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Han Y, Yang Z, Yin M, Zhang Q, Tian L, Wu H. Exploring product maturation, microbial communities and antibiotic resistance gene abundances during food waste and cattle manure co-composting. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 951:175704. [PMID: 39214357 DOI: 10.1016/j.scitotenv.2024.175704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 08/17/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]
Abstract
This study proposed combining food waste (FW) and cattle manure (CM) in composting to improve the product maturity. The findings suggested that the inclusion of CM effectively extended the thermophilic stage, facilitated the decomposition of cellulose, and enhanced the production of humus-like substances by enhancing beneficial microbial cooperation. Adding 40 % CW was optimal to reduce the nitrogen loss, increase the cellulose degradation rate to 22.07 %, increase germination index (GI) to 140 %, and reduce normalized antibiotic resistance gene (ARG) abundances. Adding CW could promote the transformation of protein-like compounds, thereby enhancing the humification process of organic substances. Structural equation modeling further verified that the temperature was the key factor affecting humification production, while the main driver for ARGs was physiochemical parameters. This study shows that co-composting of FW and CM offers the potential to promote humification, reduce ARG abundance, and improve fertilizer quality for utilization of both biowastes in the field.
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Affiliation(s)
- Ying Han
- School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, PR China; Hebei Province Key Laboratory of Deep Remediation of Heavy Metals in Water and Resource Utilization, Yanshan University, Qinhuangdao 066004, PR China.
| | - Zijian Yang
- School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, PR China
| | - Meiqi Yin
- School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, PR China
| | - Qingrui Zhang
- School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, PR China; Hebei Province Key Laboratory of Deep Remediation of Heavy Metals in Water and Resource Utilization, Yanshan University, Qinhuangdao 066004, PR China.
| | - Lili Tian
- School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, PR China; Hebei Province Key Laboratory of Deep Remediation of Heavy Metals in Water and Resource Utilization, Yanshan University, Qinhuangdao 066004, PR China
| | - Hao Wu
- School of Environmental and Chemical Engineering, Yanshan University, Qinhuangdao 066004, PR China; Hebei Province Key Laboratory of Deep Remediation of Heavy Metals in Water and Resource Utilization, Yanshan University, Qinhuangdao 066004, PR China
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Jin CZ, Jin L, Liu MJ, Lee JM, Park DJ, Kim CJ. Solihabitans fulvus gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from soil. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005110] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A polyphasic taxonomic study was carried out on an actinobacterial strain (AN110305T) isolated from soil sampled in the Republic of Korea. Cells of the strain were Gram-stain-positive, aerobic, non-motile and rod-shaped. Comparative 16S rRNA gene sequence studies showed a clear affiliation of strain AN110305T with
Actinomycetia
, with highest pairwise sequence similarities to
Goodfellowiella coeruleoviolacea
DSM 43935T (97.6%),
Umezawaea tangerina
MK27-91F2T (97.0%),
Kutzneria chonburiensis
NBRC 110610T (96.9%),
Kutzneria buriramensis
A-T 1846T (96.8%),
Umezawaea endophytica
YIM 2047XT (96.8%),
Kutzneria albida
NRRL B-24060T (96.7%) and
Saccharothrix coeruleofusca
NRRL B-16115T (96.6%). Cells of strain AN110305T formed pale-yellow colonies on Reasoner's 2A agar. MK-9 (H4) (68%) and MK-10 (H4) (32%) were the predominant menaquinones. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethyl ethanolamine, hydroxy-phosphatidylethanolamine, an unidentified aminolipid and an unidentified aminophospholipid were major polar lipids. Iso-C16:0 (24.5%), anteiso-C15:0 (19.3%), anteiso-C17:0 (15.7%) and iso-C15:0 (15.2%) were the major fatty acids and meso-diaminopimelic acid was the pepdidoglycan. The cell-wall sugars were composed of galactose, glucose, mannose and ribose. The genomic DNA G+C content was 70.7 mol%. Based on genotypic and phenotypic data, strain AN110305T could be distinguished from all genera within the family
Pseudonocardiaceae
and represents a novel genus and species named Solihabitans fulvus gen. nov., sp nov. The type strain is AN110305T (=KCTC 39307T =DSM 103572T).
