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Nocardioides Silvaticus Sp. Nov., Isolated from Forest Soil

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TAXONOMIC DESCRIPTION Li et al., Int J Syst Evol Microbiol 2018;68:1–6 DOI 10.1099/ijsem.0.003079 Nocardioides silvaticus sp. nov., isolated from forest soil Chan Li, Kaixiang Shi, Yuxiao Zhang and Gejiao Wang* Abstract A Gram-stain-positive, non-motile, rod-shaped bacterial strain S-34T was isolated from forest soil. According to 16S rRNA gene sequence analysis, strain S-34T was related to Nocardioides members and showed the highest similarities to Nocardioides thalensis NCCP-696T (97.3 %) and Nocardioides panacisoli Gsoil 346T (97.0 %), Nocardioides litorisoli X-2T (96.5 %) and Nocardioides immobilis FLL521T (96.4 %). Phylogenetic trees showed that strain S-34T fell within the cluster containing strain S-34T and N. immobilis FLL521T. The levels of DNA–DNA relatedness between strain S-34T and N. thalensis CCTCC AB 2016296T and between strain S-34T and N. panacisoli KCTC 19470T were 50.6 and 58.8 %, respectively. The genome orthoANI T T T value between strain S-34 and N. immobilis CCTCC AB 2017083 was 82.4 %. Strain S-34 had LL-diaminopimelic acid in the cell-wall peptidoglycan, diphosphatidylglycerol, phosphatidylglycerol, four unknown phospholipids and one unknown lipid as the polar lipids, meanquinone-8(H4) as the only respiratory quinone and iso-C16 : 0,C17:1!8c,C17:1!6c,C17 : 0 and C17 : 0 10- T methyl (TBSA) as the major fatty acids. The genome length of strain S-34 was 4.53 Mb containing 52 contigs and with a DNA G+C content of 71.2 mol%. Strain S-34T could be distinguished from the other Nocardioides members mainly based on the data of phylogenetic analyses, DNA–DNA hybridization, polar lipids and some biochemical differences. Therefore, strain S- 34T represents a novel species of the genus Nocardioides, for which the name Nocardioides silvaticus sp. nov. is proposed. The type strain is S-34T (=KCTC 49137T=CCTCC AB 2018079T). The genus Nocardioides was proposed by Prauser et al. in normal saline solution and serial dilutions were spread on 1976 with Nocardioides albus as the type species [1]. This Reasoner’s 2A (R2A; Sigma) agar plates and incubated at genus belongs to the phylum Actinobacteria, class Actino- 28 C for 7 days. Colonies were picked and repeatedly bacteria, order Actinomycetales and family Nocardiaceae. restreaked on R2A agar plates until purity was confirmed. To date, Nocardioides contains 101 species (www.bacterio. Strain S-34T was then purified after several sub-cultivation net/nocardioides.html) with strains isolated from diverse cycles and stored at À80 C with 25 % glycerol. environments, such as seawater [2], soil [3–6], desert [7] The 16S rRNA gene fragment of strain S-34T was amplified and glacier [8]. The members of Nocardioides are Gram- by PCR using the universal bacterial primer pair, 27F and stain-positive, aerobic, with high a DNA G+C content 1492R [10] according to Fan et al. [11]. After using T-A (64.9–74.0 mol%) [1–8]. Meanquinone-8(H4) is the major cloning with a pGEM-T Easy vector (Promega), the accurate respiratory quinone and LL-diaminopimelic acid is the diag- sequence of the PCR product was obtained. The 16S rRNA nostic amino acid of the cell- wall peptidoglycan. The fatty gene sequence of strain S-34T was compared with those acid profile includes both branched- and straight-chain fatty retrieved from GenBank and EzTaxon-e server databases acids, and iso-C is the dominant fatty acid [1–8]. The 16 : 0 (www.ezbiocloud.net/identify) [12]. Alignments of the major polar lipid is phosphatidylglycerol (PG) [1–9], some sequences were performed using MEGA version 6.0 [13]. strains have diphosphatidylglycerol (DPG) [1–6, 9] and/or Phylogenetic trees were reconstructed using the neighbour- phosphatidylinositol (PI) [2, 3, 5, 7]. In this study, a novel joining (NJ) [14], maximum-likelihood (ML) [15] and max- Nocardioides-like bacterial strain, designated strain S-34T, imum-parsimony (MP) [16] methods with bootstrap values was characterized using polyphasic taxonomic tools. determined based on 1000 replications [17]. For genome Strain S-34T was isolated from soil collected at Xinxiang analysis, the genome DNA of strain S-34T and Nocardioides Forest Ecology Park (35 18¢ 13.71† N, 113 55¢ 15.05† E) immobilis CCTCC AB 2017083T were extracted and frag- in Henan Province, PR China. The soil was suspended in mented by ultrasonication. Pair-end sequencing was carried Author affiliation: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China. *Correspondence: Gejiao Wang, [email protected] Keywords: Nocardioides; Taxonomic Description; DNA hybridization; polar lipids; fatty acid. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain S-34T is MH341589. The genome accession numbers of strain S-34T and Nocardioides immobilis CCTCC AB 2017083T are QGDD00000000 and QXGH00000000, respectively. Two tables and four supplementary figures are available with the online Supplementary materials 003079 ã 2018 IUMS 1 Li et al., Int J Syst Evol Microbiol 2018;68:1–6 Nocardioides albidus THG-S11.7T (KM073954) Nocardioides kongjuensis A2-4T (DQ218275) Nocardioides caeni MN8T (FJ423551) Nocardioides nitrophenolicus NSP41T (AF005024) 95 Nocardioides daeguensis 2C1-5 T (HQ246164) 0.01 Nocardioides aromaticivorans H-1T (AB087721) 66 62 Nocardioides simplex KCTC 9106 T (AF005009) 53 Nocardioides ginsengisoli Gsoil 1124T (AB245396) Nocardioides montaniterrae SR-1T (KF955611) Nocardioides humi DCY24 T (EF623863) Nocardioides ultimimeridianus RP-B26T (FM997998) 92 Nocardioides daecheongensis KLS 2-16T (KJ135310) 55 Nocardioides maradonensis RP-B30T (FM998000) 83 Nocardioides silvaticus S34T (MH341589) Nocardioides immobilis FLL521T (KY684256) 80 Nocardioides panacisoli Gsoil 346T (FJ666101) Nocardioides thalensis NCCP-696 T (LC193943) 72 97 99 Nocardioides litorisoli x-2T (KY287237) Nocardioides tritolerans MSL-14T (EF466107) Nocardioides sonneratiae BGMRC0092T (KY655023) 100 Nocardioides pyridinolyticus OS4T (U61298) Nocardioides aquiterrae GW-9T (AF529063) 59 Nocardioides deserti SC8A-24 T (KM816582) T 56 Nocardioides marinisabuli SBS-12 (AM422448) 100 Nocardioides lianchengensis CGMCC 4.6858 T (FMZM01000025) Nocardioides opuntiae OS1-21T (FN178400) Nocardioides albus KCTC 9186 T (AF004988) Terrabacter tumescens DSM 20308 T (X83812) Fig. 1. An NJ tree based on 16S rRNA gene sequences showing the phylogenetic relationships of strain S-34T and other related strains. Terrabacter tumescens DSM 20308T was used as an outgroup member. Filled circles indicate that the corresponding nodes were also recovered in trees reconstructed with the MP tree and ML tree. Numbers at nodes indicate levels of bootstrap support based on 1000 resampled datasets. Values below 50 % are not shown. Bar, 0.01 substitutions per nucleotide position. out by Illumina Hiseq 2500 system by Wuhan Frasergen containing 52 contigs with an N50 length of 387 842 264Â Bioinformatics. sequencing depth of coverage, 4340 coding sequences, 3 rRNA operons and 49 tRNA operons. The genome length The nearly full-length 16S rRNA gene sequence of strain S- of N. immobilis CCTCC AB 2017083T was 6.52 Mb contain- 34T was determined to be 1448 bp and showed the highest ing 72 contigs with an N50 length of 166 910 840Â sequenc- sequence identities to those of Nocardioides thalensis ing depth of coverage, 6305 coding sequences, 3 rRNA NCCP-696T (97.3 %) and Nocardioides panacisoli Gsoil T T operons and 59 tRNA operons. The genome orthoANI 346 (97.0 %), following by Nocardioides litorisoli X-2 T T value between strain S-34 and N. immobilis CCTCC AB (96.5 %) and N. immobilis FLL521 (96.4 %). The NJ tree 2017083T was 82.4 %, which is below the maximum value T shows that strain S-34 is grouped with members of the for defining new species. Four closely related type strains genus Nocardioides and clustered with N. immobilis (N. thalensis CCTCC AB 2016296T, N. panacisoli KCTC T FLL521 (Fig. 1). Similar results were also obtained in the 19470T, N. litorisoli CCTCC AB 2016255T and N. immobilis ML and MP trees (Figs S1 and S2, available in the online CCTCC AB 2017083T) and the type species strain Supplementary Material). Thus, the genome of strain S-34T (Nocardioides albus KCTC 9186T), were obtained from the and N. immobilis CCTCC AB 2017083T were both collection centres and used as the reference strains in fol- sequenced. The genome length of strain S-34T was 4.53 Mb lowing analyses. 2 Li et al., Int J Syst Evol Microbiol 2018;68:1–6 Table 1. Differential phenotypic characteristics among strain S-34T and the phylogenetically related strains and the Nocardioides type species strain Strains: 1, N. silvaticus S-34T; 2, N. thalensis CCTCC AB 2016296T; 3, N. panacisoli KCTC 19470T; 4, N. litorisoli CCTCC AB 2016255T; 5, N. immobilis CCTCC AB 2017083T; 6, N. albus KCTC 9186T. All data are tested in this study except the DNA G+C contents of reference strains. All strains are posi- tive for the activity of catalase; hydrolysis of aesculin; and for the activity of alkaline phosphatase, leucine arylamidase, acid phosphatase, naphthol- AS-BI-phosphohydrolase, 4-nitrophenyl-b-D-galactopyranoside and a-galactosidase. All strains are Gram-stain-positive and negative for indole production, methyl red production and Voges–Proskauer test, Tween 20, gelatin and CM-cellulose hydrolyses; and for the activity of oxidase, phenyl- alanine deaminase, lipase (C14), trypsin, a-galactosidase, b-glucuronidase, N-acetyl-b-glucosaminidase, a-mannosidase and a-fucosidase. +, Posi-
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  • Nocardioides Deserti Sp. Nov., an Actinobacterium Isolated from Desert Soil

