon monoxide and formate cycling metabolisms were identified. Overall, this study reveals that the shallow subsurface of an oceanic core complex hosts a biosphere that is not fueled by active serpentinization reactions and by-products.

Multiple carbon incorporation strategies support microbial survival in cold subseafloor crustal fluids

Biogeochemical processes occurring in fluids that permeate oceanic crust make measurable contributions to the marine carbon cycle, but quantitative assessments of microbial impacts on this vast, subsurface carbon pool are lacking. We provide bulk and single-cell estimates of microbial biomass production from carbon and nitrogen substrates in cool, oxic basement fluids from the western flank of the Mid-Atlantic Ridge. The wide range in carbon and nitrogen incorporation rates indicates a microbial community well poised for dynamic conditions, potentially anabolizing carbon and nitrogen at rates ranging from those observed in subsurface sediments to those found in on-axis hydrothermal vent environments. Bicarbonate incorporation rates were highest where fluids are most isolated from recharging bottom seawater, suggesting that anabolism of inorganic carbon may be a potential strategy for supplementing the ancient and recalcitrant dissolved organic carbon that is prevalent in the globally distributed subseafloor crustal environment.

Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough

Microbial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.

Sampling of basement fluids via Circulation Obviation Retrofit Kits (CORKs) for dissolved gases, fluid fixation at the seafloor, and the characterization of organic carbon

The advanced instrumented GeoMICROBE sleds (Cowen et al., 2012) facilitate the collection of hydrothermal fluids and suspended particles in the subseafloor (basaltic) basement through Circulation Obviation Retrofit Kits (CORKs) installed within boreholes of the Integrated Ocean Drilling Program. The main components of the GeoMICROBE can be converted into a mobile pumping system (MPS) that is installed on the front basket of a submersible or remotely-operated-vehicle (ROV). Here, we provide details of a hydrothermal fluid-trap used on the MPS, through which a gastight sampler can withdraw fluids. We also applied the MPS to demonstrate the value of fixing samples at the seafloor in order to determine redox-sensitive dissolved iron concentrations and speciation measurements. To make the best use of the GeoMICROBE sleds, we describe a miniature and mobile version of the GeoMICROBE sled, which permits rapid turn-over and is relatively easy for preparation and operation. Similar to GeoMICROBE sleds, the Mobile GeoMICROBE (MGM) is capable of collecting fluid samples, filtration of suspended particles, and extraction of organics. We validate this approach by demonstrating the seafloor extraction of hydrophobic organics from a large volume (247L) of hydrothermal fluids.•We describe the design of a hydrothermal fluid-trap for use with a gastight sampler, as well as the use of seafloor fixation, through ROV- or submersible assisted mobile pumping systems.•We describe the design of a Mobile GeoMICROBE (MGM) that enhances large volume hydrothermal fluid sampling, suspended particle filtration, and organic matter extraction on the seafloor.•We provide an example of organic matter extracted and characterized from hydrothermal fluids via a MGM.

Indigenous Ammonia-Oxidizing Archaea in Oxic Subseafloor Oceanic Crust

Ridge flanks represent the major avenue of chemical and heat exchange between the Earth’s oceans and the lithosphere and are thought to harbor an enormous and understudied biosphere. However, little is known about the diversity and functionality of the crustal biosphere. Here, we report an indigenous community of archaea specialized in ammonia oxidation (i.e., AOA) in the oxic oceanic crust at North Pond. These AOA are the dominant archaea and are likely responsible for most of the cycling taking place in the first step of nitrification, a feasible nitrogen cycling step in the oxic basement. The crustal AOA community structure significantly differs from that in deep ocean water but is similar to that of the community in the overlying sediments in close proximity. This report links the occurrence of AOA to their metabolic activity in the oxic subseafloor crust and suggests that ecological selection and in situ proliferation may shape the microbial community structure in the rocky subsurface.

Oceanic ridge flank systems represent one of the largest and least-explored microbial habitats on Earth. Fundamental ecological questions regarding community activity, recruitment, and succession in this environment remain unanswered. Here, we investigated ammonia-oxidizing archaea (AOA) in the sediment-buried basalts on the oxic and young ridge flank at North Pond, a sediment-filled pond on the western flank of the Mid-Atlantic Ridge, and compared them with those in the overlying sediments and bottom seawater. Nitrification in the North Pond basement is thermodynamically favorable and is supported by a reaction-transport model simulating the dynamics of nitrate in the crustal fluids. Nitrification rate is estimated to account for 6% to 7% of oxygen consumption, which is similar to the ratios found in marine oxic sediments, suggesting that aerobic mineralization of organic matter is the major ammonium source for crustal nitrifiers. Using the archaeal 16S rRNA and amoA genes as phylogenetic markers, we show that AOA, composed solely of Nitrosopumilaceae, are the major archaeal dwellers at North Pond. Phylogenetic analysis reveals that the crustal AOA communities are distinct from those in the bottom seawater and the upper oxic sediments but are similar to those in the basal part of the overlying sediment column, suggesting either similar environmental selection or the dispersal of microbes across the sediment-basement interface. Additionally, quantitative abundance data suggest enrichment of the dominant Nitrosopumilaceae clade (Eta clade) in the basement compared to the seawater. This study explored AOA and their activity in the upper oceanic crust, and our results have ecological implications for the biogeochemical cycling of nitrogen in the crustal subsurface.