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Affiliation(s)
- Chun-Zhi Jin
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Long Jin
- College of Biology and the Environment, Co-Innovation Centre for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210-037, PR China
| | - Min-Jiao Liu
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Jong-Min Lee
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Dong-Jin Park
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Chang-Jin Kim
- Industrial Biomaterial Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 305-806, Republic of Korea
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Riahi HS, Heidarieh P, Fatahi-Bafghi M. Genus Pseudonocardia: What we know about its biological properties, abilities and current application in biotechnology. J Appl Microbiol 2021; 132:890-906. [PMID: 34469043 DOI: 10.1111/jam.15271] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 07/08/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022]
Abstract
The genus Pseudonocardia belongs to a group of Actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram-positive, non-motile bacteria that are commonly found in soil, plant and environment. Although this genus has a low clinical significance; however, it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti-bacterial, anti-fungal and anti-tumour effects. The use of phenotypic tests, such as gelatinase activity, starch hydrolysis, catalase and oxidase tests, as well as molecular methods, such as polymerase chain reaction, are necessary for Pseudonocardia identification at the genus and species levels.
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Affiliation(s)
- Hanieh Sadat Riahi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Parvin Heidarieh
- Department of Bacteriology and Virology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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Wang R, Wang M, Wang J, Lin Y. Habitats Are More Important Than Seasons in Shaping Soil Bacterial Communities on the Qinghai-Tibetan Plateau. Microorganisms 2021; 9:microorganisms9081595. [PMID: 34442674 PMCID: PMC8400953 DOI: 10.3390/microorganisms9081595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Both habitats and seasons can determine the dynamics of microbial communities, but the relative importance of different habitats and seasonal changes in shaping the soil bacterial community structures on a small spatial scale in permafrost areas remains controversial. In this study, we explored the relative effect of four typical alpine meadow habitats (swamp wetland, swamp meadow, meadow and mature meadow) versus seasons on soil bacterial communities based on samples from the Qinghai-Tibetan Plateau in four months (March, May, July and September). The results showed that habitats, rather than seasons explained more variation of soil bacterial composition and structure. Environmental cofactors explained the greatest proportion of bacterial variation observed and can help elucidate the driving force of seasonal changes and habitats on bacterial communities. Soil temperature played the most important role in shaping bacterial beta diversities, followed by soil total nitrogen and pH. A group of microbial biomarkers, used as indicators of different months, were identified using random forest modeling, and for which relative abundance was shaped by different environmental factors. Furthermore, seasonality in bacterial co-occurrence patterns was observed. The data showed that co-occurrence relationships changed over months. The inter-taxa connections in May and July were more pronounced than that in March and September. Bryobacter, a genus of subgroup_22 affiliated to Acidobacteria, and Pseudonocardia belonging to Actinobacteria were observed as the keystone taxa in different months in the network. These results demonstrate that the bacterial community was clustered according to the seasonal mechanism, whereas the co-occurrence relationships changed over months, which indicated complex bacterial dynamics in a permafrost grassland on the eastern edge of Qinghai-Tibetan.
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Affiliation(s)
- Rui Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Miao Wang
- Party School of the Chengdu Committee of the Chinese Communist Party, Chengdu 610110, China;
| | - Jing Wang
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
| | - Yinghua Lin
- Institute of Wetland Research, Chinese Academy of Forestry, Beijing 100091, China; (R.W.); (J.W.)
