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

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.

authors

Trembath-Reichert E,Morono Y,Ijiri A,Hoshino T,Dawson KS,Inagaki F,Orphan VJ

doi

10.1073/pnas.1707525114

subject

Has Abstract

pub_date

2017-10-31 00:00:00

pages

E9206-E9215

issue

44

eissn

0027-8424

issn

1091-6490

pii

1707525114

journal_volume

114

pub_type

杂志文章
  • Structure and function of the Bacillus hybrid enzyme GluXyn-1: native-like jellyroll fold preserved after insertion of autonomous globular domain.

    abstract::The 1,3-1,4-beta-glucanase from Bacillus macerans (wtGLU) and the 1, 4-beta-xylanase from Bacillus subtilis (wtXYN) are both single-domain jellyroll proteins catalyzing similar enzymatic reactions. In the fusion protein GluXyn-1, the two proteins are joined by insertion of the entire XYN domain into a surface loop of ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.12.6613

    authors: Aÿ J,Götz F,Borriss R,Heinemann U

    更新日期:1998-06-09 00:00:00

  • Long-term potentiation expands information content of hippocampal dentate gyrus synapses.

    abstract::An approach combining signal detection theory and precise 3D reconstructions from serial section electron microscopy (3DEM) was used to investigate synaptic plasticity and information storage capacity at medial perforant path synapses in adult hippocampal dentate gyrus in vivo. Induction of long-term potentiation (LTP...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1716189115

    authors: Bromer C,Bartol TM,Bowden JB,Hubbard DD,Hanka DC,Gonzalez PV,Kuwajima M,Mendenhall JM,Parker PH,Abraham WC,Sejnowski TJ,Harris KM

    更新日期:2018-03-06 00:00:00

  • Locations of adenovirus genes required for the replication of adenovirus-associated virus.

    abstract::We have used DNA transfection to identify several regions of the adenovirus genome needed to induce replication of the defective parvovirus, adenovirus-associated virus (AAV). Previous studies have indicated that only early adenovirus functions are needed to aid the replication of AAV. In this report, we demonstrate t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.78.3.1925

    authors: Janik JE,Huston MM,Rose JA

    更新日期:1981-03-01 00:00:00

  • Chemical composition of Earth, Venus, and Mercury.

    abstract::Model compositions of Earth, Venus, and Mercury are calculated from the premise that planets and chondrites underwent four identical fractionation processes in the solar nebula. Because elements of similar properties stay together in these processes, five constraints suffice to define the composition of a planet: mass...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.12.6973

    authors: Morgan JW,Anders E

    更新日期:1980-12-01 00:00:00

  • Hypermutability of CpG dinucleotides in the propeptide-encoding sequence of the human albumin gene.

    abstract::An electrophoretically slow albumin variant was detected with a phenotype frequency of about 1:1000 in Sweden and was also found in a family of Scottish descent from Kaikoura, New Zealand, and in five families in Tradate, Italy. Structural study established that the major variant component was arginyl-albumin, in whic...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.10.3909

    authors: Brennan SO,Arai K,Madison J,Laurell CB,Galliano M,Watkins S,Peach R,Myles T,George P,Putnam FW

    更新日期:1990-05-01 00:00:00

  • An unusual cytokine:Ig-domain interaction revealed in the crystal structure of leukemia inhibitory factor (LIF) in complex with the LIF receptor.

    abstract::Leukemia inhibitory factor (LIF) receptor is a cell surface receptor that mediates the actions of LIF and other IL-6 type cytokines through the formation of high-affinity signaling complexes with gp130. Here we present the crystal structure of a complex of mouse LIF receptor with human LIF at 4.0 A resolution. The str...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0705577104

    authors: Huyton T,Zhang JG,Luo CS,Lou MZ,Hilton DJ,Nicola NA,Garrett TP

    更新日期:2007-07-31 00:00:00

  • Two-dimensional Raman-terahertz spectroscopy of water.

