Comparative Genome Analysis of a Novel Alkaliphilic Actinobacterial Species Nesterenkonia haasae

Aguilar-Barajas E, Díaz-Pérez C, Ramírez-Díaz MI, Riveros-Rosas H, Cervantes C. Bacterial transport of sulfate, molybdate, and related oxyanions. Biometals. 2011 Aug; 24(4):687–707. https://doi.org/10.1007/s10534-011-9421-x Aguilar-Barajas E Díaz-Pérez C Ramírez-Díaz MI Riveros-Rosas H Cervantes C Bacterial transport of sulfate, molybdate, and related oxyanions Biometals 2011 Aug 244687 707 https://doi.org/10.1007/s10534-011-9421-x10.1007/s10534-011-9421-x21301930Search in Google Scholar

Aliyu H, De Maayer P, Cowan D. The genome of the Antarctic polyextremophile Nesterenkonia sp. AN1 reveals adaptive strategies for survival under multiple stress conditions. FEMS Microbiol Ecol. 2016 Apr;92(4):fiw032. https://doi.org/10.1093/femsec/fiw032 Aliyu H De Maayer P Cowan D The genome of the Antarctic polyextremophile Nesterenkonia sp AN1 reveals adaptive strategies for survival under multiple stress conditions. FEMS Microbiol Ecol 2016 Apr924fiw032 https://doi.org/10.1093/femsec/fiw03210.1093/femsec/fiw03226884466Search in Google Scholar

Amiri H, Azarbaijani R, Parsa Yeganeh L, Shahzadeh Fazeli A, Tabatabaei M, Salekdeh GH, Karimi K. Nesterenkonia sp. strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions. Sci Rep. 2016 Jan 4;6:18408. https://doi.org/10.1038/srep18408 Amiri H Azarbaijani R Parsa Yeganeh L Shahzadeh Fazeli A Tabatabaei M Salekdeh GH Karimi K Nesterenkonia sp strain F, a halophilic bacterium producing acetone, butanol, and ethanol under aerobic conditions. Sci Rep 2016 Jan 4618408 https://doi.org/10.1038/srep1840810.1038/srep18408469873726725518Search in Google Scholar

Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M, Goto S, Ogata H. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics. 2020 Apr 1;36(7):2251–2252. https://doi.org/10.1093/bioinformatics/btz859 Aramaki T Blanc-Mathieu R Endo H Ohkubo K Kanehisa M Goto S Ogata H KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold Bioinformatics 2020 Apr 13672251 2252 https://doi.org/10.1093/bioinformatics/btz85910.1093/bioinformatics/btz859714184531742321Search in Google Scholar

Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008 Feb 8;9:75. https://doi.org/10.1186/1471-2164-9-75 Aziz RK Bartels D Best AA DeJongh M Disz T Edwards RA Formsma K Gerdes S Glass EM Kubal M et al The RAST Server: rapid annotations using subsystems technology BMC Genomics 2008 Feb 8975 https://doi.org/10.1186/1471-2164-9-7510.1186/1471-2164-9-75226569818261238Search in Google Scholar

Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, Weber T. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 2021 Jul 2; 49(W1):W29–W35. https://doi.org/10.1093/nar/gkab335 Blin K Shaw S Kloosterman AM Charlop-Powers Z van Wezel GP Medema MH Weber T antiSMASH 6.0: improving cluster detection and comparison capabilities Nucleic Acids Res 2021 Jul 2 49W1W29 W35 https://doi.org/10.1093/nar/gkab33510.1093/nar/gkab335826275533978755Search in Google Scholar

Boch J, Kempf B, Schmid R, Bremer E. Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis: characterization of the gbsAB genes. J Bacteriol. 1996 Sep;178(17):5121–5129. https://doi.org/10.1128/jb.178.17.5121-5129.1996 Boch J Kempf B Schmid R Bremer E Synthesis of the osmoprotectant glycine betaine in Bacillus subtilis: characterization of the gbsAB genes J Bacteriol 1996 Sep178175121 5129 https://doi.org/10.1128/jb.178.17.5121-5129.199610.1128/jb.178.17.5121-5129.19961783078752328Search in Google Scholar

Bursy J, Kuhlmann AU, Pittelkow M, Hartmann H, Jebbar M, Pierik AJ, Bremer E. Synthesis and uptake of the compatible solutes ectoine and 5-hydroxyectoine by Streptomyces coelicolor A3(2) in response to salt and heat stresses. Appl Environ Microbiol. 2008 Dec; 74(23):7286–7296. https://doi.org/10.1128/AEM.00768-08 Bursy J Kuhlmann AU Pittelkow M Hartmann H Jebbar M Pierik AJ Bremer E Synthesis and uptake of the compatible solutes ectoine and 5-hydroxyectoine by Streptomyces coelicolor A3(2) in response to salt and heat stresses Appl Environ Microbiol 2008 Dec 74237286 7296 https://doi.org/10.1128/AEM.00768-0810.1128/AEM.00768-08259290718849444Search in Google Scholar

