We present the draft genome sequence for Bacillus sp. strain PF3, Bacillus sp.
ABSTRACT
We present the draft genome sequence for Bacillus sp. strain PF3, Bacillus sp. strain K6W, Cellulomonas sp. strain B12, Cellulomonas sp. strain K38, Cellulomonas sp. strain K39, and Cellulomonas sp. strain K42B. These bacteria were isolated from contaminated soils, and their genomes contain genes related to chromate transport and reduction.
ANNOUNCEMENT
Previously, bacteria were isolated from soil at a Department of Transportation site (Seymore, IN) that was contaminated with chromium (1, 2). Chromium is a heavy metal and has two naturally occurring oxidation states, Cr(III) and Cr(VI), the latter being more soluble and toxic than the other (3, 4). To gain a better understanding of bacterial tolerance (resistance and/or reduction) to Cr(VI), bacteria from chromium-contaminated soils were isolated on 50% tryptic soy agar (TSA) amended with 0.25 mM Cr(VI) (K2CrO4). Here, we present the draft genome sequences of multiple Cr(VI)-tolerant bacteria (Bacillus sp. strain PF3, Bacillus sp. strain K6W, Cellulomonas sp. strain B12, Cellulomonas sp. strain K38, Cellulomonas sp. strain K39, and Cellulomonas sp. strain K42B) and examine their genomic potential to tolerate chromate.
Genomic DNA was extracted using the FastDNA spin kit (MP Biomedical, Santa Ana, CA). The DNA was sequenced using a whole-genome shotgun sequencing method utilizing the Illumina HiSeq 2000 platform at the Cincinnati Children’s Hospital Medical Center’s Genetic Variation and Gene Discovery Core facility. Adapters and primers on the raw reads were trimmed using Trimmomatic 0.33 (5), and the quality was checked using FastQC 0.11.3 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). R2 reads had low quality, so the reads were cut (length of 70 bp) and then passed through a quality filter (-Q, 33; -q, 30; -p, 50) with the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Reads were then subsampled to 4 million reads (more reads did not increase assembly quality) with seqtk (https://github.com/lh3/seqtk) and then assembled with SPAdes 3.11.1 (6, 7). The resulting assemblies were quality assessed with QUAST 3.0 (8) and CheckM (9). For the Bacillus strains, the total length of each assembly ranged from 5.1 to 5.2 Mb with a GC content of 35% and N50 values of 130,611 bp (K6W) and 53,321 bp (PF5) (Table 1). The Cellulomonas strains had total lengths ranging from 3.6 to 4.1 Mb, GC content of 74%, and N50 values ranging from 2,844 to 5,917 bp (Table 1). CheckM estimated that all 6 environmental isolates had >95% completion and <5% contamination (Table 1).
TABLE 1.
Assembly and annotation quality control and assessment dataa
| Strain | Total length (bp) |
GC (%) |
No. of contigs |
Largest contig (bp) |
N50 (bp) | Comp. (%)b |
Contam. (%)c |
Annotated gene count |
Annotated Pfam count |
WGS accession numberd |
|---|---|---|---|---|---|---|---|---|---|---|
| Bacillus sp. K6W | 5,254,820 | 35 | 124 | 421,542 | 130,611 | 99 | 0 | 5,386 | 4,440 | QMGC00000000 |
| Bacillus sp. PF5 | 5,148,681 | 35 | 184 | 296,030 | 53,321 | 99 | 0 | 5,260 | 4,298 | QMGB00000000 |
| Cellulomonas sp. B12 | 3,640,453 | 74 | 1,788 | 43,552 | 2,844 | 97 | 4 | 3,467 | 2,636 | QMGD00000000 |
| Cellulomonas sp. K38 | 3,883,871 | 74 | 1,811 | 39,943 | 3,096 | 95 | 2 | 3,827 | 2,820 | QMGE00000000 |
| Cellulomonas sp. K39 | 4,007,628 | 74 | 1,277 | 31,101 | 5,078 | 98 | 1 | 4,113 | 2,991 | QMGF00000000 |
| Cellulomonas sp. K42B | 4,103,616 | 74 | 1,158 | 36,569 | 5,917 | 99 | 2 | 4,194 | 3,078 | QMGG00000000 |
Strain heterogeneity was 0 for each strain listed.
Comp., completion.
Contam., contamination.
DDBJ/ENA/GenBank whole-genome shotgun project.