IMPORTANCE Ridge flanks represent the major avenue of chemical and heat exchange between the Earth’s oceans and the lithosphere and are thought to harbor an enormous and understudied biosphere. However, little is known about the diversity and functionality of the crustal biosphere. Here, we report an indigenous community of archaea specialized in ammonia oxidation (i.e., AOA) in the oxic oceanic crust at North Pond. These AOA are the dominant archaea and are likely responsible for most of the cycling taking place in the first step of nitrification, a feasible nitrogen cycling step in the oxic basement. The crustal AOA community structure significantly differs from that in deep ocean water but is similar to that of the community in the overlying sediments in close proximity. This report links the occurrence of AOA to their metabolic activity in the oxic subseafloor crust and suggests that ecological selection and in situ proliferation may shape the microbial community structure in the rocky subsurface.

Ecology of Subseafloor Crustal Biofilms

The crustal subseafloor is the least explored and largest biome on Earth. Interrogating crustal life is difficult due to habitat inaccessibility, low-biomass and contamination challenges. Subseafloor observatories have facilitated the study of planktonic life in crustal aquifers, however, studies of life in crust-attached biofilms are rare. Here, we investigate biofilms grown on various minerals at different temperatures over 1-6 years at subseafloor observatories in the Eastern Pacific. To mitigate potential sequence contamination, we developed a new bioinformatics tool - TaxonSluice. We explore ecological factors driving community structure and potential function of biofilms by comparing our sequence data to previous amplicon and metagenomic surveys of this habitat. We reveal that biofilm community structure is driven by temperature rather than minerology, and that rare planktonic lineages colonize the crustal biofilms. Based on 16S rRNA gene overlap, we partition metagenome assembled genomes into planktonic and biofilm fractions and suggest that there are functional differences between these community types, emphasizing the need to separately examine each to accurately describe subseafloor microbe-rock-fluid processes. Lastly, we report that some rare lineages present in our warm and anoxic study site are also found in cold and oxic crustal fluids in the Mid-Atlantic Ridge, suggesting global crustal biogeography patterns.

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere

The exploration of Earth's terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage's evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.

Carbon fixation and energy metabolisms of a subseafloor olivine biofilm

Earth's largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon metabolisms in the deep thermal basaltic aquifer are poorly understood. Anaerobic carbon fixation pathways such as the Wood-Ljungdahl pathway, which uses hydrogen (H₂) and CO₂, may be common in thermal aquifers since water-rock reactions can produce H₂ in hydrothermal environments and bicarbonate is abundant in seawater. To test this, we reconstructed the metabolisms of eleven bacterial and archaeal metagenome-assembled genomes from an olivine biofilm obtained from a Juan de Fuca Ridge basaltic aquifer. We found that the dominant carbon fixation pathway was the Wood-Ljungdahl pathway, which was present in seven of the eight bacterial genomes. Anaerobic respiration appears to be driven by sulfate reduction, and one bacterial genome contained a complete nitrogen fixation pathway. This study reveals the potential pathways for carbon and energy flux in the deep anoxic thermal aquifer ecosystem, and suggests that ancient H₂-based chemolithoautotrophy, which once dominated Earth's early biosphere, may thus remain one of the dominant metabolisms in the suboceanic aquifer today.

Tunnel Formation in Basalt Glass

We propose a model whereby microscopic tunnels form in basalt glass in response to a natural proton flux from seawater into the glass. This flux is generated by the alteration of the glass as protons from water replace cations in the glass. In our proton gradient model, cells are gateways through which protons enter and alter the glass and through which cations leave the glass. In the process, tunnels are formed, and cells derive energy from the proton and ion fluxes. Proton flux from seawater into basalt glass would have occurred on Earth as soon as water accumulated on the surface and would have preceded biological redox catalysis. Tunnels in modern basalts are similar to tunnels in Archean basalts, which may be our earliest physical evidence of life. Proton gradients like those described in this paper certainly exist on other planetary bodies where silicate rocks are exposed to acidic to slightly alkaline water.

