First investigation of the microbiology of the deepest layer of ocean crust

Microbial interactions with phosphorus containing glasses representative of vitrified radioactive waste

The presence of phosphorus in borosilicate glass (at 0.1 - 1.3 mol% P2O5) and in iron-phosphate glass (at 53 mol% P2O5) stimulated the growth and metabolic activity of anaerobic bacteria in model systems. Dissolution of these phosphorus containing glasses was either inhibited or accelerated by microbial metabolic activity, depending on the solution chemistry and the glass composition. The breakdown of organic carbon to volatile fatty acids increased glass dissolution. The interaction of microbially reduced Fe(II) with phosphorus-containing glass under anoxic conditions decreased dissolution rates, whereas the interaction of Fe(III) with phosphorus-containing glass under oxic conditions increased glass dissolution. Phosphorus addition to borosilicate glasses did not significantly affect the microbial species present, however, the diversity of the microbial community was enhanced on the surface of the iron phosphate glass. Results demonstrate the potential for microbes to influence the geochemistry of radioactive waste disposal environments with implication for wasteform durability.

The rocky road to organics needs drying

How simple abiotic organic compounds evolve toward more complex molecules of potentially prebiotic importance remains a missing key to establish where life possibly emerged. The limited variety of abiotic organics, their low concentrations and the possible pathways identified so far in hydrothermal fluids have long hampered a unifying theory of a hydrothermal origin for the emergence of life on Earth. Here we present an alternative road to abiotic organic synthesis and diversification in hydrothermal environments, which involves magmatic degassing and water-consuming mineral reactions occurring in mineral microcavities. This combination gathers key gases (N₂, H₂, CH₄, CH₃SH) and various polyaromatic materials associated with nanodiamonds and mineral products of olivine hydration (serpentinization). This endogenous assemblage results from re-speciation and drying of cooling C-O-S-H-N fluids entrapped below 600 °C-2 kbars in rocks forming the present-day oceanic lithosphere. Serpentinization dries out the system toward macromolecular carbon condensation, while olivine pods keep ingredients trapped until they are remobilized for further reactions at shallower levels. Results greatly extend our understanding of the forms of abiotic organic carbon available in hydrothermal environments and open new pathways for organic synthesis encompassing the role of minerals and drying. Such processes are expected in other planetary bodies wherever olivine-rich magmatic systems get cooled down and hydrated.

Aqueously altered igneous rocks sampled on the floor of Jezero crater, Mars

The Perseverance rover landed in Jezero crater, Mars, to investigate ancient lake and river deposits. We report observations of the crater floor, below the crater's sedimentary delta, finding the floor consists of igneous rocks altered by water. The lowest exposed unit, informally named Séítah, is a coarsely crystalline olivine-rich rock, which accumulated at the base of a magma body. Fe-Mg carbonates along grain boundaries indicate reactions with CO₂-rich water, under water-poor conditions. Overlying Séítah is a unit informally named Máaz, which we interpret as lava flows or the chemical complement to Séítah in a layered igneous body. Voids in these rocks contain sulfates and perchlorates, likely introduced by later near-surface brine evaporation. Core samples of these rocks were stored aboard Perseverance for potential return to Earth.

Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals

Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.

The Deep Rocky Biosphere: New Geomicrobiological Insights and Prospects

Rocks that react with liquid water are widespread but spatiotemporally limited throughout the solar system, except for Earth. Rock-forming minerals with high iron content and accessory minerals with high amounts of radioactive elements are essential to support rock-hosted microbial life by supplying organics, molecular hydrogen, and/or oxidants. Recent technological advances have broadened our understanding of the rocky biosphere, where microbial inhabitation appears to be difficult without nutrient and energy inputs from minerals. In particular, microbial proliferation in igneous rock basements has been revealed using innovative geomicrobiological techniques. These recent findings have dramatically changed our perspective on the nature and the extent of microbial life in the rocky biosphere, microbial interactions with minerals, and the influence of external factors on habitability. This study aimed to gather information from scientific and/or technological innovations, such as omics-based and single-cell level characterizations, targeting deep rocky habitats of organisms with minimal dependence on photosynthesis. By synthesizing pieces of rock-hosted life, we can explore the evo-phylogeny and ecophysiology of microbial life on Earth and the life’s potential on other planetary bodies.

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.

Microbial Residents of the Atlantis Massif's Shallow Serpentinite Subsurface

The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.

