Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

Ankita Kothari; Simon Roux; Hanqiao Zhang; Anatori Prieto; Drishti Soneja; John-Marc Chandonia; Sarah Spencer; Xiaoqin Wu; Sara Altenburg; Matthew W. Fields; Adam M. Deutschbauer; Adam P. Arkin; Eric J. Alm; Romy Chakraborty; Aindrila Mukhopadhyay

doi:10.1128/mSystems.00537-21

mSystems (Jun 2021)

Ecogenomics of Groundwater Phages Suggests Niche Differentiation Linked to Specific Environmental Tolerance

Ankita Kothari,
Simon Roux,
Hanqiao Zhang,
Anatori Prieto,
Drishti Soneja,
John-Marc Chandonia,
Sarah Spencer,
Xiaoqin Wu,
Sara Altenburg,
Matthew W. Fields,
Adam M. Deutschbauer,
Adam P. Arkin,
Eric J. Alm,
Romy Chakraborty,
Aindrila Mukhopadhyay

Affiliations

Ankita Kothari: ORCiD; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Simon Roux: Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Hanqiao Zhang: Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Anatori Prieto: Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Drishti Soneja: Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA
John-Marc Chandonia: ORCiD; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Sarah Spencer: Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Xiaoqin Wu: ORCiD; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Sara Altenburg: Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
Matthew W. Fields: ORCiD; Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
Adam M. Deutschbauer: ORCiD; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Adam P. Arkin: ORCiD; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Eric J. Alm: ORCiD; Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
Romy Chakraborty: ORCiD; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Aindrila Mukhopadhyay: ORCiD; Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, California, USA

DOI: https://doi.org/10.1128/mSystems.00537-21
Journal volume & issue: Vol. 6, no. 3

Abstract

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To our knowledge, this is the first study to identify the bacteriophage distribution in a groundwater ecosystem shedding light on their prevalence and distribution across metal-contaminated and background sites. Our study is uniquely based on selective sequencing of solely the extrachromosomal elements of a microbiome followed by analysis for viral signatures, thus establishing a more focused approach for phage identifications.

Published in mSystems

ISSN: 2379-5077 (Online)
Publisher: American Society for Microbiology
Country of publisher: United States
LCC subjects: Science: Microbiology
Website: https://journals.asm.org/journal/msystems

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