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The upper oceanic crust is mainly composed of basaltic lava that constitutes one of the largest habitable zones on Earth. However, the nature of deep microbial life in oceanic crust remains poorly understood, especially where old cold basaltic rock interacts with seawater beneath sediment. Here we show that microbial cells are densely concentrated in Fe-rich smectite on fracture surfaces and veins in 33.5- and 104-million-year-old (Ma) subseafloor basaltic rock. The Fe-rich smectite is locally enriched in organic carbon. Nanoscale solid characterizations reveal the organic carbon to be microbial cells within the Fe-rich smectite, with cell densities locally exceeding 10¹⁰ cells/cm³. Dominance of heterotrophic bacteria indicated by analyses of DNA sequences and lipids supports the importance of organic matter as carbon and energy sources in subseafloor basalt. Given the prominence of basaltic lava on Earth and Mars, microbial life could be habitable where subsurface basaltic rocks interact with liquid water.

Source: http://dx.doi.org/10.1038/s42003-020-0860-1

Publications > Journal Article

Microbiology Resource Announcements

Draft Genome Sequences of Penicillium spp. from Deeply Buried Oligotrophic Marine Sediments

Authors: Morgan S. Sobol, Tatsuhiko Hoshino, Taiki Futagami, Fumio Inagaki, Brandi Kiel Reese

Published: February 7, 2019

C-DEBI Contribution Number: 458

Abstract

Here, we report genome sequences of two Penicillium isolates from below the seafloor of the oligotrophic South Pacific Gyre. These genomes are the first reported for fungi from deeply buried marine sediment. Both genomes will provide valuable information regarding the role of fungi and carbon cycling in the energy-limited subsurface biosphere.

Source: http://dx.doi.org/10.1128/mra.01613-18

Publications > Journal Article

Proceedings of the National Academy of Sciences

Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds

Authors: Elizabeth Trembath-Reichert, Yuki Morono, Akira Ijiri, Tatsuhiko Hoshino, Katherine S. Dawson, Fumio Inagaki, Victoria J. Orphan

Published: October 3, 2017

C-DEBI Contribution Number: 389

Abstract

The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of ¹³C- or ¹⁵N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates.

Source: http://dx.doi.org/10.1073/pnas.1707525114

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Awards

Awards > Research Exchange Grants

Award Dates: March 17, 2015 — April 10, 2015

Determination of deep biosphere cell activity and identity utilizing the state of the art low-biomass, single cell techniques developed at JAMSTEC in their class 10,000 clean room

PI: Elizabeth Trembath-Reichert (California Institute of Technology)

Advisor: Victoria J. Orphan (California Institute of Technology)

Host: Fumio Inagaki (JAMSTEC)

Publications > Journal Article

Science

Exploring deep microbial life in coal-bearing sediment down to 2.5 km below the ocean floor

Published: July 23, 2015

C-DEBI Contribution Number: 310

Abstract

Microbial life inhabits deeply buried marine sediments, but the extent of this vast ecosystem remains poorly constrained. Here we provide evidence for the existence of microbial communities in ~40° to 60°C sediment associated with lignite coal beds at ~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers, cultivation data, and gas compositions. Concentrations of indigenous microbial cells below 1.5 km ranged from <10 to ~10⁴ cells cm⁻³. Peak concentrations occurred in lignite layers, where communities differed markedly from shallower subseafloor communities and instead resembled organotrophic communities in forest soils. This suggests that terrigenous sediments retain indigenous community members tens of millions of years after burial in the seabed.

Source: http://dx.doi.org/10.1126/science.aaa6882

Related Items

Awards

Awards > Research Exchange Grants

Award Dates: March 17, 2015 — April 10, 2015

Determination of deep biosphere cell activity and identity utilizing the state of the art low-biomass, single cell techniques developed at JAMSTEC in their class 10,000 clean room

PI: Elizabeth Trembath-Reichert (California Institute of Technology)

Advisor: Victoria J. Orphan (California Institute of Technology)

Host: Fumio Inagaki (JAMSTEC)

Person: Tatsuhiko Hoshino

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