Chander AM, Nair RG, Kaur G, Kochhar R, Dhawan DK, Bhadada SK, Mayilraj S. Genome insight and comparative pathogenomic analysis of Nesterenkonia jeotgali strain CD08_7 Isolated from duodenal mucosa of celiac disease patient. Front Microbiol. 2017 Feb 2;8:129. https://doi.org/10.3389/fmicb.2017.00129 Chander AM Nair RG Kaur G Kochhar R Dhawan DK Bhadada SK Mayilraj S Genome insight and comparative pathogenomic analysis of Nesterenkonia jeotgali strain CD08_7 Isolated from duodenal mucosa of celiac disease patient Front Microbiol 2017 Feb 28129 https://doi.org/10.3389/fmicb.2017.0012910.3389/fmicb.2017.00129528833528210247Search in Google Scholar

Chavarría M, Nikel PI, Pérez-Pantoja D, de Lorenzo V. The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress. Environ Microbiol. 2013 Jun; 15(6):1772–17785. https://doi.org/10.1111/1462-2920.12069 Chavarría M Nikel PI Pérez-Pantoja D de Lorenzo V The Entner-Doudoroff pathway empowers Pseudomonas putida KT2440 with a high tolerance to oxidative stress Environ Microbiol 2013 Jun 1561772 17785 https://doi.org/10.1111/1462-2920.1206910.1111/1462-2920.1206923301697Search in Google Scholar

Chen Y, Wang F. Insights on nitrate respiration by Shewanella. Front. Mar. Sci. 2015;1:80. https://doi.org/10.3389/fmars.2014.00080 Chen Y Wang F Insights on nitrate respiration by Shewanella Front. Mar. Sci 2015180 https://doi.org/10.3389/fmars.2014.0008010.3389/fmars.2014.00080Search in Google Scholar

Chole P, Ravi L, Krishnan K. Isolation of thermophilic Actinobacteria from different habitats. In: Dharumadurai D, editor. Methods in Actinobacteriology. Springer Protocols Handbooks. New York (USA): Humana; 2022. https://doi.org/10.1007/978-1-0716-1728-1_23 Chole P Ravi L Krishnan K Isolation of thermophilic Actinobacteria from different habitats. In: Dharumadurai D, editor. Methods in Actinobacteriology. Springer Protocols Handbooks New York (USA) Humana 2022 https://doi.org/10.1007/978-1-0716-1728-1_2310.1007/978-1-0716-1728-1_23Search in Google Scholar

Collins MD, Lawson PA, Labrenz M, Tindall BJ, Weiss N, Hirsch P. Nesterenkonia lacusekhoensis sp. nov. isolated from hypersaline Ekho Lake, East Antarctica, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol. 2002 Jul;52(Pt 4):1145–1150. https://doi.org/10.1099/00207713-52-4-1145 Collins MD Lawson PA Labrenz M Tindall BJ Weiss N Hirsch P Nesterenkonia lacusekhoensis sp nov. isolated from hypersaline Ekho Lake, East Antarctica, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol 2002 Jul52Pt 41145 1150 https://doi.org/10.1099/00207713-52-4-114510.1099/00207713-52-4-114512148619Search in Google Scholar

Dai D, Lu H, Xing P, Wu Q. Comparative genomic analyses of the genus Nesterenkonia unravels the genomic adaptation to polar extreme environments. Microorganisms. 2022 Jan 21;10(2):233. https://doi.org/10.3390/microorganisms10020233 Dai D Lu H Xing P Wu Q Comparative genomic analyses of the genus Nesterenkonia unravels the genomic adaptation to polar extreme environments Microorganisms 2022 Jan 21102233 https://doi.org/10.3390/microorganisms1002023310.3390/microorganisms10020233887537635208688Search in Google Scholar

Delgado O, Quillaguamán J, Bakhtiar S, Mattiasson B, Gessesse A, Hatti-Kaul R. Nesterenkonia aethiopica sp. nov. an alkaliphilic, moderate halophile isolated from an Ethiopian soda lake. Int J Syst Evol Microbiol. 2006 Jun;56(6):1229–1232. https://doi.org/10.1099/ijs.0.63633-0 Delgado O Quillaguamán J Bakhtiar S Mattiasson B Gessesse A Hatti-Kaul R Nesterenkonia aethiopica sp nov. an alkaliphilic, moderate halophile isolated from an Ethiopian soda lake. Int J Syst Evol Microbiol 2006 Jun5661229 1232 https://doi.org/10.1099/ijs.0.63633-010.1099/ijs.0.63633-016738096Search in Google Scholar

Delmont TO, Eren AM. Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ. 2018 Jan 25;6:e4320. https://doi.org/10.7717/peerj.4320 Delmont TO Eren AM Linking pangenomes and metagenomes: the Prochlorococcus metapangenome PeerJ 2018 Jan 256e4320 https://doi.org/10.7717/peerj.432010.7717/peerj.4320580431929423345Search in Google Scholar

Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004 Mar 19;32(5): 1792–1797. https://doi.org/10.1093/nar/gkh340 Edgar RC MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res 2004 Mar 19325 1792 1797 https://doi.org/10.1093/nar/gkh34010.1093/nar/gkh34039033715034147Search in Google Scholar

