Undisturbed hot springs inside Yellowstone National Park remain a dynamic biome for novel cellulolytic thermophiles. We report here the draft genome sequence of one of these isolates, Bacillus altitudinis YNP4-TSU

Li, Hui

O\u27Hair, Joshua A.

Scholz, Matthew

Thapa, Santosh

Zhou, Suping

English

Digital Scholarship @ Tennessee State University

Tennessee State University Digital Scholarship @ Tennessee State University Agricultural and Environmental Sciences Faculty Research Department of Agricultural and Environmental Sciences 7-13-2017 Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park Joshua A. O'Hair Tennessee State University Hui Li Tennessee State University Santosh Thapa Tennessee State University Matthew Scholz Vanderbilt University Suping Zhou Tennessee State University Follow this and additional works at: https://digitalscholarship.tnstate.edu/agricultural-and-environmental-sciences-faculty  Part of the Ecology and Evolutionary Biology Commons, Genetics Commons, and the Microbiology Commons Recommended Citation OHair JA, Li H, Thapa S, Scholz M, Zhou S. 2017. Draft genome sequence of Bacillus altitudinis YNP4-TSU, isolated from Yellowstone National Park. Genome Announc 5:e00631-17. https://doi.org/10.1128/genomeA.00631-17. This Article is brought to you for free and open access by the Department of Agricultural and Environmental Sciences at Digital Scholarship @ Tennessee State University. It has been accepted for inclusion in Agricultural and Environmental Sciences Faculty Research by an authorized administrator of Digital Scholarship @ Tennessee State University. For more information, please contact XGE@Tnstate.edu. Draft Genome Sequence of Bacillusaltitudinis YNP4-TSU, Isolated fromYellowstone National ParkJoshua A. OHair,a Hui Li,a Santosh Thapa,a Matthew Scholz,b Suping ZhouaDepartment of Agricultural and Environmental Sciences, Tennessee State University, Nashville, Tennessee,USAa; Vanderbilt Technologies for Advanced Genetics (VANTAGE), Vanderbilt University Medical Center,Nashville, Tennessee, USAbABSTRACT Undisturbed hot springs inside Yellowstone National Park remain a dy-namic biome for novel cellulolytic thermophiles. We report here the draft genomesequence of one of these isolates, Bacillus altitudinis YNP4-TSU.A new strain, Bacillus altitudinis YNP4-TSU, was isolated from Whiterock Springs (lat44.780233, long 110.69805), which is inside Yellowstone National Park, USA. The rathernew species B. altitudinis was first discovered in 2006 from cryogenic tubes taken at 41 kmin the atmosphere (1). Since then, only six other B. altitudinis strains, including YNP4-TSU,have been deposited in the NCBI genome database (retrieved May 12, 2017). This specieshas the ability to produce spores that can withstand some of the most extreme environ-ments, ranging from atmospheric radiation (1) to geothermal heated springs.B. altitudinis YNP4-TSU was isolated by vacuum filtration in 0.22 m Milliporesystems from water samples of 59°C and a pH of 2.3. Filters containing unknownamounts of specimens were then cut and transferred to nutrient agar (2). Areas withsubstantial growth were then re-streaked and incubated at 37°C to produce individualcolonies. B. altitudinis YNP4-TSU tested positive for extracellular endoglucanase activityon 10% carboxymethylcellulose (CMC) under the Congo red assay (3). After positivecellulase testing, whole genomic DNA was extracted using the GenElute SigmaGenomic DNA kit for Gram-positive strains (Sigma, USA) (3). For genome sequencing,libraries were prepared with Illumina TruSeq DNA Nano sample kits using indexedadaptors (Illumina). Pooled libraries were subjected to 150-bp paired-end sequencingaccording to the manufacturer’s protocol (Illumina HiSeq3000). Bcl2fastq2 conversionsoftware (Illumina) was used to generate demultiplexed Fastq files. This work wasperformed at the Vanderbilt Technologies for Advanced Genomics (VANTAGE) atVanderbilt University (Nashville, TN, USA). Raw reads were then trimmed to removebases of Q average  3 using Burrows–Wheeler alignment (4). De novo assembly wasperformed using SPAdes version 3.7.1 (5) with default parameters and the “-careful”flag. The draft genome of