Exploration of deep terrestrial subsurface microbiome in Late Cretaceous Deccan traps and underlying Archean basement, India

Scientific deep drilling at Koyna, western India provides a unique opportunity to explore microbial life within deep biosphere hosted by ~65 Myr old Deccan basalt and Archaean granitic basement. Characteristic low organic carbon content, mafic/felsic nature but distinct trend in sulfate and nitrate concentrations demarcates the basaltic and granitic zones as distinct ecological habitats. Quantitative PCR indicates a depth independent distribution of microorganisms predominated by bacteria. Abundance of dsrB and mcrA genes are relatively higher (at least one order of magnitude) in basalt compared to granite. Bacterial communities are dominated by Alpha-, Beta-, Gammaproteobacteria, Actinobacteria and Firmicutes, whereas Euryarchaeota is the major archaeal group. Strong correlation among the abundance of autotrophic and heterotrophic taxa is noted. Bacteria known for nitrite, sulfur and hydrogen oxidation represent the autotrophs. Fermentative, nitrate/sulfate reducing and methane metabolising microorganisms represent the heterotrophs. Lack of shared operational taxonomic units and distinct clustering of major taxa indicate possible community isolation. Shotgun metagenomics corroborate that chemolithoautotrophic assimilation of carbon coupled with fermentation and anaerobic respiration drive this deep biosphere. This first report on the geomicrobiology of the subsurface of Deccan traps provides an unprecedented opportunity to understand microbial composition and function in the terrestrial, igneous rock-hosted, deep biosphere.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies

Metatranscriptomics has recently been applied to investigate the active biogeochemical processes and elemental cycles, and in situ responses of microbiomes to environmental stimuli and stress factors. De novo assembly of RNA-Sequencing (RNA-Seq) data can reveal a more detailed description of the metabolic interactions amongst the active microbial communities. However, the quality of the assemblies and the depiction of the metabolic network provided by various de novo assemblers have not yet been thoroughly assessed. In this study, we compared 15 de novo metatranscriptomic assemblies for a fracture fluid sample collected from a borehole located at 1.34 km below land surface in a South African gold mine. These assemblies were constructed from total, non-coding, and coding reads using five de novo transcriptomic assemblers (Trans-ABySS, Trinity, Oases, IDBA-tran, and Rockhopper). They were evaluated based on the number of transcripts, transcript length, range of transcript coverage, continuity, percentage of transcripts with confident annotation assignments, as well as taxonomic and functional diversity patterns. The results showed that these parameters varied considerably among the assemblies, with Trans-ABySS and Trinity generating the best assemblies for non-coding and coding RNA reads, respectively, because the high number of transcripts assembled covered a wide expression range, and captured extensively the taxonomic and metabolic gene diversity, respectively. We concluded that the choice of de novo transcriptomic assemblers impacts substantially the taxonomic and functional compositions. Care should be taken to obtain high-quality assemblies for informing the in situ metabolic landscape.

The deep, hot biosphere: Twenty-five years of retrospection

Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H₂, CH₄, and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth's subsurface in the form of a deep subsurface microbiome initiative.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb₃- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface

Earth's deep subsurface biosphere (DSB) is home to a vast number and wide variety of microorganisms. Although difficult to access and sample, deep subsurface environments have been probed through drilling programs, exploration of mines and sampling of deeply sourced vents and springs. In an effort to understand the ecology of deep terrestrial habitats, we examined bacterial diversity in the Sanford Underground Research Facility (SURF), the former Homestake gold mine, in South Dakota, USA. Whole genomic DNA was extracted from deeply circulating groundwater and corresponding host rock (at a depth of 1.45 km below ground surface). Pyrotag DNA sequencing of the 16S rRNA gene revealed diverse communities of putative chemolithoautotrophs, aerobic and anaerobic heterotrophs, numerous candidate phyla and unique rock-associated microbial assemblage. There was a clear and near-total separation of communities between SURF deeply circulating fracture fluids and SURF host-rocks. Sequencing data from SURF compared against five similarly sequenced terrestrial subsurface sites in Europe and North America revealed classes Clostridia and Betaproteobacteria were dominant in terrestrial fluids. This study presents a unique analysis showing differences in terrestrial subsurface microbial communities between fracture fluids and host rock through which those fluids permeate.

Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327) to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae). These variations occur in relation to the type of sediment (clays versus carbonate-rich) and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.

Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community

The terrestrial deep subsurface is a huge repository of microbial biomass, but in relation to its size and physical heterogeneity, few sites have been investigated in detail. Here, we applied a culture-independent metagenomic approach to characterize the microbial community composition in deep (1500 meters below surface) terrestrial fluids. Samples were collected from a former gold mine in Lead, South Dakota, USA, now Sanford Underground Research Facility (SURF). We reconstructed 74 genomes from metagenomes (MAGs), enabling the identification of common metabolic pathways. Sulfate and nitrate/nitrite reduction were the most common putative energy metabolisms. Complete pathways for autotrophic carbon fixation were found in more than half of the MAGs, with the reductive acetyl-CoA pathway by far the most common. Nearly 40% (29 of 74) of the recovered MAGs belong to bacterial phyla without any cultivated members-microbial dark matter. Three of our MAGs constitute two novel phyla previously only identified in 16 S rRNA gene surveys. The uniqueness of this data set-its physical depth in the terrestrial subsurface, the relative abundance and completeness of microbial dark matter genomes and the overall diversity of this physically deep, dark, community-make it an invaluable addition to our knowledge of deep subsurface microbial ecology.