The Atlantis Massif rises 4,000 m above the seafloor near the Mid-Atlantic Ridge and consists of rocks uplifted from Earth’s lower crust and upper mantle. Exposure of the mantle rocks to seawater leads to their alteration into serpentinites. These aqueous geochemical reactions, collectively known as the process of serpentinization, are exothermic and are associated with the release of hydrogen gas (H₂), methane (CH₄), and small organic molecules. The biological consequences of this flux of energy and organic compounds from the Atlantis Massif were explored by International Ocean Discovery Program (IODP) Expedition 357, which used seabed drills to collect continuous sequences of shallow (<16 m below seafloor) marine serpentinites and mafic assemblages. Here, we report the census of microbial diversity in samples of the drill cores, as measured by environmental 16S rRNA gene amplicon sequencing. The problem of contamination of subsurface samples was a primary concern during all stages of this project, starting from the initial study design, continuing to the collection of samples from the seafloor, handling the samples shipboard and in the lab, preparing the samples for DNA extraction, and analyzing the DNA sequence data. To distinguish endemic microbial taxa of serpentinite subsurface rocks from seawater residents and other potential contaminants, the distributions of individual 16S rRNA gene sequences among all samples were evaluated, taking into consideration both presence/absence and relative abundances. Our results highlight a few candidate residents of the shallow serpentinite subsurface, including uncultured representatives of the Thermoplasmata, Acidobacteria, Acidimicrobia, and Chloroflexi.

IMPORTANCE The International Ocean Discovery Program Expedition 357—“Serpentinization and Life”—utilized seabed drills to collect rocks from the oceanic crust. The recovered rock cores represent the shallow serpentinite subsurface of the Atlantis Massif, where reactions between uplifted mantle rocks and water, collectively known as serpentinization, produce environmental conditions that can stimulate biological activity and are thought to be analogous to environments that were prevalent on the early Earth and perhaps other planets. The methodology and results of this project have implications for life detection experiments, including sample return missions, and provide a window into the diversity of microbial communities inhabiting subseafloor serpentinites.

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.

Habitability of the marine serpentinite subsurface: a case study of the Lost City hydrothermal field

The Lost City hydrothermal field is a dramatic example of the biological potential of serpentinization. Microbial life is prevalent throughout the Lost City chimneys, powered by the hydrogen gas and organic molecules produced by serpentinization and its associated geochemical reactions. Microbial life in the serpentinite subsurface below the Lost City chimneys, however, is unlikely to be as dense or active. The marine serpentinite subsurface poses serious challenges for microbial activity, including low porosities, the combination of stressors of elevated temperature, high pH and a lack of bioavailable ∑CO₂. A better understanding of the biological opportunities and challenges in serpentinizing systems would provide important insights into the total habitable volume of Earth's crust and for the potential of the origin and persistence of life in Earth's subsurface environments. Furthermore, the limitations to life in serpentinizing subsurface environments on Earth have significant implications for the habitability of subsurface environments on ocean worlds such as Europa and Enceladus. Here, we review the requirements and limitations of life in serpentinizing systems, informed by our research at the Lost City and the underwater mountain on which it resides, the Atlantis Massif. This article is part of a discussion meeting issue 'Serpentinite in the Earth System'.

Ice Binding Proteins: Diverse Biological Roles and Applications in Different Types of Industry

More than 80% of Earth’s surface is exposed periodically or continuously to temperatures below 5 °C. Organisms that can live in these areas are called psychrophilic or psychrotolerant. They have evolved many adaptations that allow them to survive low temperatures. One of the most interesting modifications is production of specific substances that prevent living organisms from freezing. Psychrophiles can synthesize special peptides and proteins that modulate the growth of ice crystals and are generally called ice binding proteins (IBPs). Among them, antifreeze proteins (AFPs) inhibit the formation of large ice grains inside the cells that may damage cellular organelles or cause cell death. AFPs, with their unique properties of thermal hysteresis (TH) and ice recrystallization inhibition (IRI), have become one of the promising tools in industrial applications like cryobiology, food storage, and others. Attention of the industry was also caught by another group of IBPs exhibiting a different activity—ice-nucleating proteins (INPs). This review summarizes the current state of art and possible utilizations of the large group of IBPs.

Fossilized Endolithic Microorganisms in Pillow Lavas from the Troodos Ophiolite, Cyprus

The last decade has revealed the igneous oceanic crust to host a more abundant and diverse biota than previously expected. These underexplored rock-hosted deep ecosystems dominated Earth’s biosphere prior to plants colonized land in the Ordovician, thus the fossil record of deep endoliths holds invaluable clues to early life and the work to decrypt them needs to be intensified. Here, we present fossilized microorganisms found in open and sealed pore spaces in pillow lavas from the Troodos Ophiolite (91 Ma) on Cyprus. A fungal interpretation is inferred upon the microorganisms based on characteristic morphological features. Geochemical conditions are reconstructed using data from mineralogy, fluid inclusions and the fossils themselves. Mineralogy indicates at least three hydrothermal events and a continuous increase of temperature and pH. Precipitation of 1) celadonite and saponite together with the microbial introduction was followed by 2) Na and Ca zeolites resulting in clay adherence on the microorganisms as protection, and finally 3) Ca carbonates resulted in final fossilization and preservation of the organisms in-situ. Deciphering the fossil record of the deep subseafloor biosphere is a challenging task, but when successful, can unlock doors to life’s cryptic past.

