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Title: Diversity of methanotroph communities in a basalt aquifer

Abstract

Methanotrophic bacteria play an important role in global cycling of carbon and co-metabolism of contaminants. Methanotrophs from pristine regions of the Snake River Plain Aquifer (SRPA; Idaho, USA) were studied in order to gain insight into the native groundwater communities’ genetic potential to carry out TCE co-metabolism. Wells were selected that were proximal to a TCE plume believed to be undergoing natural attenuation. Methane concentrations ranged from 1 to >1000 nM. Carbon isotope ratiosand diversity data together suggest that the SRPA contains active communities of methanotrophs that oxidize microbially produced methane. Microorganisms removed from groundwater by filtration were used as inocula for enrichments or frozen immediately and DNA was subsequently extracted for molecular characterization. Primers that specifically target methanotroph 16S rRNA genes or genes that code for subunits of soluble or particulate methane monooxygenase, mmoX and pmoA, respectively, were used to characterize the indigenous methanotrophs via PCR, cloning, RFLP analysis, and sequencing. Type I methanotroph clones aligned with Methylomonas, Methylocaldum, and Methylobacter sequences and a distinct 16S rRNA phylogenetic lineage grouped near Methylobacter. The majority of clone sequences in type II methanotroph 16S rRNA, pmoA, and mmoX gene libraries grouped closely with sequences in the Methylocystis genus. A subset ofmore » the type II methanotroph clones from the aquifer had sequences that aligned most closely to Methylosinus trichosporium OB3b and Methylocystis spp., known TCE-co-metabolizing methanotrophs.« less

Authors:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
920210
Report Number(s):
PNNL-SA-43415
Journal ID: ISSN 0168-6496; FMECEZ; KP1301010; TRN: US200818%%1100
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
FEMS Microbiology Ecology, 48:333-344
Additional Journal Information:
Journal Volume: 48; Journal ID: ISSN 0168-6496
Country of Publication:
United States
Language:
English
Subject:
03 NATURAL GAS; AQUIFERS; BASALT; CARBON; CARBON ISOTOPES; CLONING; COMMUNITIES; DNA; FILTRATION; GENES; GENETICS; METHANE; METHANOTROPHIC BACTERIA; MICROORGANISMS; NATURAL ATTENUATION; PARTICULATES; PLUMES; SNAKE RIVER PLAIN; TARGETS

Citation Formats

Newby, Deborah T, Reed, David W, Petzke, L M, Igoe, A L, Delwiche, Mark E, Roberto, Francisco F, McKinley, James P, Whiticar, M J, and Colwell, F S. Diversity of methanotroph communities in a basalt aquifer. United States: N. p., 2004. Web. doi:10.1016/j.femsec.2004.02.001.
Newby, Deborah T, Reed, David W, Petzke, L M, Igoe, A L, Delwiche, Mark E, Roberto, Francisco F, McKinley, James P, Whiticar, M J, & Colwell, F S. Diversity of methanotroph communities in a basalt aquifer. United States. https://doi.org/10.1016/j.femsec.2004.02.001
Newby, Deborah T, Reed, David W, Petzke, L M, Igoe, A L, Delwiche, Mark E, Roberto, Francisco F, McKinley, James P, Whiticar, M J, and Colwell, F S. Wed . "Diversity of methanotroph communities in a basalt aquifer". United States. https://doi.org/10.1016/j.femsec.2004.02.001.
@article{osti_920210,
title = {Diversity of methanotroph communities in a basalt aquifer},
author = {Newby, Deborah T and Reed, David W and Petzke, L M and Igoe, A L and Delwiche, Mark E and Roberto, Francisco F and McKinley, James P and Whiticar, M J and Colwell, F S},
abstractNote = {Methanotrophic bacteria play an important role in global cycling of carbon and co-metabolism of contaminants. Methanotrophs from pristine regions of the Snake River Plain Aquifer (SRPA; Idaho, USA) were studied in order to gain insight into the native groundwater communities’ genetic potential to carry out TCE co-metabolism. Wells were selected that were proximal to a TCE plume believed to be undergoing natural attenuation. Methane concentrations ranged from 1 to >1000 nM. Carbon isotope ratiosand diversity data together suggest that the SRPA contains active communities of methanotrophs that oxidize microbially produced methane. Microorganisms removed from groundwater by filtration were used as inocula for enrichments or frozen immediately and DNA was subsequently extracted for molecular characterization. Primers that specifically target methanotroph 16S rRNA genes or genes that code for subunits of soluble or particulate methane monooxygenase, mmoX and pmoA, respectively, were used to characterize the indigenous methanotrophs via PCR, cloning, RFLP analysis, and sequencing. Type I methanotroph clones aligned with Methylomonas, Methylocaldum, and Methylobacter sequences and a distinct 16S rRNA phylogenetic lineage grouped near Methylobacter. The majority of clone sequences in type II methanotroph 16S rRNA, pmoA, and mmoX gene libraries grouped closely with sequences in the Methylocystis genus. A subset of the type II methanotroph clones from the aquifer had sequences that aligned most closely to Methylosinus trichosporium OB3b and Methylocystis spp., known TCE-co-metabolizing methanotrophs.},
doi = {10.1016/j.femsec.2004.02.001},
url = {https://www.osti.gov/biblio/920210}, journal = {FEMS Microbiology Ecology, 48:333-344},
issn = {0168-6496},
number = ,
volume = 48,
place = {United States},
year = {2004},
month = {12}
}