Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176)

Kormas, Konstantinos Ar.; Smith, David C.; Edgcomb, Virginia P.; Teske, Andreas

doi:10.1016/s0168-6496(03)00128-4

Cited by 128 publications

(130 citation statements)

References 48 publications

(64 reference statements)

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“…DGGE bands 38-1, 63-1 and 43-2 represented populations that were detected in all sediment horizons analyzed. These populations were also closely related to populations detected at the Nankai Trough (Kormas et al 2003), in Mediterranean mud volcanoes (GenBank accession no. AY592406) and hydrate bearing sediments at the Cascadia Margin (Inagaki et al 2006b).…”

Section: Dgge Analysis Of Bacterial Diversitysupporting

confidence: 60%

Microbial diversity in deep sediments of the Benguela Upwelling System

Schäfer¹,

Ferdelman²,

Fossing³

et al. 2007

Aquat. Microb. Ecol.

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Section: Dgge Analysis Of Bacterial Diversitysupporting

confidence: 60%

Microbial diversity in deep sediments of the Benguela Upwelling System

Schäfer¹,

Ferdelman²,

Fossing³

et al. 2007

Aquat. Microb. Ecol.

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“…The target region lies within helices H885 and H17 in the central part of the 16S rRNA molecule. Primer Ar9R is near identical to ARC927R (Kormas et al, 2003); the only difference is an additional C at the 3 terminus in Ar9. ARC915R is a slightly altered version of the primer UNIV915R (Zheng et al, 1996) that target specifically the archaea.…”

Section: Primer Mismatchesmentioning

confidence: 97%

Uncultured archaea in deep marine subsurface sediments: have we caught them all?

2007

Self Cite

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Deep marine subsurface sediments represent a novel archaeal biosphere with unknown physiology; the sedimentary subsurface harbors numerous novel phylogenetic lineages of archaea that are at present uncultured. Archaeal 16S rRNA analyses of deep subsurface sediments demonstrate their global occurrence and wide habitat range, including deep subsurface sediments, methane seeps and organic-rich coastal sediments. These subsurface archaeal lineages were discovered by PCR of extracted environmental DNA; their detection ultimately depends on the specificity of the archaeal PCR 16S rRNA primers. Surprisingly high mismatch frequencies for some archaeal PCR primers result in amplification bias against the corresponding archaeal lineages; this review presents some examples. Obviously, most archaeal 16S rRNA PCR primers were developed either before the discovery of these deep subsurface archaeal lineages, or without taking their sequence variants into account. PCR surveys with multiple primer combinations, revision and updates of primers whenever possible, and increasing use of PCR-independent methods in molecular microbial ecology will contribute to a more comprehensive view of subsurface archaeal communities.

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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

209

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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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Molecular analysis of deep subsurface microbial communities in Nankai Trough sediments (ODP Leg 190, Site 1176)

Cited by 128 publications

References 48 publications

Microbial diversity in deep sediments of the Benguela Upwelling System

Microbial diversity in deep sediments of the Benguela Upwelling System

Uncultured archaea in deep marine subsurface sediments: have we caught them all?

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

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