Methane-oxidizing bacteria in a California upland grassland soil: Diversity and response to simulated global change

Hans Peter Horz, Virginia I Rich, Sharon Avrahami, Brendan J M Bohannan

Research output: Contribution to journalArticle

113 Citations (Scopus)

Abstract

We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to "RA 14" or "WB5FH-A," which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of non-synonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.

Original languageEnglish (US)
Pages (from-to)2642-2652
Number of pages11
JournalApplied and Environmental Microbiology
Volume71
Issue number5
DOIs
StatePublished - May 2005
Externally publishedYes

Fingerprint

Methylococcaceae
methanotrophs
upland soils
grassland soil
grassland soils
methane monooxygenase
global change
Soil
methane
bacterium
Temperature
relative abundance
Methane
air temperature
Genes
Sequence Analysis
Nucleotides
Clone Cells
gene
Amino Acids

ASJC Scopus subject areas

  • Environmental Science(all)
  • Biotechnology
  • Microbiology

Cite this

Methane-oxidizing bacteria in a California upland grassland soil : Diversity and response to simulated global change. / Horz, Hans Peter; Rich, Virginia I; Avrahami, Sharon; Bohannan, Brendan J M.

In: Applied and Environmental Microbiology, Vol. 71, No. 5, 05.2005, p. 2642-2652.

Research output: Contribution to journalArticle

@article{11aa59dd0b78458fa82cc451cf9fe354,
title = "Methane-oxidizing bacteria in a California upland grassland soil: Diversity and response to simulated global change",
abstract = "We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to {"}RA 14{"} or {"}WB5FH-A,{"} which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of non-synonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.",
author = "Horz, {Hans Peter} and Rich, {Virginia I} and Sharon Avrahami and Bohannan, {Brendan J M}",
year = "2005",
month = "5",
doi = "10.1128/AEM.71.5.2642-2652.2005",
language = "English (US)",
volume = "71",
pages = "2642--2652",
journal = "Applied and Environmental Microbiology",
issn = "0099-2240",
publisher = "American Society for Microbiology",
number = "5",

}

TY - JOUR

T1 - Methane-oxidizing bacteria in a California upland grassland soil

T2 - Diversity and response to simulated global change

AU - Horz, Hans Peter

AU - Rich, Virginia I

AU - Avrahami, Sharon

AU - Bohannan, Brendan J M

PY - 2005/5

Y1 - 2005/5

N2 - We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to "RA 14" or "WB5FH-A," which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of non-synonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.

AB - We investigated the diversity of methane-oxidizing bacteria (i.e., methanotrophs) in an annual upland grassland in northern California, using comparative sequence analysis of the pmoA gene. In addition to identifying type II methanotrophs commonly found in soils, we discovered three novel pmoA lineages for which no cultivated members have been previously reported. These novel pmoA clades clustered together either with clone sequences related to "RA 14" or "WB5FH-A," which both represent clusters of environmentally retrieved sequences of putative atmospheric methane oxidizers. Conservation of amino acid residues and rates of non-synonymous versus synonymous nucleotide substitution in these novel lineages suggests that the pmoA genes in these clades code for functionally active methane monooxygenases. The novel clades responded to simulated global changes differently than the type II methanotrophs. We observed that the relative abundance of type II methanotrophs declined in response to increased precipitation and increased atmospheric temperature, with a significant antagonistic interaction between these factors such that the effect of both together was less than that expected from their individual effects. Two of the novel clades were not observed to respond significantly to these environmental changes, while one of the novel clades had an opposite response, increasing in relative abundance in response to increased precipitation and atmospheric temperature, with a significant antagonistic interaction between these factors.

UR - http://www.scopus.com/inward/record.url?scp=18444409388&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=18444409388&partnerID=8YFLogxK

U2 - 10.1128/AEM.71.5.2642-2652.2005

DO - 10.1128/AEM.71.5.2642-2652.2005

M3 - Article

C2 - 15870356

AN - SCOPUS:18444409388

VL - 71

SP - 2642

EP - 2652

JO - Applied and Environmental Microbiology

JF - Applied and Environmental Microbiology

SN - 0099-2240

IS - 5

ER -