A primary aim of microbial ecology is to determine patterns and drivers of community distribution, interaction, and assembly amidst complexity and uncertainty. Microbial community composition has been shown to change across gradients of environment, geographic distance, salinity, temperature, oxygen, nutrients, pH, day length, and biotic factors 1-6 . These patterns have been identified mostly by focusing on one sample type and region at a time, with insights extra polated across environments and geography to produce generalized principles. To assess how microbes are distributed across environments globally-or whether microbial community dynamics follow funda mental ecological 'laws' at a planetary scale-requires either a massive monolithic cross environment survey or a practical methodology for coordinating many independent surveys. New studies of microbial environments are rapidly accumulating; however, our ability to extract meaningful information from across datasets is outstripped by the rate of data generation. Previous meta analyses have suggested robust gen eral trends in community composition, including the importance of salinity 1 and animal association 2 . These findings, although derived from relatively small and uncontrolled sample sets, support the util ity of meta analysis to reveal basic patterns of microbial diversity and suggest that a scalable and accessible analytical framework is needed.The Earth Microbiome Project (EMP, http://www.earthmicrobiome. org) was founded in 2010 to sample the Earth's microbial communities at an unprecedented scale in order to advance our understanding of the organizing biogeographic principles that govern microbial commu nity structure 7,8 . We recognized that open and collaborative science, including scientific crowdsourcing and standardized methods 8 , would help to reduce technical variation among individual studies, which can overwhelm biological variation and make general trends difficult to detect 9 . Comprising around 100 studies, over half of which have yielded peer reviewed publications (Supplementary Table 1), the EMP has now dwarfed by 100 fold the sampling and sequencing depth of earlier meta analysis efforts 1,2 ; concurrently, powerful analysis tools have been developed, opening a new and larger window into the distri bution of microbial diversity on Earth. In establishing a scalable frame work to catalogue microbiota globally, we provide both a resource for the exploration of myriad questions and a starting point for the guided acquisition of new data to answer them. As an example of using this Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of r...

The serpentinite-hosted Lost City hydrothermal field is a remarkable submarine ecosystem in which geological, chemical, and biological processes are intimately interlinked. Reactions between seawater and upper mantle peridotite produce methane- and hydrogen-rich fluids, with temperatures ranging from <40 degrees to 90 degrees C at pH 9 to 11, and carbonate chimneys 30 to 60 meters tall. A low diversity of microorganisms related to methane-cycling Archaea thrive in the warm porous interiors of the edifices. Macrofaunal communities show a degree of species diversity at least as high as that of black smoker vent sites along the Mid-Atlantic Ridge, but they lack the high biomasses of chemosynthetic organisms that are typical of volcanically driven systems.

Evidence is growing that hydrothermal venting occurs not only along mid-ocean ridges but also on old regions of the oceanic crust away from spreading centres. Here we report the discovery of an extensive hydrothermal field at 30 degrees N near the eastern intersection of the Mid-Atlantic Ridge and the Atlantis fracture zone. The vent field--named 'Lost City'--is distinctly different from all other known sea-floor hydrothermal fields in that it is located on 1.5-Myr-old crust, nearly 15 km from the spreading axis, and may be driven by the heat of exothermic serpentinization reactions between sea water and mantle rocks. It is located on a dome-like massif and is dominated by steep-sided carbonate chimneys, rather than the sulphide structures typical of 'black smoker' hydrothermal fields. We found that vent fluids are relatively cool (40-75 degrees C) and alkaline (pH 9.0-9.8), supporting dense microbial communities that include anaerobic thermophiles. Because the geological characteristics of the Atlantis massif are similar to numerous areas of old crust along the Mid-Atlantic, Indian and Arctic ridges, these results indicate that a much larger portion of the oceanic crust may support hydrothermal activity and microbial life than previously thought.

Hydrothermal venting and the formation of carbonate chimneys in the Lost City hydrothermal field (LCHF) are driven predominantly by serpentinization reactions and cooling of mantle rocks, resulting in a highly reducing, high-pH environment with abundant dissolved hydrogen and methane. Phylogenetic and terminal restriction fragment length polymorphism analyses of 16S rRNA genes in fluids and carbonate material from this site indicate the presence of organisms similar to sulfur-oxidizing, sulfate-reducing, and methane-oxidizing Bacteria as well as methanogenic and anaerobic methane-oxidizing Archaea. The presence of these metabolic groups indicates that microbial cycling of sulfur and methane may be the dominant biogeochemical processes active within this ultramafic rock-hosted environment. 16S rRNA gene sequences grouping within the Methylobacter and Thiomicrospira clades were recovered from a chemically diverse suite of carbonate chimney and fluid samples. In contrast, 16S rRNA genes corresponding to the Lost City Methanosarcinales phylotype were found exclusively in high-temperature chimneys, while a phylotype of anaerobic methanotrophic Archaea (ANME-1) was restricted to lower-temperature, less vigorously venting sites. A hyperthermophilic habitat beneath the LCHF may be reflected by 16S rRNA gene sequences belonging to Thermococcales and uncultured Crenarchaeota identified in vent fluids. The finding of a diverse microbial ecosystem supported by the interaction of high-temperature, high-pH fluids resulting from serpentinization reactions in the subsurface provides insight into the biogeochemistry of what may be a pervasive process in ultramafic subseafloor environments.The Lost City hydrothermal field (LCHF) is located near the summit of the Atlantis Massif at a water depth of ϳ750 m (37, 38). Long-lived faulting and extensive uplift at the massif have resulted in the exposure of magnesium-rich, variably altered ultramafic rocks with lesser gabbroic material that is 1.5 to 2 million years of age. Fluid circulation within the massif is driven by serpentinization reactions and the cooling of the underlying mantle rocks. These reactions result in a combination of extreme conditions never before seen in the marine environment, which include venting of high-pH (from pH 9 to 11), 40 to 91°C hydrothermal fluids with high concentrations of dissolved hydrogen (H 2 ), methane (CH 4 ), and other lowmolecular-weight hydrocarbons (38). Mixing of the warm, high-pH fluids with seawater results in carbonate precipitation and growth of chimneys, which tower up to 60 m above the surrounding seafloor (38). Carbon-14 radioisotopic dating indicates that hydrothermal activity has been ongoing for at least 30,000 years (17). A large percentage of exposed seafloor on and near slow-and ultraslow-spreading ridges is likely to contain ultramafic rocks similar to those that host the LCHF (4, 12, 14). Therefore, this system offers a unique opportunity to study an ultramafic-rock-hosted submarine ecosystem that may be both widespread and ...

