Evidence map›Paper›PMID 36053980›Full record

ArticleEnvironmental microbiology2022

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

Jennifer L Goff, Elizabeth G Szink, Michael P Thorgersen, Andrew D Putt, Yupeng Fan, Lauren M Lui, Torben N Nielsen, Kristopher A Hunt, Jonathan P Michael, Yajiao Wang and 10 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Environmental microbiology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors.

Jennifer L GoffDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.ORCID 0000-0002-9089-9632
Elizabeth G SzinkDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
Michael P ThorgersenDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
Andrew D PuttEarth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA.
Yupeng FanInstitute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
Lauren M LuiEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Torben N NielsenEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Kristopher A HuntCivil and Environmental Engineering, University of Washington, Seattle, Washington, USA.
Jonathan P MichaelInstitute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
Yajiao WangInstitute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
Daliang NingInstitute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
Ying FuInstitute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
Joy D Van NostrandInstitute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
Farris L PooleDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
John-Marc ChandoniaEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Terry C HazenEarth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA.ORCID 0000-0002-2536-9993
David A StahlCivil and Environmental Engineering, University of Washington, Seattle, Washington, USA.ORCID 0000-0003-3051-841X
Jizhong ZhouInstitute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA.
Adam P ArkinEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.ORCID 0000-0002-9796-5014
Michael W W AdamsDepartment of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.ORCID 0000-0003-0881-8870

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Bacillus cereusMetals, HeavyGenomicsPhylogenyRNA, Ribosomal, 16SMetals, HeavyRNA, Ribosomal, 16S

Identifiers

PMID36053980
PMCPMC9805006

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.