Edouard S, Sankar S, Dangui NP, Lagier JC, Michelle C, Raoult D, Fournier PE. Genome sequence and description of Nesterenkonia massiliensis sp. nov. strain NP 1(T.). Stand Genomic Sci. 2014 Apr 1; 9(3):866–882. https://doi.org/10.4056/sigs.5631022 Edouard S Sankar S Dangui NP Lagier JC Michelle C Raoult D Fournier PE Genome sequence and description of Nesterenkonia massiliensis sp nov. strain NP 1(T.). Stand Genomic Sci 2014 Apr 1 93866 882 https://doi.org/10.4056/sigs.563102210.4056/sigs.5631022414899125197469Search in Google Scholar

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015 Oct 8;3:e1319. https://doi.org/10.7717/peerj.1319 Eren AM Esen ÖC Quince C Vineis JH Morrison HG Sogin ML Delmont TO Anvi’o: an advanced analysis and visualization platform for ‘omics data PeerJ 2015 Oct 83e1319 https://doi.org/10.7717/peerj.131910.7717/peerj.1319461481026500826Search in Google Scholar

Finore I, Orlando P, Di Donato P, Leone L, Nicolaus B, Poli A. Nesterenkonia aurantiaca sp. nov. an alkaliphilic actinobacterium isolated from Antarctica. Int J Syst Evol Microbiol. 2016 Mar;66(3): 1554–1560. https://doi.org/10.1099/ijsem.0.000917 Finore I Orlando P Di Donato P Leone L Nicolaus B Poli A Nesterenkonia aurantiaca sp nov. an alkaliphilic actinobacterium isolated from Antarctica. Int J Syst Evol Microbiol 2016 Mar663 1554 1560 https://doi.org/10.1099/ijsem.0.00091710.1099/ijsem.0.00091726813578Search in Google Scholar

Frikha-Dammak D, Ayadi H, Hakim-Rekik I, Belbahri L, Maalej S. Genome analysis of the salt-resistant Paludifilum halophilum DSM 102817^T reveals genes involved in flux-tuning of ectoines and unexplored bioactive secondary metabolites. World J Microbiol Biotechnol. 2021 Sep 22;37(10):178. https://doi.org/10.1007/s11274-021-03147-7 Frikha-Dammak D Ayadi H Hakim-Rekik I Belbahri L Maalej S Genome analysis of the salt-resistant Paludifilum halophilum DSM 102817^T reveals genes involved in flux-tuning of ectoines and unexplored bioactive secondary metabolites World J Microbiol Biotechnol 2021 Sep 223710178 https://doi.org/10.1007/s11274-021-03147-710.1007/s11274-021-03147-734549358Search in Google Scholar

Govender L, Naidoo L, Setati ME. Nesterenkonia suensis sp. nov. a haloalkaliphilic actinobacterium isolated from a salt pan. Int J Syst Evol Microbiol. 2013 Jan;63(Pt_1):41–46. https://doi.org/10.1099/ijs.0.035006-0 Govender L Naidoo L Setati ME Nesterenkonia suensis sp nov. a haloalkaliphilic actinobacterium isolated from a salt pan. Int J Syst Evol Microbiol 2013 Jan63Pt_141 46 https://doi.org/10.1099/ijs.0.035006-010.1099/ijs.0.035006-022328610Search in Google Scholar

Grant JR, Arantes AS, Stothard P. Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics. 2012 May 23;13:202. https://doi.org/10.1186/1471-2164-13-202 Grant JR Arantes AS Stothard P Comparing thousands of circular genomes using the CGView Comparison Tool BMC Genomics 2012 May 2313202 https://doi.org/10.1186/1471-2164-13-20210.1186/1471-2164-13-202346935022621371Search in Google Scholar

Guerrero-Garzón JF, Zehl M, Schneider O, Rückert C, Busche T, Kalinowski J, Bredholt H, Zotchev SB. Streptomyces spp. from the marine sponge Antho dichotoma: Analyses of secondary metabolite biosynthesis gene clusters and some of their products. Front Micro-biol. 2020 Mar 18;11:437. https://doi.org/10.3389/fmicb.2020.00437 Guerrero-Garzón JF Zehl M Schneider O Rückert C Busche T Kalinowski J Bredholt H Zotchev SB Streptomyces spp from the marine sponge Antho dichotoma: Analyses of secondary metabolite biosynthesis gene clusters and some of their products. Front Micro-biol 2020 Mar 1811437 https://doi.org/10.3389/fmicb.2020.0043710.3389/fmicb.2020.00437709358732256483Search in Google Scholar

He L, Xiao Y, Gebreselassie N, Zhang F, Antoniewiez MR, Tang YJ, Peng L. Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on ¹³C-metabolic flux analysis. Biotechnol Bioeng. 2014 Mar;111(3):575–585. https://doi.org/10.1002/bit.25124 He L Xiao Y Gebreselassie N Zhang F Antoniewiez MR Tang YJ Peng L Central metabolic responses to the overproduction of fatty acids in Escherichia coli based on ¹³C-metabolic flux analysis Biotechnol Bioeng 2014 Mar1113575 585 https://doi.org/10.1002/bit.2512410.1002/bit.25124590167724122357Search in Google Scholar

Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EE, Sale KL, Keasling JD, Mukhopadhyay A, Tang YJ. Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants. Biotechnol Biofuels. 2016 Oct 10;9:212. https://doi.org/10.1186/s13068-016-0630-y Hollinshead WD Rodriguez S Martin HG Wang G Baidoo EE Sale KL Keasling JD Mukhopadhyay A Tang YJ Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants Biotechnol Biofuels 2016 Oct 109212 https://doi.org/10.1186/s13068-016-0630-y10.1186/s13068-016-0630-y505726127766116Search in Google Scholar