    abstract::Two-dimensional Raman-terahertz (THz) spectroscopy is presented as a multidimensional spectroscopy directly in the far-IR regime. The method is used to explore the dynamics of the collective intermolecular modes of liquid water at ambient temperatures that emerge from the hydrogen-bond networks water forming. Two-dime...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1317459110

    authors: Savolainen J,Ahmed S,Hamm P

    更新日期:2013-12-17 00:00:00

  • Light chains of myosins from white, red, and cardiac muscles.

    abstract::Purified preparations of rabbit skeletal white, red, and cardiac muscle myosin (WM, RM, and CM) were subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Significant differences in both the molecular weights and number of light chains in these myosins were found. WM has three distinct light-chain co...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.68.5.946

    authors: Sarkar S,Sreter FA,Gergely J

    更新日期:1971-05-01 00:00:00

  • Probing the instabilities in the dynamics of helical fragments from mouse PrPC.

    abstract::The first step in the formation of the protease resistant form (PrPSc) of prion proteins involves a conformational transition of the monomeric cellular form of PrPC to a more stable aggregation prone state PrPC*. A search of PDBselect and Escherichia coli and yeast genomes shows that the exact pattern of charges in he...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0404235101

    authors: Dima RI,Thirumalai D

    更新日期:2004-10-26 00:00:00

  • Masking the 5' terminal nucleotides of the hepatitis C virus genome by an unconventional microRNA-target RNA complex.

    abstract::Hepatitis C virus subverts liver-specific microRNA, miR-122, to upregulate viral RNA abundance in both infected cultured cells and in the liver of infected chimpanzees. These findings have identified miR-122 as an attractive antiviral target. Thus, it is imperative to know whether a distinct functional complex exists ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1012464108

    authors: Machlin ES,Sarnow P,Sagan SM

    更新日期:2011-02-22 00:00:00

  • Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes.

    abstract::The human proteome contains a plethora of short linear motifs (SLiMs) that serve as binding interfaces for modular protein domains. Such interactions are crucial for signaling and other cellular processes, but are difficult to detect because of their low to moderate affinities. Here we developed a dedicated approach, ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1312296111

    authors: Ivarsson Y,Arnold R,McLaughlin M,Nim S,Joshi R,Ray D,Liu B,Teyra J,Pawson T,Moffat J,Li SS,Sidhu SS,Kim PM

    更新日期:2014-02-18 00:00:00

  • Cloning of cDNAs that encode human mast cell carboxypeptidase A, and comparison of the protein with mouse mast cell carboxypeptidase A and rat pancreatic carboxypeptidases.

    abstract::Human skin and lung mast cells and rodent peritoneal mast cells contain a carboxypeptidase in their secretory granules. We have screened human lung cDNA libraries with a mouse mast cell carboxypeptidase A (MC-CPA) cDNA probe to isolate a near-full-length cDNA that encodes human MC-CPA. The 5' end of the human MC-CPA t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.23.9480

    authors: Reynolds DS,Gurley DS,Stevens RL,Sugarbaker DJ,Austen KF,Serafin WE

    更新日期:1989-12-01 00:00:00

  • Regulatory γ1 subunits defy symmetry in functional modulation of BK channels.

    abstract::Structural symmetry is a hallmark of homomeric ion channels. Nonobligatory regulatory proteins can also critically define the precise functional role of such channels. For instance, the pore-forming subunit of the large conductance voltage and calcium-activated potassium (BK, Slo1, or KCa1.1) channels encoded by a sin...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1804560115

    authors: Gonzalez-Perez V,Ben Johny M,Xia XM,Lingle CJ

    更新日期:2018-10-02 00:00:00

  • Local maternal control of seed size by KLUH/CYP78A5-dependent growth signaling.

    abstract::Seed development in plants involves the coordinated growth of the embryo, endosperm, and maternal tissue. Several genes have been identified that influence seed size by acting maternally, such as AUXIN RESPONSE FACTOR2, APETALA2, and DA1. However, given the lack of gain-of-function effects of these genes on seed size,...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0907024106

    authors: Adamski NM,Anastasiou E,Eriksson S,O'Neill CM,Lenhard M

    更新日期:2009-11-24 00:00:00

  • A cascade of cytokines mediates mechanical inflammatory hypernociception in mice.

