1
|
Park S, Kim I, Chhetri G, Jung Y, Woo H, Seo T. Cellulomonas alba sp. nov. and Cellulomonas edaphi sp. nov., isolated from wetland soils. Int J Syst Evol Microbiol 2024; 74. [PMID: 38214698 DOI: 10.1099/ijsem.0.006235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Two novel strains were isolated from wetland soils in Goyang, Republic of Korea. The two Gram-stain-positive, facultatively anaerobic, rod-shaped bacterial-type strains were designated MW4T and MW9T. Phylogenomic analysis based on whole-genome sequences suggested that both strains belonged to the genus Cellulomonas. The cells of strain MW4T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 6.0-10.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The cells of strain MW9T were non-motile and grew at 20-40 °C (optimum, 35 °C), at pH 5.0-9.0 (optimum, pH 8.0) and in the presence of 0-1.0% NaCl (optimum, 0 %). The average nucleotide identity (77.1-88.1 %) and digital DNA-DNA hybridization values (21.0-34.8 %) between the two novel strains and with their closely related strains fell within the range for the genus Cellulomonas. The novel strains MW4T and MW9T and reference strains possessed alkane synthesis gene clusters (oleA, oleB, oleC and oleD). Phylogenomic, phylogenetic, average nucleotide identity, digital DNA-DNA hybridization, physiological and biochemical data indicated that the novel strains were distinct from other members of the family Cellulomonadaceae. We propose the names Cellulomonas alba sp. nov. (type strain MW4T=KACC 23260T=TBRC 17645T) and Cellulomons edaphi sp. nov. (type strain MW9T=KACC 23261T=TBRC 17646T) for the two strains.
Collapse
Affiliation(s)
- Sunho Park
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yonghee Jung
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Haejin Woo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| |
Collapse
|
2
|
Wijayawardene NN, Dai DQ, Jayasinghe PK, Gunasekara SS, Nagano Y, Tibpromma S, Suwannarach N, Boonyuen N. Ecological and Oceanographic Perspectives in Future Marine Fungal Taxonomy. J Fungi (Basel) 2022; 8:1141. [PMID: 36354908 PMCID: PMC9696965 DOI: 10.3390/jof8111141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2023] Open
Abstract
Marine fungi are an ecological rather than a taxonomic group that has been widely researched. Significant progress has been made in documenting their phylogeny, biodiversity, ultrastructure, ecology, physiology, and capacity for degradation of lignocellulosic compounds. This review (concept paper) summarizes the current knowledge of marine fungal diversity and provides an integrated and comprehensive view of their ecological roles in the world's oceans. Novel terms for 'semi marine fungi' and 'marine fungi' are proposed based on the existence of fungi in various oceanic environments. The major maritime currents and upwelling that affect species diversity are discussed. This paper also forecasts under-explored regions with a greater diversity of marine taxa based on oceanic currents. The prospects for marine and semi-marine mycology are highlighted, notably, technological developments in culture-independent sequencing approaches for strengthening our present understanding of marine fungi's ecological roles.
