Lipingzhangella rawalii sp. nov., a novel halophile isolated from Sambhar Salt Lake, Rajasthan, India.
Genome sequencing
Halophile
Saline ecosystem
Sambhar Salt Lake
Journal
Archives of microbiology
ISSN: 1432-072X
Titre abrégé: Arch Microbiol
Pays: Germany
ID NLM: 0410427
Informations de publication
Date de publication:
15 Dec 2023
15 Dec 2023
Historique:
received:
09
10
2023
accepted:
17
11
2023
revised:
17
11
2023
medline:
15
12
2023
pubmed:
15
12
2023
entrez:
15
12
2023
Statut:
epublish
Résumé
A haloalkaliphilic actinobacterial strain LS1_29
Identifiants
pubmed: 38100061
doi: 10.1007/s00203-023-03757-9
pii: 10.1007/s00203-023-03757-9
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
22Subventions
Organisme : Science and Engineering Research Board
ID : SRG/2022/000126
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.
Références
Andrews S (2010) FastQC: a quality control tool for high throughput sequence data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ .
Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genomics. https://doi.org/10.1186/1471-2164-9-75
doi: 10.1186/1471-2164-9-75
pubmed: 18261238
pmcid: 2265698
Blin K, Shaw S, Augustijn HE et al (2023) antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 51:W46–W50. https://doi.org/10.1093/nar/gkad344
doi: 10.1093/nar/gkad344
pubmed: 37140036
pmcid: 10320115
Bosi E, Donati B, Galardini M et al (2015) MeDuSa: a multi-draft based scaffolder. Bioinformatics 31:2443–2451. https://doi.org/10.1093/bioinformatics/btv171
doi: 10.1093/bioinformatics/btv171
pubmed: 25810435
Brettin T, Davis JJ, Disz T et al (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. https://doi.org/10.1038/srep08365
doi: 10.1038/srep08365
pubmed: 25666585
pmcid: 4322359
Chang X, Liu W, Zhang X-H (2011) Spinactinospora alkalitolerans gen. nov., sp. nov., an actinomycete isolated from marine sediment. Int J Syst Evol Microbiol 61:2805–2810. https://doi.org/10.1099/ijs.0.027383-0
doi: 10.1099/ijs.0.027383-0
pubmed: 21216917
Chang X, Liu W, Zhang X-H (2012) Salinactinospora qingdaonensis gen. nov., sp. nov., a halophilic actinomycete isolated from a salt pond. Int J Syst Evol Microbiol 62:954–959. https://doi.org/10.1099/ijs.0.031088-0
doi: 10.1099/ijs.0.031088-0
pubmed: 21669918
Chklovski A, Parks DH, Woodcroft BJ, Tyson GW (2023) CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods 20:1203–1212. https://doi.org/10.1038/s41592-023-01940-w
doi: 10.1038/s41592-023-01940-w
pubmed: 37500759
Chun J, Oren A, Ventosa A et al (2018) Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 68:461–466. https://doi.org/10.1099/ijsem.0.002516
doi: 10.1099/ijsem.0.002516
pubmed: 29292687
Claverías FP, Serna-Cardona N, Cumsille A et al (2022) Spiractinospora alimapuensis gen. nov., sp. nov., isolated from marine sediment of Valparaíso Bay (Chile) and proposal for reclassification of two species of the genus Nocardiopsis. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.005207
doi: 10.1099/ijsem.0.005207
pubmed: 35085063
Cui XL, Mao PH, Zeng M et al (2001) Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 51:357–363. https://doi.org/10.1099/00207713-51-2-357
doi: 10.1099/00207713-51-2-357
pubmed: 11321080
Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668. https://doi.org/10.1086/282802
doi: 10.1086/282802