YNP4-TSU was assembled into 67 contigs with a total genomesize of 3,749,504 bp (N50, 172,320) and a GC content of 45.0%. Automated annotationwas performed with the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version3.3 and yielded 3,734 coding genes, 72 tRNAs, and 16 rRNAs. Annotation predictedseveral endoglucanase, exoglucanase, and cellobiase genes, which upon an NCBInucleotide BLAST search (retrieved April 25, 2017) revealed many novel gene-encodingsequences (6). These potential enzymes may have an important role on future biomassfermentation, which is why a further examination of the enzymatic rates will helpdetermine the cellulolytic capabilities of B. altitudinis YNP4-TSU.Accession number(s). The whole-genome shotgun project reported here has beendeposited at DDBJ/EMBL/GenBank under the accession number MEDE00000000. Theversion reported here is the first version, MEDE01000000.Received 16 May 2017 Accepted 18 May2017 Published 13 July 2017Citation OHair JA, Li H, Thapa S, Scholz M,Zhou S. 2017. Draft genome sequence ofBacillus altitudinis YNP4-TSU, isolated fromYellowstone National Park. Genome Announc5:e00631-17. https://doi.org/10.1128/genomeA.00631-17.Copyright © 2017 OHair et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Suping Zhou,zsuping@tnstate.edu.PROKARYOTEScrossmVolume 5 Issue 28 e00631-17 genomea.asm.org 1Downloaded from https://journals.asm.org/journal/genomea on 16 June 2021 by 173.233.240.6.ACKNOWLEDGMENTSWe thank the Yellowstone National Park for access to sensitive hydrothermal areasunder permit YELL-2015-SCI-6074. We especially thank Stacey Gunther and Sarah Haasfor their help in coordinating permits and providing guidance on field sampling atYellowstone National Park. The Vanderbilt VANTAGE Core provided technical assistancefor this work. VANTAGE is supported in part by a CTSA grant (5UL1 RR024975-03), theVanderbilt Ingram Cancer Center (P30 CA68485), the Vanderbilt Vision Center (P30EY08126), and NIH/NCRR (G20 RR030956). We also give special thanks to Olivia Kouesfor her assistance at VANTAGE and to Sarabjit Bhatti for assisting with the lab analysisat Tennessee State University. Any opinions, findings, and conclusions or recommen-dations expressed in this material are those of the author(s) and do not reflect the viewsof the U.S. Department of Agriculture or the National Park Service.REFERENCES1. Shivaji S, Chaturvedi P, Suresh K, Reddy GSN, Dutt CB, Wainwright M,Narlikar JV, Bhargava PM. 2006. Bacillus aerius sp. nov., Bacillus aerophilussp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov.,isolated from cryogenic tubes used for collecting air samples from highaltitudes. Int J Syst Evol Microbiol 56:1465–1473. https://doi.org/10.1099/ijs.0.64029-0.2. O’Hair JA, Li H, Thapa S, Scholz MB, Zhou S. 2017. Draft genome sequenceof Bacillus licheniformis strain YNP1-TSU, isolated from Whiterock Springsin Yellowstone National Park. Genome Announc 5(9):e01496-16. https://doi.org/10.1128/genomeA.01496-16.3. Li H, Zhou S, Johnson T, Vercruysse K, Ropelewski AJ, Thannhauser TW.2014. Draft genome sequence of new Bacillus cereus strain tsu1. GenomeAnnounc 2(6):e01294-14. https://doi.org/10.1128/genomeA.01294-14.4. Li H, Durbin R. 2009. Fast and accurate short read alignment withBurrows–Wheeler transform. Bioinformatics 25:1754 –1760. https://doi.org/10.1093/bioinformatics/btp324.5. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, LesinVM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome as-sembly algorithm and its applications to single-cell sequencing. J ComputBiol 19:455– 477. https://doi.org/10.1089/cmb.2012.0021.6. NCBI Resource Coordinators. 2016. Database resources of the NationalCenter for Biotechnology Information. Nucleic Acids Research 44:D7–D19.https://doi.org/10.1093/nar/gkv1290.OHair et al.Volume 5 Issue 28 e00631-17 genomea.asm.org 2Downloaded from https://journals.asm.org/journal/genomea on 16 June 2021 by 173.233.240.6.

Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park

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Draft Genome Sequence of Bacillus altitudinis YNP4-TSU, Isolated from Yellowstone National Park

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