- Correspondence: ; Tel.: +86-13671160455
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Zuo J, Zu M, Liu L, Song X, Yuan Y. Composition and diversity of bacterial communities in the rhizosphere of the Chinese medicinal herb Dendrobium. BMC PLANT BIOLOGY 2021; 21:127. [PMID: 33663379 PMCID: PMC7931511 DOI: 10.1186/s12870-021-02893-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 02/18/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Dendrobium is a precious herbal that belongs to Orchidaceae and is widely used as health care traditional Chinese medicine in Asia. Although orchids are mycorrhizal plants, most research still focuses on endophytes, and there is still large amount unknown about rhizosphere microorganisms. To investigate the rhizosphere microbial community of different Dendrobium species during the maturity stage, we used high-throughput sequencing to analyze microbial community in rhizosphere soil during the maturity stage of three kinds of Dendrobium species. RESULTS In our study, a total of 240,320 sequences and 11,179 OTUs were obtained from these three Dendrobium species. According to the analysis of OTU annotation results, different Dendrobium rhizosphere soil bacteria include 2 kingdoms, 63 phyla, 72 classes, 159 orders, 309 families, 850 genera and 663 species. Among all sequences, the dominant bacterial phyla (relative abundance > 1%) were Proteobacteria, Actinobacteria, Bacteroidetes, Acidobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, Chloroflexi, and Gemmatimonadetes. And through WGCNA analysis, we found the hub flora was also belong to Acidobacteria, Actinobacteria and Proteobacteria. CONCLUSIONS We found that the rhizosphere bacterial communities of the three kinds of Dendrobium have significant differences, and that the main species of rhizosphere microorganisms of Dendrobium are concentrated in the Proteobacteria, Actinobacteria, and Bacteroidetes. Moreover, the smaller the bacterial level, the greater the difference among Dendrobium species. These results fill knowledge gaps in the rhizosphere microbial community of Dendrobium and provide a theoretical basis for the subsequent mining of microbial functions and the study of biological fertilizers.
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Affiliation(s)
- Jiajia Zuo
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 China
| | - Mengting Zu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 China
| | - Lei Liu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 China
| | - Xiaomei Song
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 China
| | - Yingdan Yuan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, 225009 China
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Song J, Qiu S, Zhao J, Han C, Wang Y, Sun X, Jiang S, Wang X, Xiang W. Pseudonocardia tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Antonie van Leeuwenhoek 2018; 112:765-773. [PMID: 30536164 DOI: 10.1007/s10482-018-01210-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 12/01/2018] [Indexed: 11/29/2022]
Abstract
An aerobic, non-motile, Gram-stain positive actinomycete, designated strain NEAU-YY211T, was isolated from the rhizosphere soil of wheat (Triticum aestivum L.) collected from Zhumadian, Henan Province, mid-eastern China, and characterised taxonomically using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequence indicated that strain NEAU-YY211T belongs to the genus Pseudonocardia, showing high similarities with respect to Pseudonocardia ammonioxydans H9T (99.1%) and Pseudonocardia antitumoralis SCSIO 01299T (99.0%), respectively. The cell wall was found to contain meso-diaminopimelic acid and the whole cell sugars were identified as arabinose and galactose. The predominant menaquinone of strain NEAU-YY211T was identified as MK-8(H4) and the major fatty acids were identified as iso-C16:0, C17:1ω8c and iso-C16:1. The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unidentified phospholipid. The G+C content of the genomic DNA was determined to be 72.6 mol%. Levels of DNA-DNA relatedness with P. ammonioxydans JCM 12462T and P. antitumoralis DSM 45322T were 54.5 ± 3.5% and 49.8 ± 2.5% (mean ± SD), respectively. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate can be distinguished from closely related type strains and thus represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia tritici sp. nov. is proposed. The type strain is NEAU-YY211T (= DSM 106068T = CGMCC 4.7474T).
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Affiliation(s)
- Jia Song
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Shiwen Qiu
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Junwei Zhao
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Chuanyu Han
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Ying Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xiujun Sun
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Shanwen Jiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China
| | - Xiangjing Wang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China.
| | - Wensheng Xiang
- Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, No. 59 Mucai Street, Xiangfang District, Harbin, 150030, People's Republic of China. .,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China.
