Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment

Goff, Jennifer; Lui, Lauren M.; Nielsen, Torben; Thorgersen, Michael P.; Szink, Elizabeth G; Chandonia, John-Marc; Poole, Farris L.; Zhou, Jizhong; Hazen, Terry C.; Arkin, Adam P.; Adams, Michael W. W.

doi:10.1128/mra.00145-22

Cited by 7 publications

(16 citation statements)

References 8 publications

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“…The mass spectrometer is operated in data independent mode with a duty cycle of 3 MS1 survey scans and 45 MS2 scans. For data analysis, the raw data was analyzed by searching against a FASTA sequence database (library-free mode) containing the proteins from the genome of interest [31,35] and common proteomic contaminants. DIA-NN automatically generates a set of decoy precursors out of the sequence database for negative controls and subsequently utilizes deep neural networks to obtain q-values to distinguish between target and decoy precursors [34].…”

Section: Proteomic Analysismentioning

confidence: 99%

Mixed heavy metal stress induces global iron starvation response

et al. 2022

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Multiple heavy metal contamination is an increasingly common global problem. Heavy metals have the potential to disrupt microbially mediated biogeochemical cycling. However, systems-level studies on the effects of combinations of heavy metals on bacteria are lacking. For this study, we focused on the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) subsurface which is contaminated with several heavy metals and high concentrations of nitrate. Using a native Bacillus cereus isolate that represents a dominant species at this site, we assessed the combined impact of eight metal contaminants, all at site-relevant concentrations, on cell processes through an integrated multi-omics approach that included discovery proteomics, targeted metabolomics, and targeted gene-expression profiling. The combination of eight metals impacted cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Exposure to the metal mixture elicited a global iron starvation response not observed during individual metal exposures. This disruption of iron homeostasis resulted in decreased activity of the iron-cofactor-containing nitrate and nitrite reductases, both of which are important in biological nitrate removal at the site. We propose that the combinatorial effects of simultaneous exposure to multiple heavy metals is an underappreciated yet significant form of cell stress in the environment with the potential to disrupt global nutrient cycles and to impede bioremediation efforts at mixed waste sites. Our work underscores the need to shift from single- to multi-metal studies for assessing and predicting the impacts of complex contaminants on microbial systems.

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Section: Proteomic Analysismentioning

confidence: 99%

Mixed heavy metal stress induces global iron starvation response

et al. 2022

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“…The full‐length 16S rRNA gene sequence was retrieved from the strain CPTF genome (Goff, Lui, et al, 2022 ). The strain CPTF 16S rRNA gene V4 region sequence was compared to the ORR sediment 16S rRNA gene V4 region amplicon sequence variants (ASVs) using a BLASTn search with default parameters.…”

Section: Methodsmentioning

confidence: 99%

“…Genome sequencing and phylogeny. The strain CPTF genome was previously sequenced using a combination of long-read nanopore technology and Illumina short reads to obtain a high quality completed genome (Goff et al, 2022b). Phylogeny was determined by average nucleotide identity (ANI) using the "Classify Microbes with GTDB-Tk".…”

Section: Genomic Analysismentioning

confidence: 99%

“…Bacillus cereus str. CPT56D-587-MTF (referred to as strain CPTF) was isolated as described previously by Goff, Lui, et al (2022). CPTF was routinely streaked out on LB plates and grown overnight at 30 C. A single isolated colony was inoculated into LB broth and grown overnight shaking at 200 rpm at 30 C. The overnight culture was diluted 100-fold into a defined medium for further experimentation.…”

Section: Media and Culture Conditionsmentioning

confidence: 99%

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

Goff

Szink

Thorgersen

et al. 2022

Environmental Microbiology

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We isolated a Bacillus cereus strain (CPTF) that represents a dominant community member of a mixed waste contaminated subsurface site as determined by 16S rRNA gene (V4 region) amplicon sequence variant profiling. Pangenomic analysis of the B. cereus group revealed significant genomic expansion in strain CPTF that was largely attributable to plasmid acquisition and transposable element mobilization. We further This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record. Please cite this article as

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“…Bacillus cereus str. CPT56D-587-MTF (referred to as strain CPTF) [30] was routinely streaked out on LB plates and grown overnight at 30 ºC. A single isolated colony was inoculated into LB broth and grown overnight shaking at 200 rpm at 30 ºC.…”

Section: Methodsmentioning

confidence: 99%

Mixed Heavy Metals Stress Induces Global Iron Starvation as Revealed by System Level Multi-Omic Analyses

Goff

Chen

Thorgersen

et al. 2022

Preprint

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Globally, multiple heavy metal contamination is an increasingly common problem. As heavy metals have the potential to disrupt microbially-mediated biogeochemical cycling, it is critical to understand their impact on microbial physiology. However, systems-level studies on the effects of a combination of heavy metals on bacteria are lacking. Here, we use a native Bacillus cereus isolate from the subsurface of the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA)- representing a highly abundant species at the site - to assess the combined impact of eight metal contaminants. Using this metal mixture and individual metals, all at concentrations based on the ORR site geochemistry, we performed growth experiments and proteomic analyses of the B. cereus strain, in combination with targeted MS-based metabolomics and gene expression profiling. The combination of eight metals impacts cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Specifically, exposure to the metal mixture elicited global iron starvation responses not observed in any of the individual metal treatments. As nitrate is also a significant contaminant at the ORR site and nitrate and nitrite reductases are iron-containing enzymes, we also examined the effects of the metal mixture on reduction of nitrogen oxides. We found that the metal mixture inhibits the activity of these enzymes through a combination of direct enzymatic damage and post-transcriptional and post-translational regulation. Altogether, these data suggest that metal mixture studies are critical for understanding how multiple rather than individual metals influence microbial processes in the environment.

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Complete Genome Sequence of Bacillus cereus Strain CPT56D-587-MTF, Isolated from a Nitrate- and Metal-Contaminated Subsurface Environment

Cited by 7 publications

References 8 publications

Mixed heavy metal stress induces global iron starvation response

Mixed heavy metal stress induces global iron starvation response

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

Mixed Heavy Metals Stress Induces Global Iron Starvation as Revealed by System Level Multi-Omic Analyses

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