Guo L, Tuo L, Habden X et al (2015) Allosalinactinospora lopnorensis gen. nov., sp. nov., a new member of the family Nocardiopsaceae isolated from soil. Int J Syst Evol Microbiol 65:206–213. https://doi.org/10.1099/ijs.0.055160-0
doi: 10.1099/ijs.0.055160-0
pubmed: 25332211
Jani K, Khare K, Senik S et al (2018) Corynebacterium godavarianum sp. nov., isolated from the Godavari river. India Int J Syst Evol Microbiol 68:241–247. https://doi.org/10.1099/ijsem.0.002491
doi: 10.1099/ijsem.0.002491
pubmed: 29148360
Kajale S, Deshpande N, Pali S et al (2020a) Natrialba swarupiae sp. nov., a halophilic archaeon isolated from a hypersaline lake in India. Int J Syst Evol Microbiol 70:1876–1881. https://doi.org/10.1099/ijsem.0.003986
doi: 10.1099/ijsem.0.003986
pubmed: 31967950
Kajale S, Deshpande N, Shouche Y, Sharma A (2020b) Cultivation of diverse microorganisms from hypersaline lake and impact of delay in sample processing on cell viability. Curr Microbiol 77:716–721. https://doi.org/10.1007/s00284-019-01857-8
doi: 10.1007/s00284-019-01857-8
pubmed: 31912221
Kämpfer P, Schäfer J, Lodders N, Martin K (2010) Murinocardiopsis flavida gen. nov., sp. nov., an actinomycete isolated from indoor walls. Int J Syst Evol Microbiol 60:1729–1734. https://doi.org/10.1099/ijs.0.015990-0
doi: 10.1099/ijs.0.015990-0
pubmed: 19734281
Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. https://doi.org/10.1016/j.jmb.2015.11.006
doi: 10.1016/j.jmb.2015.11.006
pubmed: 26585406
Kroppenstedt RM, Evtushenko LI (2006) The family Nocardiopsaceae. The Prokaryotes. Springer New York, New York, NY, pp 754–795. https://doi.org/10.1007/0-387-30743-5_29
doi: 10.1007/0-387-30743-5_29
Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley & Sons, New York, pp 115–175
Lee I, Ouk Kim Y, Park S-C, Chun J (2016) OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 66:1100–1103. https://doi.org/10.1099/ijsem.0.000760
doi: 10.1099/ijsem.0.000760
pubmed: 26585518
Lefort V, Desper R, Gascuel O (2015) FastME 2.0: a comprehensive, accurate, and fast distance-based phylogeny inference program: table 1. Mol Biol Evol 32:2798–2800. https://doi.org/10.1093/molbev/msv150
doi: 10.1093/molbev/msv150
pubmed: 26130081
pmcid: 4576710
Liu M-J, Zhu W-Y, Li J et al (2015) Actinorugispora endophytica gen. nov., sp. nov., an actinomycete isolated from Daucus carota. Int J Syst Evol Microbiol 65:2562–2568. https://doi.org/10.1099/ijs.0.000304
doi: 10.1099/ijs.0.000304
pubmed: 25948617
Meier-Kolthoff JP, Göker M (2019) TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun. https://doi.org/10.1038/s41467-019-10210-3
doi: 10.1038/s41467-019-10210-3
pubmed: 31097708
pmcid: 6522516
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
doi: 10.1186/1471-2105-14-60
Meyer J (1976) Nocardiopsis, a new genus of the order actinomycetales. Int J Syst Bacteriol 26:487–493. https://doi.org/10.1099/00207713-26-4-487
doi: 10.1099/00207713-26-4-487
Mikheenko A, Prjibelski A, Saveliev V et al (2018) Versatile genome assembly evaluation with QUAST-LG. Bioinformatics 34:i142–i150. https://doi.org/10.1093/bioinformatics/bty266
doi: 10.1093/bioinformatics/bty266
pubmed: 29949969
pmcid: 6022658
Ng ZY, Fang B-Z, Li W-J, Tan GYA (2019) Marinitenerispora sediminis gen. nov., sp. nov., a member of the family Nocardiopsaceae isolated from marine sediment. Int J Syst Evol Microbiol 69:3031–3040. https://doi.org/10.1099/ijsem.0.003587
doi: 10.1099/ijsem.0.003587
pubmed: 31310190