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7
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Alvarado P, Huang Y, Wang J, Garrido I, Leiva S. Phylogeny and bioactivity of epiphytic Gram-positive bacteria isolated from three co-occurring antarctic macroalgae. Antonie Van Leeuwenhoek 2018; 111:1543-1555. [PMID: 29460205 DOI: 10.1007/s10482-018-1044-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 02/07/2018] [Indexed: 12/25/2022]
Abstract
Marine macroalgae are emerging as an untapped source of novel microbial diversity and, therefore, of new bioactive secondary metabolites. This study was aimed at assessing the diversity and antimicrobial activity of the culturable Gram-positive bacteria associated with the surface of three co-occurring Antarctic macroalgae. Specimens of Adenocystis utricularis (brown alga), Iridaea cordata (red alga) and Monostroma hariotii (green alga) were collected from the intertidal zone of King George Island, Antarctica. Gram-positive bacteria were investigated by cultivation-based methods and 16S rRNA gene sequencing, and screened for antimicrobial activity against a panel of pathogenic microorganisms. Isolates were found to belong to 12 families, with a dominance of Microbacteriaceae and Micrococcaceae. Seventeen genera of Actinobacteria and 2 of Firmicutes were cultured from the three macroalgae, containing 29 phylotypes. Three phylotypes within Actinobacteria were regarded as potentially novel species. Sixteen isolates belonging to the genera Agrococcus, Arthrobacter, Micrococcus, Pseudarthrobacter, Pseudonocardia, Sanguibacter, Staphylococcus, Streptomyces and Tessaracoccus exhibited antibiotic activity against at least one of the indicator strains. The bacterial phylotype composition was distinct among the three macroalgae species, suggesting that these macroalgae host species-specific Gram-positive associates. The results highlight the importance of Antarctic macroalgae as a rich source of Gram-positive bacterial diversity and potentially novel species, and a reservoir of bacteria producing biologically active compounds with pharmacological potential.
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Affiliation(s)
- Pamela Alvarado
- Universidad Tecnológica de Chile INACAP, Avenida René Soriano 2382, Osorno, Chile
| | - Ying Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ignacio Garrido
- Département de Biologie et Québec-Océan, Université Laval, Pavillon Alexandre-Vachon 1045, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
- Centro FONDAP de Investigaciones en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Sergio Leiva
- Instituto de Bioquímica & Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
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Chanama S, Janphen S, Suriyachadkun C, Chanama M. Pseudonocardia mangrovi sp. nov., isolated from soil. Int J Syst Evol Microbiol 2018; 68:2949-2955. [PMID: 30040061 DOI: 10.1099/ijsem.0.002927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-positive, aerobic actinomycete, designated strain SMC 195T, was isolated from soil collected from a mangrove forest in Thailand. The strain produced extensively branched substrate and aerial mycelia. The substrate mycelium was fragmented into rod-shaped elements, and spore chains consisting of smooth and rod-shaped spores were formed on the aerial mycelium. The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that SMC 195T represented a member of the genus Pseudonocardia, and the most closely phylogenetically related species were Pseudonocardia yuanmonensisJCM 18055T (99.2 % 16S rRNA gene sequence similarity), Pseudonocardia halophobicaNRRL B-16514T (98.9 %) and Pseudonocardia kujensisNRRL B-24890T (98.7 %). However, the DNA-DNA relatedness values between SMC 195Tand the closest phylogenetically related species were significantly below 70 %. The G+C content of the genomic DNA was 74±0.8 mol%. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars consisted of arabinose, galactose, glucose, rhamnose and ribose. The menaquinone was MK-8(H4) only. The major cellular fatty acid was the branched fatty acid iso-C16 : 0 (33.6 %). The polar lipids detected were phosphatidylethanolamine, phosphatidylmethylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol and unidentified glycolipids. On the basis of the results from phenotypic, chemotaxonomic and genotypic studies, it is concluded that SMC 195T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia mangrovi sp. nov. is proposed. The type strain is SMC 195T (=TBRC 7778T=NBRC 113150T).