Hydrostatic Pressure Helps to Cultivate an Original Anaerobic Bacterium From the Atlantis Massif Subseafloor (IODP Expedition 357): Petrocella atlantisensis gen. nov. sp. nov

Rock-hosted subseafloor habitats are very challenging for life, and current knowledge about microorganisms inhabiting such lithic environments is still limited. This study explored the cultivable microbial diversity in anaerobic enrichment cultures from cores recovered during the International Ocean Discovery Program (IODP) Expedition 357 from the Atlantis Massif (Mid-Atlantic Ridge, 30°N). 16S rRNA gene survey of enrichment cultures grown at 10–25°C and pH 8.5 showed that Firmicutes and Proteobacteria were generally dominant. However, cultivable microbial diversity significantly differed depending on incubation at atmospheric pressure (0.1 MPa), or hydrostatic pressures (HP) mimicking the in situ pressure conditions (8.2 or 14.0 MPa). An original, strictly anaerobic bacterium designated 70B-A^T was isolated from core M0070C-3R1 (1150 meter below sea level; 3.5 m below seafloor) only from cultures performed at 14.0 MPa. This strain named Petrocella atlantisensis is a novel species of a new genus within the newly described family Vallitaleaceae (order Clostridiales, phylum Firmicutes). It is a mesophilic, moderately halotolerant and piezophilic chemoorganotroph, able to grow by fermentation of carbohydrates and proteinaceous compounds. Its 3.5 Mb genome contains numerous genes for ABC transporters of sugars and amino acids, and pathways for fermentation of mono- and di-saccharides and amino acids were identified. Genes encoding multimeric [FeFe] hydrogenases and a Rnf complex form the basis to explain hydrogen and energy production in strain 70B-A^T. This study outlines the importance of using hydrostatic pressure in culture experiments for isolation and characterization of autochthonous piezophilic microorganisms from subseafloor rocks.

Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities

The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.

While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions.

IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.

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.

A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico in 2010 resulted in serious damage to local marine and coastal environments. In addition to the physical removal and chemical dispersion of spilled oil, biodegradation by indigenous microorganisms was regarded as the most effective way for cleaning up residual oil. Different microbiological methods were applied to investigate the changes and responses of bacterial communities after the DWH oil spills. By summarizing and analyzing these microbiological methods, giving recommendations and proposing some methods that have not been used, this review aims to provide constructive guidelines for microbiological studies after environmental disasters, especially those involving organic pollutants.

Fungi in Deep Subsurface Environments

The igneous crust of the oceans and the continents represents the major part of Earth's lithosphere and has recently been recognized as a substantial, yet underexplored, microbial habitat. While prokaryotes have been the focus of most investigations, microeukaryotes have been surprisingly neglected. However, recent work acknowledges eukaryotes, and in particular fungi, as common inhabitants of the deep biosphere, including the deep igneous provinces. The fossil record of the subseafloor igneous crust, and to some extent the continental bedrock, establishes fungi or fungus-like organisms as inhabitants of deep rock since at least the Paleoproterozoic, which challenges the present notion of early fungal evolution. Additionally, deep fungi have been shown to play an important ecological role engaging in symbiosis-like relationships with prokaryotes, decomposing organic matter, and being responsible for mineral weathering and formation, thus mediating mobilization of biogeochemically important elements. In this review, we aim at covering the abundance and diversity of fungi in the various igneous rock provinces on Earth as well as describing the ecological impact of deep fungi. We further discuss what consequences recent findings might have for the understanding of the fungal distribution in extensive anoxic environments and for early fungal evolution.

High reactivity of deep biota under anthropogenic CO2 injection into basalt

Basalts are recognized as one of the major habitats on Earth, harboring diverse and active microbial populations. Inconsistently, this living component is rarely considered in engineering operations carried out in these environments. This includes carbon capture and storage (CCS) technologies that seek to offset anthropogenic CO₂ emissions into the atmosphere by burying this greenhouse gas in the subsurface. Here, we show that deep ecosystems respond quickly to field operations associated with CO₂ injections based on a microbiological survey of a basaltic CCS site. Acidic CO₂-charged groundwater results in a marked decrease (by ~ 2.5–4) in microbial richness despite observable blooms of lithoautotrophic iron-oxidizing Betaproteobacteria and degraders of aromatic compounds, which hence impact the aquifer redox state and the carbon fate. Host-basalt dissolution releases nutrients and energy sources, which sustain the growth of autotrophic and heterotrophic species whose activities may have consequences on mineral storage.

The impacts of carbon capture and storage (CCS) on subsurface microorganisms are poorly understood. Here, the authors show that deep ecosystems respond quickly to CO2 injections and that the environmental consequences of their metabolic activities need to be properly assessed for sustainable CCS in basalt.

