First Investigation of the Microbiology of the Deepest Layer of Ocean Crust

We would like to thank Frederick (Rick) Colwell for input on molecular analyses in low biomass environments, Donna Blackman, Benoît Ildefonse, Adélie Delacour, and Gretchen Früh-Green for discussions regarding geological and geochemical aspects of this manuscript, and the Integrated Ocean Drilling Program Expeditions 304/305 Science Party. We would also like to thank Captain Alex Simpson and the entire crew of the JOIDES Resolution.Conceived and designed the experiments: OUM MRF SJG. Performed the experiments: OUM TN MR JDVN AM. Analyzed the data: OUM TN MR JDVN AM. Contributed reagents/materials/analysis tools: TN MR JZ MRF SJG. Wrote the paper: OUM.The gabbroic layer comprises the majority of ocean crust. Opportunities to sample this expansive crustal environment are rare because of the technological demands of deep ocean drilling; thus, gabbroic microbial communities have not yet been studied. During the Integrated Ocean Drilling Program Expeditions 304 and 305, igneous rock samples were collected from 0.45-1391.01 meters below seafloor at Hole 1309D, located on the Atlantis Massif (30 °N, 42 °W). Microbial diversity in the rocks was analyzed by denaturing gradient gel electrophoresis and sequencing (Expedition 304), and terminal restriction fragment length polymorphism, cloning and sequencing, and functional gene microarray analysis (Expedition 305). The gabbroic microbial community was relatively depauperate, consisting of a low diversity of proteobacterial lineages closely related to Bacteria from hydrocarbon-dominated environments and to known hydrocarbon degraders, and there was little evidence of Archaea. Functional gene diversity in the gabbroic samples was analyzed with a microarray for metabolic genes (“GeoChip”), producing further evidence of genomic potential for hydrocarbon degradation - genes for aerobic methane and toluene oxidation. Genes coding for anaerobic respirations, such as nitrate reduction, sulfate reduction, and metal reduction, as well as genes for carbon fixation, nitrogen fixation, and ammonium-oxidation, were also present. Our results suggest that the gabbroic layer hosts a microbial community that can degrade hydrocarbons and fix carbon and nitrogen, and has the potential to employ a diversity of non-oxygen electron acceptors. This rare glimpse of the gabbroic ecosystem provides further support for the recent finding of hydrocarbons in deep ocean gabbro from Hole 1309D. It has been hypothesized that these hydrocarbons might originate abiotically from serpentinization reactions that are occurring deep in the Earth's crust, raising the possibility that the lithic microbial community reported here might utilize carbon sources produced independently of the surface biosphere.Yeshttp://www.plosone.org/static/editorial#pee

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art ‘meta-omic’ techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments

Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage

Anaerobic oxidation of methane (AOM) is critical for controlling the flux of methane from anoxic environments. AOM coupled to iron1, manganese1 and sulphate2 reduction have been demonstrated in consortia containing anaerobic methanotrophic (ANME) archaea. More recently it has been shown that the bacterium Candidatus ‘Methylomirabilis oxyfera’ can couple AOM to nitrite reduction through an intra-aerobic methane oxidation pathway3. Bioreactors capable of AOM coupled to denitrification have resulted in the enrichment of ‘M. oxyfera’ and a novel ANME lineage, ANME-2d4,5. However, as ‘M. oxyfera’ can independently couple AOM to denitrification, the role of ANME-2d in the process is unresolved. Here, a bioreactor fed with nitrate, ammonium and methane was dominated by a single ANME-2d population performing nitrate-driven AOM. Metagenomic, single-cell genomic and metatranscriptomic analyses combined with bioreactor performance and 13C- and 15N-labelling experiments show that ANME-2d is capable of independent AOM through reverse methanogenesis using nitrate as the terminal electron acceptor. Comparative analyses reveal that the genes for nitrate reduction were transferred laterally from a bacterial donor, suggesting selection for this novel process within ANME-2d. Nitrite produced by ANME-2d is reduced to dinitrogen gas through a syntrophic relationship with an anaerobic ammonium-oxidizing bacterium, effectively outcompeting ‘M. oxyfera’ in the system. We propose the name Candidatus ‘Methanoperedens nitroreducens’ for the ANME-2d population and the family Candidatus ‘Methanoperedenaceae’ for the ANME-2d lineage. We predict that ‘M. nitroreducens’ and other members of the ‘Methanoperedenaceae’ have an important role in linking the global carbon and nitrogen cycles in anoxic environments

Anaerobic Methane Oxidizers

The anaerobic oxidation of methane (AOM) with sulfate as the final electron acceptor according to (CH4 + SO4 2− → HCO3 − + HS− + H2O) is the major sink of methane in the oceans and hence a significant process in the global carbon cycle and methane budget. Anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) are assumed to act as a syntrophic consortium where the archaeal partner activates and metabolizes methane, leading to an intermediate that is scavenged as electron donor by the sulfate-reducing partner. All known anaerobic methanotrophs are related to the methanogenic Euryarchaeota. Recently, much has been learned about the distribution, activity, and physiology of the ANME, however, not a single member of these groups has been obtained in culture and the biochemical functioning of AOM remains unknown

Anaerobic Methane Oxidizers

The anaerobic oxidation of methane (AOM) with sulfate as the final electron acceptor according to the net reaction CH4 + SO42- -> HCO3- -> HS- + H2O is the major sink of methane in the ocean floor and hence a significant process in the marine methane budget and the global carbon cycle. Since its discovery, much has been learned about the distribution of the AOM process, its activity in different settings, and connections to other metabolic reactions in the seafloor. AOM is performed by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Since all known ANME and most of their partner bacteria have so far resisted isolation, the physiology of both organisms has been largely inferred from culture-independent approaches on natural enrichments or enrichment cultures. All known ANME are related to methanogenic Euryarchaeota, and as such they reverse the methanogenesis pathway to activate and completely oxidize methane. The reducing equivalents are shuttled to the partner bacteria, which use them for sulfate reduction. Recently, evidence has been found for ANME that can use nitrate or iron as electron acceptors. The exact mechanisms for the required exchange of reducing equivalents in AOM and their genetic codes are yet poorly understood, but recently discovered accumulations of cytochromes and nanowire connections in the intercellular space of the consortia suggest direct electron transfer between both partners