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Affiliation(s)
- Suchart Chanama
- 1Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Suphansa Janphen
- 2Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
| | - Chanwit Suriyachadkun
- 3BIOTEC Culture Collection, Bioresources Technology Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), 113 Thailand Science Park, Thanon Phahonyothin, Tambon Khlong Nueng, Amphoe Khlong Luang, Pathum Thani 12120, Thailand
| | - Manee Chanama
- 2Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok 10400, Thailand
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Sujarit K, Sujada N, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong S. Pseudonocardia thailandensis sp. nov., an actinomycete isolated from a subterranean termite nest. Int J Syst Evol Microbiol 2017; 67:2773-2778. [DOI: 10.1099/ijsem.0.002017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Kanaporn Sujarit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nikhom Sujada
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
| | - Wasu Pathom-Aree
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
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10
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Yang Q, Franco CMM, Zhang W. Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification. Appl Microbiol Biotechnol 2015; 99:8731-40. [PMID: 26245685 DOI: 10.1007/s00253-015-6875-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 11/26/2022]
Abstract
Experiments were designed to validate the two common DNA extraction protocols (CTAB-based method and DNeasy Blood & Tissue Kit) used to effectively recover actinobacterial DNA from sponge samples in order to study the sponge-associated actinobacterial diversity. This was done by artificially spiking sponge samples with actinobacteria (spores, mycelia and a combination of the two). Our results demonstrated that both DNA extraction methods were effective in obtaining DNA from the sponge samples as well as the sponge samples spiked with different amounts of actinobacteria. However, it was noted that in the presence of the sponge, the bacterial 16S rRNA gene could not be amplified unless the combined DNA template was diluted. To test the hypothesis that the extracted sponge DNA contained inhibitors, dilutions of the DNA extracts were tested for six sponge species representing five orders. The results suggested that the inhibitors were co-extracted with the sponge DNA, and a high dilution of this DNA was required for the successful PCR amplification for most of the samples. The optimized PCR conditions, including primer selection, PCR reaction system and program optimization, further improved the PCR performance. However, no single PCR condition was found to be suitable for the diverse sponge samples using various primer sets. These results highlight for the first time that the DNA extraction methods used are effective in obtaining actinobacterial DNA and that the presence of inhibitors in the sponge DNA requires high dilution coupled with fine tuning of the PCR conditions to achieve success in the study of sponge-associated actinobacterial diversity.
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Affiliation(s)
- Qi Yang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia
| | - Christopher M M Franco
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
| | - Wei Zhang
- Centre for Marine Bioproducts Development, Adelaide, SA, 5042, Australia.
- Department of Medical Biotechnology, School of Medicine, Flinders University, Adelaide, SA, 5042, Australia.
- Centre for Marine Drugs, Renji Hospital, Shanghai Jiaotong University, Shanghai, 200240, China.
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11
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Hamedi J, Mohammadipanah F. Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria. J Ind Microbiol Biotechnol 2014; 42:157-71. [PMID: 25410828 DOI: 10.1007/s10295-014-1537-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/06/2014] [Indexed: 11/25/2022]
Abstract
Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.
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Affiliation(s)
- Javad Hamedi
- Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, 14155-6455, Tehran, Iran,
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Sahin N, Veyisoglu A, Tatar D, Spröer C, Cetin D, Guven K, Klenk HP. Pseudonocardia cypriaca sp. nov., Pseudonocardia salamisensis sp. nov., Pseudonocardia hierapolitana sp. nov. and Pseudonocardia kujensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2014; 64:1703-1711. [PMID: 24523445 DOI: 10.1099/ijs.0.059824-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of four novel actinomycetes isolated from soil samples, designated KT2142T, PM2084T, K236T and A4038T, were established by using a polyphasic approach. The organisms had chemical and morphological features that were consistent with their classification in the genus Pseudonocardia. Whole-cell hydrolysates of the four strains contained meso-diaminopimelic acid and arabinose and galactose as the diagnostic sugars (cell-wall type IV). Their predominant menaquinone was found to be MK-8(H4). The major fatty acid was iso-C16:0. 16S rRNA gene sequence data supported the classification of the isolates in the genus Pseudonocardia and showed that they formed four distinct branches within the genus. DNA-DNA relatedness studies between the isolates and their phylogenetic neighbours showed that they belonged to distinct genomic species. The four isolates were readily distinguished from one another and from the type strains of species classified in the genus Pseudonocardia based on a combination of phenotypic and genotypic properties. In conclusion, it is proposed that the four isolates be classified in four novel species of the genus Pseudonocardia, for which the names Pseudonocardia cypriaca sp. nov. (type strain KT2142T=KCTC 29067T=DSM 45511T=NRRL B-24882T), Pseudonocardia hierapolitana sp. nov. (type strain PM2084T=KCTC 29068T=DSM 45671T=NRRL B-24879T), Pseudonocardia salamisensis sp. nov. (type strain K236T=KCTC 29100T=DSM 45717T) and Pseudonocardia kujensis sp. nov. (type strain A4038T=KCTC 29062T=DSM 45670T=NRRL B-24890T) are proposed.
