Title: Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

Abstract

Soils are reservoirs of antibiotic resistance genes (ARGs), but environmental dynamics of ARGs are largely unknown. Long-term disturbances offer opportunities to examine microbiome responses at scales relevant for both ecological and evolutionary processes and can be insightful for studying ARGs. We examined ARGs in soils overlying the underground coal seam fire in Centralia, PA, which has been burning since 1962. As the fire progresses, previously hot soils can recover to ambient temperatures, which creates a gradient of fire impact. We examined metagenomes from surface soils along this gradient to examine ARGs using a gene-targeted assembler. We targeted 35 clinically relevant ARGs and two horizontal gene transfer-related genes (intI and repA). We detected 17 ARGs in Centralia: AAC6-Ia, adeB, bla_A, bla_B, bla_C, cmlA, dfra12, intI, sul2, tetA, tetW, tetX, tolC, vanA, vanH, vanX and vanZ. The diversity and abundance of bla_A, bla_B, dfra12 and tolC decreased with soil temperature, and changes in ARGs were largely explained by changes in community structure. We observed sequence-specific biogeography along the temperature gradient and observed compositional shifts in bla_A, dfra12 and intI. These results suggest that increased temperatures can reduce soil ARGs but that this is largely due to a concomitant reduction in community-level diversity.

Authors:

Dunivin, T. K. ^[1]; Shade, A.  ^[2]

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• Search DOE PAGES for ORCID "0000-0002-7189-3067"

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+ Show Author Affiliations

1. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Environmental and Integrative Toxicological Sciences Doctoral Program, Michigan State University, East Lansing, MI 48824, USA
2. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA, Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA, Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA

Publication Date:

Thu Feb 01 00:00:00 EST 2018

Research Org.:

USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Michigan State Univ., East Lansing, MI (United States)

Sponsoring Org.:

USDOE Office of Science (SC)

OSTI Identifier:

1457202

Alternate Identifier(s):

OSTI ID: 1904110

Grant/Contract Number:  

AC02-05CH11231

Resource Type:

Published Article

Journal Name:

FEMS Microbiology Ecology (Online)

Additional Journal Information:

Journal Name: FEMS Microbiology Ecology (Online) Journal Volume: 94 Journal Issue: 3; Journal ID: ISSN 1574-6941

Publisher:

Oxford University Press

Country of Publication:

Netherlands

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; thermophile; gene-targeted assembly; metagenome; rplB; coal fire