Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.
ABSTRACT
Asinibacterium sp. strains OR43 and OR53 belong to the phylum Bacteroidetes and were isolated from subsurface sediments in Oak Ridge, TN. Both strains grow at elevated levels of heavy metals. Here, we present the closed genome sequence of Asinibacterium sp. strain OR53 and the draft genome sequence of Asinibacterium sp. strain OR43.
ANNOUNCEMENT
Asinibacterium sp. strains OR43 and OR53 (formerly Sediminibacterium sp. strains OR43 and OR53) are Gram-negative, nonmotile, aerobic bacteria. The type strain Asinibacterium lactis was isolated from donkey milk powder (1). Closely related genera include Sediminibacterium, Vibrionimonas, and Hydrotalea (2–6). Related sequences (16S rRNA) were detected ubiquitously in the environment but most notably in sites contaminated with hydrocarbons, heavy metals, and/or radionucleotides (7–14). The genome sequences will provide insight into the potential role of Asinibacterium sp. strains OR43 and OR53 in the bioremediation of heavy metals.
Asinibacterium sp. strains OR43 and OR53 were isolated from the contaminated subsurface sediment at the Integrated Field Research Challenge (IFRC) in Oak Ridge, TN, with the diffusion chamber approach (7). Both strains have a very similar physiology and are able to grow in the presence of uranium equal to the concentrations in their original environment (7, 15) (R. M. Brzoska and A. Bollmann, unpublished data). Prior to DNA isolation, the strains were grown in 0.1× Luria-Bertani broth at 27°C (7). Genomic DNA was isolated with the JETFLEX genomic DNA purification kit from GenoMed (Loehne, Germany) according to the manufacturer’s recommendations. Genome sequence data for both genomes were obtained with the Illumina HiSeq 2000 platform with paired-end technology (2 × 150 bp) (16). The data produced 18,342,342 reads generating 3,005 Mbp (strain OR43) and 21,794,720 reads generating 3,269 Mbp (strain OR53). The genome sequences were assembled with ALLPATHS version R37654 (strain OR43) and version R39750 (strain OR53) (17), Velvet version 1.1.05 (18), and Phrap version 4.24 (High Performance Software LLC) (only strain OR53). Prodigal 2.5 was used for gene calling (19). The genomes were annotated with the DOE Joint Genome Institute (JGI) Annotation Pipeline (20, 21) and further analyzed with the Integrated Microbial Genomes and Microbiomes database and comparative analysis system (IMG/M) at the Joint Genome Institute in Walnut Creek, CA (22).
The genome size for Asinibacterium sp. strain OR43 was 3,768,016 bp in 12 scaffolds with a GC content of 45.7%, and that for Asinibacterium sp. strain OR53 was 3,715,967 bp in 1 scaffold with a GC content of 45.4%. Asinibacterium sp. strain OR43 had 2,473 proteins with predicted functions out of 3,284 protein-coding sequences, while Asinibacterium sp. strain OR53 had 2,464 proteins with predicted functions out of 3,281 protein-coding sequences. The genomes contained predicted heavy-metal efflux pumps and sensing proteins. The average nucleotide identity (ANI) between the genomes was calculated with the Microbial Species Identifier (MiSI) method (23) at 96.4%, which indicated that the genomes were the same species and very closely related. Further analysis is needed to determine the mechanism of Asinibacterium spp. to withstand and grow in the presence of uranium.
Data availability.
This whole-genome project has been deposited at DDBJ/EMBL/GenBank under the accession numbers ATYE00000000 (Asinibacterium sp. strain OR43) and AZXP00000000 (Asinibacterium sp. strain OR53). The raw reads were deposited in the SRA under SRP078705 (Asinibacterium sp. strain OR53) and SRP078706 (Asinibacterium sp. strain OR43).
ACKNOWLEDGMENTS
This work was conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, which is supported by the Office of Science of the U.S. Department of Energy under contract number DE-AC02-05CH11231.
We thank Eveline Brambilla (Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) for her help with the isolation of the genomic DNA.
