Abstract
The taxonomic position of a filamentous actinobacterial strain, isolate H45T, recovered from a high altitude Atacama Desert gravel soil, was established using a polyphasic approach. The strain, which is known to produce novel dienes, has chemotaxonomic and morphological properties typical of the genus Lentzea and formed a distinct branch in the Lentzea 16S rRNA gene tree that is closely related to the type strain of Lentzea kentuckyensis. The two strains were distinguished using a combination of phenotypic properties and by a DNA:DNA relatedness value of 37.6 ± 4.0%. On the basis of these genotypic and phenotypic data it is proposed that isolate H45T (=NCIMB 4966T = NRRL B-65282T) be classified in the genus Lentzea as Lentzea chajnantorensis sp. nov.
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Bull AT, Asenjo JA, Goodfellow M, Gómez-Silva B (2016) The Atacama Desert: technical resources and the growing importance of novel microbial diversity. Ann Rev Microbiol 70:215–234. doi:10.1146/annurev-micro-102215-095236
Busarakam K, Bull AT, Girard G, Labeda DP, van Wezel GP, Goodfellow M (2014) Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees. Antonie Van Leeuwenhoek 105:849–861. doi:10.1007/s10482-014-0139-y
Cao C, Zhou X, Qin S, Tao F, Jiang J, Lian B (2015) Lentzea guizhouensis sp. nov., a novel lithophilous actinobacterium isolated from limestone from the Karst area, Guizhou. China Antonie van Leeuwenhoek 108:1365–1372. doi:10.1007/s10482-015-0589-x
Cashion P, Holder-Franklin MA, McCully J, Franklin M (1977) A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466. doi:10.1016/0003-2697(77)90720-5
Collins MD, Goodfellow M, Minnikin DE, Alderson G (1985) Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 58:77–86. doi:10.1111/j.1365-2672.1985.tb01431.x
De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133–142. doi:10.1111/j.1432-1033.1970.tb00830.x
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184–192. doi:10.1016/S0723-2020(83)80048-4
Kim SB, Goodfellow M (2002) Streptomyces thermospinisporus sp. nov., a moderately thermophilic carboxydotrophic streptomycete isolated from soil. Int J Syst Evol Microbiol 52:1225–1228. doi:10.1099/00207713-52-4-1225
Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Kuykendall LD, Roy MA, O’Neill JJ, Devine TE (1988) Fatty acids, antibiotic resistance and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Evolut Microbiol 38:358–361. doi:10.1099/00207713-38-4-358
Labeda DP (2012) Genus XI. Lentzea Yassin, Rainey, Brzezinka, Jahnke, Weissbrodt, Budzikiewicz, Stackebrandt, and Schaal 1995, 362vp emend. Labeda, Hatano, Kroppenstedt and Tamura 2001, 1049. In: Goodfellow M, Kämpfer P, Busse H, Trujillo ME, Suzuki K, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5. The Actinobacteria, Part B, Springer, New York, pp 1379–1383
Labeda DP, Goodfellow M (2012) Family I. Pseudonocardiaceae Embley, Smida, and Stackebrandt 1989, 205vp emend. Labeda, Goodfellow, Chun, Zhi and Li 2010a). In: Goodfellow M, Kämpfer P, Busse H, Trujillo ME, Suzuki K, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn. The Actinobacteria, Part B, Springer, New York, pp 1302–1305
Labeda DP, Hatano K, Kroppenstedt RM, Tamura T (2001) Revival of the genus Lentzea and proposal for Lechevalieria gen. nov. Int J Syst Evolut Microbiol 51:1045–1050. doi:10.1099/00207713-51-3-1045
Labeda DP, Donahue JM, Sells S, Kroppenstedt RM (2007) Lentzea kentuckyensis sp. nov., of equine origin. Int J Syst Evol Microbiol 57:1780–1783
Lechevalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 2:435–443
Lee SD, Kim ES, Roe JH, Kim JH, Kang SO, Hah YC (2000) Saccharothrix violacea sp. nov., isolated from a gold mine cave, and Saccharothrix albidocapillata comb. nov. Int J Syst Evol Microbiol 50:1315–1323
Miller LT (1982) Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 16:584–586