Horikoshi K, Akiba T. Alkalophilic microorganisms: A new microbial world. Tokyo (Japan): Japan Scientific Societies Press; Berlin, Heidelberg (Germany): Springer-Verlag; 1982. Horikoshi K Akiba T Alkalophilic microorganisms: A new microbial world Tokyo (Japan) Japan Scientific Societies Press; Berlin, Heidelberg (Germany): Springer-Verlag; 1982Search in Google Scholar

Horikoshi, K. Production of alkaline enzymes by alkalophilic microorganisms: Part II. Alkaline amylase produced by Bacillus No. A-40-2. Agric Biol Chem. 1971;35(11):1783–1791. https://doi.org/10.1080/00021369.1971.10860143 Horikoshi K Production of alkaline enzymes by alkalophilic microorganisms: Part II Alkaline amylase produced by Bacillus No. A-40-2. Agric Biol Chem 197135111783 1791 https://doi.org/10.1080/00021369.1971.1086014310.1271/bbb1961.36.285Search in Google Scholar

Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018 Nov 30; 9(1): 5114. https://doi.org/10.1038/s41467-018-07641-9 Jain C Rodriguez-R LM Phillippy AM Konstantinidis KT Aluru S High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries Nat Commun 2018 Nov 30 91 5114 https://doi.org/10.1038/s41467-018-07641-910.1038/s41467-018-07641-9626947830504855Search in Google Scholar

Jones BE, Grant WD, Duckworth AW, Schumann P, Weiss N, Stackebrandt E. Cellulomonas bogoriensis sp. nov. an alkaliphilic cellulomonad. Int J Syst Evol Microbiol. 2005 Jul;55(4):1711–1714. https://doi.org/10.1099/ijs.0.63646-0 Jones BE Grant WD Duckworth AW Schumann P Weiss N Stackebrandt E Cellulomonas bogoriensis sp nov. an alkaliphilic cellulomonad. Int J Syst Evol Microbiol 2005 Jul5541711 1714 https://doi.org/10.1099/ijs.0.63646-010.1099/ijs.0.63646-016014506Search in Google Scholar

Kaari M, Baskaran, A, Venugopal G, Manikkam R, Bhaskar PV. Isolation of psychrophilic and psychrotolerant Actinobacteria. In: Dharumadurai D, editor. Methods in Actinobacteriology. Springer Protocols Handbooks. New York (USA): Humana; 2022. https://doi.org/10.1007/978-1-0716-1728-1_21 Kaari M Baskaran A Venugopal G Manikkam R Bhaskar PV Isolation of psychrophilic and psychrotolerant Actinobacteria In Dharumadurai D editor Methods in Actinobacteriology. Springer Protocols Handbooks New York (USA) Humana 2022 https://doi.org/10.1007/978-1-0716-1728-1_2110.1007/978-1-0716-1728-1_21Search in Google Scholar

Koch AL. Were Gram-positive rods the first bacteria? Trends Micro-biol. 2003 Apr; 11(4):166–170. https://doi.org/10.1016/s0966-842x(03)00063-5 Koch AL Were Gram-positive rods the first bacteria? Trends Micro-biol 2003 Apr 114166 170 https://doi.org/10.1016/s0966-842x(03)00063-510.1016/S0966-842X(03)00063-5Search in Google Scholar

Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets. Mol Biol Evol. 2016 Jul;33(7):1870–1874. https://doi.org/10.1093/molbev/msw054 Kumar S Stecher G Tamura K MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for bigger datasets Mol Biol Evol 2016 Jul3371870 1874 https://doi.org/10.1093/molbev/msw05410.1093/molbev/msw054Search in Google Scholar

Li WJ, Chen HH, Kim CJ, Zhang YQ, Park DJ, Lee JC, Xu LH, Jiang CL. Nesterenkonia sandarakina sp. nov. and Nesterenkonia lutea sp. nov. novel actinobacteria, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol. 2005 Jan;55(1):463–466. https://doi.org/10.1099/ijs.0.63281-0 Li WJ Chen HH Kim CJ Zhang YQ Park DJ Lee JC Xu LH Jiang CL Nesterenkonia sandarakina sp nov. and Nesterenkonia lutea sp. nov. novel actinobacteria, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol 2005 Jan551463 466 https://doi.org/10.1099/ijs.0.63281-010.1099/ijs.0.63281-0Search in Google Scholar

Li WJ, Zhang YQ, Schumann P, Liu HY, Yu LY, Zhang YQ, Stackebrandt E, Xu LH, Jiang CL. Nesterenkonia halophila sp. nov. a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil. Int J Syst Evol Microbiol. 2008 Jun;58(6):1359–1363. https://doi.org/10.1099/ijs.0.64226-0 Li WJ Zhang YQ Schumann P Liu HY Yu LY Zhang YQ Stackebrandt E Xu LH Jiang CL Nesterenkonia halophila sp nov. a moderately halophilic, alkalitolerant actinobacterium isolated from a saline soil. Int J Syst Evol Microbiol 2008 Jun5861359 1363 https://doi.org/10.1099/ijs.0.64226-010.1099/ijs.0.64226-0Search in Google Scholar