Collapse
Affiliation(s)
- Nalin N. Wijayawardene
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
- Section of Genetics, Institute for Research and Development in Health and Social Care, No: 393/3, Lily Avenue, Off Robert Gunawardane Mawatha, Battaramulla 10120, Sri Lanka
- National Institute of Fundamental Studies, Hantana Road, Kandy 20000, Sri Lanka
| | - Don-Qin Dai
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Prabath K. Jayasinghe
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Sudheera S. Gunasekara
- National Aquatic Resources Research and Development Agency (NARA), Crow Island, Colombo 00150, Sri Lanka
| | - Yuriko Nagano
- Deep-Sea Biodiversity Research Group, Marine Biodiversity and Environmental Assessment Research Center, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Saowaluck Tibpromma
- Centre for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing 655011, China
| | - Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nattawut Boonyuen
- Plant Microbe Interaction Research Team (APMT), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| |
Collapse
|
3
|
Zhang G, Yang J, Lai XH, Jin D, Lu S, Liu L, Cheng Y, Pu J, Yang C, Liu Y, Ye L, Xu J. Cellulomonas dongxiuzhuiae sp. nov., Cellulomonas wangleii sp. nov. and Cellulomonas fengjieae sp. nov., isolated from the intestinal contents of Marmota himalayana. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Six Gram-stain-positive, aerobic or facultative anaerobic, catalase-positive, urease- and oxidase-negative, rod-shaped bacteria (zg-ZUI157T/zg-ZUI40, zg-ZUI222T/zg-ZUI199 and zg-ZUI188T/ zg-ZUI168) were characterized by a polyphasic approach. Optimal growth of the six strains was observed at pH 7.0 and 28 °C. Phylogenetic analyses based on the 16S rRNA gene and 247 core genes revealed that they belong to genus
Cellulomonas
. The three type strains have low digital DNA-DNA hybridization (19.3–30.1%) and average nucleotide identity values (78.0-85.5%) with all available genomes in the genus
Cellulomonas
, and a DNA G+C content range of 73.0-74.6 mol%. The major fatty acids detected in strain pairs zg-ZUI157T/zg-ZUI40 and zg-ZUI 222T/zg-ZUI199 were C16:0, anteiso-C15:0 and anteiso A-C15:1, and C16:0, anteiso-C15:0, anteiso A-C15:1 and anteiso-C17:0 in strain pair zg-ZUI188T/zg-ZUI168. Diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol mannosides were the major polar lipids detected in the three novel species. MK-9(H4) was the predominant quinone detected in strains zg-ZUI222T (87.4 %) and zg-ZUI188T (91.4 %), and MK-9(H4) (49.1 %) and MK-8 (43.4 %) in strain zg-ZUI157T. The cell-wall sugars detected in the three novel species mainly contained rhamnose. The cell-wall peptidoglycan type of the three novel species was A4β, with an inferred l-Orn–d-Asp interpeptide bridge for strains zg-ZUI157T and zg-ZUI222T, and l-Orn–d-Glu for strain zg-ZUI188T. Based on the results of the phenotypic, phylogenetic, genomic hybridization, average nucleotide identity and chemotaxonomic analyses, the six strains should be classified as belonging to three novel
Cellulomonas
species, for which the names Cellulomonas dongxiuzhuiae sp. nov. (zg-ZUI157T=GDMCC 1.2559T=KCTC 49678T), Cellulomonas wangleii sp. nov. (zg-ZUI222T=GDMCC 1.2501T=KCTC 49675T) and Cellulomonas fengjieae sp. nov. (zg-ZUI188T=GDMCC 1.2563T=KCTC 49674T) are proposed.
Collapse
Affiliation(s)
- Gui Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jing Yang
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Xin-He Lai
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu 476000, PR China
| | - Dong Jin
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Shan Lu
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yanpeng Cheng
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Caixin Yang
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Yue Liu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Lin Ye
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| | - Jianguo Xu
- Institute of Public Health, Nankai University, Tianjin 300071, PR China
- Shanghai Institute for Emerging and Re-emerging Infectious Diseases, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 102206, PR China
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan 030001, PR China
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
| |
Collapse
|
4
|
Zhang SS, Xu JF, Sun XL, Guo W, Liu ZS. Cellulomonas taurus sp. nov., a novel bacteria with multiple hydrolase activity isolated from livestock, and potential application in wastewater treatment. Antonie van Leeuwenhoek 2021; 114:527-538. [PMID: 33710455 DOI: 10.1007/s10482-021-01538-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/08/2021] [Indexed: 11/29/2022]
Abstract