    Nocardioides Deserti Sp. Nov., an Actinobacterium Isolated from Desert Soil

    International Journal of Systematic and Evolutionary Microbiology (2015), 65, 1604–1610 DOI 10.1099/ijs.0.000147 Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil Li Tuo,1 Yan-Ping Dong,1,2 Xugela Habden,3 Jia-Meng Liu,1 Lin Guo,1 Xian-Fu Liu,4 Li Chen,4 Zhong-Ke Jiang,1 Shao-Wei Liu,1 Yu-Bin Zhang,2 Yu-Qin Zhang1 and Cheng-Hang Sun1 Correspondence 1Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Yu-Qin Zhang Medical College, Beijing 100050, PR China [email protected] 2College of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, Cheng-Hang Sun PR China [email protected] 3College of Life Science and Chemistry, Xinjiang Normal University, Urumchi 830054, PR China 4Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China A rod- or coccus-shaped, non-spore-forming actinobacterium, designated strain SC8A-24T, was isolated from a soil sample collected from the rhizosphere of Alhagi sparsifolia on the southern edge of the Taklimakan desert, Xinjiang, China, and examined by a polyphasic approach to clarify its taxonomic position. This actinobacterium was Gram-staining-positive and aerobic. Substrate and aerial mycelia were not observed, and no diffusible pigments were observed on the media tested. Strain SC8A-24T grew optimally without NaCl at 28–30 6C and pH 7.0–8.0. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain SC8A-24T belonged to the genus Nocardioides and shared the highest 16S rRNA gene sequence similarity with Nocardioides salarius CL-Z59T (96.51 %), N.
  • Nocardioides Sp. Strain WSN05-2, Isolated from a Wheat Field, Degrades Deoxynivalenol, Producing the Novel Intermediate 3-Epi-Deoxynivalenol

    Nocardioides Sp. Strain WSN05-2, Isolated from a Wheat Field, Degrades Deoxynivalenol, Producing the Novel Intermediate 3-Epi-Deoxynivalenol