The assembled genomes were annotated by the Department of Energy’s Joint Genome Institute Integrated Microbial Genomes (IMG) system (10). Annotated gene counts ranged from 3,467 to 5,386, and Pfam gene counts ranged from 2,623 to 4,440 (Table 1). Only Cellulomonas sp. strains K38 and B12 had annotated chromate reductases that are NAD(P)H-dependent flavin mononucleotide (FMN) reductases. The Cr(VI)-reducing bacterium Pseudomonas putida KT2440 uses a NAD(P)H reductase, chrR, to enzymatically reduce Cr(VI) (11). Both Bacillus sp. strains had annotated chromate transporters. Pseudomonas aeruginosa uses a chromate transporter, chrA, to provide resistance to Cr(VI) (12). All environmental isolates had annotated genes coding cobalt-zinc-cadmium efflux system proteins, which have been linked to heavy metal tolerance in other bacteria (13, 14). Therefore, the genomes provide evidence of how these environmental isolates tolerate chromate and suggest tolerance to other heavy metals.
Data availability.
The raw sequencing reads have been deposited in the Sequence Read Archive (SRA) under the accession number SRP120551. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers QMGB00000000 to QMGG00000000, as listed in Table 1. Integrated Microbial Genomes (IMG) annotations have the Genomes Online Database (GOLD) study identification (ID) number Gs0130379.
ACKNOWLEDGMENTS
Funding was provided by the Central Michigan University (CMU) College of Science and Engineering. The U.S. Environmental Protection Agency, through its Office of Research and Development, collaborated in the research described here. Any opinions expressed in this paper are those of the authors and do not necessarily reflect the views of the agency; therefore, no official endorsement should be inferred.
Any mention of trade names or commercial products does not constitute endorsement or recommendation for use.
Footnotes
This article is contribution number 105 of the CMU Institute for Great Lakes Research.
REFERENCES
- 1.Kourtev PS, Nakatsu CH, Konopka A. 2009. Inhibition of nitrate reduction by chromium(VI) in anaerobic soil microcosms. Appl Environ Microbiol 75:6249–6257. doi: 10.1128/AEM.00347-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Henson MW, Santo Domingo JW, Kourtev PS, Jensen RV, Dunn JA, Learman DR. 2015. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment. PeerJ 3:e1395. doi: 10.7717/peerj.1395. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Bartlett RJ. 1991. Chromium cycling in soils and water—links, gaps, and methods. Environ Health Perspect 92:17–24. doi: 10.1289/ehp.919217. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Cheng Y, Holman H-Y, Lin Z. 2012. Remediation of chromium and uranium contamination by microbial activity. Elements 8:107–112. doi: 10.2113/gselements.8.2.107. [DOI] [Google Scholar]
- 5.Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi: 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, Prjibelski AD, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, Clingenpeel SR, Woyke T, Mclean JS, Lasken R, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714–737. doi: 10.1089/cmb.2013.0084. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075. doi: 10.1093/bioinformatics/btt086. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25:1043–1055. doi: 10.1101/gr.186072.114. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang JH, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. 2012. IMG: the Integrated Microbial Genomes Database and comparative analysis system. Nucleic Acids Res 40:D115–D122. doi: 10.1093/nar/gkr1044. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Park CH, Keyhan M, Wielinga B, Fendorf S, Matin A. 2000. Purification to homogeneity and characterization of a novel Pseudomonas putida chromate reductase. Appl Environ Microbiol 66:1788–1795. doi: 10.1128/AEM.66.5.1788-1795.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Cervantes C, Ohtake H, Chu L, Misra TK, Silver S. 1990. Cloning, nucleotide sequence, and expression of the chromate resistance determinant of Pseudomonas aeruginosa plasmid pUM505. J Bacteriol 172:287–291. doi: 10.1128/jb.172.1.287-291.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Nies DH. 1995. The cobalt, zinc, and cadmium efflux system CzcABC from Alcaligenes eutrophus functions as a cation-proton antiporter in Escherichia coli. J Bacteriol 177:2707–2712. doi: 10.1128/jb.177.10.2707-2712.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Manara A, DalCorso G, Baliardini C, Farinati S, Cecconi D, Furini A. 2012. Pseudomonas putida response to cadmium: changes in membrane and cytosolic proteomes. J Proteome Res 11:4169–4179. doi: 10.1021/pr300281f. [DOI] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The raw sequencing reads have been deposited in the Sequence Read Archive (SRA) under the accession number SRP120551. This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers QMGB00000000 to QMGG00000000, as listed in Table 1. Integrated Microbial Genomes (IMG) annotations have the Genomes Online Database (GOLD) study identification (ID) number Gs0130379.