Diversity and survival of artificial lifeforms under sedimentation and random motion

Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures emerge in cellular automata and are often used to represent molecules or living organisms. They converge generally towards homogeneous stationary soups of still-life creatures. It is hard for an observer to believe they are similar to living systems, in particular because nothing is moving anymore within such simulated environments after few computation steps, because they present isotropic spatial organisation, because the diversity of self-maintained morphologies is poor, and because when stationary states are reached the creatures are immortal. Natural living systems, on the contrary, are composed of a high diversity of creatures in interaction having limited lifetimes and generally present a certain anisotropy of their spatial organisation, in particular frontiers and interfaces. In the present work, we propose that the presence of directional weak fields such as gravity may counter-balance the excess of mixing and disorder caused by Brownian motion and favour the appearance of specific regions, i.e. different strata or environmental layers, in which physical-chemical conditions favour the emergence and the survival of self-maintained spatial structures including living systems. We test this hypothesis by way of numerical simulations of a very simplified ecosystem model. We use the well-known Game of Life to which we add rules simulating both sedimentation forces and thermal agitation. We show that this leads to more active (vitality and biodiversity) and robust (survival) dynamics. This effectively suggests that coupling such physical processes to reactive systems allows the separation of environments into different milieux and could constitute a simple mechanism to form ecosystem frontiers or elementary interfaces that would protect and favour the development of fragile auto-poietic systems.

Submarine Basaltic Glass Colonization by the Heterotrophic Fe(II)-Oxidizing and Siderophore-Producing Deep-Sea Bacterium Pseudomonas stutzeri VS-10: The Potential Role of Basalt in Enhancing Growth

Phylogenetically and metabolically diverse bacterial communities have been found in association with submarine basaltic glass surfaces. The driving forces behind basalt colonization are for the most part unknown. It remains ambiguous if basalt provides ecological advantages beyond representing a substrate for surface colonization, such as supplying nutrients and/or energy. Pseudomonas stutzeri VS-10, a metabolically versatile bacterium isolated from Vailulu'u Seamount, was used as a model organism to investigate the physiological responses observed when biofilms are established on basaltic glasses. In Fe-limited heterotrophic media, P. stutzeri VS-10 exhibited elevated growth in the presence of basaltic glass. Diffusion chamber experiments demonstrated that physical attachment or contact of soluble metabolites such as siderophores with the basaltic glass plays a pivotal role in this process. Electrochemical data indicated that P. stutzeri VS-10 is able to use solid substrates (electrodes) as terminal electron donors and acceptors. Siderophore production and heterotrophic Fe(II) oxidation are discussed as potential mechanisms enhancing growth of P. stutzeri VS-10 on glass surfaces. In correlation with that we discuss the possibility that metabolic versatility could represent a common and beneficial physiological trait in marine microbial communities being subject to oligotrophic and rapidly changing deep-sea conditions.

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H₂, CH₄, Ca²⁺, Mg²⁺, NO3-, SO42-, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.

Molecular determinant of the effects of hydrostatic pressure on protein folding stability

Hydrostatic pressure is an important environmental variable that plays an essential role in biological adaptation for many extremophilic organisms (for example, piezophiles). Increase in hydrostatic pressure, much like increase in temperature, perturbs the thermodynamic equilibrium between native and unfolded states of proteins. Experimentally, it has been observed that increase in hydrostatic pressure can both increase and decrease protein stability. These observations suggest that volume changes upon protein unfolding can be both positive and negative. The molecular details of this difference in sign of volume changes have been puzzling the field for the past 50 years. Here we present a comprehensive thermodynamic model that provides in-depth analysis of the contribution of various molecular determinants to the volume changes upon protein unfolding. Comparison with experimental data shows that the model allows quantitative predictions of volume changes upon protein unfolding, thus paving the way to proteome-wide computational comparison of proteins from different extremophilic organisms.

Proteins can be both stabilized and destabilized by pressure. Here the authors analyse the factors contributing to both negative and positive protein volume change upon denaturation, and shed light on the molecular determinants allowing proteins to be stable at high pressures.

Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank

The deep marine biosphere has over the past decades been exposed as an immense habitat for microorganisms with wide-reaching implications for our understanding of life on Earth. Recent advances in knowledge concerning this biosphere have been achieved mainly through extensive microbial and geochemical studies of deep marine sediments. However, the oceanic crust buried beneath the sediments, is still largely unexplored with respect to even the most fundamental questions related to microbial life. Here, we present quantitative and qualitative data related to the microbial inventory from 33 deeply buried basaltic rocks collected at two different locations, penetrating 300 vertical meters into the upper oceanic crust on the west flank of the Mid-Atlantic spreading ridge. We use quantitative PCR and sequencing of 16S rRNA gene amplicons to estimate cell abundances and to profile the community structure. Our data suggest that the number of cells is relatively stable at ~10⁴ per gram of rock irrespectively of sampling site and depth. Further, we show that Proteobacteria, especially Gammaproteobacteria dominate the microbial assemblage across all investigated samples, with Archaea, in general, represented by < 1% of the community. In addition, we show that the communities within the crust are distinct from the overlying sediment. However, many of their respective microbial inhabitants are shared between the two biomes, but with markedly different relative distributions. Our study provides fundamental information with respect to abundance, distribution, and identity of microorganisms in the upper oceanic crust.

