Ecophysiological and genomic analyses of a representative isolate of highly abundant Bacillus cereus strains in contaminated subsurface sediments
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Sep 01, 2022
- Source ID
- 10.1111/1462-2920.16173
Entities
People
- Andrew D. Putt
- Daliang Ning
- David A Stahl
- Elizabeth G. Szink
- Farris L. Poole Ii
- Jennifer L. Goff
- Jizhong Zhou
- John‐marc Chandonia
- Jonathan P. Michael
- Joy D. Van Nostrand
- Kristopher A Hunt
- Lauren M. Lui
- Michael P. Thorgersen
- Michael W. W. Adams
- Terry C Hazen
- Torben N. Nielsen
- Yajiao Wang
- Ying Fu
- Yupeng Fan
Organizations
- Lawrence Berkeley National Laboratory
- Oak Ridge National Laboratory
- Office of Biological and Environmental Research
- Office of Science
- United States Department of Energy
- University of California, Berkeley
- University of Oklahoma
- University of Tennessee
- University of Washington