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems

It is generally accepted that diverse, poorly characterized microorganisms reside deep within Earth’s crust. One such lineage of deep subsurface-dwelling bacteria is an uncultivated member of the Firmicutes phylum that can dominate molecular surveys from both marine and continental rock fracture fluids, sometimes forming the sole member of a single-species microbiome. Here, we reconstructed a genome from basalt-hosted fluids of the deep subseafloor along the eastern Juan de Fuca Ridge flank and used a phylogenomic analysis to show that, despite vast differences in geographic origin and habitat, it forms a monophyletic clade with the terrestrial deep subsurface genome of “Candidatus Desulforudis audaxviator” MP104C. While a limited number of differences were observed between the marine genome of “Candidatus Desulfopertinax cowenii” modA32 and its terrestrial relative that may be of potential adaptive importance, here it is revealed that the two are remarkably similar thermophiles possessing the genetic capacity for motility, sporulation, hydrogenotrophy, chemoorganotrophy, dissimilatory sulfate reduction, and the ability to fix inorganic carbon via the Wood-Ljungdahl pathway for chemoautotrophic growth. Our results provide insights into the genetic repertoire within marine and terrestrial members of a bacterial lineage that is widespread in the global deep subsurface biosphere, and provides a natural means to investigate adaptations specific to these two environments.

Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids

The global deep subsurface biosphere is one of the largest reservoirs for microbial life on our planet. This study takes advantage of new sampling technologies and couples them with improvements to DNA sequencing and associated informatics tools to reconstruct the genomes of uncultivated Bacteria and Archaea from fluids collected deep within the Juan de Fuca Ridge subseafloor. Here, we generated two metagenomes from borehole observatories located 311 meters apart and, using binning tools, retrieved 98 genomes from metagenomes (GFMs). Of the GFMs, 31 were estimated to be >90% complete, while an additional 17 were >70% complete. Phylogenomic analysis revealed 53 bacterial and 45 archaeal GFMs, of which nearly all were distantly related to known cultivated isolates. In the GFMs, abundant Bacteria included Chloroflexi, Nitrospirae, Acetothermia (OP1), EM3, Aminicenantes (OP8), Gammaproteobacteria, and Deltaproteobacteria, while abundant Archaea included Archaeoglobi, Bathyarchaeota (MCG), and Marine Benthic Group E (MBG-E). These data are the first GFMs reconstructed from the deep basaltic subseafloor biosphere, and provide a dataset available for further interrogation.

Viruses in the Oceanic Basement

Microbial life has been detected well into the igneous crust of the seafloor (i.e., the oceanic basement), but there have been no reports confirming the presence of viruses in this habitat. To detect and characterize an ocean basement virome, geothermally heated fluid samples (ca. 60 to 65°C) were collected from 117 to 292 m deep into the ocean basement using seafloor observatories installed in two boreholes (Integrated Ocean Drilling Program [IODP] U1362A and U1362B) drilled in the eastern sediment-covered flank of the Juan de Fuca Ridge. Concentrations of virus-like particles in the fluid samples were on the order of 0.2 × 10⁵ to 2 × 10⁵ ml⁻¹ (n = 8), higher than prokaryote-like cells in the same samples by a factor of 9 on average (range, 1.5 to 27). Electron microscopy revealed diverse viral morphotypes similar to those of viruses known to infect bacteria and thermophilic archaea. An analysis of virus-like sequences in basement microbial metagenomes suggests that those from archaeon-infecting viruses were the most common (63 to 80%). Complete genomes of a putative archaeon-infecting virus and a prophage within an archaeal scaffold were identified among the assembled sequences, and sequence analysis suggests that they represent lineages divergent from known thermophilic viruses. Of the clustered regularly interspaced short palindromic repeat (CRISPR)-containing scaffolds in the metagenomes for which a taxonomy could be inferred (163 out of 737), 51 to 55% appeared to be archaeal and 45 to 49% appeared to be bacterial. These results imply that the warmed, highly altered fluids in deeply buried ocean basement harbor a distinct assemblage of novel viruses, including many that infect archaea, and that these viruses are active participants in the ecology of the basement microbiome.

