Methane oxidation by an extremely acidophilic bacterium of the phylum Verrucomicrobia.
Aerobic methanotrophic bacteria consume methane as it diffuses away from methanogenic zones of soil and sediment. They act as a biofilter to reduce methane emissions to the atmosphere, and they are therefore targets in strategies to combat global climate change. No cultured methanotroph grows optimally below pH 5, but some environments with active methane cycles are very acidic. Here we describe an extremely acidophilic methanotroph that grows optimally at pH 2.0-2.5. Unlike the known methanotrophs, it does not belong to the phylum Proteobacteria but rather to the Verrucomicrobia, a widespread and diverse bacterial phylum that primarily comprises uncultivated species with unknown genotypes. Analysis of its draft genome detected genes encoding particulate methane monooxygenase that were homologous to genes found in methanotrophic proteobacteria. However, known genetic modules for methanol and formaldehyde oxidation were incomplete or missing, suggesting that the bacterium uses some novel methylotrophic pathways. Phylogenetic analysis of its three pmoA genes (encoding a subunit of particulate methane monooxygenase) placed them into a distinct cluster from proteobacterial homologues. This indicates an ancient divergence of Verrucomicrobia and Proteobacteria methanotrophs rather than a recent horizontal gene transfer of methanotrophic ability. The findings show that methanotrophy in the Bacteria is more taxonomically, ecologically and genetically diverse than previously thought, and that previous studies have failed to assess the full diversity of methanotrophs in acidic environments.
Dunfield
Peter F
PF
GNS Science, Extremophile Research Group, Private Bag 2000, Taupo, New Zealand. p.dunfield@gns.cri.nz
Yuryev
Anton
A
Senin
Pavel
P
Smirnova
Angela V
AV
Stott
Matthew B
MB
Hou
Shaobin
S
Ly
Binh
B
Saw
Jimmy H
JH
Zhou
Zhemin
Z
Ren
Yan
Y
Wang
Jianmei
J
Mountain
Bruce W
BW
Crowe
Michelle A
MA
Weatherby
Tina M
TM
Bodelier
Paul L E
PL
Liesack
Werner
W
Feng
Lu
L
Wang
Lei
L
Alam
Maqsudul
M
D000143:Acids / Q000378:metabolism; D001419:Bacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics / Q000378:metabolism*; D019015:Geologic Sediments / Q000382:microbiology; D006863:Hydrogen-Ion Concentration; D008697:Methane / Q000378:metabolism*; D008969:Molecular Sequence Data; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010100:Oxygen / Q000378:metabolism; D010105:Oxygenases / Q000235:genetics; D010313:Partial Pressure; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013696:Temperature
D000143:Acids; D012336:RNA, Ribosomal, 16S; D010088:Oxidoreductases; D010105:Oxygenases; C021555:methane monooxygenase; C045582:ammonia monooxygenase; D008697:Methane; D010100:Oxygen