Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190

Newberry, Carole J.; Webster, Gordon; Cragg, Barry A.; Parkes, Ronald John; Weightman, Andrew J.; Fry, John C.

doi:10.1111/j.1462-2920.2004.00568.x

Cited by 183 publications

(191 citation statements)

References 80 publications

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“…Contrary to our expectations, the methanogen isolates from subseafloor sediments were very closely related to previously characterized (cultivated) methanogens. Although the novelty of the isolated methanogens is unfortunately low from a taxonomic perspective, our results are consistent with previous culture-independent molecular studies, which have also detected sequences closely related to previously isolated methanogens, such as Methanosarcina and Methanobrevibacter (for example, Marchesi et al, 2001;Newberry et al, 2004). Among the bacterial isolates, strains MO-CFX1 and MO-CFX2 belonging to the Chloroflexi subphylum I, and strains MO-SPC1 and MO-SPC2 belonging to the genus Spirochaeta are of note (Figures 5a-d) because these bacterial components have been frequently reported as some of the predominant microbial components in marine subsurface environments (for example, Toffin et al, 2004;Inagaki et al, 2006;Fry et al, 2008;Webster et al, 2009).…”

supporting

confidence: 81%

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

et al. 2011

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Microbial methanogenesis in subseafloor sediments is a key process in the carbon cycle on the Earth. However, the cultivation-dependent evidences have been poorly demonstrated. Here we report the cultivation of a methanogenic microbial consortium from subseafloor sediments using a continuous-flow-type bioreactor with polyurethane sponges as microbial habitats, called down-flow hanging sponge (DHS) reactor. We anaerobically incubated methane-rich core sediments collected from off Shimokita Peninsula, Japan, for 826 days in the reactor at 10 1C. Synthetic seawater supplemented with glucose, yeast extract, acetate and propionate as potential energy sources was provided into the reactor. After 289 days of operation, microbiological methane production became evident. Fluorescence in situ hybridization analysis revealed the presence of metabolically active microbial cells with various morphologies in the reactor. DNA-and RNA-based phylogenetic analyses targeting 16S rRNA indicated the successful growth of phylogenetically diverse microbial components during cultivation in the reactor. Most of the phylotypes in the reactor, once it made methane, were more closely related to culture sequences than to the subsurface environmental sequence. Potentially methanogenic phylotypes related to the genera Methanobacterium, Methanococcoides and Methanosarcina were predominantly detected concomitantly with methane production, while uncultured archaeal phylotypes were also detected. Using the methanogenic community enrichment as subsequent inocula, traditional batch-type cultivations led to the successful isolation of several anaerobic microbes including those methanogens. Our results substantiate that the DHS bioreactor is a useful system for the enrichment of numerous fastidious microbes from subseafloor sediments and will enable the physiological and ecological characterization of pure cultures of previously uncultivated subseafloor microbial life.

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confidence: 81%

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

et al. 2011

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“…These strains are closely related to the recently isolated Carnobacterium pleistocenium (42) and to Antarctic isolates of the family Carnobacteriaceae (22). Members of this family have been previously detected in rRNA surveys of deep-ocean sediments (38), but this is the first report of a piezophilic isolate of this species as well as the first grampositive piezophile ever identified. The pressure range for growth of AT7 and AT12 was 0.1 to 60 MPa, with an optimum at 15 MPa (58).…”