REFERENCES
- 1.Lee D-G, Park J-M, Kang H, Hong S-Y, Lee KR, Chang H-B, Trujillo ME. 2013. Asinibacterium lactis gen. nov., sp. nov., a member of the family Chitinophagaceae, isolated from donkey (Equus asinus) milk. Int J Syst Evol Microbiol 63:3180–3185. doi: 10.1099/ijs.0.047639-0. [DOI] [PubMed] [Google Scholar]
- 2.Albert RA, Zitomer D, Dollhopf M, Schauer-Gimenez AE, Struble C, King M, Son S, Langer S, Busse H-J. 2014. Proposal of Vibrionimonas magnilacihabitans gen. nov., sp. nov., a curved Gram-stain-negative bacterium isolated from lake water. Int J Syst Evol Microbiol 64:613–620. doi: 10.1099/ijs.0.056663-0. [DOI] [PubMed] [Google Scholar]
- 3.Qu J-H, Yuan H-L. 2008. Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir. Int J Syst Evol Microbiol 58:2191–2194. doi: 10.1099/ijs.0.65514-0. [DOI] [PubMed] [Google Scholar]
- 4.Kim Y-J, Nguyen N-L, Weon H-Y, Yang D-C. 2013. Sediminibacterium ginsengisoli sp. nov., isolated from soil of a ginseng field, and emended descriptions of the genus Sediminibacterium and of Sediminibacterium salmoneum. Int J Syst Evol Microbiol 63:905–912. doi: 10.1099/ijs.0.038554-0. [DOI] [PubMed] [Google Scholar]
- 5.Kämpfer P, Lodders N, Falsen E. 2011. Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov. Int J Syst Evol Microbiol 61:518–523. doi: 10.1099/ijs.0.023002-0. [DOI] [PubMed] [Google Scholar]
- 6.Albuquerque L, Rainey FA, Nobre MF, da Costa MS. 2012. Hydrotalea sandarakina sp. nov., isolated from a hot spring runoff, and emended descriptions of the genus Hydrotalea and the species Hydrotalea flava. Int J Syst Evol Microbiol 62:1603–1608. doi: 10.1099/ijs.0.034496-0. [DOI] [PubMed] [Google Scholar]
- 7.Bollmann A, Palumbo AV, Lewis K, Epstein SS. 2010. Isolation and physiology of bacteria from contaminated subsurface sediments. Appl Environ Microbiol 76:7413–7419. doi: 10.1128/AEM.00376-10. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Ayarza JM, Figuerola ELM, Erijman L. 2014. Draft genome sequences of type strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. strain C3, a novel strain isolated from activated sludge. Genome Announc 2:e01073-13. doi: 10.1128/genomeA.01073-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Singleton DR, Richardson SD, Aitken MD. 2011. Pyrosequence analysis of bacteria communities in aerobic bioreactors treating polycyclic aromatic hydrocarbon-contaminated soil. Biodegradation 22:1061–1073. doi: 10.1007/s10532-011-9463-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W, Chang SH, Chang HW, Watson D, Brodie EL, Hazen TC, Keller M. 2006. Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72:3291–3301. doi: 10.1128/AEM.72.5.3291-3301.2006. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Laplante K, Sébastien B, Derome N. 2013. Parallel changes of taxonomic interaction networks in lacustrine bacterial communities by a polymetalic perturbation. Evol Appl 6:643–659. doi: 10.1111/eva.12050. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Al-Awadhi H, Dashti N, Khanafer M, Al-Mailem D, Ali N, Radwan S. 2013. Bias problems in culture-independent analysis of environmental bacterial communities: a representative study of hydrocarbonoclastic bacteria. SpringerPlus 2:369. doi: 10.1186/2193-1801-2-369. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Dhal PK, Islam E, Kazy SK, Sar P. 2011. Culture-independent molecular analysis of bacteria diversity in uranium-ore/-mine waste-contaminated and non-contaminated sites from uranium mines. 3 Biotech 1:261–272. doi: 10.1007/s13205-011-0034-4. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 14.Callbeck CM, Agrawal A, Voordouw G. 2013. Acetate production from oil under sulfate-reducing conditions in bioreactors injected with sulfate and nitrate. Appl Environ Microbiol 79:5059–5068. doi: 10.1128/AEM.01251-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 15.Brzoska RM, Bollmann A. 2016. The long-term effect of uranium and pH on the community composition of an artificial consortium. FEMS Microbiol Ecol 92:fiv158. doi: 10.1093/femsec/fiv158. [DOI] [PubMed] [Google Scholar]
- 16.Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433–438. doi: 10.1517/14622416.5.4.433. [DOI] [PubMed] [Google Scholar]
- 17.MacCallum I, Przybylski D, Gnerre S, Burton J, Shlyakhter I, Gnirke A, Malek J, McKernan K, Ranade S, Shea TP, Williams L, Young S, Nusbaum C, Jaffe DB. 2009. ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads. Genome Biol 10:R103. doi: 10.1186/gb-2009-10-10-r103. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 18.Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829. doi: 10.1101/gr.074492.107. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19.Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119. doi: 10.1186/1471-2105-11-119. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 20.Huntemann M, Ivanova NN, Mavromatis K, Tripp HJ, Paez-Espino D, Palaniappan K, Szeto E, Pillay M, Chen I-MA, Pati A, Nielsen T, Markowitz VM, Kyrpides NC. 2015. The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). Stand Genomic Sci 10:86. doi: 10.1186/s40793-015-0077-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 21.Chen I-MA, Markowitz VM, Palaniappan K, Szeto E, Chu K, Huang J, Ratner A, Pillay M, Hadjithomas M, Huntemann M, Mikhailova N, Ovchinnikova G, Ivanova NN, Kyrpides N. 2016. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. BMC Genomics 17:307. doi: 10.1186/s12864-016-2629-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 22.Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, Huntemann M, Varghese N, White JR, Seshadri R, Smirnova T, Kirton E, Jungbluth SP, Woyke T, Eloe-Fadrosh EA, Ivanova NN, Kyrpides NC. 2019. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 47:D666–D677. doi: 10.1093/nar/gky901. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 23.Varghese NJ, Mukherjee S, Ivanova N, Konstantinidis KT, Mavrommatis K, Kyrpides NC, Pati A. 2015. Microbial species delineation using whole genome sequences. Nucleic Acids Res 43:6761–6771. doi: 10.1093/nar/gkv657. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
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Data Availability Statement
This whole-genome project has been deposited at DDBJ/EMBL/GenBank under the accession numbers ATYE00000000 (Asinibacterium sp. strain OR43) and AZXP00000000 (Asinibacterium sp. strain OR53). The raw reads were deposited in the SRA under SRP078705 (Asinibacterium sp. strain OR53) and SRP078706 (Asinibacterium sp. strain OR43).