    Appl Microbiol Biotechnol (2011) 89:419–427 DOI 10.1007/s00253-010-2857-z ENVIRONMENTAL BIOTECHNOLOGY Nocardioides sp. strain WSN05-2, isolated from a wheat field, degrades deoxynivalenol, producing the novel intermediate 3-epi-deoxynivalenol Yoko Ikunaga & Ikuo Sato & Stephanie Grond & Nobutaka Numaziri & Shigenobu Yoshida & Hiroko Yamaya & Syuntaro Hiradate & Morifumi Hasegawa & Hiroaki Toshima & Motoo Koitabashi & Michihiro Ito & Petr Karlovsky & Seiya Tsushima Received: 18 May 2010 /Revised: 1 August 2010 /Accepted: 31 August 2010 /Published online: 21 September 2010 # Springer-Verlag 2010 Abstract The mycotoxin deoxynivalenol (DON) causes supernatant. The metabolite was identified as 3-epi- serious problems worldwide in the production of crops such deoxynivalenol (3-epi-DON) by mass spectrometry and as wheat and barley because of its toxicity toward humans 1Hand13C nuclear magnetic resonance analysis. The and livestock. A bacterial culture capable of degrading amount of DON on wheat grain was reduced by about DON was obtained from soil samples collected in wheat 90% at 7 days after inoculation with WSN05-2. This is the fields using an enrichment culture procedure. The isolated first report of a Nocardioides sp.strainabletodegrade bacterium, designated strain WSN05-2, completely removed DON and of the yet unknown 3-epi-DON as an intermediate 1,000 μg/mL of DON from the culture medium after in the degradation of DON by a microorganism. incubation for 10 days. On the basis of phylogenetic studies, WSN05-2 was classified as a bacterium belonging to the Keywords Fusarium graminearum . Trichothecenes . genus Nocardioides. WSN05-2 showed significant growth in Deoxynivalenol . Mycotoxin degradation . Nocardioides culture medium with DON as the sole carbon source.
  • Different Genome-Wide Transcriptome Responses of Nocardioides Simplex VKM Ac- 2033D to Phytosterol and Cortisone 21- Acetate Victoria Yu Shtratnikova1* , Mikhail I

    Different Genome-Wide Transcriptome Responses of Nocardioides Simplex VKM Ac- 2033D to Phytosterol and Cortisone 21- Acetate Victoria Yu Shtratnikova1* , Mikhail I

    Shtratnikova et al. BMC Biotechnology (2021) 21:7 https://doi.org/10.1186/s12896-021-00668-9 RESEARCH ARTICLE Open Access Different genome-wide transcriptome responses of Nocardioides simplex VKM Ac- 2033D to phytosterol and cortisone 21- acetate Victoria Yu Shtratnikova1* , Mikhail I. Sсhelkunov2,3 , Victoria V. Fokina4,5 , Eugeny Y. Bragin4 , Andrey A. Shutov 4,5 and Marina V. Donova4,5 Abstract Background: Bacterial degradation/transformation of steroids is widely investigated to create biotechnologically relevant strains for industrial application. The strain of Nocardioides simplex VKM Ac-2033D is well known mainly for its superior 3-ketosteroid Δ1-dehydrogenase activity towards various 3-oxosteroids and other important reactions of sterol degradation. However, its biocatalytic capacities and the molecular fundamentals of its activity towards natural sterols and synthetic steroids were not fully understood. In this study, a comparative investigation of the genome-wide transcriptome profiling of the N. simplex VKM Ac-2033D grown on phytosterol, or in the presence of cortisone 21-acetate was performed with RNA-seq. Results: Although the gene patterns induced by phytosterol generally resemble the gene sets involved in phytosterol degradation pathways in mycolic acid rich actinobacteria such as Mycolicibacterium, Mycobacterium and Rhodococcus species, the differences in gene organization and previously unreported genes with high expression level were revealed. Transcription of the genes related to KstR- and KstR2-regulons was mainly enhanced in response to phytosterol, and the role in steroid catabolism is predicted for some dozens of the genes in N. simplex. New transcription factors binding motifs and new candidate transcription regulators of steroid catabolism were predicted in N.