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Chantavorakit T, Suriyachadkun C, Hong K, Duangmal K. Nocardiopsis suaedae sp. nov. and Nocardiopsis endophytica sp. nov., two novel halophilic actinobacteria isolated from halophytes. Int J Syst Evol Microbiol 2023; 73. [PMID: 37347684 DOI: 10.1099/ijsem.0.005948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
A polyphasic approach was used to describe two halophilic actinobacterial strains, designated LSu2-4T and RSe5-2T, which were isolated from halophytes [Suaeda maritima (L.) Dum. and Sesuvium portulacastrum (L.) L.] collected from Prachuap Khiri Khan province, Thailand. Comparative analysis of 16S rRNA gene sequences showed that strains LSu2-4T and RSe5-2T were assigned to the genus Nocardiopsis, with Nocardiopsis chromatogenes YIM 90109T(99.2 and 99.2 % similarities, respectively) and Nocardiopsis halophila DSM 44494T(99.0 and 98.8 % similarities, respectively) being their closely related strains. Whereas the 16S rRNA gene sequence similarity between LSu2-4T and RSe5-2T was 99.4 %. Phylogenetic and phylogenomic analyses based on 16S rRNA gene and whole-genome sequences revealed that both strains clustered with N. chromatogenes YIM 90109T and N. halophila DSM 44494T. The average nucleotide identity (ANI) based on blast, ANI based on MUMmer and digital DNA-DNA hybridization (dDDH) relatedness values between the two strains and their closest type strains were below the threshold values for identifying a novel species. Morphological characteristics and chemotaxonomic features of both strains were typical for the genus Nocardiopsis by formed well-developed substrate mycelia and aerial mycelia which fragmented into rod-shaped spores. Whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were variously hydrogenated with 10 isoprene units and contained phosphatidylcholine in their polar lipid profiles. Major fatty acids were iso-C16:0 and 10-methyl C18:0. In silico analysis predicted that the genomes of LSu2-4T and RSe5-2T contained genes associated with stress responses and biosynthetic gene clusters encoding diverse bioactive metabolites. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strains LSu2-4T and RSe5-2T represents two novel species of the genus Nocardiopsis, for which the names Nocardiopsis suaedae sp. nov. (type strain LSu2-4T=TBRC 16415T=NBRC 115855T) and Nocardiopsis endophytica sp. nov. (type strain RSe5-2T=TBRC 16416T=NBRC 115856T) are proposed.
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Affiliation(s)
- Tanatorn Chantavorakit
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
| | - Chanwit Suriyachadkun
- Thailand Bioresource Research Center (TBRC), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani 12120, Thailand
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, PR China
| | - Kannika Duangmal
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University (BDCKU), Bangkok 10900, Thailand
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Messaoudi O, Wink J, Bendahou M. Diversity of Actinobacteria Isolated from Date Palms Rhizosphere and Saline Environments: Isolation, Identification and Biological Activity Evaluation. Microorganisms 2020; 8:E1853. [PMID: 33255541 PMCID: PMC7760371 DOI: 10.3390/microorganisms8121853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 01/20/2023] Open
Abstract
The diversity of cultural Actinobacteria in two types of Algerian Sahara environments, including saline environments and date palms rhizosphere, was investigated. In this study, a total of 40 strains of actinomycetes was isolated from different soil samples, using a rehydration and centrifugation method. Molecular identification, based on 16S rRNA gene sequence analysis, revealed that these isolates were affiliated to six clusters corresponding to eight genera, including Streptomyces, Nocardiopsis, Saccharopolyspora, Actinomadura, Actinocorallia, Micromonospora, Couchioplanes, and Planomonospora. A taxonomic analysis, based on the morphological, physiological, biochemical, and molecular investigation, of selected strains, which belong to the rare Actinobacteria, was undertaken. Four strains (CG3, A111, A93, and A79) were found to form distinct phyletic lines and represent new actinobacterial taxa. An assessment of antimicrobial proprieties of the 40 obtained actinomycetes strains, showed moderate to strong antimicrobial activities against fungi and bacteria. This study demonstrated the richness of Algerian Sahara with rare Actinobacteria, which can provide novel bioactive metabolites, to solving some of the most challenging problems of the day, such as multi-drug resistance.