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Affiliation(s)
- Nevzat Sahin
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Aysel Veyisoglu
- Department of Molecular Biology and Genetics, Faculty of Sciences, Canik Basari University, 55080 Samsun, Turkey.,Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Demet Tatar
- Department of Biology, Faculty of Art and Science, Ondokuz Mayis University, 55139 Kurupelit-Samsun, Turkey
| | - Cathrin Spröer
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
| | - Demet Cetin
- Science Teaching Programme, Gazi Faculty of Education, Gazi University, Ankara, Turkey
| | - Kiymet Guven
- Anadolu University, Faculty of Science, Biology Department, 26470 Eskisehir, Turkey
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany
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Bouizgarne B, Ait Ben Aouamar A. Diversity of Plant Associated Actinobacteria. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2014. [DOI: 10.1007/978-3-319-05936-5_3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM, Tian XP, Zhang S, Li WJ. Pseudonocardia sediminis sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2013; 64:745-750. [PMID: 24198055 DOI: 10.1099/ijs.0.057844-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic actinomycete, designated strain YIM M13141(T), was isolated from a marine sediment sample from the South China Sea, and its taxonomic position was determined using a polyphasic approach. The strain produced branched substrate mycelium and aerial hyphae, but no diffusible pigments were produced on the media tested. At maturity, substrate mycelium was fragmented and spore chains were formed on aerial hyphae and substrate mycelium. Optimum growth occurred at 28 °C, 1-3% (w/v) NaCl and pH 7.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Pseudonocardia, showing highest levels of similarity with respect to Pseudonocardia sichuanensis KLBMP 1115(T) (97.1%), Pseudonocardia tetrahydrofuranoxydans K1(T) (97.1%) and Pseudonocardia kunmingensis YIM 63158(T) (97.0%). Whole-organism hydrolysates of the strain contained meso-diaminopimelic acid and the sugars galactose, glucose, mannose and arabinose. The predominant menaquinone was MK-8(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylethanolamine, two unknown phosphoglycolipids and two glycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 73.1 mol%. DNA-DNA relatedness with P. tetrahydrofuranoxydans DSM 44239(T) was 42.8 ± 3.5% (mean±sd). Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia sediminis sp. nov. is proposed. The type strain is YIM M13141(T) ( = DSM 45779(T) = JCM 18540(T)).
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Affiliation(s)
- Dao-Feng Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China.,Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Zhao Jiang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
| | - Bing-Bing Liu
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Xiao-Mei Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Xin-Peng Tian
- Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Si Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, CAS; RNAM Center for Marine Microbiology, CAS; Guangdong Key Laboratory of Marine Materia Medica; South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301, PR China
| | - Wen-Jun Li
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China.,Key Laboratory of Biogeography and Bioresource in Arid Land, CAS, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürűmqi 830011, PR China
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Kaewkla O, Franco CMM. Rational approaches to improving the isolation of endophytic actinobacteria from Australian native trees. MICROBIAL ECOLOGY 2013; 65:384-393. [PMID: 22976339 DOI: 10.1007/s00248-012-0113-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 08/14/2012] [Indexed: 06/01/2023]
Abstract
In recent years, new actinobacterial species have been isolated as endophytes of plants and shrubs and are sought after both for their role as potential producers of new drug candidates for the pharmaceutical industry and as biocontrol inoculants for sustainable agriculture. Molecular-based approaches to the study of microbial ecology generally reveal a broader microbial diversity than can be obtained by cultivation methods. This study aimed to improve the success of isolating individual members of the actinobacterial population as pure cultures as well as improving the ability to characterise the large numbers obtained in pure culture. To achieve this objective, our study successfully employed rational and holistic approaches including the use of isolation media with low concentrations of nutrients normally available to the microorganism in the plant, plating larger quantities of plant sample, incubating isolation plates for up to 16 weeks, excising colonies when they are visible and choosing Australian endemic trees as the source of the actinobacteria. A hierarchy of polyphasic methods based on culture morphology, amplified 16S rRNA gene restriction analysis and limited sequencing was used to classify all 576 actinobacterial isolates from leaf, stem and root samples of two eucalypts: a Grey Box and Red Gum, a native apricot tree and a native pine tree. The classification revealed that, in addition to 413 Streptomyces spp., isolates belonged to 16 other actinobacterial genera: Actinomadura (two strains), Actinomycetospora (six), Actinopolymorpha (two), Amycolatopsis (six), Gordonia (one), Kribbella (25), Micromonospora (six), Nocardia (ten), Nocardioides (11), Nocardiopsis (one), Nonomuraea (one), Polymorphospora (two), Promicromonospora (51), Pseudonocardia (36), Williamsia (two) and a novel genus Flindersiella (one). In order to prove novelty, 12 strains were characterised fully to the species level based on polyphasic taxonomy. One strain represented a novel genus in the family Nocardioides, and the other 11 strains were accepted as novel species. In summary, the holistic isolation strategies were successful in obtaining significant culturable actinobacterial diversity within Australian native trees that includes rare and novel species.