A Gram-positive, smooth, sub-transparent, faint yellow,0.5-0.7 µm diameter, rod shaped aerobic or facultative aerobic strain P40-2Twas isolated from livestock farms in Northeast China. Strain P40-2T grew at 25-40 °C (optimum 30-38 °C), and in 0-4% (w/v) NaCl (optimum 0%) in LB medium. Based on 16S rRNA gene sequence analysis, strain P40-2T belongs to the class Cellulomonas and is most closely related to C. denverensis strain W6929, C. pakistanensis strain NCCP-11and C. hominis strain CE40.DNA-DNA hybridization rate of strain P40-2T was 29%, and the ANI with C.denverensisstrainW6929 was 85.33%. The genome is 3437431 bp long with a G + C content of 71.99%. Of the 3177 predicted genes, 3119 were protein-coding genes and 58 were RNA encoding genes. The chemotaxonomic data: menaquinone was MK-9(H4), anteiso-C15: 0, C16:0 and anteiso-C17: 0 were the major cellular fatty acids, and the main cell-wall amino acids were ornithine,alanine, glycine and glutamate. The cell wall peptidogly can sugars included glucose, rhamnose, galactose and mannose. The polar lipid present were DPG, PG, PE, and PIM. On the basis of DNA-DNA relatedness, phylogenetic position, complete genome sequence and physiological characteristics, strain P40-2T can be differentiated from other species of the genus Cellulomonas with validly published names and thus represents a novel species, for which the name Cellulomonas taurus is proposed. The type strain is Cellulomonas taurus P40-2T (= CGMCC No.1.17732T).The acute toxicity test in mice showed that LD50 of strain P40-2T was rather high with 1.5 × 1011 CFU/mouse, which indicated low pathogenicity. Drug susceptibility showed that strainP40-2T was resistant to most antibiotics and only sensitive to six antibiotics. Strain P40-2T contained a variety of hydrolytic enzymes including the ability to hydrolyze cellulose, β-glucan, chitin, xylan, and casein. Microbial flocculant MBF-P40 for sewage was prepared with strain P40-2T, after strain P40-2T was confirmed that had good flocculation effect. MBF-P40 was used to prepare flocculation rate of 99.40%. MBF-P40 treatmented sewage from eight different sources. Flocculation rate for pig farm wastewater was 96.07%, COD removal rate is 71.05%, ammonia nitrogen removal rate is 18.22%. The result shows that MBF-P40 has a good flocculation effect, and good prospect of development and application for wastewater treatment.
Collapse
Affiliation(s)
- Sha-Sha Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education Jilin University/College of Animal Medicine, Changchun, 130062, Jilin, China
| | - Jian-Feng Xu
- Panjin Center for Inspection and Testing/Panjin CDC, Panjin, 124010, Liaoning, China
| | - Xiao-Li Sun
- Panjin Center for Inspection and Testing/Panjin CDC, Panjin, 124010, Liaoning, China
| | - Wei Guo
- Panjin Center for Inspection and Testing/Panjin CDC, Panjin, 124010, Liaoning, China
| | - Zeng-Shan Liu
- Key Laboratory of Zoonosis Research, Ministry of Education Jilin University/College of Animal Medicine, Changchun, 130062, Jilin, China.
| |
Collapse
|
5
|
Lee HJ, Kim SY, Whang KS. Cellulomonas citrea sp. nov., isolated from paddy soil. Int J Syst Evol Microbiol 2020; 70:5304-5311. [PMID: 32877326 DOI: 10.1099/ijsem.0.004409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-stain-positive, facultatively anaerobic, motile, aerobic, rod-shaped and non-spore-forming actinobacteria, strains AO-9T and AO-18, were isolated from paddy soil collected from Daejeon, Republic of Korea. Colonies were smooth, lemon-yellow and circular and 0.5-0.8×2.0-2.4 µm in diameter after 3 days of incubation at 28 °C on tryptic soy agar. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains AO-9T and AO-18 belonged to the genus Cellulomonas, showing the highest sequence similarities to Cellulomonas marina FXJ8.089T (96.6 %), Cellulomonas endophytica SYSUP0004T (96.5 %), Cellulomonas gelida DSM 20111T (96.2 %), Cellulomonas uda DSM 20107T (96.1 %), Cellulomonas rhizosphaerae NEAU-TCZ24T (96.1 %), Cellulomonas composti TR7-06T (96.0 %), Cellulomonas persica JCM 18111T (96.0 %) and less than 96 % to other closely related species. The DNA-DNA hybridization values between strains AO-9T and AO-18 were 87 %. The average nucleotide identity and digital DNA-DNA hybridization values between strain AO-9T and type strains of related species of the genus Cellulomonas were 84.0-85.8 % and 20.3-20.9 %, respectively. The major cellular fatty acids are anteiso-C15:0 (49.9 %), C14:0 (12.9 %) and iso-C14:0 (12.1 %). The predominant isoprenoid quinone was MK-9 (H4). The polar lipid profile consists of diphosphatidylglycerol, phosphatidylglycerol and one unidentified lipid. The DNA G+C content was 72.9 mol%. Based on its distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the two strains are considered to represent novel species of the genus Cellulomonas, for which the name Cellulomonas citrea sp. nov. is proposed. The type strain is AO-9T (=KACC 19069T=NBRC 112523T).
