Deep biosphere

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...

The specific topographic characteristics and complex hydrodynamics of seamounts could directly or indirectly affect the distribution and trophic status of microbes. However, little is known about the distribution patterns and associated driving forces of micro-eukaryotes in the deep seamounts. Micro-eukaryotes in the seamount sediments along the island arc of the Yap and Mariana trenches were investigated using high-throughput sequencing and quantitative PCR based on the 18S rRNA gene. Micro-eukaryotic communities from seamounts were clustered together and distinct from those of the depression, which showed comparatively lower diversity, gene abundance, endemic species, and higher proportions of decomposers and parasites...

Tiny ocean plankton (picoplankton) are fundamental for the functioning of the biosphere, but the ecological mechanisms shaping their biogeography were partially understood. Comprehending whether these microorganisms are structured by niche versus neutral processes is relevant in the context of global change. We investigate the ecological processes (selection, dispersal, and drift) structuring global-ocean picoplanktonic communities inhabiting the epipelagic (0 to 200 meters), mesopelagic (200 to 1000 meters), and bathypelagic (1000 to 4000 meters) zones...

Organic nitrogen mineralization, indispensable to soil carbon and nitrogen cycles, is the largest contributor to nitrate reservoirs in deep vadose zones. The microbial nitrogen mineralization (MNM) within deep soils, particularly in regions with intensive agricultural activities and thick soil horizons, has been largely disregarded. As such, this study aims to address this knowledge gap by investigating the chiA-harboring microbial structure and network within nine 10-m profiles beneath cultivated farmlands and two apple orchards...

The Earth's microbial biosphere extends from ambient to extreme environments, including deep-sea hydrothermal vents and subseafloor habitats. Despite efforts to understand the physiological adaptations of these microbes, our knowledge is limited due to the technological challenges associated with reproducing in situ high temperature (HT)-high hydrostatic pressure (HHP) conditions and sampling HT-HHP cultures. In the present study, we developed a new high temperature and pressure (HTP) incubation system that enabled the maintenance of HT-HHP conditions while sampling incubation medium and mostly eliminated non-biological reactions, including hydrogen generation or the leakage of small gaseous molecules...

Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities...

The rate of primary productivity is a keystone variable in driving biogeochemical cycles today and has been throughout Earth's past.1 For example, it plays a critical role in determining nutrient stoichiometry in the oceans,2 the amount of global biomass,3 and the composition of Earth's atmosphere.4 Modern estimates suggest that terrestrial and marine realms contribute near-equal amounts to global gross primary productivity (GPP).5 However, this productivity balance has shifted significantly in both recent times6 and through deep time...

Investigations of abiotic and biotic contributions to dissolved organic carbon (DOC) are required to constrain microbial habitability in continental subsurface fluids. Here we investigate a large (101-283 mg C/L) DOC pool in an ancient (>1Ga), high temperature (45-55 °C), low biomass (102 -104 cells/mL), and deep (3.2 km) brine from an uranium-enriched South African gold mine. Excitation-emission matrices (EEMs), negative electrospray ionization (-ESI) 21 tesla Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and amino acid analyses suggest the brine DOC is primarily radiolytically oxidized kerogen-rich shales or reefs, methane and ethane, with trace amounts of C3 -C6 hydrocarbons and organic sulfides...

Hadal trenches are unique geological and ecological systems located along subduction zones. Earthquake-triggered turbidites act as efficient transport pathways of organic carbon (OC), yet remineralization and transformation of OC in these systems are not comprehensively understood. Here we measure concentrations and stable- and radiocarbon isotope signatures of dissolved organic and inorganic carbon (DOC, DIC) in the subsurface sediment interstitial water along the Japan Trench axis collected during the IODP Expedition 386...

Traditional culture techniques usually retrieve a small fraction of the marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 23 samples used for isolation...

Serpentinization of peridotite provides a significant source of energy for the subseafloor biosphere and abiotic organic synthesis. The presence of diverse micrometer-scale organic matter in serpentinites offers insights into deep carbon cycling and the origin of life on Earth. It is critical to maintain stringent lab protocols in analyzing serpentinite samples, limiting the contact with organic materials that could contaminate serpentinites and cause misinterpretations. However, the extent to which these organic materials (e...

Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site-specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland...

The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits...

Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional (13 C/12 C and D/H) and multiply substituted (13 CH3 D and 12 CH2 D2 ) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration...

In recent years, strong evidence has emerged indicating the potential habitability of the subsurface of Mars. Occasional discharge events that bring subsurface fluids to the surface may carry with them the biological traces of subsurface organisms. Similar events are known to take place on Earth and are frequently associated with long-term mineralogical preservation of organic material, including DNA. Taking advantage of this process may allow for the development of life-detection strategies targeting biosignatures from the more habitable subsurface environment without the need for direct subsurface exploration...

Deep sea cold seep sediments have been discovered to harbor novel, abundant, and diverse bacterial and archaeal viruses. However, little is known about viral genetic features and evolutionary patterns in these environments. Here, we examined the evolutionary ecology of viruses across active and extinct seep stages in the area of Haima cold seeps in the South China Sea. A total of 338 viral operational taxonomic units are identified and linked to 36 bacterial and archaeal phyla. The dynamics of host-virus interactions are informed by diverse antiviral defense systems across 43 families found in 487 microbial genomes...

Microorganisms in subsurface sediments live from recalcitrant organic matter deposited thousands or millions of years ago. Their catabolic activities are low, but the deep biosphere is of global importance due to its volume. The stability of deeply buried sediments provides a natural laboratory where prokaryotic communities that live in steady state with their environments can be studied over long time scales. We tested if a balance is established between the flow of energy, the microbial community size, and the basal power requirement needed to maintain cells in sediments buried meters below the sea floor...

Glacier-fed lakes are characterized by cold temperatures, high altitudes, and nutrient-poor conditions. Despite these challenging conditions, near-surface sediments of glacier-fed lakes harbor rich microbial communities that are critical for ecosystem functioning and serve as a bridge between aquatic ecology and the deep subsurface biosphere. However, there is limited knowledge regarding the microbial communities and their assembly processes in these sediments, which are highly vulnerable to climate change...

Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals...

Anaerobic fungi are known to migrate and establish a 3D network of biofilms (microbiomes) and live invisible in the rumen and terrestrial subsurface, deep-sea - marine, and anoxic environment. They deserve our attention to understand anoxic fungal ecology and functions and develop new products and solutions. Such fungi activate unique genes to produce various polysaccharidases deemed essential for degrading plants' lignocellulosic materials. Nutrient release, recycling, and physical support by anaerobic fungi are crucial for microbiome formation...