Actinobacterium strain S63T isolated from a soil sample

collected from Spindrift Col on Signy Island

(South Orkney Islands, maritime Antarctic) is a new

species of the Intrasporangiaceae family. Here we

report a draft genome sequence with an approximate

size of 5 Mbp contained in 54 contigs (69.33% GC

content). Preliminary analysis revealed the presence

of cold active protein coding sequences, which may

indicate an adaptation to the harsh polar environment

from which the strain was isolated

Convey, P.

Gan, H.M.

Pearce, D.A.

Tan, G.Y.A.

Thomas, S.M.

Actinobacterium strain S63T isolated from a soil sample collected from Spindrift Col on Signy Island (South Orkney Islands, maritime Antarctic) is a new species of the Intrasporangiaceae family. Here we report a draft genome sequence with an approximate size of 5 Mbp contained in 54 contigs (69.33% GC content). Preliminary analysis revealed the presence of cold active protein coding sequences, which may indicate an adaptation to the harsh polar environment from which the strain was isolated

Convey, Peter

Gan, Han Ming

Pearce, David Anthony

Tan, Geok Yuan Annie

UM Digital Repository

Draft genome sequence of a novel actinobacterium from the family Intrasporangiaceae isolated from Signy Island, Antarctica

Thomas, SM

Convey, P

Pearce, DA

Tan, GYA

Deakin Research Online

Thomas, S. M.

Gan, H. M.