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Affiliation(s)
- Onuma Kaewkla
- Department of Medical Biotechnology, School of Medicine, Flinders University, Bedford Park, Adelaide, South Australia, Australia
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Cuesta G, Soler A, Alonso JL, Ruvira MA, Lucena T, Arahal DR, Goodfellow M. Pseudonocardia hispaniensis sp. nov., a novel actinomycete isolated from industrial wastewater activated sludge. Antonie van Leeuwenhoek 2012; 103:135-42. [PMID: 22899021 DOI: 10.1007/s10482-012-9792-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 08/06/2012] [Indexed: 10/28/2022]
Abstract
A novel actinomycete, designated PA3(T), was isolated from an oil refinery wastewater treatment plant, located in Palos de la Frontera, Huelva, Spain, and characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct subclade in the Pseudonocardia tree together with Pseudonocardia asaccharolytica DSM 44247(T). The chemotaxonomic properties of the isolate, for example, the presence of MK-8 (H(4)) as the predominant menaquinone and iso-C(16:0) as the major fatty acid, are consistent with its classification in the genus Pseudonocardia. DNA:DNA pairing experiments between the isolate and the type strain of P. asaccharolytica DSM 44247(T) showed that they belonged to separate genomic species. The two strains were readily distinguished using a combination of phenotypic properties. Consequently, it is proposed that isolate PA3(T) represents a novel species for which the name Pseudonocardia hispaniensis sp. nov. is proposed. The type strain is PA3(T) (= CCM 8391(T) = CECT 8030(T)).
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Affiliation(s)
- G Cuesta
- Área de Microbiología, Departamento de Biotecnología, E.T.S.I. Agronómica y Medio Natural, Universitat Politècnica de València, Camino de Vera 14, 46022, Valencia, Spain.
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Xing K, Qin S, Bian GK, Zhang YJ, Zhang WD, Dai CC, Liu CH, Li WJ, Jiang JH. Pseudonocardia nantongensis sp. nov., a novel endophytic actinomycete isolated from the coastal halophyte Tamarix chinensis Lour. Antonie van Leeuwenhoek 2012; 102:659-67. [DOI: 10.1007/s10482-012-9764-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 06/13/2012] [Indexed: 11/30/2022]
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Nie GX, Ming H, Wei DQ, Zhou EM, Tang X, Cheng J, Tang SK, Li WJ. Pseudonocardia yuanmoensis sp. nov., a novel actinobacterium isolated from soil in Yunnan, south-west China. Antonie van Leeuwenhoek 2011; 101:753-60. [DOI: 10.1007/s10482-011-9689-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
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Pseudonocardia serianimatus sp. nov., a novel actinomycete isolated from the surface-sterilized leaves of Artemisia annua L. Antonie van Leeuwenhoek 2011; 100:521-8. [DOI: 10.1007/s10482-011-9607-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 06/06/2011] [Indexed: 11/26/2022]
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Kaewkla O, Franco CMM. Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree. Int J Syst Evol Microbiol 2011; 61:742-746. [DOI: 10.1099/ijs.0.022327-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strain, designated EUM 374T, was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374T grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095T and Pseudonocardia spinosispora LM 141T, respectively, and 93–96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374T from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374T ( = DSM 45351T = ACM 5285T).