    abstract::The hypernociceptive effects of cytokines [TNF-alpha, keratinocyte-derived chemokine (KC), and IL-1beta] and their participation in carrageenan (Cg)-induced inflammatory hypernociception in mice were investigated. Nociceptor sensitization (hypernociception) was quantified with an electronic version of the von Frey fil...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0409225102

    authors: Cunha TM,Verri WA Jr,Silva JS,Poole S,Cunha FQ,Ferreira SH

    更新日期:2005-02-01 00:00:00

  • Scaling up behavioral science interventions in online education.

    abstract::Online education is rapidly expanding in response to rising demand for higher and continuing education, but many online students struggle to achieve their educational goals. Several behavioral science interventions have shown promise in raising student persistence and completion rates in a handful of courses, but evid...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1921417117

    authors: Kizilcec RF,Reich J,Yeomans M,Dann C,Brunskill E,Lopez G,Turkay S,Williams JJ,Tingley D

    更新日期:2020-06-30 00:00:00

  • Biochemical evolution III: polymerization on organophilic silica-rich surfaces, crystal-chemical modeling, formation of first cells, and geological clues.

    abstract::Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal-chemical modeling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,评审

    doi:10.1073/pnas.96.7.3479

    authors: Smith JV,Arnold FP Jr,Parsons I,Lee MR

    更新日期:1999-03-30 00:00:00

  • Poly(A) polymerase and poly(g) polymerase in wheat chloroplasts.

    abstract::Extracts of wheat chloroplasts contain a poly(A) polymerase which can polymerize AMP residues from ATP onto an RNA primer. Whole extracts of wheat leaves also contain another poly(A) polymerase which is present in much larger amount and is probably derived from the nuclei. Both polymerases can utilize as primer poly(A...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.71.2.389

    authors: Burkard G,Keller EB

    更新日期:1974-02-01 00:00:00

  • The agroecological matrix as alternative to the land-sparing/agriculture intensification model.

    abstract::Among the myriad complications involved in the current food crisis, the relationship between agriculture and the rest of nature is one of the most important yet remains only incompletely analyzed. Particularly in tropical areas, agriculture is frequently seen as the antithesis of the natural world, where the problem i...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0905455107

    authors: Perfecto I,Vandermeer J

    更新日期:2010-03-30 00:00:00

  • Monopoles and fractional vortices in chiral superconductors.

    abstract::I discuss two exotic objects that must be experimentally identified in chiral superfluids and superconductors. These are (i) the vortex with a fractional quantum number (N = 1/2 in chiral superfluids, and N = 1/2 and N = 1/4 in chiral superconductors), which plays the part of the Alice string in relativistic theories ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.97.6.2431

    authors: Volovik GE

    更新日期:2000-03-14 00:00:00

  • Site of anticonvulsant action on sodium channels: autoradiographic and electrophysiological studies in rat brain.

    abstract::The anticonvulsants phenytoin and carbamazepine interact allosterically with the batrachotoxin binding site of sodium channels. In the present study, we demonstrate an autoradiographic technique to localize the batrachotoxin binding site on sodium channels in rat brain using [3H]batrachotoxinin-A 20-alpha-benzoate (BT...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.9.3051

    authors: Worley PF,Baraban JM

    更新日期:1987-05-01 00:00:00

  • Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances.

    abstract::The reconstruction of phylogenetic trees from DNA and protein sequences is confounded by unequal rate effects. These effects can group rapidly evolving taxa with other rapidly evolving taxa, whether or not they are genealogically related. All algorithms are sensitive to these effects whenever the assumptions on which ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.4.1455

    authors: Lake JA

    更新日期:1994-02-15 00:00:00

  • Ryanodine receptor leak mediated by caspase-8 activation leads to left ventricular injury after myocardial ischemia-reperfusion.

    abstract::Myocardial ischemic disease is the major cause of death worldwide. After myocardial infarction, reperfusion of infracted heart has been an important objective of strategies to improve outcomes. However, cardiac ischemia/reperfusion (I/R) is characterized by inflammation, arrhythmias, cardiomyocyte damage, and, at the ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1100286108

    authors: Fauconnier J,Meli AC,Thireau J,Roberge S,Shan J,Sassi Y,Reiken SR,Rauzier JM,Marchand A,Chauvier D,Cassan C,Crozier C,Bideaux P,Lompré AM,Jacotot E,Marks AR,Lacampagne A

