title: Persistence of the dominant soil phylum Acidobacteria by trace gas scavenging.
abstract: The majority of microbial cells in global soils exist in a spectrum of dormant states. However, the metabolic processes that enable them to survive environmental challenges, such as nutrient-limitation, remain to be elucidated. In this work, we demonstrate that energy-starved cultures of Pyrinomonas methylaliphatogenes, an aerobic heterotrophic acidobacterium isolated from New Zealand volcanic soils, persist by scavenging the picomolar concentrations of H2 distributed throughout the atmosphere. Following the transition from exponential to stationary phase due to glucose limitation, the bacterium up-regulates by fourfold the expression of an eight-gene operon encoding an actinobacteria-type H2-uptake [NiFe]-hydrogenase. Whole-cells of the organism consume atmospheric H2 in a first-order kinetic process. Hydrogen oxidation occurred most rapidly under oxic conditions and was weakly associated with the cell membrane. We propose that atmospheric H2 scavenging serves as a mechanism to sustain the respiratory chain of P. methylaliphatogenes when organic electron donors are scarce. As the first observation of H2 oxidation to our knowledge in the Acidobacteria, the second most dominant soil phylum, this work identifies new sinks in the biogeochemical H2 cycle and suggests that trace gas oxidation may be a general mechanism for microbial persistence.
authors.affiliation: Department of Microbiology and Immunology, University of Otago, North Dunedin, Dunedin 9054, New Zealand; The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Acton, ACT 2601, Australia; chris.greening@csiro.au m.stott@gns.cri.nz.
authors.forename: Chris
authors.initials: C
authors.lastname: Greening
authors.affiliation: GNS Science, Wairakei Research Centre, Wairakei, Taupō 3352, New Zealand; Scion, Te Papa Tipu Innovation Park, Whakerewarewa, Rotorua 3010, New Zealand;
authors.forename: Carlo R
authors.initials: CR
authors.lastname: Carere
authors.affiliation: Department of Microbiology and Immunology, University of Otago, North Dunedin, Dunedin 9054, New Zealand;
authors.forename: Rowena
authors.initials: R
authors.lastname: Rushton-Green
authors.affiliation: Department of Microbiology and Immunology, University of Otago, North Dunedin, Dunedin 9054, New Zealand;
authors.forename: Liam K
authors.initials: LK
authors.lastname: Harold
authors.affiliation: Department of Microbiology and Immunology, University of Otago, North Dunedin, Dunedin 9054, New Zealand;
authors.forename: Kiel
authors.initials: K
authors.lastname: Hards
authors.affiliation: The Commonwealth Scientific and Industrial Research Organisation, Land and Water Flagship, Acton, ACT 2601, Australia;
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Taylor
authors.affiliation: Department of Microbiology and Immunology, University of Otago, North Dunedin, Dunedin 9054, New Zealand;
authors.forename: Sergio E
authors.initials: SE
authors.lastname: Morales
authors.affiliation: GNS Science, Wairakei Research Centre, Wairakei, Taupō 3352, New Zealand; chris.greening@csiro.au m.stott@gns.cri.nz.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Stott
authors.affiliation: Department of Microbiology and Immunology, University of Otago, North Dunedin, Dunedin 9054, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland Central, Auckland 1010, New Zealand.
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Cook
mesh_terms: D061271:Acidobacteria / Q000378:metabolism*; D000595:Amino Acid Sequence; D001272:Atmosphere; D002244:Carbon / Q000737:chemistry; D002849:Chromatography, Gas; D004579:Electron Transport; D004583:Electrons; D005740:Gases; D015964:Gene Expression Regulation, Bacterial; D006859:Hydrogen / Q000737:chemistry; D006864:Hydrogenase / Q000378:metabolism; D007700:Kinetics; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010100:Oxygen / Q000737:chemistry; D010802:Phylogeny; D015203:Reproducibility of Results; D017386:Sequence Homology, Amino Acid; D012987:Soil / Q000737:chemistry; D012988:Soil Microbiology
chemical_list: D005740:Gases; D012987:Soil; D002244:Carbon; D006859:Hydrogen; D006864:Hydrogenase; D010100:Oxygen
keywords: dormancy; extremophile; hydrogen; hydrogenase; rare biosphere