Liu GH, Narsing Rao MP, Dong ZY, Wang JP, Che JM, Chen QQ, Sengonca C, Liu B, Li WJ. Genome-based reclassification of Bacillus plakortidis Borchert et al. 2007 and Bacillus lehensis Ghosh et al. 2007 as a later heterotypic synonym of Bacillus oshimensis Yumoto et al. 2005; Bacillus rhizosphaerae Madhaiyan et al. 2011 as a later heterotypic synonym of Bacillus clausii Nielsen et al. 1995. Antonie Van Leeuwenhoek. 2019 Dec;112(12):1725–1730. https://doi.org/10.1007/s10482-019-01299-z Liu GH Narsing Rao MP Dong ZY Wang JP Che JM Chen QQ Sengonca C Liu B Li WJ Genome-based reclassification of Bacillus plakortidis Borchert et al. 2007 and Bacillus lehensis Ghosh et al. 2007 as a later heterotypic synonym of Bacillus oshimensis Yumoto et al. 2005; Bacillus rhizosphaerae Madhaiyan et al. 2011 as a later heterotypic synonym of Bacillus clausii Nielsen et al. 1995 Antonie Van Leeuwenhoek 2019 Dec112121725 1730 https://doi.org/10.1007/s10482-019-01299-z10.1007/s10482-019-01299-zSearch in Google Scholar

Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer rna genes in genomic sequence. Nucleic Acids Res. 1997 Mar; 25(5):955–964. https://doi.org/10.1093/nar/25.5.955 Lowe TM Eddy SR tRNAscan-SE: A program for improved detection of transfer rna genes in genomic sequence Nucleic Acids Res 1997 Mar 255955 964 https://doi.org/10.1093/nar/25.5.95510.1093/nar/25.5.955Search in Google Scholar

Machin EV, Asem MD, Salam N, Iriarte A, Langleib M, Li WJ, Menes RJ. Nesterenkonia natronophila sp. nov. an alkaliphilic actinobacterium isolated from a soda lake, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol. 2019 Jul;69(7): 1960–1966. https://doi.org/10.1099/ijsem.0.003409 Machin EV Asem MD Salam N Iriarte A Langleib M Li WJ Menes RJ Nesterenkonia natronophila sp nov. an alkaliphilic actinobacterium isolated from a soda lake, and emended description of the genus Nesterenkonia. Int J Syst Evol Microbiol 2019 Jul697 1960 1966 https://doi.org/10.1099/ijsem.0.00340910.1099/ijsem.0.003409Search in Google Scholar

Martín J, da S Sousa T, Crespo G, Palomo S, González I, Tormo JR, de la Cruz M, Anderson M, Hill RT, Vicente F, et al. Kocurin, the true structure of PM181104, an anti-methicillin-resistant Staphylococcus aureus (MRSA) thiazolyl peptide from the marine-derived bacterium Kocuria palustris. Mar Drugs. 2013 Feb 4;11(2):387–398. https://doi.org/10.3390/md11020387 Martín J da S Sousa T Crespo G Palomo S González I Tormo JR de la Cruz M Anderson M Hill RT Vicente F et al Kocurin, the true structure of PM181104, an anti-methicillin-resistant Staphylococcus aureus (MRSA) thiazolyl peptide from the marine-derived bacterium Kocuria palustris Mar Drugs 2013 Feb 4112387 398 https://doi.org/10.3390/md1102038710.3390/md11020387Search in Google Scholar

Martínez-Espinosa RM, Marhuenda-Egea FC, Bonete MJ. Assimilatory nitrate reductase from the haloarchaeon Haloferax mediterranei: purification and characterisation. FEMS Microbiol Lett. 2001 Nov 13;204(2):381–385. https://doi.org/10.1016/s0378-1097(01)00431-1 Martínez-Espinosa RM Marhuenda-Egea FC Bonete MJ Assimilatory nitrate reductase from the haloarchaeon Haloferax mediterranei: purification and characterisation FEMS Microbiol Lett 2001 Nov 132042381 385 https://doi.org/10.1016/s0378-1097(01)00431-110.1016/S0378-1097(01)00431-1Search in Google Scholar

Mehta VJ, Thumar JT, Singh SP. Production of alkaline protease from an alkaliphilic actinomycete. Bioresour Technol. 2006 Sep; 97(14): 1650–1654. https://doi.org/10.1016/j.biortech.2005.07.023 Mehta VJ Thumar JT Singh SP Production of alkaline protease from an alkaliphilic actinomycete Bioresour Technol 2006 Sep 9714 1650 1654 https://doi.org/10.1016/j.biortech.2005.07.02310.1016/j.biortech.2005.07.02316203132Search in Google Scholar

Narsing Rao MP, Li YQ, Zhang H, Dong ZY, Dhulappa A, Xiao M, Li WJ. Amycolatopsis alkalitolerans sp. nov. isolated from Gastrodia elata Blume. J Antibiot (Tokyo). 2020 Jan;73(1):35–39. https://doi.org/10.1038/s41429-019-0222-8 Narsing Rao MP Li YQ Zhang H Dong ZY Dhulappa A Xiao M Li WJ Amycolatopsis alkalitolerans sp nov. isolated from Gastrodia elata Blume. J Antibiot (Tokyo) 2020 Jan73135 39 https://doi.org/10.1038/s41429-019-0222-810.1038/s41429-019-0222-831434994Search in Google Scholar