Section: Resultsmentioning

confidence: 97%

The Unique 16S rRNA Genes of Piezophiles Reflect both Phylogeny and Adaptation

Lauro

Chastain

Blankenship

et al. 2007

Appl Environ Microbiol

124

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In the ocean's most extreme depths, pressures of 70 to 110 megapascals prevent the growth of all but the most hyperpiezophilic (pressure-loving) organisms. The physiological adaptations required for growth under these conditions are considered to be substantial. Efforts to determine specific adaptations permitting growth at extreme pressures have thus far focused on relatively few ␥-proteobacteria, in part due to the technical difficulties of obtaining piezophilic bacteria in pure culture. Here, we present the molecular phylogenies of several new piezophiles of widely differing geographic origins. Included are results from an analysis of the first deep-trench bacterial isolates recovered from the southern hemisphere (9.9-km depth) and of the first grampositive piezophilic strains. These new data allowed both phylogenetic and structural 16S rRNA comparisons among deep-ocean trench piezophiles and closely related strains not adapted to high pressure. Our results suggest that (i) the Circumpolar Deep Water acts as repository for hyperpiezophiles and drives their dissemination to deep trenches in the Pacific Ocean and (ii) the occurrence of elongated helices in the 16S rRNA genes increases with the extent of adaptation to growth at elevated pressure. These helix changes are believed to improve ribosome function under deep-sea conditions. Low temperature and high hydrostatic pressure structure deep-sea communities outside of hydrothermal vents. Tight selection by these and other environmental parameters is considered the cause of the conspicuous absence of many deep-sea taxonomic groups from the deepest ocean environments (8, 44).Both temperature and pressure exert their effects at many levels of bacterial physiology, from the structure of macromolecules to the rate of metabolic reactions. Adaptations to low temperature include alterations of membrane phospholipids, such as increased fatty acid unsaturation (43), enzymes characterized by high catalytic efficiency and reduced activation enthalpy (16,20,37,45), and high levels of cold shock proteins, RNA helicases (9), and posttranscriptional modification of tRNA molecules (15), all of which may reduce the formation of unfavorable nucleic acid secondary structures at low temperature. In contrast with enthalpy-based temperature effects, the underlying cause of pressure effects arises from the promotion of reduced system volumes, in accordance with Le Chatelier's principle (5). Despite these thermodynamic differences, low temperature and high pressure share a surprising number of influences on biological processes. For example, membrane fluidity, permeability, and phase are similarly altered by both parameters.As with psychrophiles, piezophiles ("high-pressure-loving" microbes) contain lipids with highly unsaturated fatty acids (6, 7). Indeed, the presence of unsaturated fatty acids is critical to growth ability at high pressure (3,4,19). Both low temperature and high pressure also alter protein quaternary structure (46) and nucleic acid secondary structure (50), and at ...

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“…Cells can only occupy pores larger than the cell size; the probability of finding pores of viable host size decreases with depth due to compaction, and with grain specific surface S S due to the presence of fine particles in the pore space (Phadnis and Santamarina, 2011). Nankai Trough data from other studies are included (Kormas et al, 2003;Li et al, 1999;Mills et al, 2012;Newberry et al, 2004;Reed et al, 2002). The shaded region represents results from other locations compiled in Parkes et al (1994Parkes et al ( , 2009.…”

Section: Biological Testmentioning

confidence: 99%

Hydro-bio-geomechanical properties of hydrate-bearing sediments from Nankai Trough

Santamarina

Dai

Terzariol

et al. 2015

Marine and Petroleum Geology

204

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a b s t r a c tNatural hydrate-bearing sediments from the Nankai Trough, offshore Japan, were studied using the Pressure Core Characterization Tools (PCCTs) to obtain geomechanical, hydrological, electrical, and biological properties under in situ pressure, temperature, and restored effective stress conditions. Measurement results, combined with index-property data and analytical physics-based models, provide unique insight into hydrate-bearing sediments in situ. Tested cores contain some silty-sands, but are predominantly sandy-and clayey-silts. Hydrate saturations S h range from 0.15 to 0.74, with significant concentrations in the silty-sands. Wave velocity and flexible-wall permeameter measurements on neverdepressurized pressure-core sediments suggest hydrates in the coarser-grained zones, the silty-sands where S h exceeds 0.4, contribute to soil-skeletal stability and are load-bearing. In the sandy-and clayey-silts, where S h < 0.4, the state of effective stress and stress history are significant factors determining sediment stiffness. Controlled depressurization tests show that hydrate dissociation occurs too quickly to maintain thermodynamic equilibrium, and pressureetemperature conditions track the hydrate stability boundary in pure-water, rather than that in seawater, in spite of both the in situ pore water and the water used to maintain specimen pore pressure prior to dissociation being saline. Hydrate dissociation accompanied with fines migration caused up to 2.4% vertical strain contraction. The firstever direct shear measurements on never-depressurized pressure-core specimens show hydratebearing sediments have higher sediment strength and peak friction angle than post-dissociation sediments, but the residual friction angle remains the same in both cases. Permeability measurements made before and after hydrate dissociation demonstrate that water permeability increases after dissociation, but the gain is limited by the transition from hydrate saturation before dissociation to gas saturation after dissociation. In a proof-of-concept study, sediment microbial communities were successfully extracted and stored under high-pressure, anoxic conditions. Depressurized samples of these extractions were incubated in air, where microbes exhibited temperature-dependent growth rates.Published by Elsevier Ltd.

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Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190

Cited by 183 publications

References 80 publications

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

Cultivation of methanogenic community from subseafloor sediments using a continuous-flow bioreactor

The Unique 16S rRNA Genes of Piezophiles Reflect both Phylogeny and Adaptation

Hydro-bio-geomechanical properties of hydrate-bearing sediments from Nankai Trough

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