Pseudonocardia humida sp. nov., an Actinomycete Isolated from Mangrove Soil Showing Distinct Distribution Pattern of Biosynthetic Gene Clusters.
Journal
Current microbiology
ISSN: 1432-0991
Titre abrégé: Curr Microbiol
Pays: United States
ID NLM: 7808448
Informations de publication
Date de publication:
07 Feb 2022
07 Feb 2022
Historique:
received:
02
11
2021
accepted:
24
01
2022
entrez:
7
2
2022
pubmed:
8
2
2022
medline:
10
2
2022
Statut:
epublish
Résumé
A novel actinomycete strain, designated S2-4
Identifiants
pubmed: 35129703
doi: 10.1007/s00284-022-02784-x
pii: 10.1007/s00284-022-02784-x
doi:
Substances chimiques
DNA, Bacterial
0
Fatty Acids
0
Phospholipids
0
RNA, Ribosomal, 16S
0
Soil
0
Vitamin K 2
11032-49-8
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
87Subventions
Organisme : Natural Science Foundation of Jiangsu Province
ID : BK20190703
Informations de copyright
© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Henssen A (1957) Beiträge zur Morphologie und Systematik der thermophilen Actinomyceten. Archiv Mikrobiol 26:373–414. https://doi.org/10.1007/BF00407588
doi: 10.1007/BF00407588
Warwick S, Bowen T, Mcveigh H, Embley TM (1994) A phylogenetic analysis of the family Pseudonocardiaceae and the genera Actinokineospora and Saccharothrix with 16S rRNA sequences and a proposal to combine the genera Amycolata and Pseudonocardia in an emended genus Pseudonocardia. Int J Syst Bacteriol 44(2):293–299. https://doi.org/10.1099/00207713-44-2-293
doi: 10.1099/00207713-44-2-293
pubmed: 8186093
Reichert K, Lipski A, Pradella S, Stackebrandt E, Altendorf K (1998) Pseudonocardia asaccharolytica sp. nov. and Pseudonocardia sulfidoxydans sp. nov., two new dimethyl disulfide-degrading actinomycetes and emended description of the genus Pseudonocardia. Int J Syst Bacteriol 48(2):441–449. https://doi.org/10.1099/00207713-48-2-441
Huang Y, Wang L, Lu Z, Hong L, Liu ZH, Tan GYA, Goodfellow M (2002) Proposal to combine the genera Actinobispora and Pseudonocardia in an emended genus Pseudonocardia, and description of Pseudonocardia zijingensis sp. nov.. Int J Syst Evol Microbiol 52(3):977–982. https://doi.org/10.1099/00207713-52-3-977
Park SW, Park ST, Lee JE, Kim YM (2008) Pseudonocardia carboxydivorans sp. nov., a carbon monoxide-oxidizing actinomycete, and an emended description of the genus Pseudonocardia. Int J Syst Evol Microbiol 58:2475–2478. https://doi.org/10.1099/ijs.0.65765-0
doi: 10.1099/ijs.0.65765-0
pubmed: 18984679
Huang Y, Goodfellow M (2015) Pseudonocardia. In: Trujillo ME, Dedysh S, DeVos P, Hedlund B, Kämpfer P, Rainey FA, Whitman WB (eds) Bergey’s Manual of Systematics of Archaea and Bacteria. Wiley, New Jersey, pp 1–32 https://doi.org/10.1002/9781118960608.gbm00184
Parte AC, Carbasse JS, Meier-Kolthoff JP, Reimer LC, Göker M (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612. https://doi.org/10.1099/ijsem.0.004332
doi: 10.1099/ijsem.0.004332
pubmed: 32701423
pmcid: 7723251
Grostern A, Alvarez-Cohen L (2013) RubisCO-based CO
doi: 10.1111/1462-2920.12144
pubmed: 23663433
Inoue D, Tsunoda T, Sawada K, Yamamoto N, Saito Y, Sei K, Ike M (2016) 1,4-Dioxane degradation potential of members of the genera Pseudonocardia and Rhodococcus. Biodegradation 27(4–6):277–286. https://doi.org/10.1007/s10532-016-9772-7
doi: 10.1007/s10532-016-9772-7
pubmed: 27623820
Ding T, Yang LJ, Zhang WD, Shen YH (2019) The secondary metabolites of rare actinomycetes: chemistry and bioactivity. RSC Adv 9(38):21964–21988. https://doi.org/10.1039/C9RA03579F
doi: 10.1039/C9RA03579F
Demain AL, Fang A (2001) The natural functions of secondary metabolites. In: Fiechter A (ed) History of modern biotechnology I, Avd Biochem Eng Biot. Springer, Berlin
van Bergeijk DA, Terlouw BR, Medema MH, van Wezel GP (2020) Ecology and genomics of Actinobacteria: new concepts for natural product discovery. Nat Rev Microbiol 18(10):546–558. https://doi.org/10.1038/s41579-020-0379-y
doi: 10.1038/s41579-020-0379-y
pubmed: 32483324
Huang RR, Yang SR, Zhen C, Ge XF, Chen XK, Wen ZQ, Li YN, Liu WZ (2021) Genomic molecular signatures determined characterization of Mycolicibacterium gossypii sp. nov., a fast-growing mycobacterial species isolated from cotton field soil. Antonie Van Leeuwenhoek 114:1735–1744. https://doi.org/10.1007/s10482-021-01638-z
