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Mol Ecol. 2017 Mar;26(6):1547-1556. doi: 10.1111/mec.14011. Epub 2017 Feb 10.

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms.

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Institute of Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR, USA.
Department of Land, Air and Water Resources, University of California, Davis, CA, USA.
Department of Microbiology, University of Massachusetts, Amherst, MA, USA.
United States Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
Utah Water Research Laboratory, Utah State University, Logan, UT, USA.
Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA.


Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane-cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane-cycling microorganisms responded to land use change, with the strongest responses exhibited by methane-consuming, rather than methane-producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane-cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils.


land use change; metagenomics; methane; microbial ecology; traits

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