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
Read online
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.
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