doi: 10.1007/s10482-021-01638-z
pubmed: 34392432
Monciardini P, Sosio M, Cavaletti L, Chiocchini C, Donadio S (2002) New PCR primers for the selective amplification of 16S rDNA from different groups of actinomycetes. FEMS Microbiol Ecol 42:419–429. https://doi.org/10.1111/j.1574-6941.2002.tb01031.x
doi: 10.1111/j.1574-6941.2002.tb01031.x
pubmed: 19709301
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 67:1613–1617. https://doi.org/10.1099/ijsem.0.001755
doi: 10.1099/ijsem.0.001755
pubmed: 5563544
pmcid: 5563544
Patnaik BB, Park SY, Kang SW, Hwang HJ, Wang TH, Park EB, Chung JM, Song DK, Kim C, Kim S, Lee JB, Jeong HC, Park HS, Han YS, Lee YS (2016) Transcriptome profile of the Asian Giant Hornet (Vespa mandarinia) using Illumina HiSeq 4000 sequencing: De Novo assembly, functional annotation, and discovery of SSR markers. Int J Genomics 2016:1–15. https://doi.org/10.1155/2016/4169587
doi: 10.1155/2016/4169587
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung D, Yiu S, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1(1):18. https://doi.org/10.1186/2047-217X-1-18
doi: 10.1186/2047-217X-1-18
pubmed: 23587118
pmcid: 3626529
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477. https://doi.org/10.1089/cmb.2012.0021
doi: 10.1089/cmb.2012.0021
pubmed: 22506599
pmcid: 3342519
Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJM, Birol I (2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19(6):1117–1123. https://doi.org/10.1101/gr.089532.108
doi: 10.1101/gr.089532.108
pubmed: 19251739
pmcid: 2694472
Lin SH, Liao YC (2013) CISA: contig integrator for sequence assembly of bacterial genomes. PLoS ONE 8(3):e60843. https://doi.org/10.1371/journal.pone.0060843
doi: 10.1371/journal.pone.0060843
pubmed: 23556006
pmcid: 3610655
Kim J, Na SI, Kim D, Chun J (2021) UBCG2: up-to-date bacterial core genes and pipeline for phylogenomic analysis. J Microbiol 59:609–615. https://doi.org/10.1007/s12275-021-1231-4
doi: 10.1007/s12275-021-1231-4
pubmed: 34052993
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2014) Highly parallelized inference of large genome-based phylogenies. Concurr Comput Pr Exper (Special Issue) 26:1715–1729. https://doi.org/10.1002/cpe.3112
doi: 10.1002/cpe.3112
Price MN, Dehal PS, Arkin AP (2010) FastTree 2: approximately maximum-likelihood trees for large alignments. PLoS ONE 5(3):e9490. https://doi.org/10.1371/journal.pone.0009490
doi: 10.1371/journal.pone.0009490
pubmed: 20224823
pmcid: 2835736
Letunic I, Bork P (2021) Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 49:293–296. https://doi.org/10.1093/nar/gkab301
doi: 10.1093/nar/gkab301
Meier-Kolthoff JP, Auch AF, Klenk HP, 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
Murray RGE, Doetsch RN, Robinow CF (1994) Determination and cytological light microscopy. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 32–34
Zhao GZ, Li J, Zhu WY, Li XP, Tian SZ, Zhao LX, Xu LH, Li WJ (2011) Pseudonocardia bannaensis sp. nov., a novel actinomycete isolated from the surface-sterilized roots of Artemisia annua L. Antonie Van Leeuwenhoek 100:35–42. https://doi.org/10.1007/s10482-011-9562-5
doi: 10.1007/s10482-011-9562-5
pubmed: 21336595
Koon MA, Almohammed Ali K, Speaker RM, McGrath JP, Linton EW, Steinhilb M (2019) Preparation of prokaryotic and eukaryotic organisms using chemical drying for morphological analysis in scanning electron microscopy (SEM). J Vis Exp 143:e58761. https://doi.org/10.3791/58761
doi: 10.3791/58761
Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607–654
Ichihara K, Fukubayashi Y (2010) Preparation of fatty acid methyl esters for gas-liquid chromatography. J Lipid Res 51(3):635–640. https://doi.org/10.1194/jlr.D001065
doi: 10.1194/jlr.D001065
pubmed: 19759389
pmcid: 2817593
Kämpfer P, Kroppenstedt RM (1996) Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005. https://doi.org/10.1139/m96-128
doi: 10.1139/m96-128
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett J (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2(5):233–241. https://doi.org/10.1016/0167-7012(84)90018-6