The hydrothermally active ocean basement is voluminous and likely provided conditions critical to the origins of life, but the microbiology of this vast habitat is not well understood. Viruses in particular, although integral to the origins, evolution, and ecology of all life on earth, have never been documented in basement fluids. This report provides the first estimate of free virus particles (virions) within fluids circulating through the extrusive basalt of the seafloor and describes the morphological and genetic signatures of basement viruses. These data push the known geographical limits of the virosphere deep into the ocean basement and point to a wealth of novel viral diversity, exploration of which could shed light on the early evolution of viruses.

Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation

Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e⁻⁵. None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).

An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers

Subsurface lithoautotrophic microbial ecosystems (SLiMEs) under oligotrophic conditions are typically supported by H₂ Methanogens and sulfate reducers, and the respective energy processes, are thought to be the dominant players and have been the research foci. Recent investigations showed that, in some deep, fluid-filled fractures in the Witwatersrand Basin, South Africa, methanogens contribute <5% of the total DNA and appear to produce sufficient CH₄ to support the rest of the diverse community. This paradoxical situation reflects our lack of knowledge about the in situ metabolic diversity and the overall ecological trophic structure of SLiMEs. Here, we show the active metabolic processes and interactions in one of these communities by combining metatranscriptomic assemblies, metaproteomic and stable isotopic data, and thermodynamic modeling. Dominating the active community are four autotrophic β-proteobacterial genera that are capable of oxidizing sulfur by denitrification, a process that was previously unnoticed in the deep subsurface. They co-occur with sulfate reducers, anaerobic methane oxidizers, and methanogens, which each comprise <5% of the total community. Syntrophic interactions between these microbial groups remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate in the subsurface. The dominance of sulfur oxidizers is explained by the availability of electron donors and acceptors to these microorganisms and the ability of sulfur-oxidizing denitrifiers to gain energy through concomitant S and H₂ oxidation. We demonstrate that SLiMEs support taxonomically and metabolically diverse microorganisms, which, through developing syntrophic partnerships, overcome thermodynamic barriers imposed by the environmental conditions in the deep subsurface.

Identification of Free-Living and Particle-Associated Microbial Communities Present in Hadal Regions of the Mariana Trench

Relatively few studies have described the microbial populations present in ultra-deep hadal environments, largely as a result of difficulties associated with sampling. Here we report Illumina-tag V6 16S rRNA sequence-based analyses of the free-living and particle-associated microbial communities recovered from locations within two of the deepest hadal sites on Earth, the Challenger Deep (10,918 meters below surface-mbs) and the Sirena Deep (10,667 mbs) within the Mariana Trench, as well as one control site (Ulithi Atoll, 761 mbs). Seawater samples were collected using an autonomous lander positioned ~1 m above the seafloor. The bacterial populations within the Mariana Trench bottom water samples were dissimilar to other deep-sea microbial communities, though with overlap with those of diffuse flow hydrothermal vents and deep-subsurface locations. Distinct particle-associated and free-living bacterial communities were found to exist. The hadal bacterial populations were also markedly different from one another, indicating the likelihood of different chemical conditions at the two sites. In contrast to the bacteria, the hadal archaeal communities were more similar to other less deep datasets and to each other due to an abundance of cosmopolitan deep-sea taxa. The hadal communities were enriched in 34 bacterial and 4 archaeal operational taxonomic units (OTUs) including members of the Gammaproteobacteria, Epsilonproteobacteria, Marinimicrobia, Cyanobacteria, Deltaproteobacteria, Gemmatimonadetes, Atribacteria, Spirochaetes, and Euryarchaeota. Sequences matching cultivated piezophiles were notably enriched in the Challenger Deep, especially within the particle-associated fraction, and were found in higher abundances than in other hadal studies, where they were either far less prevalent or missing. Our results indicate the importance of heterotrophy, sulfur-cycling, and methane and hydrogen utilization within the bottom waters of the deeper regions of the Mariana Trench, and highlight novel community features of these extreme habitats.

Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge

Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25°C) regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe³⁺/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement.

Temperature and Redox Effect on Mineral Colonization in Juan de Fuca Ridge Flank Subsurface Crustal Fluids

To examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for 1 year at the seafloor wellhead of a crustal borehole observatory (IODP Hole U1301A, Juan de Fuca Ridge flank) as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby IODP Hole U1301B). In comparison to previous studies at these same sites, this approach allowed assessment of the effects of temperature, fluid chemistry, and/or mineralogy on colonization patterns of different mineral substrates, and an opportunity to verify the approach of deploying colonization experiments at an observatory wellhead at the seafloor instead of within the borehole. The Hole U1301B deployment did not have biofilm growth, based on microscopy and DNA extraction, thereby confirming the integrity of the colonization design against bottom seawater intrusion. In contrast, the Hole U1301A deployment supported biofilms dominated by Epsilonproteobacteria (43.5% of 370 16S rRNA gene clone sequences) and Gammaproteobacteria (29.3%). Sequence analysis revealed overlap in microbial communities between different minerals incubated at the Hole U1301A wellhead, indicating that mineralogy did not separate biofilm structure within the 1-year colonization experiment. Differences in the Hole U1301A wellhead biofilm community composition relative to previous studies from within the borehole using similar mineral substrates suggest that temperature and the diffusion of dissolved oxygen through plastic components influenced the mineral colonization experiments positioned at the wellhead. This highlights the capacity of low abundance crustal fluid taxa to rapidly establish communities on diverse mineral substrates under changing environmental conditions such as from temperature and oxygen.

