Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts

Abstract

We used molecular techniques to analyze basalts of varying ages that were collected from the East Pacific Rise, 91 N, from the rift axis of the Juan de Fuca Ridge and from neighboring seamounts. Cluster analysis of 16S rDNA terminal restriction fragment polymorphism data revealed that basalt endoliths are distinct from seawater and that communities clustered, to some degree, based on the age of the host rock. This age-based clustering suggests that alteration processes may affect community structure. Cloning and sequencing of bacterial and archaeal 16S rRNA genes revealed 12 different phyla and subphyla associated with basalts. These include the Gemmatimonadetes, Nitrospirae, the candidate phylum SBR1093 in the bacteria, and in the Archaea Marine Benthic Group B, none of which have been previously reported in basalts. We delineated novel ocean crust clades in the c-Proteobacteria, Planctomycetes and Actinobacteria that are composed entirely of basalt-associated microflora, and may represent basalt ecotypes. Finally, microarray analysis of functional genes in basalt revealed that genes coding for previously unreported processes such as carbon fixation, methane oxidation, methanogenesis and nitrogen fixation are present, suggesting that basalts harbor previously unrecognized metabolic diversity. These novel processes could exert a profound influence on ocean chemistry.

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

“…2 GeoChip has also been applied to the study of hydrothermal vents, for which it indicated the presence of very diverse SRM populations that, along with other microorganisms, undergo rapid dynamic succession and adaptation to the steep temperature and chemical gradients across the vent chimney 115 . In addition, SRMs were detected in deep-sea basalts, suggesting the occurrence of anaerobic processes in these extremely nutrient-poor environments 116 . More recently, GeoChip has been used to investigate microbial responses to the oil spill in the Gulf of Mexico 112 .…”

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

“…Some recent studies indicate that microbial nitrogen fixation, whereby dinitrogen gas is converted into ammonium, is another source of ammonium in the dark ocean, as in the case of nitrogen fixation linked to the anaerobic oxidation of methane or sulfate reduction in marine sediments (44,107). Other genomic surveys indicate the presence of nitrogen-fixing microorganisms inhabiting the surface of seafloor-exposed basaltic crustal rocks (354). These findings indicate that nitrogen fixation may contribute more ammo-nium to the marine benthic ecosystem than previously thought, although the quantitative importance of this process is not well documented.…”

“…The microorganisms responsible for Fe oxidation on basalts are not entirely clear, although commonly occurring alpha (including Hyphomonas species)-, gamma (including Marinobacter species)-and zetaproteobacteria are potential candidates for mediating this process (134,479). Fe(III)-reducing microorganisms, including Shewanella frigimarina and Shewanella loihica, have been cultivated from basalt enrichments (346) and from seamount sampling (183), and genes involved in iron reduction, mostly cytochromes, have been documented in surveys of environmental DNA from basalts (354). Activities and rates of Fe oxidation or reduction in basalts in the environment are very poorly constrained because appropriate assays are not available.…”

“…Knowledge of metabolic reactions occurring in the oceanic crust is sparse, as accessing this environment is technologically challenging. The majority of information available derives from analyzing the quantity and speciation of chemical constituents within rocks or fluids collected from the subsurface or at the seafloor (e.g., see references 26, 474, 602, and 603), by making inferences from functional genes observed in environmental DNA (354), or from incubation of mineral substrates in the environment or in the laboratory as a proxy for natural processes (133,134,425,540,559). Additional in situ experimental techniques are in development, especially for the hard rock subsurface (159,424,425), which promise to deliver more information about processes occurring within the oceanic crust.…”

GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity

“…Currently, this technology has become a powerful and high-throughput tool for analyzing microbial communities and monitoring environmental processes and ecosystem functions (c.f., Wu et al, 2001Wu et al, , 2006Wu et al, , 2008Loy et al, 2002;TaroncherOldenburg et al, 2003;Bodrossy and Sessitsch, 2004;Rhee et al, 2004;Steward et al, 2004;Tiquia et al, 2004;Dix et al, 2006;Rodriguez-Martinez et al, 2006;He et al, 2007;Leigh et al, 2007;Yergeau et al, 2007;Zhou et al, 2008;Liang et al, 2009;Mason et al, 2009;Tas et al, 2009;Van Nostrand et al, 2009;Waldron et al, 2009;Wang et al, 2009). Especially, one of our previous functional gene arrays (FGAs), GeoChip 2.0, containing more than 24 000 probes and covering more than 10 000 gene sequences from B150 gene categories involved in key microbially mediated biogeochemical processes has been widely used to analyze microbial communities from different resources, such as soils (Yergeau et al, 2007;Zhou et al, 2008), waters Leigh et al, 2007;Tas et al, 2009;Van Nostrand et al, 2009;Waldron et al, 2009), oil fields (Liang et al, 2009), marine sediments (Wu et al, 2008), extreme environments (Mason et al, 2009;Wang et al, 2009), bioreactor systems (Rodriguez-Martinez et al, 2006) and other habitats (Kimes et al, 2010), to address a variety of questions related to biogeochemical cycles, bioremediati...…”