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul; 25(7):1043–1055. https://doi.org/10.1101/gr.186072.114 Parks DH Imelfort M Skennerton CT Hugenholtz P Tyson GW CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Genome Res 2015 Jul 2571043 1055 https://doi.org/10.1101/gr.186072.11410.14264/uql.2016.841Search in Google Scholar

Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol. 2020 Nov; 70(11):5607–5612. https://doi.org/10.1099/ijsem.0.004332 Parte AC Sardà Carbasse J Meier-Kolthoff JP Reimer LC Göker M List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ Int J Syst Evol Microbiol 2020 Nov 70115607 5612 https://doi.org/10.1099/ijsem.0.00433210.1099/ijsem.0.004332772325132701423Search in Google Scholar

Pastor JM, Salvador M, Argandoña M, Bernal V, Reina-Bueno M, Csonka LN, Iborra JL, Vargas C, Nieto JJ, Cánovas M. Ectoines in cell stress protection: Uses and biotechnological production. Biotechnol Adv. 2010 Nov-Dec;28(6):782–801. https://doi.org/10.1016/j.biotechadv.2010.06.005 Pastor JM Salvador M Argandoña M Bernal V Reina-Bueno M Csonka LN Iborra JL Vargas C Nieto JJ Cánovas M Ectoines in cell stress protection: Uses and biotechnological production Biotechnol Adv 2010 Nov-Dec286782 801 https://doi.org/10.1016/j.biotechadv.2010.06.00510.1016/j.biotechadv.2010.06.00520600783Search in Google Scholar

Patra T, Koley H, Ramamurthy T, Ghose AC, Nandy RK. The Entner-Doudoroff pathway is obligatory for gluconate utilization and contributes to the pathogenicity of Vibrio cholerae. J Bacteriol. 2012 Jul;194(13):3377–3385. https://doi.org/10.1128/JB.06379-11 Patra T Koley H Ramamurthy T Ghose AC Nandy RK The Entner-Doudoroff pathway is obligatory for gluconate utilization and contributes to the pathogenicity of Vibrio cholerae J Bacteriol 2012 Jul194133377 3385 https://doi.org/10.1128/JB.06379-1110.1128/JB.06379-11343474022544275Search in Google Scholar

Prabhu DM, Quadri SR, Cheng J, Liu L, Chen W, Yang Y, Hozzein WN, Lingappa K, Li WJ. Sinomonas mesophila sp. nov. isolated from ancient fort soil. J Antibiot (Tokyo). 2015;68(5):318–321. https://doi.org/10.1038/ja.2014.161 Prabhu DM Quadri SR Cheng J Liu L Chen W Yang Y Hozzein WN Lingappa K Li WJ Sinomonas mesophila sp nov. isolated from ancient fort soil. J Antibiot (Tokyo) 2015685318 321 https://doi.org/10.1038/ja.2014.16110.1038/ja.2014.16125464972Search in Google Scholar

Preiss L, Hicks DB, Suzuki S, Meier T, Krulwich TA. Alkaliphilic bacteria with impact on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis. Front Bioeng Biotechnol. 2015 Jun 3;3:75. https://doi.org/10.3389/fbioe.2015.00075 Preiss L Hicks DB Suzuki S Meier T Krulwich TA Alkaliphilic bacteria with impact on industrial applications, concepts of early life forms, and bioenergetics of ATP synthesis Front Bioeng Biotechnol 2015 Jun 3375 https://doi.org/10.3389/fbioe.2015.0007510.3389/fbioe.2015.00075445347726090360Search in Google Scholar

Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK.Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods. 2016 Nov; 8(1):12–24. https://doi.org/10.1039/C5AY02550H Pritchard L Glover RH Humphris S Elphinstone JG Toth IK Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens Anal Methods 2016 Nov 8112 24 https://doi.org/10.1039/C5AY02550H10.1039/C5AY02550HSearch in Google Scholar

Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA. 2009 Nov 10;106(45):19126–19131. https://doi.org/10.1073/pnas.0906412106 Richter M Rosselló-Móra R Shifting the genomic gold standard for the prokaryotic species definition Proc Natl Acad Sci USA 2009 Nov 101064519126 19131 https://doi.org/10.1073/pnas.090641210610.1073/pnas.0906412106277642519855009Search in Google Scholar

Rytter H, Jamet A, Ziveri J, Ramond E, Coureuil M, Lagouge-Roussey P, Euphrasie D, Tros F, Goudin N, Chhuon C, et al. The pentose phosphate pathway constitutes a major metabolic hub in pathogenic Francisella. PLoS Pathog. 2021 Aug 2;17(8):e1009326. https://doi.org/10.1371/journal.ppat.1009326 Rytter H Jamet A Ziveri J Ramond E Coureuil M Lagouge-Roussey P Euphrasie D Tros F Goudin N Chhuon C et al The pentose phosphate pathway constitutes a major metabolic hub in pathogenic Francisella PLoS Pathog 2021 Aug 2178e1009326 https://doi.org/10.1371/journal.ppat.100932610.1371/journal.ppat.1009326836058834339477Search in Google Scholar