Collapse
Affiliation(s)
- Hyo-Jin Lee
- Department of Microbiology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea.,Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Song-Yeon Kim
- Department of Microbiology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea.,Department of Microbiology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| |
Collapse
|
6
|
Li YQ, Zhang H, Xiao M, Dong ZY, Zhang JY, Narsing Rao MP, Li WJ. Cellulomonas endophytica sp. nov., isolated from Gastrodia elata Blume. Int J Syst Evol Microbiol 2020; 70:3091-3095. [PMID: 32238231 DOI: 10.1099/ijsem.0.004133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, facultatively anaerobic and non-motile strain, designated SYSUP0004T, was isolated from the tubers of Gastrodia elata Blume collected from Yunnan Province, PR China. The 16S rRNA gene sequence result showed that the strain SYSUP0004T shared low similarity (97.7 %) with the type strain of Cellulomonas marina. SYSUP0004T grew at pH 6.0-9.0 (optimum, pH 8.0), temperature 4-30 °C (optimum, 28 °C) and could tolerate NaCl up to 4 % w/v (optimum in the absence of NaCl). The cell-wall peptidoglycan type was A4β with an interpeptide bridge l-ornithine-d-glutamic acid. Cell-wall sugars were mannose, ribose, glucose, galactose and fucose. The menaquinone was MK-9(H4). The major fatty acids were anteiso-C15:0, anteiso-C15 : 1 A, C16 : 0 and anteiso-C17 : 0. The polar lipids of SYSUP0004T were diphosphatidylglycerol, unidentified phosphoglycolipid, phosphatidylinositol mannosides and unidentified glycolipid. The genomic DNA G+C content was 76.5 %. The average nucleotide identity values between SYSUP0004T and members of the genus Cellulomonas were below the cut-off level (95-96 %) recommended as the ANI criterion for interspecies identity. Thus, based on the above results strain SYSUP0004T represents a novel species of the genus Cellulomonas, for which the name Cellulomonas endophytica sp. nov. is proposed. The type strain, SYSUP0004T (=KCTC 49025T=CGMCC 1.16405T).
Collapse
Affiliation(s)
- Yan-Qiong Li
- Kunming Medical University Haiyuan College, Kunming, PR China
| | - Hui Zhang
- Kunming Medical University Haiyuan College, Kunming, PR China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Zhou-Yan Dong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Jing-Yi Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China.,Department of Biotechnology, Dayananda Sagar College of Engineering (Affiliated to Visvesvaraya Technological University, Belagavi), Bangalore, Karnataka, India
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat- Sen University, Guangzhou, PR China.,CAS Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Urumqi, Xinjiang, PR China
| |
Collapse
|
7
|
Cellulomonas aurantiaca sp. nov., isolated from a soil sample from a tangerine field. Antonie van Leeuwenhoek 2019; 112:1623-1632. [DOI: 10.1007/s10482-019-01288-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 06/13/2019] [Indexed: 10/26/2022]
|
8
|
Subramani R, Sipkema D. Marine Rare Actinomycetes: A Promising Source of Structurally Diverse and Unique Novel Natural Products. Mar Drugs 2019; 17:E249. [PMID: 31035452 PMCID: PMC6562664 DOI: 10.3390/md17050249] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Rare actinomycetes are prolific in the marine environment; however, knowledge about their diversity, distribution and biochemistry is limited. Marine rare actinomycetes represent a rather untapped source of chemically diverse secondary metabolites and novel bioactive compounds. In this review, we aim to summarize the present knowledge on the isolation, diversity, distribution and natural product discovery of marine rare actinomycetes reported from mid-2013 to 2017. A total of 97 new species, representing 9 novel genera and belonging to 27 families of marine rare actinomycetes have been reported, with the highest numbers of novel isolates from the families Pseudonocardiaceae, Demequinaceae, Micromonosporaceae and Nocardioidaceae. Additionally, this study reviewed 167 new bioactive compounds produced by 58 different rare actinomycete species representing 24 genera. Most of the compounds produced by the marine rare actinomycetes present antibacterial, antifungal, antiparasitic, anticancer or antimalarial activities. The highest numbers of natural products were derived from the genera Nocardiopsis, Micromonospora, Salinispora and Pseudonocardia. Members of the genus Micromonospora were revealed to be the richest source of chemically diverse and unique bioactive natural products.