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Affiliation(s)
- Omar Messaoudi
- Laboratory of Applied Microbiology in Food, Biomedical and Environment, Abou Bekr Belkaïd University, 13000 Tlemcen, Algeria;
- Department of Biology, Faculty of Science, University of Amar Telidji, 03000 Laghouat, Algeria
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Joachim Wink
- Microbial Strain Collection, Helmholtz Centre for Infection Research GmbH (HZI), Inhoffenstrasse 7, 38124 Braunschweig, Germany;
| | - Mourad Bendahou
- Laboratory of Applied Microbiology in Food, Biomedical and Environment, Abou Bekr Belkaïd University, 13000 Tlemcen, Algeria;
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Tandon K, Baatar B, Chiang PW, Dashdondog N, Oyuntsetseg B, Tang SL. A Large-Scale Survey of the Bacterial Communities in Lakes of Western Mongolia with Varying Salinity Regimes. Microorganisms 2020; 8:E1729. [PMID: 33158252 PMCID: PMC7716208 DOI: 10.3390/microorganisms8111729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
In recent years, climate change coupled with anthropogenic activities has led to monumental changes in saline lakes which are rapidly drying up across the globe and particularly in Central Asia. The landlocked country of Mongolia is rich in lakes which have remained primarily undisturbed by human impact, and many of these lakes have varying salinity regimes and are located across various geographical landscapes. In this study, we sampled 18 lakes with varying salinity regimes (hyperhaline, mesohaline, oligohaline, and polyhaline) covering 7000 km of western Mongolia and its various geographical landscapes (Gobi Desert, forests, and steppe). We identified that the bacterial communities that dominate these lakes are significantly influenced by salinity (p < 0.001) and geographical landscape (p < 0.001). Further, only five zOTUs were shared in all the lakes across the salinity regimes, providing evidence that both local and regional factors govern the community assembly and composition. Furthermore, the bacterial communities of hyperhaline lakes were significantly positively correlated with salinity (ANOVA, p < 0.001) and arsenic concentrations (ANOVA, p < 0.001), whereas bacterial communities of mesohaline and polyhaline lakes situated in forest and steppe landscapes were positively correlated with temperature (ANOVA, p < 0.001) and altitude (ANOVA, p < 0.001), respectively. Functional predictions based on the 16S rRNA gene indicated enrichment of KEGG Ontology terms related to transporters for osmoprotection and -regulation. Overall, our study provides a comprehensive view of the bacterial diversity and community composition present in these lakes, which might be lost in the future.
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Affiliation(s)
- Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Bayanmunkh Baatar
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
- School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia;
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
| | - Narangarvuu Dashdondog
- School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia;
| | - Bolormaa Oyuntsetseg
- School of Arts and Sciences, National University of Mongolia, Ulaanbaatar 14201, Mongolia;
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan; (K.T.); (B.B.); (P.-W.C.)
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
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Erikstad HA, Ceballos RM, Smestad NB, Birkeland NK. Global Biogeographic Distribution Patterns of Thermoacidophilic Verrucomicrobia Methanotrophs Suggest Allopatric Evolution. Front Microbiol 2019; 10:1129. [PMID: 31191475 PMCID: PMC6549252 DOI: 10.3389/fmicb.2019.01129] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/03/2019] [Indexed: 12/13/2022] Open
Abstract
Thermoacidophilic methane-oxidizing Verrucomicrobia of the candidate genus Methylacidiphilum represent a bacterial taxon adapted to highly acidic (pH 1–4) and moderate temperature (∼65°C) methane-containing geothermal environments. Their apparent ubiquity in acidic terrestrial volcanic areas makes them ideal model organisms to study prokaryotic biogeography. Three Methylacidiphilum species isolated from distantly-separated geothermal regions in Russia, New Zealand, and Italy were previously described. We have explored the intra-taxon phylogenetic patterns of these organisms based on comparative genome analyses and phenotypic comparisons with six new Verrucomicrobia methanotroph isolates from other globally-separated acidic geothermal locations. Comparison of rRNA and particulate methane monooxygenase (pmoCAB) operon sequences indicates a close phylogenetic relationship among the new isolates as well as with the previously characterized strains. All share similar cell morphology including the presence of extensive intracellular inclusion bodies and lack of intracellular membrane systems, which are typical for proteobacterial methanotrophs. However, genome sequence comparisons and concatenated MLST-based phylogenetic analyses separate the new isolates into three distinct species-level groups. Three recently processed isolates from the Azores (each from geographically-separate hot springs within the region) and a single isolate from Iceland are highly similar, sharing more than 88% in silico genome homology with each other as well as with the previous isolate, Methylacidiphilum fumariolicum strain SolV, from Italy. These appear to constitute a distinct European/Atlantic clade. However, two of the new isolates – one from the Yellowstone National Park (United States) and another from The Philippines – constitute separate and novel Methylacidiphilum species. There is no clear correlation between fatty acid profiles and geographic distance between origins, or any phylogenetic relationship. Serological analysis using antiserum raised against M. kamchatkense strain Kam1 revealed large differences in the degree of cross-reactivity with no correlation with other factors. However, the genetic distance between the strains does correlate to the distance between their geographic origins and suggests a global biogeographic pattern shaped by an isolation-by-distance mechanism. These results further confirm terrestrial geothermal springs as isolated islands featuring allopatric prokaryotic speciation.