Pearce, David

Northumbria University Research Portal

NERC Open Research Archive

SPECIAL SECTION: ASIAN FORUM FOR POLAR SCIENCES  CURRENT SCIENCE, VOL. 115, NO. 9, 10 NOVEMBER 2018 1695*For correspondence. (e-mail: gyatan@um.edu.my) Draft genome sequence of a novel actino-bacterium from the family Intrasporangiaceae  isolated from Signy Island, Antarctica  S. M. Thomas1,2, P. Convey2,5, H. M. Gan3,4, D. A. Pearce2,5,6 and G. Y. A. Tan1,2,* 1Institute of Biological Sciences, and 2National Antarctic Research Centre, University of Malaya, 50603 Kuala Lumpur, Malaysia 3Genomics Facility, Tropical and Medicine Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway,  Selangor, Malaysia 4Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong 3220, Australia 5British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 OET, United Kingdom 6Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University at Newcastle,  Newcastle-upon-Tyne, NE1 8ST, United Kingdom  Actinobacterium strain S63T isolated from a soil sam-ple collected from Spindrift Col on Signy Island (South Orkney Islands, maritime Antarctic) is a new species of the Intrasporangiaceae family. Here we  report a draft genome sequence with an approximate size of 5 Mbp contained in 54 contigs (69.33% GC content). Preliminary analysis revealed the presence of cold active protein coding sequences, which may indicate an adaptation to the harsh polar environment from which the strain was isolated.  Keywords: Actinobacteria, Antarctic soil, Humibacil-lus.  SIGNY Island is located in the South Orkney Islands  archipelago in the Atlantic sector of the Southern Ocean. The island is well known for its seals, penguins, skuas and other birds, as well as being a paradigmatic example of the terrestrial vegetation and ecosystems of the mari-time Antarctic1. Within its maximum dimensions (6.5 × 5 km), most terrestrial microbial communities here have a strong marine influence, receiving nutritional and water input through sea-spray and the movement of marine  vertebrates. Culture-dependent and culture-independent studies increasingly indicate that diverse microbial life thrives, despite the environmental pressures of Antarctica2,3. It is clear that various Antarctic microbial communities harbour new and previously undescribed species4,5. Here we report the draft genome sequence of strain S63T, a novel species of the family Intrasporangiaceae, isolated from a soil sample collected from Signy Island.  Soils from Signy Island have yielded a diversity of bacteria6, one of which is Actinobacterium strain S63T. This strain was isolated from a sample collected from Spindrift Col on Signy Island, Antarctica. It was isolated on Starch Casein Nitrate agar7 supplemented with 2% NaCl and incubated at 15°C for up to 4 months.  Strain S63T is a Gram-positive coccoid bacterium. The strain is catalase positive, aerobic, non-motile and non-spore forming. The diaminopimelic acid isomer in the cell wall peptidoglycan is LL-DAP. This strain also pro-duces amylase and lipase at 15°C, but does not produce biosurfactants in the drop-collapsing test8. Additional phenotypic information supporting the novelty of the strain is being documented for a future publication.  Total genomic DNA extraction was carried out using the MG™ DNA purification kit (Macrogen Inc., Korea) following the manufacturer’s instructions. Genomic DNA was fragmented using adaptive focused acoustic techno-logy (AFA, Covaris) to a target size of 250 bp. The frag-mented DNA was then end-repaired, ligated to Truseq adapters, and PCR-enriched using Truseq PCR master mix and a primer cocktail following the manufacturer’s protocol (TruSeq DNA sample preparation kit, Illumina, CA, USA). The final sequencing library was quantified using qPCR according to the qPCR quantification proto-col guide (KAPA Library Quantification kits for illumina sequencing platforms) and the library size was confirmed using the Agilent 1000 DNA kit on an Agilent 2100 Bio-analyzer (Agilent Technologies, Böblingen, Germany). The resulting library was sequenced using a standard flow cell, and 200 cycles (100 paired end) on the illumina  HiSeq2000 platform.  A total of 47,882,286 paired-end reads (4.79 Gbp) were generated on the HiSeq, of which only 6 million reads were subsequently subsampled for de novo assem-bly to reduce the generation of spurious contigs due to overly high sequencing depth9. Genome assembly was performed using Spades version 3.8.1 with the ‘careful’ option enabled10. The draft assembly was subsequently improved using in silico scaffolding and gap-closing11,12. The final draft genome has an accumulated length of 5,023,713 bp (69.33% GC, 120 × genome coverage)  contained in 54 contigs with an N50 of 194,740 bp.  SPECIAL SECTION: ASIAN FORUM FOR POLAR SCIENCES  CURRENT SCIENCE, VOL. 115, NO. 9, 10 NOVEMBER 2018 1696Annotation was performed using the NCBI Prokaryotic Genome Annotation Pipeline, leading to the prediction of 4529 coding sequences. Among these, 2671 had anno-tated functions and 1858 were hypothetical proteins. One copy of each ribosomal RNA (5S, 16S and 23S) was identified in the draft genome, along with 47 tRNAs and 3 ncRNAs.  