Collapse
Affiliation(s)
- Ramesh Subramani
- School of Biological and Chemical Sciences, Faculty of Science, Technology & Environment, The University of the South Pacific, Laucala Campus, Private Mail Bag, Suva, Republic of Fiji.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands.
| |
Collapse
|
9
|
Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 421] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
Collapse
Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| |
Collapse
|
10
|
Sun X, Li J, Du J, Xiao H, Ni J. Cellulomonas macrotermitis sp. nov., a chitinolytic and cellulolytic bacterium isolated from the hindgut of a fungus-growing termite. Antonie van Leeuwenhoek 2017; 111:471-478. [DOI: 10.1007/s10482-017-0968-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 10/21/2017] [Indexed: 10/18/2022]
|
11
|
Wei XL, Lin YB, Xu L, Han MS, Dong DH, Chen WM, Wang L, Wei GH. Bacillus radicibactersp. nov., a new bacterium isolated from root nodule ofOxytropis ochrocephalaBunge. J Basic Microbiol 2015. [DOI: 10.1002/jobm.201400940] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiu Li Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| | - Yan Bing Lin
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| | - Lin Xu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| | - Meng Sha Han
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| | - Dan Hong Dong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| | - Wei Min Chen
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| | - Li Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| | - Ge Hong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau College of Life Sciences; Northwest A&F University; Yangling 712100 Shaanxi China
| |
Collapse
|
12
|
Wei XL, Han MS, Xia CC, Ding SL, Xu L, Lin YB, Wang L, Wei GH. Diaphorobacter ruginosibacter sp. nov., isolated from soybean root nodule, and emended description of the genus Diaphorobacter. Arch Microbiol 2015; 197:683-92. [PMID: 25763990 DOI: 10.1007/s00203-015-1102-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/01/2015] [Accepted: 03/03/2015] [Indexed: 10/23/2022]
Abstract
A gram-negative bacterium designated BN30(T), which is motile with a polar flagellum, non-endospores forming, oxidase- and catalase-positive, was isolated from soybean root nodule. The organism is facultative anaerobic and surface-wrinkled rod. It can grow at 10-40 °C, pH 6-8 and 6 % (w/v) NaCl. BLASTn search based on 16S rRNA gene sequence revealed that the strain is closely related to Diaphorobacter aerolatus 8604S-37(T), Alicycliphilus denitrificans K601(T), Simplicispira limi EMB325(T), Diaphorobacter nitroreducens NA10B(T) and Diaphorobacter oryzae RF3(T), which all belonged to the family Comamonadaceae in class Betaproteobacteria. Phylogenetic analysis showed that the strain formed a firm clade with three Diaphorobacter species, being closest to Diaphorobacter aerolatus 8604S-37(T) with similarity of 98.64 %. DNA-DNA relatedness values between strain BN30(T) and five reference strains ranged from 11.5 to 35.9 %. All the results of phylogenetic analysis, chemotaxonomical data (predominant fatty acids are C16:0, sum feature 3, sum feature 8 and C17:0 cyclo; major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol; major quinone is Q-8; G+C of total DNA is 65.2 %), physiological and phenotypic results supported that BN30(T) represented a novel species within the genus Diaphorobacter. The name Diaphorobacter ruginosibacter was proposed, and the type strain is BN30(T) (=ACCC06116(T) = DSM 27467(T)).
