Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments

Journal Article · 31 August 2022 · Environmental Microbiology

DOI: https://doi.org/10.1111/1462-2920.16173 · OSTI ID:1885081

Goff, Jennifer L.  ^[1]; Szink, Elizabeth G. ^[1]; Thorgersen, Michael P. ^[1]; Putt, Andrew D. ^[2]; Fan, Yupeng ^[3]; Lui, Lauren M. ^[4]; Nielsen, Torben N. ^[4]; Hunt, Kristopher A. ^[5]; Michael, Jonathan P. ^[3]; Wang, Yajiao ^[3]; Ning, Daliang ^[3]; Fu, Ying ^[3]; Van Nostrand, Joy D. ^[3]; Poole, II, Farris L. ^[1]; Chandonia, John‐Marc ^[4]; Hazen, Terry C.  ^[6]; Stahl, David A.  ^[5]; Zhou, Jizhong ^[7]; Arkin, Adam P.  ^[8]; Adams, Michael W. W.  ^[1]

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1. Department of Biochemistry and Molecular Biology University of Georgia Athens Georgia USA
2. Earth and Planetary Sciences University of Tennessee Knoxville Tennessee USA
3. Institute for Environmental Genomics University of Oklahoma Norman Oklahoma USA
4. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley California USA
5. Civil and Environmental Engineering University of Washington Seattle Washington USA
6. Earth and Planetary Sciences University of Tennessee Knoxville Tennessee USA, Genome Sciences Division Oak Ridge National Lab Oak Ridge Tennessee USA, Department of Civil and Environmental Engineering University of Tennessee Knoxville Tennessee USA
7. Institute for Environmental Genomics University of Oklahoma Norman Oklahoma USA, Department of Microbiology and Plant Biology University of Oklahoma Norman Oklahoma USA, School of Civil Engineering and Environmental Sciences University of Oklahoma Norman Oklahoma USA, Earth and Environmental Sciences Lawrence Berkley National Laboratory Berkeley California USA
8. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley California USA, Department of Bioengineering University of California at Berkeley Berkeley California USA

Abstract Bacillus cereus strain CPT56D‐587‐MTF (CPTF) was isolated from the highly contaminated Oak Ridge Reservation (ORR) subsurface. This site is contaminated with high levels of nitric acid and multiple heavy metals. Amplicon sequencing of the 16S rRNA genes (V4 region) in sediment from this area revealed an amplicon sequence variant (ASV) with 100% identity to the CPTF 16S rRNA sequence. Notably, this CPTF‐matching ASV had the highest relative abundance in this community survey, with a median relative abundance of 3.77% and comprised 20%–40% of reads in some samples. Pangenomic analysis revealed that strain CPTF has expanded genomic content compared to other B. cereus species—largely due to plasmid acquisition and expansion of transposable elements. This suggests that these features are important for rapid adaptation to native environmental stressors. We connected genotype to phenotype in the context of the unique geochemistry of the site. These analyses revealed that certain genes (e.g. nitrate reductase, heavy metal efflux pumps) that allow this strain to successfully occupy the geochemically heterogenous microniches of its native site are characteristic of the B. cereus species while others such as acid tolerance are mobile genetic element associated and are generally unique to strain CPTF.

• Research Organization: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
• Sponsoring Organization: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1885081
• Journal Information: Environmental Microbiology, Journal Name: Environmental Microbiology Journal Issue: 11 Vol. 24; ISSN 1462-2912
• Publisher: Wiley-BlackwellCopyright Statement
• Country of Publication: United Kingdom
• Language: English