Abstract
Rhizobium sp. GHKF11 is an organophosphate-degrading bacterial strain that was isolated from farmland soil in Pecan Grove, Texas, USA. In addition to a capacity for pesticide degradation, GHKF11 shares conserved traits with other Rhizobium spp., including heavy metal resistance and transport genes that may have significant agricultural biotechnology applications.
GENOME ANNOUNCEMENT
Soil bacteria that live within the rhizosphere of plants often form symbiotic relationships with their plant hosts, significantly enhancing their nutrient uptake, fixing nitrogen, and promoting plant growth. Of these soil bacteria, strains that are resistant to the toxicological effects of common pesticides and heavy metals and aid in the soil detoxification of these compounds are particularly desirable to agricultural biotechnology (1, 2). Here, we report a draft genome sequence of an organophosphate-degrading strain of a Rhizobium sp., isolated from farmland soil in Pecan Grove, Texas, USA, through an environmental sampling research module undertaken by University of Houston biotechnology undergraduates (3). This strain, designated GHKF11, is related to Rhizobium sp. UR51a and shares many of its plant-promoting characteristics, including genes involved in nodulation, nitrogen fixation, and the production of siderophores (4). GHKF11 also possesses a battery of resistance genes against metals and metalloids, such as copper, cobalt, nickel, and arsenic. With the addition of its phosphotriesterase activity against organophosphates, the GHKF11 strain shows considerable potential for aiding in the remediation of both pesticide- and metal-contaminated soils.
The genome sequencing of GHKF11 was performed through Illumina MiSeq paired-end sequencing with a final sequencing coverage of 326.38×. Sequence reads were checked for quality using FastQC (5) and filtered using BBTools (6) with a minimum Phred score of 20. Paired-end reads were assembled into 61 contigs with the SPAdes version 3.7 program (7). Preliminary reference-based annotation using PATRIC (8) web resources was carried out to identify conserved pathways. Final de novo annotation was performed with Prokka (9) and the NCBI Prokaryotic Genome Automatic Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genome/annotation_prok). The metabolic pathways of aromatic and heterocyclic compounds were examined through KEGG databases (10). This draft genome of strain GHKF11 comprises a total of 5,290,899 bp encoding for 4,899 protein-coding sequences, of which 97 are pseudogenes, 1,059 are annotated as hypothetical proteins, and 3,840 form known functional proteins. The genome has a GC content of 59.12% and contains 4 rRNA (three complete, two partial), 50 tRNA, and 4 ncRNA loci.
Nucleotide sequence accession numbers.
The Rhizobium sp. GHKF11 whole-genome shotgun project has the project accession number LVFG00000000. This version of the project (01) has the accession number LVFG01000000, and consists of sequences LVFG01000001 to LVFG0100061.
ACKNOWLEDGMENT
The authors acknowledge efforts of Brian Iken in sample preparation.
Funding Statement
Funding for this work was provided for by the National Science Foundation (NSF) (award no. 1505403).
The NSF had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Footnotes
Citation Iyer R, Damania A. 2016. Draft genome sequence of Rhizobium sp. GHKF11, isolated from farmland soil in Pecan Grove, Texas. Genome Announc 4(4):e00682-16. doi:10.1128/genomeA.00682-16.
REFERENCES
- 1.Glick BR. 2012. Plant growth-promoting bacteria: mechanisms and applications. Scientifica 2012:963401. doi: 10.6064/2012/963401. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Khan MS, Zaidi A, Wani PA, Oves M. 2009. Role of plant growth promoting rhizobacteria in the remediation of metal contaminated soils. Environ Chem Lett 7:1–19. doi: 10.1007/s10311-008-0155-0. [DOI] [Google Scholar]
- 3.Iyer R, Smith K, Kudrle B, Leon A. 2015. Detection and location of OP-degrading activity: A model to integrate education and research. N Biotechnol 32:403–411. doi: 10.1016/j.nbt.2015.03.010. [DOI] [PubMed] [Google Scholar]
- 4.De Souza R, Sant’Anna FH, Ambrosini A, Tadra-Sfeir M, Faoro H, Pedrosa FO, Souza EM, Passaglia LM. 2015. Genome of rhizobium sp. UR51a, isolated from rice cropped in southern Brazilian Fields. Genome Announc 3(2):e00249-15. doi: 10.1128/genomeA.00249-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc.
- 6.Bushnell B. BBMap short read aligner. https://sourceforge.net/projects/bbmap/.
- 7.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]
- 8.Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJC, Seung YH, Zhang C, Zhang Y, Sobral BW. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581–D591. doi: 10.1093/nar/gkt1099. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 10.Kanehisa M, Goto S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28:27–30. doi: 10.1093/nar/28.1.27. [DOI] [PMC free article] [PubMed] [Google Scholar]