Diversity and Metabolic Potentials of Subsurface Crustal Microorganisms from the Western Flank of the Mid-Atlantic Ridge

Deep-sea oceanic crust constitutes the largest region of the earth’s surface. Accumulating evidence suggests that unique microbial communities are supported by iron cycling processes, particularly in the young (<10 million-year old), cool (<25°C) subsurface oceanic crust. To test this hypothesis, we investigated the microbial abundance, diversity, and metabolic potentials in the sediment-buried crust from “North Pond” on western flank of the Mid-Atlantic Ridge. Three lithologic units along basement Hole U1383C were found, which typically hosted ∼10⁴ cells cm^-3 of basaltic rock, with higher cell densities occurring between 115 and 145 m below seafloor. Similar bacterial community structures, which are dominated by Gammaproteobacterial and Sphingobacterial species closely related to iron oxidizers, were detected regardless of variations in sampling depth. The metabolic potentials of the crust microbiota were assayed by metagenomic analysis of two basalt enrichments which showed similar bacterial structure with the original sample. Genes coding for energy metabolism involved in hydrocarbon degradation, dissimilatory nitrate reduction to ammonium, denitrification and hydrogen oxidation were identified. Compared with other marine environments, the metagenomes from the basalt-hosted environments were enriched in pathways for Fe³⁺ uptake, siderophore synthesis and uptake, and Fe transport, suggesting that iron metabolism is an important energy production and conservation mechanism in this system. Overall, we provide evidence that the North Pond crustal biosphere is dominated by unique bacterial groups with the potential for iron-related biogeochemical cycles.

A distinct and active bacterial community in cold oxygenated fluids circulating beneath the western flank of the Mid-Atlantic ridge

The rock-hosted, oceanic crustal aquifer is one of the largest ecosystems on Earth, yet little is known about its indigenous microorganisms. Here we provide the first phylogenetic and functional description of an active microbial community residing in the cold oxic crustal aquifer. Using subseafloor observatories, we recovered crustal fluids and found that the geochemical composition is similar to bottom seawater, as are cell abundances. However, based on relative abundances and functional potential of key bacterial groups, the crustal fluid microbial community is heterogeneous and markedly distinct from seawater. Potential rates of autotrophy and heterotrophy in the crust exceeded those of seawater, especially at elevated temperatures (25 °C) and deeper in the crust. Together, these results reveal an active, distinct, and diverse bacterial community engaged in both heterotrophy and autotrophy in the oxygenated crustal aquifer, providing key insight into the role of microbial communities in the ubiquitous cold dark subseafloor biosphere.

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt

Although little is known regarding microbial life within our planet's rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity.

Radiolytic Hydrogen Production in the Subseafloor Basaltic Aquifer

Hydrogen (H2) is produced in geological settings by dissociation of water due to radiation from radioactive decay of naturally occurring uranium ((238)U, (235)U), thorium ((232)Th) and potassium ((40)K). To quantify the potential significance of radiolytic H2 as an electron donor for microbes within the South Pacific subseafloor basaltic aquifer, we use radionuclide concentrations of 43 basalt samples from IODP Expedition 329 to calculate radiolytic H2 production rates in basement fractures. The samples are from three sites with very different basement ages and a wide range of alteration types. U, Th, and K concentrations vary by up to an order of magnitude from sample to sample at each site. Comparison of our samples to each other and to the results of previous studies of unaltered East Pacific Rise basalt suggests that significant variations in radionuclide concentrations are due to differences in initial (unaltered basalt) concentrations (which can vary between eruptive events) and post-emplacement alteration. However, there is no clear relationship between alteration type and calculated radiolytic yields. Local maxima in U, Th, and K produce hotspots of H2 production, causing calculated radiolytic rates to differ by up to a factor of 80 from sample to sample. Fracture width also greatly influences H2 production, where microfractures are hotspots for radiolytic H2 production. For example, H2 production rates normalized to water volume are 190 times higher in 1 μm wide fractures than in fractures that are 10 cm wide. To assess the importance of water radiolysis for microbial communities in subseafloor basaltic aquifers, we compare electron transfer rates from radiolysis to rates from iron oxidation in subseafloor basalt. Radiolysis appears likely to be a more important electron donor source than iron oxidation in old (>10 Ma) basement basalt. Radiolytic H2 production in the volume of water adjacent to a square cm of the most radioactive SPG basalt may support as many as 1500 cells.