Sadeghi A, Soltani BM, Nekouei MK, Jouzani GS, Mirzaei HH, Sadeghizadeh M. Diversity of the ectoines biosynthesis genes in the salt tolerant Streptomyces and evidence for inductive effect of ectoines on their accumulation. Microbiol Res. 2014 Sep-Oct; 169(9–10):699–708. https://doi.org/10.1016/j.micres.2014.02.005 Sadeghi A Soltani BM Nekouei MK Jouzani GS Mirzaei HH Sadeghizadeh M Diversity of the ectoines biosynthesis genes in the salt tolerant Streptomyces and evidence for inductive effect of ectoines on their accumulation Microbiol Res 2014 Sep-Oct 1699–10699 708 https://doi.org/10.1016/j.micres.2014.02.00510.1016/j.micres.2014.02.00524629523Search in Google Scholar

Sarethy IP, Saxena Y, Kapoor A, Sharma M, Sharma SK, Gupta V, Gupta S. Alkaliphilic bacteria: applications in industrial biotechnology. J Ind Microbiol Biotechnol. 2011 Jul;38(7):769–790. https://doi.org/10.1007/s10295-011-0968-x Sarethy IP Saxena Y Kapoor A Sharma M Sharma SK Gupta V Gupta S Alkaliphilic bacteria: applications in industrial biotechnology J Ind Microbiol Biotechnol 2011 Jul387769 790 https://doi.org/10.1007/s10295-011-0968-x10.1007/s10295-011-0968-x21479938Search in Google Scholar

Shafiei M, Ziaee AA, Amoozegar MA. Purification and characterization of a halophilic α-amylase with increased activity in the presence of organic solvents from the moderately halophilic Nesterenkonia sp. strain F. Extremophiles. 2012 Jul;16(4):627–635. https://doi.org/10.1007/s00792-012-0462-z Shafiei M Ziaee AA Amoozegar MA Purification and characterization of a halophilic α-amylase with increased activity in the presence of organic solvents from the moderately halophilic Nesterenkonia sp strain F. Extremophiles 2012 Jul164627 635 https://doi.org/10.1007/s00792-012-0462-z10.1007/s00792-012-0462-z22592324Search in Google Scholar

Shafiei M, Ziaee AA, Amoozegar MA. Purification and characterization of an organic-solvent-tolerant halophilic α-amylase from the moderately halophilic Nesterenkonia sp. strain F. J Ind Microbiol Biotechnol. 2011 Feb;38(2):275–281. https://doi.org/10.1007/s10295-010-0770-1 Shafiei M Ziaee AA Amoozegar MA Purification and characterization of an organic-solvent-tolerant halophilic α-amylase from the moderately halophilic Nesterenkonia sp strain F. J Ind Microbiol Biotechnol 2011 Feb382275 281 https://doi.org/10.1007/s10295-010-0770-110.1007/s10295-010-0770-120593298Search in Google Scholar

Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actino-bacteria: biology and potential applications. Front Microbiol. 2015 Sep 25;6:1014. https://doi.org/10.3389/fmicb.2015.01014 Shivlata L Satyanarayana T Thermophilic and alkaliphilic Actino-bacteria: biology and potential applications Front Microbiol 2015 Sep 2561014 https://doi.org/10.3389/fmicb.2015.0101410.3389/fmicb.2015.01014458525026441937Search in Google Scholar

Silver S, Walderhaug M. Gene regulation of plasmid- and chromosome-determined inorganic ion transport in bacteria. Microbiol Rev. 1992 Mar;56(1):195–228. https://doi.org/10.1128/mr.56.1.195-228.1992 Silver S Walderhaug M Gene regulation of plasmid- and chromosome-determined inorganic ion transport in bacteria Microbiol Rev 1992 Mar561195 228 https://doi.org/10.1128/mr.56.1.195-228.199210.1128/mr.56.1.195-228.19923728611579110Search in Google Scholar

Stackebrandt E, Koch C, Gvozdiak O, Schumann P. Taxonomic dissection of the genus Micrococcus Kocuria gen. nov. Nesterenkonia gen. nov. Kytococcus gen. nov. Dermacoccus gen. nov. and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol. 1995;45(4):682–692. https://doi.org/10.1099/00207713-45-4-682 Stackebrandt E Koch C Gvozdiak O Schumann P Taxonomic dissection of the genus Micrococcus Kocuria gen nov. Nesterenkonia gen. nov. Kytococcus gen. nov. Dermacoccus gen. nov. and Micrococcus Cohn 1872 gen. emend. Int J Syst Bacteriol. 1995454682 692 https://doi.org/10.1099/00207713-45-4-68210.1099/00207713-45-4-6827547287Search in Google Scholar

Taber WA. Evidence for the existence of acid-sensitive actinomycetes in soil. Can J Microbiol. 1960 Oct;6(5):534–544. https://doi.org/10.1139/m60-058 Taber WA Evidence for the existence of acid-sensitive actinomycetes in soil Can J Microbiol 1960 Oct65534 544 https://doi.org/10.1139/m60-05810.1139/m60-058Search in Google Scholar

