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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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Palma-Cano LE, Piñon-Castillo HA, Tarango-Rivero SH, Carbon A, Salas-Leiva J, Muñoz-Castellanos LN, Cravo-Laureau C, Duran R, Orrantia-Borunda E. Effect of organic and conventional farming on soil bacterial diversity of pecan tree (Carya illinoensis K. Kosh) orchard across two phenological stages. Lett Appl Microbiol 2021; 72:556-569. [PMID: 33453128 DOI: 10.1111/lam.13452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/29/2020] [Accepted: 01/11/2021] [Indexed: 12/19/2022]
Abstract
We described the bacterial diversity of walnut grove soils under organic and conventional farming. The bacterial communities of rhizospheric and nonrhizospheric soils of pecan tree (Carya illinoensis K. Koch) were compared considering two phenological stages (sprouting and ripening). Sixteen operational taxonomic units (OTUs) were identified significantly more abundant according to the plant development, only one according to the farming condition, and none according to the soil origin. The OTUs specificaly abundant according to plant development included Actinobateria (2) and Betaproteobacteria (1) related OTUs more abundant at the sprouting stage, while at the fruit ripening (FR) stage the more abundant OTUs were related to Actinobacteria (6), Alphaproteobacteria (6), and unclassified Bacteria (1). The Gaiellaceae OTU18 (Actinobacteria) was more abundant under conventional farming. Thus, our study revealed that the plant development stage was the main factor shaping the bacterial community structure, while less influence was noticed for the farming condition. The bacterial communities exhibited specific metabolic capacities, a large range of carbon sources being used at the FR stage. The identified OTUs specifically more abundant represent indicators providing useful information on soil condition, potential tools for the management of soil bacterial communities.
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Affiliation(s)
- L E Palma-Cano
- Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - H A Piñon-Castillo
- Facultad de Ciencias Químicas de la Universidad Autónoma de Chihuahua, Chihuahua, México
| | | | - A Carbon
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM, UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - J Salas-Leiva
- Centro de Investigación en Materiales Avanzados, Chihuahua, México.,Cátedra-CONACyT, Centro de Investigación en Materiales Avanzados, Chihuahua, México
| | - L N Muñoz-Castellanos
- Facultad de Ciencias Químicas de la Universidad Autónoma de Chihuahua, Chihuahua, México
| | - C Cravo-Laureau
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM, UMR CNRS 5254, Bat. IBEAS, Pau, France
| | - R Duran
- Université de Pau et des Pays de l'Adour, UPPA/E2S, IPREM, UMR CNRS 5254, Bat. IBEAS, Pau, France
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Goh KM, Shahar S, Chan KG, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current Status and Potential Applications of Underexplored Prokaryotes. Microorganisms 2019; 7:E468. [PMID: 31635256 PMCID: PMC6843859 DOI: 10.3390/microorganisms7100468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
- International Genome Centre, Jiangsu University, ZhenJiang 212013, China.
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Syazwani Itri Amran
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Mohd Helmi Sani
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
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Sun Y, Chen HH, Sun HM, Ai MJ, Su J, Yu LY, Zhang YQ. Naumannella huperziae sp. nov., an endophytic actinobacterium isolated from Huperzia serrata (Thunb.). Int J Syst Evol Microbiol 2017. [DOI: 10.1099/ijsem.0.001882] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Ye Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Hua-Hong Chen
- Department of Chemistry, Chuxiong Normal College, Chuxiong, Yunnan 675000, PR China
| | - Hong-Min Sun
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Meng-Jie Ai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Jing Su
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Li-Yan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
| | - Yu-Qin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, PR China
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