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Affiliation(s)
- Onuma Kaewkla
- Department of Medical Biotechnology, Flinders University, Bedford Park, Australia
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Pseudonocardia bannaensis sp. nov., a novel actinomycete isolated from the surface-sterilized roots of Artemisia annua L. Antonie van Leeuwenhoek 2011; 100:35-42. [DOI: 10.1007/s10482-011-9562-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
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Zhao GZ, Li J, Huang HY, Zhu WY, Park DJ, Kim CJ, Xu LH, Li WJ. Pseudonocardia kunmingensis sp. nov., an actinobacterium isolated from surface-sterilized roots of Artemisia annua L. Int J Syst Evol Microbiol 2010; 61:2292-2297. [PMID: 20971834 DOI: 10.1099/ijs.0.027607-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, aerobic, actinobacterial strain with rod-shaped spores, designated YIM 63158(T), was isolated from the surface-sterilized roots of Artemisia annua L. collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 63158(T) belonged to the genus Pseudonocardia. The closest neighbours were 'Pseudonocardia sichuanensis' KLBMP 1115 (99.9 % 16S rRNA gene sequence similarity), Pseudonocardia adelaidensis EUM 221(T) (99.1 %) and Pseudonocardia zijingensis DSM 44774(T) (98.8 %); sequence similarities to other members of the genus Pseudonocardia ranged from 98.6 to 94.4 %. The chemotaxonomic characteristics, such as the cell-wall diaminopimelic acid, whole-cell sugars, fatty acid components and major menaquinones, suggested that the isolate belonged to the genus Pseudonocardia. The G+C content of the genomic DNA was 73.3 mol%. On the basis of physiological, biochemical and chemotaxonomic data, including low DNA-DNA relatedness between the isolate and other members of the genus Pseudonocardia, it is proposed that strain YIM 63158(T) represents a novel species in this genus, with the name Pseudonocardia kunmingensis sp. nov. The type strain is YIM 63158(T) ( = DSM 45301(T) = CCTCC AA 208078(T)). [corrected].
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Affiliation(s)
- Guo-Zhen Zhao
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Jie Li
- Key Laboratory of Marine Bio-resources Sustainable Utilization/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.,The Key Laboratory for Microbial Resources of the Ministry of Education, PR China and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Hai-Yu Huang
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Wen-Yong Zhu
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Dong-Jin Park
- Korea Research Institutes of Biosciences and Biotechnology 52, Eoeun-dong, Yuseong gu, Daejeon, 305-333, Republic of Korea
| | - Chang-Jin Kim
- Korea Research Institutes of Biosciences and Biotechnology 52, Eoeun-dong, Yuseong gu, Daejeon, 305-333, Republic of Korea
| | - Li-Hua Xu
- The Key Laboratory for Microbial Resources of the Ministry of Education, PR China and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
| | - Wen-Jun Li
- Key Laboratory of Marine Bio-resources Sustainable Utilization/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, PR China.,The Key Laboratory for Microbial Resources of the Ministry of Education, PR China and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, PR China
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Biodiversity, bioactive natural products and biotechnological potential of plant-associated endophytic actinobacteria. Appl Microbiol Biotechnol 2010; 89:457-73. [DOI: 10.1007/s00253-010-2923-6] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 09/24/2010] [Accepted: 09/26/2010] [Indexed: 01/23/2023]
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Pseudonocardia sichuanensis sp. nov., a novel endophytic actinomycete isolated from the root of Jatropha curcas L. Antonie van Leeuwenhoek 2010; 99:395-401. [PMID: 20827574 DOI: 10.1007/s10482-010-9504-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/31/2010] [Indexed: 10/19/2022]
Abstract
A novel isolate, designated strain KLBMP 1115(T) was isolated from the surface-sterilized root of oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China. Characterization of the isolate was based on a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain KLBMP 1115(T) belongs to the phylogenetic cluster of the genus Pseudonocardia and was most closely related to Pseudonocardia adelaidensis EUM 221(T) (98.9%) and Pseudonocardia zijingensis DSM 44774(T) (98.6%), whereas the DNA-DNA relatedness values between strain KLBMP 1115(T) and the two type strains were 47.3 and 39.7%, respectively. Levels of lower similarities to the type strains of other recognized Pseudonocardia species ranged from 94.4 to 98.4%. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-8(H(4)). The major fatty acids of strain KLBMP 1115(T) was iso-C(16:0). The chemotaxonomic properties of strain KLBMP 1115(T) were consistent with those shared by members of the genus Pseudonocardia. On the basis of the phenotypic features and the DNA-DNA hybridization data, strain KLBMP 1115(T) represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia sichuanensis sp. nov. is proposed. The type strain is KLBMP 1115(T) (=KCTC 19781(T) = CCTCC AA 2010002(T)).
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