Anaerobic Fungi: A Potential Source of Biological H2 in the Oceanic Crust

The recent recognition of fungi in the oceanic igneous crust challenges the understanding of this environment as being exclusively prokaryotic and forces reconsiderations of the ecology of the deep biosphere. Anoxic provinces in the igneous crust are abundant and increase with age and depth of the crust. The presence of anaerobic fungi in deep-sea sediments and on the seafloor introduces a type of organism with attributes of geobiological significance not previously accounted for. Anaerobic fungi are best known from the rumen of herbivores where they produce molecular hydrogen, which in turn stimulates the growth of methanogens. The symbiotic cooperation between anaerobic fungi and methanogens in the rumen enhance the metabolic rate and growth of both. Methanogens and other hydrogen-consuming anaerobic archaea are known from subseafloor basalt; however, the abiotic production of hydrogen is questioned to be sufficient to support such communities. Alternatively, biologically produced hydrogen could serve as a continuous source. Here, we propose anaerobic fungi as a source of bioavailable hydrogen in the oceanic crust, and a close interplay between anaerobic fungi and hydrogen-driven prokaryotes.

The Ability of Microbial Community of Lake Baikal Bottom Sediments Associated with Gas Discharge to Carry Out the Transformation of Organic Matter under Thermobaric Conditions

The ability to compare the composition and metabolic potential of microbial communities inhabiting the subsurface sediment in geographically distinct locations is one of the keys to understanding the evolution and function of the subsurface biosphere. Prospective areas for study of the subsurface biosphere are the sites of hydrocarbon discharges on the bottom of the Lake Baikal rift, where ascending fluxes of gas-saturated fluids and oil from deep layers of bottom sediments seep into near-surface sediment. The samples of surface sediments collected in the area of the Posolskaya Bank methane seep were cultured for 17 months under thermobaric conditions (80°C, 5 MPa) with the addition of complementary organic substrate, and a different composition for the gas phase. After incubation, the presence of intact cells of microorganisms, organic matter transformation and the formation of oil biomarkers was confirmed in the samples, with the addition of Baikal diatom alga Synedra acus detritus, and gas mixture CH₄:H₂:CO₂. Taxonomic assignment of the 16S rRNA sequence data indicates that the predominant sequences in the enrichment were Sphingomonas (55.3%), Solirubrobacter (27.5%) and Arthrobacter (16.6%). At the same time, in heat-killed sediment and in sediment without any additional substrates, which were cultivated in a CH₄ atmosphere, no geochemical changes were detected, nor the presence of intact cells and 16S rRNA sequences of Bacteria and Archaea. This data may suggest that the decomposition of organic matter under culturing conditions could be performed by microorganisms from low-temperature sediment layers. One possible explanation of this phenomenon is migration of the representatives of the deep thermophilic community through fault zones in the near surface sediment layers, together with gas-bearing fluids.

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.

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.

Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes

Fractures in the deep subsurface of Earth's crust are inhabited by diverse microbial communities that participate in biogeochemical cycles of the Earth. Life on Earth, which arose c. 3.5-4.0 billion years ago, reaches down at least 5 km in the crust. Deep mines, caves, and boreholes have provided scientists with opportunities to sample deep subsurface microbiomes and to obtain information on the species diversity and functions. A wide variety of bacteria, archaea, eukaryotes, and viruses are now known to reside in the crust, but their functions are still largely unknown. The crust at different depths has varying geological composition and hosts endemic microbiomes accordingly. The diversity is driven by geological formations and gases evolving from deeper depths. Cooperation among different species is still mostly unexplored, but viruses are known to restrict density of bacterial and archaeal populations. Due to the complex growth requirements of the deep subsurface microbiomes, the new knowledge about their diversity and functions is mostly obtained by molecular methods, eg, meta'omics'. Geomicrobiology is a multidisciplinary research area combining disciplines from geology, mineralogy, geochemistry, and microbiology. Geomicrobiology is concerned with the interaction of microorganisms and geological processes. At the surface of mineralogical or rock surfaces, geomicrobial processes occur mainly under aerobic conditions. In the deep subsurface, however, the environmental conditions are reducing and anaerobic. The present chapter describes the world of microbiomes in deep terrestrial geological environments as well as metagenomic and metatranscriptomic methods suitable for studies of these enigmatic communities.

In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust

The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 10⁵ cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.

A Fungal-Prokaryotic Consortium at the Basalt-Zeolite Interface in Subseafloor Igneous Crust

We have after half a century of coordinated scientific drilling gained insight into Earth´s largest microbial habitat, the subseafloor igneous crust, but still lack substantial understanding regarding its abundance, diversity and ecology. Here we describe a fossilized microbial consortium of prokaryotes and fungi at the basalt-zeolite interface of fractured subseafloor basalts from a depth of 240 m below seafloor (mbsf). The microbial consortium and its relationship with the surrounding physical environment are revealed by synchrotron-based X-ray tomographic microscopy (SRXTM), environmental scanning electron microscopy (ESEM), and Raman spectroscopy. The base of the consortium is represented by microstromatolites—remains of bacterial communities that oxidized reduced iron directly from the basalt. The microstromatolites and the surrounding basalt were overlaid by fungal cells and hyphae. The consortium was overgrown by hydrothermally formed zeolites but remained alive and active during this event. After its formation, fungal hyphae bored in the zeolite, producing millimetre-long tunnels through the mineral substrate. The dissolution could either serve to extract metals like Ca, Na and K essential for fungal growth and metabolism, or be a response to environmental stress owing to the mineral overgrowth. Our results show how microbial life may be maintained in a nutrient-poor and extreme environment by close ecological interplay and reveal an effective strategy for nutrient extraction from minerals. The prokaryotic portion of the consortium served as a carbon source for the eukaryotic portion. Such an approach may be a prerequisite for prokaryotic-eukaryotic colonisation of, and persistence in, subseafloor igneous crust.