    更新日期:2011-08-09 00:00:00

  • Nerves in the spine of a sea urchin: a neglected division of the echinoderm nervous system.

    abstract::Electrical stimulation of the primary spines (greater than 10 cm long) of the tropical sea urchin Diadema antillarum elicits graded compound action potentials that are conducted at a constant speed of approximately equal to 27 cm/sec. Ion substitution experiments suggest that these are due to the summation of calcium ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.5.1555

    authors: Smith DS,Brink D,del Castillo J

    更新日期:1985-03-01 00:00:00

  • Insulin stimulation of SREBP-1c processing in transgenic rat hepatocytes requires p70 S6-kinase.

    abstract::Insulin activates sterol regulatory element-binding protein-1c (SREBP-1c) in liver, thereby increasing fatty acid and triglyceride synthesis. We created a line of transgenic rats that produce epitope-tagged human SREBP-1c in liver under control of the constitutive apolipoprotein E promoter/enhancer. This system allows...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1213343109

    authors: Owen JL,Zhang Y,Bae SH,Farooqi MS,Liang G,Hammer RE,Goldstein JL,Brown MS

    更新日期:2012-10-02 00:00:00

  • Nucleosome positioning by genomic excluding-energy barriers.

    abstract::Recent genome-wide nucleosome mappings along with bioinformatics studies have confirmed that the DNA sequence plays a more important role in the collective organization of nucleosomes in vivo than previously thought. Yet in living cells, this organization also results from the action of various external factors like D...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0909511106

    authors: Milani P,Chevereau G,Vaillant C,Audit B,Haftek-Terreau Z,Marilley M,Bouvet P,Argoul F,Arneodo A

    更新日期:2009-12-29 00:00:00

  • Hearing in the crocodilia.

    abstract::Measurements of auditory sensitivity in terms of the cochlear potentials were made in young specimens of three species of crocodilians, Caiman crocodilus and Alligator mississipiensis of the subfamily Alligatorinae and Crocodylus acutus of the subfamily Crocodylinae. These species show considerable similarity in their...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.68.7.1498

    authors: Wever EG

    更新日期:1971-07-01 00:00:00

  • Dynamic antibody responses to the Mycobacterium tuberculosis proteome.

    abstract::Considerable effort has been directed toward controlling tuberculosis, which kills almost two million people yearly. High on the research agenda is the discovery of biomarkers of active tuberculosis (TB) for diagnosis and for monitoring treatment outcome. Rational biomarker discovery requires understanding host-pathog...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1009080107

    authors: Kunnath-Velayudhan S,Salamon H,Wang HY,Davidow AL,Molina DM,Huynh VT,Cirillo DM,Michel G,Talbot EA,Perkins MD,Felgner PL,Liang X,Gennaro ML

    更新日期:2010-08-17 00:00:00

  • An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency.

    abstract::Mammalian SWI/SNF [also called BAF (Brg/Brahma-associated factors)] ATP-dependent chromatin remodeling complexes are essential for formation of the totipotent and pluripotent cells of the early embryo. In addition, subunits of this complex have been recovered in screens for genes required for nuclear reprogramming in ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0812889106

    authors: Ho L,Ronan JL,Wu J,Staahl BT,Chen L,Kuo A,Lessard J,Nesvizhskii AI,Ranish J,Crabtree GR

    更新日期:2009-03-31 00:00:00

  • Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors.

    abstract::Eukaryotes engage in a multitude of beneficial and deleterious interactions with bacteria. Hamiltonella defensa, an endosymbiont of aphids and other sap-feeding insects, protects its aphid host from attack by parasitoid wasps. Thus H. defensa is only conditionally beneficial to hosts, unlike ancient nutritional symbio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0900194106

    authors: Degnan PH,Yu Y,Sisneros N,Wing RA,Moran NA

    更新日期:2009-06-02 00:00:00