doi: 10.1016/0167-7012(84)90018-6
Komagata K, Suzuki KI (1988) 4 Lipid and cell-wall analysis in bacterial systematics. Method Microbiol 19:161–207. https://doi.org/10.1016/S0580-9517(08)70410-0
doi: 10.1016/S0580-9517(08)70410-0
Rouser G, Fleischer S, Yamamoto A (1970) Two dimensional thin layer chromatographic separation of polar lipids and determination of phospholipids by phosphorus analysis of spots. Lipids 5(5):494–496. https://doi.org/10.1007/BF02531316
doi: 10.1007/BF02531316
pubmed: 5483450
Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, Weber T (2021) antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 49:29–35. https://doi.org/10.1093/nar/gkab335
doi: 10.1093/nar/gkab335
Ziemert N, Weber T, Medema MH (2020) Genome mining approaches to bacterial natural product discovery. In: Liu HW, Begley TP (eds) Comprehensive natural products III, Elsevier, pp 19–33. https://doi.org/10.1016/B978-0-12-409547-2.14627-X
vander Meersche Y, Cretin G, de Brevern AG, Gelly JC, Galochkina T (2021) MEDUSA: prediction of protein flexibility from sequence. J Mol Biol 433(11):166882. https://doi.org/10.1016/j.jmb.2021.166882
doi: 10.1016/j.jmb.2021.166882
pubmed: 33972018
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, Costa MS, Rooney AP, Yi H, Xu XW, Meyer SD, Trujillo ME (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
Nolof G, Hirsch P (1962) Nocardia hydrocarbonoxydans n. spec., ein oligocarbophiler Actinomycet. Archiv für Mikrobiologie 44(3):266–277. https://doi.org/10.1007/BF00510948
Lechevalier MP, Prauser H, Labeda DP, Ruan JS (1986) Two new genera of Nocardioform actinomycetes: Amycolata gen. nov. and Amycolatopsis gen. nov. Int J Syst Bacteriol 36(1):29–37. https://doi.org/10.1099/00207713-36-1-29
Kämpfer P, Kohlweyer U, Thiemer B, Andreesen JR (2006) Pseudonocardia tetrahydrofuranoxydans sp. nov.. Int J Syst Evol Microbiol 56(7):1535–1538. https://doi.org/10.1099/ijs.0.64199-0
Zhang GY, Wang LN, Li JL, Zhou Y (2017) Pseudonocardia profundimaris sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 67(6):1693–1697. https://doi.org/10.1099/ijsem.0.001849
Zhao GZ, Li J, Huang HY, Zhu WY, Park DJ, Kim CJ, Xu LH, Li WJ (2011) Pseudonocardia kunmingensis sp. nov., an actinobacterium isolated from surface-sterilized roots of Artemisia annua L. Int J Syst Evol Microbiol 61:2292–2297. https://doi.org/10.1099/ijs.0.027607-0
doi: 10.1099/ijs.0.027607-0
pubmed: 20971834
Hirsch P (1958) Stoffwechselphysiologische Untersuchungen an Nocardia petroleophila n. sp. Archiv Mikrobiol 29(4):368–393. https://doi.org/10.1007/BF00571596
Mo P, Zhao YL, Liu J, Xu ZG, Gao J (2021) Pseudonocardia broussonetiae sp. nov., an endophytic actinomycete isolated from the roots of Broussonetia papyrifera. Int J Syst Evol Microbiol 71(3):1–6. https://doi.org/10.1099/ijsem.0.004680
Trujillo ME, Idris H, Riesco R, Nouioui I, Igual JM, Bull AT, Goodfellow M (2017) Pseudonocardia nigra sp. nov., isolated from Atacama Desert rock. Int J Syst Evol Microbiol 67(8):2980–2985. https://doi.org/10.1099/ijsem.0.002063
Xu LH, Jin X, Mao PH, Lu ZF, Cui XL, Jiang CL (1999) Three new species of the genus Actinobispora of the family Pseudonocardiaceae, Actinobispora alaniniphila sp. nov., Actinobispora aurantiaca sp. nov. and Actinobispora xinjiangensis sp. nov. Int J Syst Evol Microbiol 49(2):881–886. https://doi.org/10.1099/00207713-49-2-881
Klaysubun C, Lipun K, Duangmal K (2020) Pseudonocardia acidicola sp. nov., a novel actinomycete isolated from peat swamp forest soil. Int J Syst Evol Microbiol 70(11):5648–5653. https://doi.org/10.1099/ijsem.0.004459
Yang XQ, Feng P, Yin Y, Bushley K, Spatafora JW, Wang CS (2018) Cyclosporine biosynthesis in Tolypocladium inflatum benefits fungal adaptation to the environment. mBio 9(5):e01211–18. https://doi.org/10.1128/mBio.01211-18
Pastor JM, Salvador M, Argandoña M, Bernal V, Reina-Bueno M, Csonka LN, Iborra JL, Vargas C, Nieto JJ, Cánovas M (2010) Ectoines in cell stress protection: uses and biotechnological production. Biotechnol Adv 28(6):782–801. https://doi.org/10.1016/j.biotechadv.2010.06.005
doi: 10.1016/j.biotechadv.2010.06.005
pubmed: 20600783