A Hierarchical System for Evaluating the Biogenicity of Metavolcanic- and Ultramafic-Hosted Microalteration Textures in the Search for Extraterrestrial Life

The low-temperature alteration of submarine volcanic glasses has been argued to involve the activity of microorganisms, and analogous fluid-rock-microbial-mediated alteration has also been postulated on Mars. However, establishing the extent to which microbes are involved in volcanic glass alteration has proven to be difficult, and the reliability of resulting textural biosignatures is debated, particularly in the early rock record. We therefore propose a hierarchical scheme to evaluate the biogenicity of candidate textural biosignatures found in altered terrestrial and extraterrestrial basaltic glasses and serpentinized ultramafic rocks. The hierarchical scheme is formulated to give increasing confidence of a biogenic origin and involves (i) investigation of the textural context and syngenicity of the candidate biosignature; (ii) characterization of the morphology and size range of the microtextures; (iii) mapping of the geological and physicochemical variables controlling the occurrence and preservation of the microtextures; (iv) in situ investigation of chemical signatures that are syngenetic to the microtexture; and (v) identification of growth patterns suggestive of biological behavior and redox variations in the host minerals. The scheme results in five categories of candidate biosignature as follows: Category 1 indicates preservation of very weak evidence for biogenicity, Categories 2 through 4 indicate evidence for increasing confidence of a biogenic origin, and Category 5 indicates that biogenic origin is most likely. We apply this hierarchical approach to examine the evidence for a biogenic origin of several examples, including candidate bacterial encrustations in altered pillow lavas, granular and tubular microtextures in volcanic glass from the subseafloor and a Phanerozoic ophiolite, mineralized microtextures in Archean metavolcanic glass, and alteration textures in olivines of the martian meteorite Yamato 000593. The aim of this hierarchical approach is to provide a framework for identifying robust biosignatures of microbial life in the altered oceanic crust on Earth, and in extraterrestrial altered mafic-ultramafic rocks, particularly on Mars.

Carbon fixation by basalt-hosted microbial communities

Oceanic crust is a massive potential habitat for microbial life on Earth, yet our understanding of this ecosystem is limited due to difficulty in access. In particular, measurements of rates of microbial activity are sparse. We used stable carbon isotope incubations of crustal samples, coupled with functional gene analyses, to examine the potential for carbon fixation on oceanic crust. Both seafloor-exposed and subseafloor basalts were recovered from different mid-ocean ridge and hot spot environments (i.e., the Juan de Fuca Ridge, the Mid-Atlantic Ridge, and the Loihi Seamount) and incubated with (13)C-labeled bicarbonate. Seafloor-exposed basalts revealed incorporation of (13)C-label into organic matter over time, though the degree of incorporation was heterogeneous. The incorporation of (13)C into biomass was inconclusive in subseafloor basalts. Translating these measurements into potential rates of carbon fixation indicated that 0.1-10 nmol C g(-1) rock d(-1) could be fixed by seafloor-exposed rocks. When scaled to the global production of oceanic crust, this suggests carbon fixation rates of 10(9)-10(12) g C year(-1), which matches earlier predictions based on thermodynamic calculations. Functional gene analyses indicate that the Calvin cycle is likely the dominant biochemical mechanism for carbon fixation in basalt-hosted biofilms, although the reductive acetyl-CoA pathway and reverse TCA cycle likely play some role in net carbon fixation. These results provide empirical evidence for autotrophy in oceanic crust, suggesting that basalt-hosted autotrophy could be a significant contributor of organic matter in this remote and vast environment.

Fast-folding proteins under stress

Proteins are subject to a variety of stresses in biological organisms, including pressure and temperature, which are the easiest stresses to simulate by molecular dynamics. We discuss the effect of pressure and thermal stress on very-fast-folding model proteins, whose in vitro folding can be fully simulated on computers and compared with experiments. We then discuss experiments that can be used to subject proteins to low- and high-temperature unfolding, as well as low- and high-pressure unfolding. Pressure and temperature are prototypical perturbations that illustrate how close many proteins are to instability, a property that cells can exploit to control protein function. We conclude by reviewing some recent in-cell experiments, and progress being made in simulating and measuring protein stability and function inside live cells.