Olson RD, Assaf R, Brettin T et al (2023) Introducing the bacterial and viral bioinformatics resource center (BV-BRC): a resource combining PATRIC, IRD and ViPR. Nucleic Acids Res 51:D678–D689. https://doi.org/10.1093/nar/gkac1003
doi: 10.1093/nar/gkac1003
pubmed: 36350631
Rainey FA, Ward-Rainey N, Kroppenstedt RM, Stackebrandt E (1996) The genus nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal of Nocardiopsaceae fam. nov. Int J Syst Bacteriol 46:1088–1092. https://doi.org/10.1099/00207713-46-4-1088
doi: 10.1099/00207713-46-4-1088
pubmed: 8863440
Rodriguez-R, Konstantinidis KK (2016) The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Prepr 4:e1900-1901
Sahay H, Mahfooz S, Singh AK et al (2012) Exploration and characterization of agriculturally and industrially important haloalkaliphilic bacteria from environmental samples of hypersaline Sambhar lake, India. World J Microbiol Biotechnol 28:3207–3217. https://doi.org/10.1007/s11274-012-1131-1
doi: 10.1007/s11274-012-1131-1
pubmed: 22828794
Sharma A, Shouche Y (2014) Microbial culture collection (MCC) and international depositary authority (IDA) at national centre for cell science, Pune. Indian J Microbiol 54:129–133. https://doi.org/10.1007/s12088-014-0447-y
doi: 10.1007/s12088-014-0447-y
pubmed: 25320411
pmcid: 4188496
Sharma A, Jani K, Feng G-D et al (2018) Subsaxibacter sediminis sp. nov., isolated from Arctic glacial sediment and emended description of the genus Subsaxibacter. Int J Syst Evol Microbiol 68:1678–1682. https://doi.org/10.1099/ijsem.0.002729
doi: 10.1099/ijsem.0.002729
pubmed: 29561259
Tamura K, Stecher G, Kumar S (2021) MEGA11: Molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
doi: 10.1093/molbev/msab120
pubmed: 33892491
pmcid: 8233496
Tang S-K, Tian X-P, Zhi X-Y et al (2008) Haloactinospora alba gen. nov., sp. nov., a halophilic filamentous actinomycete of the family Nocardiopsaceae. Int J Syst Evol Microbiol 58:2075–2080. https://doi.org/10.1099/ijs.0.65531-0
doi: 10.1099/ijs.0.65531-0
pubmed: 18768607
Tian X-P, Tang S-K, Dong J-D et al (2009) Marinactinospora thermotolerans gen. nov., sp. nov., a marine actinomycete isolated from a sediment in the northern South China Sea. Int J Syst Evol Microbiol 59:948–952. https://doi.org/10.1099/ijs.0.005231-0
doi: 10.1099/ijs.0.005231-0
pubmed: 19406773
Upasani V, Desai S (1990) Sambhar Salt lake: chemical composition of the brines and studies on haloalkaliphilic archaebacteria. Arch Microbiol. https://doi.org/10.1007/bf00248841
doi: 10.1007/bf00248841
Walker BJ, Abeel T, Shea T et al (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9:e112963. https://doi.org/10.1371/journal.pone.0112963
doi: 10.1371/journal.pone.0112963
pubmed: 25409509
pmcid: 4237348
Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13:e1005595. https://doi.org/10.1371/journal.pcbi.1005595
doi: 10.1371/journal.pcbi.1005595
pubmed: 28594827
pmcid: 5481147
Yoon S-H, Ha S-M, Kwon S et al (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
doi: 10.1099/ijsem.0.001755
pubmed: 28005526
pmcid: 5563544
Zhang Z, Wang Y, Ruan J (1998) Reclassification of thermomonospora and microtetraspora. Int J Syst Bacteriol 48:411–422. https://doi.org/10.1099/00207713-48-2-411
doi: 10.1099/00207713-48-2-411
pubmed: 9731279
Zhang Y-G, Lu X-H, Ding Y-B et al (2016) Lipingzhangella halophila gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 66:4071–4076. https://doi.org/10.1099/ijsem.0.001312
doi: 10.1099/ijsem.0.001312
pubmed: 27412719