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

BACKGROUND

The rapid development of sequencing technologies has provided access to environments that were either once thought inhospitable to life altogether or that contain too few cells to be analyzed using genomics approaches. While 16S rRNA gene microbial community sequencing has revolutionized our understanding of community composition and diversity over time and space, it only provides a crude estimate of microbial functional and metabolic potential. Alternatively, shotgun metagenomics allows comprehensive sampling of all genetic material in an environment, without any underlying primer biases. Until recently, one of the major bottlenecks of shotgun metagenomics has been the requirement for large initial DNA template quantities during library preparation.

RESULTS

Here, we investigate the effects of varying template concentrations across three low biomass library preparation protocols on their ability to accurately reconstruct a mock microbial community of known composition. We analyze the effects of input DNA quantity and library preparation method on library insert size, GC content, community composition, assembly quality and metagenomic binning. We found that library preparation method and the amount of starting material had significant impacts on the mock community metagenomes. In particular, GC content shifted towards more GC rich sequences at the lower input quantities regardless of library prep method, the number of low quality reads that could not be mapped to the reference genomes increased with decreasing input quantities, and the different library preparation methods had an impact on overall metagenomic community composition.

CONCLUSIONS

This benchmark study provides recommendations for library creation of representative and minimally biased metagenome shotgun sequencing, enabling insights into functional attributes of low biomass ecosystem microbial communities.

Temperature and pressure adaptation of a sulfate reducer from the deep subsurface

Microbial life in deep marine subsurface faces increasing temperatures and hydrostatic pressure with depth. In this study, we have examined growth characteristics and temperature-related adaptation of the Desulfovibrio indonesiensis strain P23 to the in situ pressure of 30 MPa. The strain originates from the deep subsurface of the eastern flank of the Juan de Fuca Ridge (IODP Site U1301). The organism was isolated at 20°C and atmospheric pressure from ~61°C-warm sediments approximately 5 m above the sediment-basement interface. In comparison to standard laboratory conditions (20°C and 0.1 MPa), faster growth was recorded when incubated at in situ pressure and high temperature (45°C), while cell filamentation was induced by further compression. The maximum growth temperature shifted from 48°C at atmospheric pressure to 50°C under high-pressure conditions. Complementary cellular lipid analyses revealed a two-step response of membrane viscosity to increasing temperature with an exchange of unsaturated by saturated fatty acids and subsequent change from branched to unbranched alkyl moieties. While temperature had a stronger effect on the degree of fatty acid saturation and restructuring of main phospholipids, pressure mainly affected branching and length of side chains. The simultaneous decrease of temperature and pressure to ambient laboratory conditions allowed the cultivation of our moderately thermophilic strain. This may in turn be one key to a successful isolation of microorganisms from the deep subsurface adapted to high temperature and pressure.

Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

Activity and phylogenetic diversity of sulfate-reducing microorganisms in low-temperature subsurface fluids within the upper oceanic crust

The basaltic ocean crust is the largest aquifer system on Earth, yet the rates of biological activity in this environment are unknown. Low-temperature (<100°C) fluid samples were investigated from two borehole observatories in the Juan de Fuca Ridge (JFR) flank, representing a range of upper oceanic basement thermal and geochemical properties. Microbial sulfate reduction rates (SRR) were measured in laboratory incubations with ³⁵S-sulfate over a range of temperatures and the identity of the corresponding sulfate-reducing microorganisms (SRM) was studied by analyzing the sequence diversity of the functional marker dissimilatory (bi)sulfite reductase (dsrAB) gene. We found that microbial sulfate reduction was limited by the decreasing availability of organic electron donors in higher temperature, more altered fluids. Thermodynamic calculations indicate energetic constraints for metabolism, which together with relatively higher cell-specific SRR reveal increased maintenance requirements, consistent with novel species-level dsrAB phylotypes of thermophilic SRM. Our estimates suggest that microbially-mediated sulfate reduction may account for the removal of organic matter in fluids within the upper oceanic crust and underscore the potential quantitative impact of microbial processes in deep subsurface marine crustal fluids on marine and global biogeochemical carbon cycling.