Minnikin DE, Alshamaony L, Goodfellow M (1975) Differentiation of Mycobacterium, Nocardia and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 88:200–204
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Murray PR, Baron EJ, Pfalter MA, Tenover FC, Yolken RH (1999) Manual of Clinical Microbiology, 7th edn. ASM Press, Washington
O’Donnell AG, Falconer C, Goodfellow M, Ward AC, Williams E (1993) Biosystematics and diversity amongst novel carboxydotrophic actinomycetes. Antonie Van Leeuwenhoek 64:325–340. doi:10.1007/BF00873091
Okoro CK, Bull AT, Mutreja A, Rong X, Huang Y, Goodfellow M (2010) Lechevalieria atacamensis sp. nov., Lechevalieria deserti sp. nov. and Lechevalieria roselyniae sp. nov., isolated from hyperarid soils. Int J Syst Evol Microbiol 60:296–300
Sasamura S, Kobayashi M, Muramatsu H, Yoshimura S, Kinoshita T, Ohki H, Okada K, Deai Y, Yamagishi Y, Hashimoto M (2015) Bioconversion of FR901459, a novel derivative of cyclosporin A, by Lentzea sp. 7887. J Antibiot 68:511–520. doi:10.1038/ja.2015.19
Sasser MJ (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Microbial ID Inc, Newark
Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340
Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Vaas LAI, Sikorski J, Michael V, Göker M, Klenk HP (2012) Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS ONE 7:e34846. doi:10.1371/journal.pone.0034846
Vaas LAI, Sikorski J, Hofner B, Fiebig A, Buddruhs N, Klenk HP, Göker M (2013) opm: an R package for analysing OmniLog® phenotype microarray data. Bioinformatics. doi:10.1093/bioinformatics/btt291
Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464. doi:10.1099/00207713-37-4-463
Wichner D, Idris H, Houssen WE, McEwan AR, Bull AT, Asenjo JA, Goodfellow M, Jaspars M, Ebel R, Rateb ME (2017) Isolation and anti-HIV-1 integrase activity of lentzeosides A-F from extremotolerant Lentzea sp. H45, a strain isolated from a high-altitude Atacama Desert soil. J Antibiot (Tokyo)
Williams ST, Goodfellow M, Alderson G, Wellington EMH, Sneath PHA, Sackin MJ (1983) Numerical classification of Streptomyces and related genera. J Gen Microbiol 129:1743–1813
Yassin AF, Rainey FA, Brzezinka H, Jahnke KD, Weissbrodt H, Budzikiewicz H, Stackebrandt E, Schaal KP (1995) Lentzea gen. nov., a new genus of the order Actinomycetales. Int J Syst Evol Microbiol 45:357–363. doi:10.1099/00207713-45-2-357
Yoon, SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol
Yuan LJ, Zhang YQ, Yu LY, Liu HY, Guan Y, Lee JC, Kim CJ, Zhang YQ (2010) Alloactinosynnema album gen. nov., sp. nov., a member of the family Actinosynnemataceae isolated from soil. Int J Syst Evol Microbiol 60:39–43. doi:10.1099/ijs.0.010744-0
Zakharova OS, Zenova GM, Zvyagintsev DG (2003) Some approaches to the selective isolation of actinomycetes of the genus Actinomadura from soil. Microbiology 72:110–113. doi:10.1023/A:1022294526830
Zhang J, Xie Q, Liu Z, Goodfellow M (2007) Lechevalieria fradiae sp. nov., a novel actinomycete isolated from soil in China. Int J Syst Evol Microbiol 57:832–836
Acknowledgements
This study was partly funded through a UK Newton Project for UK-Chile collaboration (T I CCA 586). Thanks are due to the staff of the European Southern Observatory for permission and assistance in collecting soil samples from Cerro Chajnantor. H.I. is indebted to the Malaysian Government for a Ph.D. scholarship and M.G. for an Emeritus Fellowship from the Leverhulme Trust. The authors are indebted to Dr. Maria del Carmen Montero-Calasanz for help in interpreting the BIOLOG data.
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Idris, H., Nouioui, I., Asenjo, J.A. et al. Lentzea chajnantorensis sp. nov., an actinobacterium from a very high altitude Cerro Chajnantor gravel soil in northern Chile. Antonie van Leeuwenhoek 110, 795–802 (2017). https://doi.org/10.1007/s10482-017-0851-5
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DOI: https://doi.org/10.1007/s10482-017-0851-5