Thumar JT, Dhulia K, Singh SP. Isolation and partial purification of an antimicrobial agent from halotolerant alkaliphilic Streptomyces aburaviensis strain Kut-8. World J Microbiol Biotechnol. 2010 Mar; 26:2081–2087. https://doi.org/10.1007/s11274-010-0394-7 Thumar JT Dhulia K Singh SP Isolation and partial purification of an antimicrobial agent from halotolerant alkaliphilic Streptomyces aburaviensis strain Kut-8 World J Microbiol Biotechnol 2010 Mar 262081 2087 https://doi.org/10.1007/s11274-010-0394-710.1007/s11274-010-0394-7Search in Google Scholar

van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. In: van Helden J, Toussaint A, Thieffry D, editors. Bacterial molecular networks. Methods in molecular biology, vol. 804. New York (USA): Springer; 2012. p. 281–295. https://doi.org/10.1007/978-1-61779-361-5_15 van Dongen S Abreu-Goodger C Using MCL to extract clusters from networks. In: van Helden J, Toussaint A, Thieffry D, editors. Bacterial molecular networks. Methods in molecular biology, vol. 804 New York (USA) Springer 2012 p 281–295 https://doi.org/10.1007/978-1-61779-361-5_1510.1007/978-1-61779-361-5_1522144159Search in Google Scholar

Wang HF, Zhang YG, Chen JY, Hozzein WN, Li L, Wadaan MAM, Zhang YM, Li WJ. Nesterenkonia rhizosphaerae sp. nov. an alkaliphilic actinobacterium isolated from rhizosphere soil in a saline-alkaline desert. Int J Syst Evol Microbiol. 2014 Dec;64(Pt_12):4021–4026. https://doi.org/10.1099/ijs.0.066894-0 Wang HF Zhang YG Chen JY Hozzein WN Li L Wadaan MAM Zhang YM Li WJ Nesterenkonia rhizosphaerae sp nov. an alkaliphilic actinobacterium isolated from rhizosphere soil in a saline-alkaline desert. Int J Syst Evol Microbiol 2014 Dec64Pt_124021 4026 https://doi.org/10.1099/ijs.0.066894-010.1099/ijs.0.066894-025225260Search in Google Scholar

Wang S, Sun L, Wei D, Salam N, Fang BZ, Dong ZY, Hao XY, Zhang M, Zhang Z, Li WJ. Nesterenkonia haasae sp. nov. an alkaliphilic actinobacterium isolated from a degraded pasture in Songnen Plain. Arch Microbiol. 2021 Apr;203(3):959–966. https://doi.org/10.1007/s00203-020-02073-w Wang S Sun L Wei D Salam N Fang BZ Dong ZY Hao XY Zhang M Zhang Z Li WJ Nesterenkonia haasae sp nov. an alkaliphilic actinobacterium isolated from a degraded pasture in Songnen Plain. Arch Microbiol 2021 Apr2033959 966 https://doi.org/10.1007/s00203-020-02073-w10.1007/s00203-020-02073-w33104820Search in Google Scholar

Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, Goh KM. Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses. Sci Rep. 2016 Sep 19;6:33660. https://doi.org/10.1038/srep33660 Yaakop AS Chan KG Ee R Lim YL Lee SK Manan FA Goh KM Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses Sci Rep 2016 Sep 19633660 https://doi.org/10.1038/srep3366010.1038/srep33660502756527641516Search in Google Scholar

Yoon JH, Jung SY, Kim W, Nam SW, Oh TK. Nesterenkonia jeotgali sp. nov. isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol. 2006 Nov;56(11):2587–2592. https://doi.org/10.1099/ijs.0.64266-0 Yoon JH Jung SY Kim W Nam SW Oh TK Nesterenkonia jeotgali sp nov. isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2006 Nov56112587 2592 https://doi.org/10.1099/ijs.0.64266-010.1099/ijs.0.64266-017082396Search in Google Scholar

Zheng Z, Gao S, He Y, Li Z, Li Y, Cai X, Gu W, Wang G. The enhancement of the oxidative pentose phosphate pathway maybe involved in resolving imbalance between photosystem I and II in Dunaliella salina Algal Res. 2017 Sep;26:402–408. https://doi.org/10.1016/j.algal.2017.07.024 Zheng Z Gao S He Y Li Z Li Y Cai X Gu W Wang G The enhancement of the oxidative pentose phosphate pathway maybe involved in resolving imbalance between photosystem I and II in Dunaliella salina Algal Res 2017 Sep26402 408 https://doi.org/10.1016/j.algal.2017.07.02410.1016/j.algal.2017.07.024Search in Google Scholar

Zhu D, Liu J, Han R, Shen G, Long Q, Wei X, Liu D. Identification and characterization of ectoine biosynthesis genes and heterologous expression of the ectABC gene cluster from Halomonas sp. QHL1, a moderately halophilic bacterium isolated from Qinghai Lake. J Microbiol. 2014 Feb;52(2):139–147. https://doi.org/10.1007/s12275-014-3389-5 Zhu D Liu J Han R Shen G Long Q Wei X Liu D Identification and characterization of ectoine biosynthesis genes and heterologous expression of the ectABC gene cluster from Halomonas sp QHL1, a moderately halophilic bacterium isolated from Qinghai Lake. J Microbiol 2014 Feb522139 147 https://doi.org/10.1007/s12275-014-3389-510.1007/s12275-014-3389-524500478Search in Google Scholar