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Affiliation(s)
| | - Ruben Michael Ceballos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
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Namsaraev ZB. Microbial Communities of the Central Asian Lakes as Indicators of Climatic and Ecological Changes in the Region. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718040148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Zhao F, Qin YH, Zheng X, Zhao HW, Chai DY, Li W, Pu MX, Zuo XS, Qian W, Ni P, Zhang Y, Mei H, He ST. Biogeography and Adaptive evolution of Streptomyces Strains from saline environments. Sci Rep 2016; 6:32718. [PMID: 27596681 PMCID: PMC5011734 DOI: 10.1038/srep32718] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/15/2016] [Indexed: 12/23/2022] Open
Abstract
The genus Streptomyces is a widespread genus within the phylum Actinobacteria and has been isolated from various environments worldwide. However, little is known about whether biogeography affects distributional pattern of Streptomyces in salty environments. Such information is essential for understanding the ecology of Streptomyces. Here we analyzed four house-keeping genes (16S rRNA, rpoB, recA and atpD) and salty-tolerance related genes (ectA-ectD) of 38 Streptomyces strains isolated from saline environments in Yunnan and Xinjiang Provinces of western China. The obtained Streptomyces strains were classified into three operational taxonomic units, each comprising habitat-specific geno- and ecotype STs. In combination with expressional variations of salty-tolerance related genes, the statistical analyses showed that spatial distance and environmental factors substantially influenced Streptomyces distribution in saline environments: the former had stronger influence at large spatial scales (>700 km), whereas the latter was influential at large (>700 km) and small spatial scales (<700 km). Plus, the quantitative analyses of salty-tolerence related genes (ectA-D) indicated that Streptomyces strains from salt lakes have higher expression of ectA-D genes and could accumulate larger quantities of ectoine and hydroxyectoine than strains from salt mines, which could help them resist to salinity in the hypersaline environments.
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Affiliation(s)
- Fei Zhao
- Pharmaceutical deparment, Henan Province People's Hospital, No.7, Wei Wu Road, Zhengzhou, Henan, 450003, China
| | - Yu-Hua Qin
- Pharmaceutical deparment, Henan Province People's Hospital, No.7, Wei Wu Road, Zhengzhou, Henan, 450003, China
| | - Xin Zheng
- Yunnan WALVAX Biotechnology Co., Ltd, Kunming, 650106, China
| | - Hong-Wei Zhao
- Pharmaceutical deparment, Henan Province People's Hospital, No.7, Wei Wu Road, Zhengzhou, Henan, 450003, China
| | - Dong-Yan Chai
- Pharmaceutical deparment, Henan Province People's Hospital, No.7, Wei Wu Road, Zhengzhou, Henan, 450003, China
| | - Wei Li
- Yuxi WALVAX Biotechnology Co., Ltd, Kunming, 653100, China
| | - Ming-Xiang Pu
- Yunnan WALVAX Biotechnology Co., Ltd, Kunming, 650106, China
| | - Xing-Sheng Zuo
- Pharmaceutical deparment, Henan Province People's Hospital, No.7, Wei Wu Road, Zhengzhou, Henan, 450003, China
| | - Wen Qian
- Yunnan WALVAX Biotechnology Co., Ltd, Kunming, 650106, China
| | - Ping Ni
- Yunnan WALVAX Biotechnology Co., Ltd, Kunming, 650106, China
| | - Yong Zhang
- Eryuan No. one high school, Dali Bai nationality Prefecture, 671202, China
| | - Han Mei
- Yunnan Weather Modification Center, Kunming, 650034, China
| | - Song-Tao He
- Pharmaceutical deparment, Henan Province People's Hospital, No.7, Wei Wu Road, Zhengzhou, Henan, 450003, China.,Yunnan WALVAX Biotechnology Co., Ltd, Kunming, 650106, China.,Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
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