Oxygen consumption rates in subseafloor basaltic crust derived from a reaction transport model

Oceanic crust is the largest potential habitat for life on Earth and may contain a significant fraction of Earth's total microbial biomass; yet, empirical analysis of reaction rates in basaltic crust is lacking. Here we report the first assessment of oxygen consumption in young (~8 Ma) and cool (<25 °C) basaltic crust, which we calculate from modelling dissolved oxygen and strontium pore water gradients in basal sediments collected during Integrated Ocean Drilling Program Expedition 336 to 'North Pond' on the western flank of the Mid-Atlantic Ridge. Dissolved oxygen is completely consumed within the upper to middle section of the sediment column, with an increase in concentration towards the sediment-basement interface, indicating an upward supply from oxic fluids circulating within the crust. A parametric reaction transport model of oxygen behaviour in upper basement suggests oxygen consumption rates of 1 nmol  cm(-3)ROCK d(-1) or less in young and cool basaltic crust.

Phylogenetic diversity of microorganisms in subseafloor crustal fluids from Holes 1025C and 1026B along the Juan de Fuca Ridge flank

To expand investigations into the phylogenetic diversity of microorganisms inhabiting the subseafloor biosphere, basalt-hosted crustal fluids were sampled from Circulation Obviation Retrofit Kits (CORKs) affixed to Holes 1025C and 1026B along the Juan de Fuca Ridge (JdFR) flank using a clean fluid pumping system. These boreholes penetrate the crustal aquifer of young ocean crust (1.24 and 3.51 million years old, respectively), but differ with respect to borehole depth and temperature at the sediment-basement interface (147 m and 39°C vs. 295 m and 64°C, respectively). Cloning and sequencing of PCR-amplified small subunit ribosomal RNA genes revealed that fluids retrieved from Hole 1025C were dominated by relatives of the genus Desulfobulbus of the Deltaproteobacteria (56% of clones) and Candidatus Desulforudis of the Firmicutes (17%). Fluids sampled from Hole 1026B also contained plausible deep subseafloor inhabitants amongst the most abundant clone lineages; however, both geochemical analysis and microbial community structure reveal the borehole to be compromised by bottom seawater intrusion. Regardless, this study provides independent support for previous observations seeking to identify phylogenetic groups of microorganisms common to the deep ocean crustal biosphere, and extends previous observations by identifying additional lineages that may be prevalent in this unique environment.

Microbial activity in the marine deep biosphere: progress and prospects

The vast marine deep biosphere consists of microbial habitats within sediment, pore waters, upper basaltic crust and the fluids that circulate throughout it. A wide range of temperature, pressure, pH, and electron donor and acceptor conditions exists—all of which can combine to affect carbon and nutrient cycling and result in gradients on spatial scales ranging from millimeters to kilometers. Diverse and mostly uncharacterized microorganisms live in these habitats, and potentially play a role in mediating global scale biogeochemical processes. Quantifying the rates at which microbial activity in the subsurface occurs is a challenging endeavor, yet developing an understanding of these rates is essential to determine the impact of subsurface life on Earth's global biogeochemical cycles, and for understanding how microorganisms in these “extreme” environments survive (or even thrive). Here, we synthesize recent advances and discoveries pertaining to microbial activity in the marine deep subsurface, and we highlight topics about which there is still little understanding and suggest potential paths forward to address them. This publication is the result of a workshop held in August 2012 by the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) “theme team” on microbial activity (www.darkenergybiosphere.org).

Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico

The Naica Mine in northern Mexico is famous for its giant gypsum crystals, which may reach up to 11 m long and contain fluid inclusions that might have captured microorganisms during their formation. These crystals formed under particularly stable geochemical conditions in cavities filled by low salinity hydrothermal water at 54-58°C. We have explored the microbial diversity associated to these deep, saline hydrothermal waters collected in the deepest (ca. 700-760 m) mineshafts by amplifying, cloning and sequencing small-subunit ribosomal RNA genes using primers specific for archaea, bacteria, and eukaryotes. Eukaryotes were not detectable in the samples and the prokaryotic diversity identified was very low. Two archaeal operational taxonomic units (OTUs) were detected in one sample. They clustered with, respectively, basal Thaumarchaeota lineages and with a large clade of environmental sequences branching at the base of the Thermoplasmatales within the Euryarchaeota. Bacterial sequences belonged to the Candidate Division OP3, Firmicutes and the Alpha- and Beta-proteobacteria. Most of the lineages detected appear autochthonous to the Naica system, since they had as closest representatives environmental sequences retrieved from deep sediments or the deep subsurface. In addition, the high GC content of 16S rRNA gene sequences belonging to the archaea and to some OP3 OTUs suggests that at least these lineages are thermophilic. Attempts to amplify diagnostic functional genes for methanogenesis (mcrA) and sulfate reduction (dsrAB) were unsuccessful, suggesting that those activities, if present, are not important in the aquifer. By contrast, genes encoding archaeal ammonium monooxygenase (AamoA) were amplified, suggesting that Naica Thaumarchaeota are involved in nitrification. These organisms are likely thermophilic chemolithoautotrophs adapted to thrive in an extremely energy-limited environment.