Collapse
Affiliation(s)
- Xiu Li Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Ren F, Zhang L, Song L, Xu S, Xi L, Huang L, Huang Y, Dai X. Fulvimarina
manganoxydans sp. nov., isolated from a deep-sea hydrothermal plume in the south-west Indian Ocean. Int J Syst Evol Microbiol 2014; 64:2920-2925. [DOI: 10.1099/ijs.0.060558-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, Mn(II)-oxidizing, Gram-negative bacterium, strain 8047T, was isolated from a deep-sea hydrothermal vent plume in the south-west Indian Ocean. The strain was rod-shaped and motile with a terminal flagellum, and formed yellowish colonies. It produced catalase and oxidase, hydrolysed gelatin and reduced nitrate. 16S rRNA gene sequence analysis showed that strain 8047T belonged to the order
Rhizobiales
of the class
Alphaproteobacteria
, and was phylogenetically most closely related to the genus
Fulvimarina
, sharing 94.4 % sequence identity with the type strain of the type species. The taxonomic affiliation of strain 8047T was supported by phylogenetic analysis of four additional housekeeping genes, gyrB, recA, rpoC and rpoB. The predominant respiratory lipoquinone of strain 8047T was Q-10, the major fatty acid was C18 : 1ω7c and the DNA G+C content was 61.7 mol%. On the basis of the phenotypic and genotypic characteristics determined in this study, strain 8047T represents a novel species within the genus
Fulvimarina
, for which the name Fulvimarina manganoxydans sp. nov. is proposed. The type strain is strain 8047T ( = CGMCC1.10972T = JCM 18890T).
Collapse
Affiliation(s)
- Fei Ren
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Limin Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lei Song
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Shiyao Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Lijun Xi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| |
Collapse
|
14
|
Ahmed I, Kudo T, Abbas S, Ehsan M, Iino T, Fujiwara T, Ohkuma M. Cellulomonas pakistanensis sp. nov., a moderately halotolerant Actinobacteria. Int J Syst Evol Microbiol 2014; 64:2305-2311. [PMID: 24733176 DOI: 10.1099/ijs.0.059063-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
A rod-shaped, motile, facultatively anaerobic and moderately halotolerant plant-growth-promoting actinobacterial strain, designated NCCP-11(T), was isolated from paddy grains. To delineate its taxonomic position, the strain was subjected to a polyphasic characterization. Cells of strain NCCP-11(T) grew at 10-37 °C (optimum 28-32 °C), at pH 6-9 (optimum pH 7) and in 0-12% (w/v) NaCl (optimum 1-2%) in broth medium. Based on 16S rRNA gene sequence analysis, strain NCCP-11(T) showed highest similarity to the type strains of Cellulomonas hominis (98.99%) and Cellulomonas denverensis (98.09 %) and less than 97 % with other closely related taxa. The chemotaxonomic data [major menaquinone: MK-9(H4); cell-wall peptidoglycan: type A4β; major fatty acids: anteiso-C15 : 0, C16 : 0, C14 : 0 and anteiso-C17 : 0; major polar lipids: diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositolmannosides and two unknown polar lipids] also supported the affiliation of strain NCCP-11(T) to the genus Cellulomonas. The level of DNA-DNA relatedness between strain NCCP-11(T) and the two type strains mentioned above was less than 42.7%. On the basis of DNA-DNA relatedness, physiological and biochemical characteristics and phylogenetic position, strain NCCP-11(T) can be differentiated from species of the genus Cellulomonas with validly published names and thus represents a novel species, for which the name Cellulomonas pakistanensis sp. nov. is proposed. The type strain is NCCP-11(T) ( = DSM 24792(T) = JCM 18755(T) = KCTC 19798(T)).
Collapse
Affiliation(s)
- Iftikhar Ahmed
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- National Culture Collection of Pakistan, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad-45500, Pakistan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Saira Abbas
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- National Culture Collection of Pakistan, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad-45500, Pakistan
| | - Muhammad Ehsan
- National Culture Collection of Pakistan, National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad-45500, Pakistan
| | - Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Toru Fujiwara
- Laboratory of Plant Nutrition and Fertilizers, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| |
Collapse
|