Zygomycetes in Vesicular Basanites from Vesteris Seamount, Greenland Basin--A New Type of Cryptoendolithic Fungi

Fungi have been recognized as a frequent colonizer of subseafloor basalt but a substantial understanding of their abundance, diversity and ecological role in this environment is still lacking. Here we report fossilized cryptoendolithic fungal communities represented by mainly Zygomycetes and minor Ascomycetes in vesicles of dredged volcanic rocks (basanites) from the Vesteris Seamount in the Greenland Basin. Zygomycetes had not been reported from subseafloor basalt previously. Different stages in zygospore formation are documented in the studied samples, representing a reproduction cycle. Spore structures of both Zygomycetes and Ascomycetes are mineralized by romanechite-like Mn oxide phases, indicating an involvement in Mn(II) oxidation to form Mn(III,VI) oxides. Zygospores still exhibit a core of carbonaceous matter due to their resistance to degradation. The fungi are closely associated with fossiliferous marine sediments that have been introduced into the vesicles. At the contact to sediment infillings, fungi produced haustoria that penetrated and scavenged on the remains of fragmented marine organisms. It is most likely that such marine debris is the main carbon source for fungi in shallow volcanic rocks, which favored the establishment of vital colonies.

Biogenic Mn-Oxides in Subseafloor Basalts

The deep biosphere of the subseafloor basalts is recognized as a major scientific frontier in disciplines like biology, geology, and oceanography. Recently, the presence of fungi in these environments has involved a change of view regarding diversity and ecology. Here, we describe fossilized fungal communities in vugs in subseafloor basalts from a depth of 936.65 metres below seafloor at the Detroit Seamount, Pacific Ocean. These fungal communities are closely associated with botryoidal Mn oxides composed of todorokite. Analyses of the Mn oxides by Electron Paramagnetic Resonance spectroscopy (EPR) indicate a biogenic signature. We suggest, based on mineralogical, morphological and EPR data, a biological origin of the botryoidal Mn oxides. Our results show that fungi are involved in Mn cycling at great depths in the seafloor and we introduce EPR as a means to easily identify biogenic Mn oxides in these environments.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20,273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

Trends and future challenges in sampling the deep terrestrial biosphere

Research in the deep terrestrial biosphere is driven by interest in novel biodiversity and metabolisms, biogeochemical cycling, and the impact of human activities on this ecosystem. As this interest continues to grow, it is important to ensure that when subsurface investigations are proposed, materials recovered from the subsurface are sampled and preserved in an appropriate manner to limit contamination and ensure preservation of accurate microbial, geochemical, and mineralogical signatures. On February 20th, 2014, a workshop on "Trends and Future Challenges in Sampling The Deep Subsurface" was coordinated in Columbus, Ohio by The Ohio State University and West Virginia University faculty, and sponsored by The Ohio State University and the Sloan Foundation's Deep Carbon Observatory. The workshop aims were to identify and develop best practices for the collection, preservation, and analysis of terrestrial deep rock samples. This document summarizes the information shared during this workshop.

Microorganisms persist at record depths in the subseafloor of the Canterbury Basin

The subsurface realm is colonized by microbial communities to depths of >1000 meters below the seafloor (m.b.sf.), but little is known about overall diversity and microbial distribution patterns at the most profound depths. Here we show that not only Bacteria and Archaea but also Eukarya occur at record depths in the subseafloor of the Canterbury Basin. Shifts in microbial community composition along a core of nearly 2 km reflect vertical taxa zonation influenced by sediment depth. Representatives of some microbial taxa were also cultivated using methods mimicking in situ conditions. These results suggest that diverse microorganisms persist down to 1922 m.b.sf. in the seafloor of the Canterbury Basin and extend the previously known depth limits of microbial evidence (i) from 159 to 1740 m.b.sf. for Eukarya and (ii) from 518 to 1922 m.b.sf. for Bacteria.

GeoChip 4: a functional gene-array-based high-throughput environmental technology for microbial community analysis

Micro-organisms play critical roles in many important biogeochemical processes in the Earth's biosphere. However, understanding and characterizing the functional capacity of microbial communities are still difficult due to the extremely diverse and often uncultivable nature of most micro-organisms. In this study, we developed a new functional gene array, GeoChip 4, for analysing the functional diversity, composition, structure, metabolic potential/activity and dynamics of microbial communities. GeoChip 4 contained approximately 82 000 probes covering 141 995 coding sequences from 410 functional gene families related to microbial carbon (C), nitrogen (N), sulphur (S), and phosphorus (P) cycling, energy metabolism, antibiotic resistance, metal resistance/reduction, organic remediation, stress responses, bacteriophage and virulence. A total of 173 archaeal, 4138 bacterial, 404 eukaryotic and 252 viral strains were targeted, providing the ability to analyse targeted functional gene families of micro-organisms included in all four domains. Experimental assessment using different amounts of DNA suggested that as little as 500 ng environmental DNA was required for good hybridization, and the signal intensities detected were well correlated with the DNA amount used. GeoChip 4 was then applied to study the effect of long-term warming on soil microbial communities at a Central Oklahoma site, with results indicating that microbial communities respond to long-term warming by enriching carbon degradation, nutrient cycling (nitrogen and phosphorous) and stress response gene families. To the best of our knowledge, GeoChip 4 is the most comprehensive functional gene array for microbial community analysis.