Based on 16S rRNA gene sequence analysis and BLAST results from the NCBI database, the strain was found to share <97% similarity with Humibacillus xan-thopallidus KV-663T, the only validly described member of that genus. Four predicted proteins in the genome of strain S63T were annotated as cold-shock proteins (Locus tags: BA895_07505, BA895_14940, BA895_17625 and BA895_20550). Subsequent protein domain analysis  using InterProScan confirmed the presence of protein domains commonly found in cold-shock proteins such as IPR011129, IPR002059 and IPR012156, indicating  potential capability of the strain to resist the extreme  environment stresses of Antarctica.  Strain S63T also possesses genes coding for enzymes involved in the conversion of maltose to trehalose. Treha-lose is a source of energy as well as a cryoprotectant and and is involved in anhydrobiosis in many groups of  organisms13. It could, in this case, assist this bacterium to withstand prolonged desiccation. The genome also con-tained alpha-amylase and glucoamylase genes, which are a part of the gene complex for the biosynthesis of tre-halose. Production of trehalose may also increase survival of cold stress, as shown in an Arthrobacter sp. isolated from an Alpine permafrost sample, which was found to accumulate trehalose upon cold shock14.  The strain has been deposited in the DSMZ culture col-lection as DSM 29435T. The partial 16S rRNA gene  sequence (1366 bp) has been deposited in the NCBI GenBank database under the accession number KJ547654. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the NCBI Ref-erence Sequence: NZ_MAST00000000.1.   1. Smith, R. I. L., Signy Island as a paradigm of biological and environmental change in Antarctic terrestrial ecosystems. In Antarctic Ecosystems. Ecological Change and Conservation (eds Kerry, K. R. and Hempel, G.), Springer, Berlin, 1990, pp. 32–50. 2. Cavicchioli, R., Microbial ecology of Antarctic aquatic systems. Nat. Rev. Microbiol., 2015, 13, 691–706. 3. Cowan, D. A. and Tow, L. A., Endangered Antarctic environ-ments. Annu. Rev. Microbiol., 2004, 58, 649–690. 4. Babalola, O. O., Kirby, B. M., Le Roes-Hill, M., Cook, A. E., Cary, S. C., Burton, S. G. and Cowan, D. A., Phylogenetic analy-sis of actinobacterial populations associated with Antarctic dry valley mineral soils. Environ. Microbiol., 2009, 11, 566–576. 5. Chong, C. W., Goh, Y. S., Convey, P., Pearce, D. A. and Tan, I. K. P., Spatial pattern in Antarctica: what can we learn from  Antarctic bacterial isolates? Extremophiles, 2013, 17, 733–745. 6. Pan, S. Y., Tan, G. Y. A., Convey, P., Pearce, D. A. and Tan, I. K. P., Diversity and bioactivity of actinomycetes from Signy Island terrestrial soils, maritime Antarctic. Adv. Polar Sci., 2013, 24, 208–212. 7. Küster, E. and Williams, S., Selection of media for isolation of streptomycetes. Nature, 1964, 202, 928–929. 8. Thomas, S., Biodiversity and Bioactivity of Antarctic Actinobacte-ria, M Sc thesis, University of Malaya, 2017. 9. Gan, H. M., Lee, Y. P. and Austin, C. M., Nanopore long-read guided complete genome assembly of Hydrogenophaga inter-media and genomic insights into 4-aminobenzenesulfonate,  p-aminobenzoic acid and hydrogen metabolism in the genus  Hydrogenophaga. Front. Microbiol., 2017, 8, 1880. 10. Nurk, S. et al., Assembling genomes and mini-metagenomes from highly chimeric reads. In Proceedings of the 17th Annual Interna-tional Conference on Research in Computational Molecular Bio-logy (eds Deng, M., Jiang, R., Sun, F. and Zhang, X.), 2013, Springer, Berlin, pp. 158–170. 11. Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D. and Pirovano, W., Scaffolding pre-assembled contigs using SSPACE. In Bioin-formatics, Oxford, England, 2011, vol. 27, pp. 578–579. 12. Boetzer, M. and Pirovano, W., Toward almost closed genomes with GapFiller. Genome Biol., 2012, 13, 1. 13. Everatt, M. J., Convey, P., Bale, J. S., Worland, M. R. and  Hayward, S. A. L., Responses of invertebrates to temperature and water stress: a polar perspective. J. Therm. Biol., 2014, 54, 118–132. 14. Chen, X. M. et al., Regulation of expression of trehalose-6-phosphate synthase during cold shock in Arthrobacter strain A3. Extremophiles, 2011, 15, 499–508.   ACKNOWLEDGEMENTS. We acknowledge the University of  Malaya Research Grant (RP002E-13SUS & RP007-2012D) and the Ministry of Science, Technology and Innovation Flagship Grant (FP0712E012). P.C. is supported by Natural Environment Research Council core funding to the British Antarctic Survey’s ‘Biodiversity, Evolution and Adaptation’ Team. P.C. and D.A.P. are also supported by Visiting Professorships to the University of Malaya.  doi: 10.18520/cs/v115/i9/1695-1696     

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Draft genome sequence of a novel actinobacterium from the family Intrasporangiaceae isolated from Signy Island, Antarctica

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