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A large, intact sulfide chimney, designated Finn, was recovered from the Mothra Vent Field on the Juan de Fuca Ridge in 1998. Finn was venting 302°C fluids on the seafloor and contained complex mineralogical zones surrounding a large open central conduit. Examination of microorganisms within these zones, followed by community analysis with oligonucleotide probes, showed that there were variations in the abundance and diversity of eubacteria and archaea from the exterior to the interior of the chimney. The microbial abundance based upon epifluorescence microscopy and quantitative fatty acid analyses varied from >10 8 cells/g of sulfide 2 to 10 cm within the chimney wall to <10 5 cells/g in interior zones. Direct microscopic observation indicated that microorganisms were attached to mineral surfaces throughout the structure. Whole-cell hybridization results revealed that there was a transition from a mixed community of eubacteria and archaea near the cool exterior of the chimney to primarily archaea near the warm interior. Archaeal diversity was examined in three zones of Finn by cloning and sequencing of the 16S rRNA gene. The majority of sequences from the exterior of the chimney were related to marine group I of the Crenarchaeota and uncultured Euryarchaeota from benthic marine environments. In contrast, clone libraries from interior regions of the chimney contained sequences closely related to methanogens, Thermococcales, and Archaeoglobales, in addition to uncultured crenarchaeal phylotypes obtained from deep subsurface sites. These observations of microbial communities within an active hydrothermal chimney provide insight into the microbial ecology within such structures and may facilitate follow-up exploration into expanding the known upper temperature limits of life.Volcanic and tectonic activity associated with midocean ridge spreading centers supports widespread hydrothermal activity that occurs over lateral distances of hundreds of kilometers and extends deep into the subseafloor (15). Thermal and chemical gradients created by mixing of hydrothermal fluids with seawater and fluid interactions with heated rock support microbial life uniquely adapted to specific extreme environments (30,48). Sulfide edifices present in marine hydrothermal systems are the seafloor products of hydrothermal circulation, where they serve as conduits for hot, metal-enriched fluids. These structures have steep temperature and chemistry gradients similar to those suspected to exist in the subseafloor, but the gradients are condensed into much smaller spatial scales (15,18,30). Previously, researchers have investigated the microbial biomass and diversity within the walls of vent chimneys and associated structures by using culture-based, microscopic, and molecular methods (24,26,44,50,51). Thermophilic and hyperthermophilic microorganisms are commonly cultured from pieces of chimneys from the deep-sea environment (24,30,44). In addition, intact cells have been observed in small pieces of sulfide chimneys, porous beehive structures...

The recently discovered Lost City Hydrothermal Field (LCHF) represents a new type of submarine hydrothermal system driven primarily by exothermic serpentinization reactions in ultramafic oceanic crust. Highly reducing, alkaline hydrothermal environments at the LCHF produce considerable quantities of hydrogen, methane and organic molecules through chemo- and biosynthetic reactions. Here, we report the first analyses of microbial communities inhabiting carbonate chimneys awash in warm, high pH fluids at the LCHF and the predominance of a single group of methane-metabolizing Archaea. The predominant phylotype, related to the Methanosarcinales, formed tens of micrometre-thick biofilms in regions adjacent to hydrothermal flow. Exterior portions of active structures harboured a diverse microbial community composed primarily of filamentous Eubacteria that resembled sulphide-oxidizing species. Inactive samples, away from regions of hydrothermal flow, contained phylotypes related to pelagic microorganisms. The abundance of organisms linked to the volatile chemistry at the LCHF hints that similar metabolic processes may operate in the subseafloor. These results expand the range of known geological settings that support biological activity to include submarine hydrothermal systems that are not dependent upon magmatic heat sources.

Ultramafic rocks in the Earth’s mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). In order to assess the potential for microbial H2 utilization fueled by serpentinization, we conducted metagenomic surveys of a marine serpentinite-hosted hydrothermal chimney (at the Lost City hydrothermal field) and two continental serpentinite-hosted alkaline seeps (at the Tablelands Ophiolite, Newfoundland). Novel [NiFe]-hydrogenase sequences were identified at both the marine and continental sites, and in both cases, phylogenetic analyses indicated aerobic, potentially autotrophic Betaproteobacteria belonging to order Burkholderiales as the most likely H2-oxidizers. Both sites also yielded metagenomic evidence for microbial H2 production catalyzed by [FeFe]-hydrogenases in anaerobic Gram-positive bacteria belonging to order Clostridiales. In addition, we present metagenomic evidence at both sites for aerobic carbon monoxide utilization and anaerobic carbon fixation via the Wood–Ljungdahl pathway. In general, our results point to H2-oxidizing Betaproteobacteria thriving in shallow, oxic–anoxic transition zones and the anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These data demonstrate the feasibility of metagenomic investigations into novel subsurface habitats via surface-exposed seeps and indicate the potential for H2-powered primary production in serpentinite-hosted subsurface habitats.