Microscale mapping of alteration conditions and potential biosignatures in basaltic-ultramafic rocks on early Earth and beyond

Subseafloor environments preserved in Archean greenstone belts provide an analogue for investigating potential subsurface habitats on Mars. The c. 3.5-3.4 Ga pillow lava metabasalts of the mid-Archean Barberton greenstone belt, South Africa, have been argued to contain the earliest evidence for microbial subseafloor life. This includes candidate trace fossils in the form of titanite microtextures, and sulfur isotopic signatures of pyrite preserved in metabasaltic glass of the c. 3.472 Ga Hooggenoeg Formation. It has been contended that similar microtextures in altered martian basalts may represent potential extraterrestrial biosignatures of microbe-fluid-rock interaction. But despite numerous studies describing these putative early traces of life, a detailed metamorphic characterization of the microtextures and their host alteration conditions in the ancient pillow lava metabasites is lacking. Here, we present a new nondestructive technique with which to study the in situ metamorphic alteration conditions associated with potential biosignatures in mafic-ultramafic rocks of the Hooggenoeg Formation. Our approach combines quantitative microscale compositional mapping by electron microprobe with inverse thermodynamic modeling to derive low-temperature chlorite crystallization conditions. We found that the titanite microtextures formed under subgreenschist to greenschist facies conditions. Two chlorite temperature groups were identified in the maps surrounding the titanite microtextures and record peak metamorphic conditions at 315 ± 40°C (XFe3+(chlorite) = 25-34%) and lower-temperature chlorite veins/microdomains at T = 210 ± 40°C (lower XFe3+(chlorite) = 40-45%). These results provide the first metamorphic constraints in textural context on the Barberton titanite microtextures and thereby improve our understanding of the local preservation conditions of these potential biosignatures. We suggest that this approach may prove to be an important tool in future studies to assess the biogenicity of these earliest candidate traces of life on Earth. Furthermore, we propose that this mapping approach could also be used to investigate altered mafic-ultramafic extraterrestrial samples containing candidate biosignatures.

A microarray for assessing transcription from pelagic marine microbial taxa

Metagenomic approaches have revealed unprecedented genetic diversity within microbial communities across vast expanses of the world's oceans. Linking this genetic diversity with key metabolic and cellular activities of microbial assemblages is a fundamental challenge. Here we report on a collaborative effort to design MicroTOOLs (Microbiological Targets for Ocean Observing Laboratories), a high-density oligonucleotide microarray that targets functional genes of diverse taxa in pelagic and coastal marine microbial communities. MicroTOOLs integrates nucleotide sequence information from disparate data types: genomes, PCR-amplicons, metagenomes, and metatranscriptomes. It targets 19 400 unique sequences over 145 different genes that are relevant to stress responses and microbial metabolism across the three domains of life and viruses. MicroTOOLs was used in a proof-of-concept experiment that compared the functional responses of microbial communities following Fe and P enrichments of surface water samples from the North Pacific Subtropical Gyre. We detected transcription of 68% of the gene targets across major taxonomic groups, and the pattern of transcription indicated relief from Fe limitation and transition to N limitation in some taxa. Prochlorococcus (eHLI), Synechococcus (sub-cluster 5.3) and Alphaproteobacteria SAR11 clade (HIMB59) showed the strongest responses to the Fe enrichment. In addition, members of uncharacterized lineages also responded. The MicroTOOLs microarray provides a robust tool for comprehensive characterization of major functional groups of microbes in the open ocean, and the design can be easily amended for specific environments and research questions.

Taxonomically and functionally diverse microbial communities in deep crystalline rocks of the Fennoscandian shield

Microbial life in the nutrient-limited and low-permeability continental crystalline crust is abundant but remains relatively unexplored. Using high-throughput sequencing to assess the 16S rRNA gene diversity, we found diverse bacterial and archaeal communities along a 2516-m-deep drill hole in continental crystalline crust in Outokumpu, Finland. These communities varied at different sampling depths in response to prevailing lithology and hydrogeochemistry. Further analysis by shotgun metagenomic sequencing revealed variable carbon and nutrient utilization strategies as well as specific functional and physiological adaptations uniquely associated with specific environmental conditions. Altogether, our results show that predominant geological and hydrogeochemical conditions, including the existence and connectivity of fracture systems and the low amounts of available energy, have a key role in controlling microbial ecology and evolution in the nutrient and energy-poor deep crustal biosphere.

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).

Pressure as an environmental parameter for microbial life--a review

Microbial life has been prevailing in the biosphere for the last 3.8 Ga at least. Throughout most of the Earth's history it has experienced a range of pressures; both dynamic pressure when the young Earth was heavily bombarded, and static pressure in subsurface environments that could have served as a refuge and where microbial life nowadays flourishes. In this review, we discuss the extent of high-pressure habitats in early and modern times and provide a short overview of microbial survival under dynamic pressures. We summarize the current knowledge about the impact of microbial activity on biogeochemical cycles under pressures characteristic of the deep subsurface. We evaluate the possibility that pressure can be a limiting parameter for life at depth. Finally, we discuss the open questions and knowledge gaps that exist in the field of high-pressure geomicrobiology.