Journal of Microbiology

Journal Articles

Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea: Sanjit Chandra Debnath , Ahmed Mohammed Abdo Miyah , Can Chen , Huan Sheng , Xue-Wei Xu , Yue-Hong Wu , Dao-Qiong Zheng , Jin-Zhong Xu , Ya-Nan Di , Pin-Mei Wang , Li Shen; J. Microbiol. 2019;57(12):1065-1072. Published online September 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9194-4

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A yellow pigmented, Gram-stain-negative, aerobic bacterium designated A5.7T was studied to evaluate the taxonomic position following the modern polyphasic approach. The strain was isolated from sediments near Zhairuo Island, which is situated in the East China Sea. Cells were non-spore forming rods without flagella but showed motility by gliding. Growth was observed at 15–35°C (optimum 28°C), pH 6.0–9.0 (optimum pH 6.5) and 0–2% (w/v) NaCl (optimum 0–0.5%) in LB broth. The major respiratory quinone of A5.7T was menaquinone 6. The major polar lipid of A5.7T was phosphatidylethanolamine and the predominant fatty acids (> 5%) were iso-C15:0, iso-C17:0 3-OH, C15:1 ω6c, iso-C15:0 3-OH, iso-C15:1 G, summed feature 3 (C16:1 ω7c and/or C16:1 ω6c) and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Flavobacterium and shares the highest sequence similarities with Flavobacterium sharifuzzamanii A7.6T (98.5%), Flavobacterium tistrianum GB 56.1T (98.3%), Flavobacterium nitrogenifigens NXU-44T (97.8%), Flavobacterium anhuiense D3T (97.6%), Flavobacterium ginsenosidimutans THG 01T (97.6%), and Flavobacterium foetidum CJ42T (97.6%). Digital DNA-DNA hybridization and average nucleotide identity values between the strain and its closest phylogenetic neighbors showed the ranges from 19.6 to 34.1% and 73.7 to 87.9%, respectively. Therefore, based on polyphasic characteristics, strain A5.7T represents a novel species of the genus Flavobacterium for which the name Flavobacterium zhairuonensis sp. nov. is proposed. The type strain is A5.7T (= KCTC 62406T = MCCC 1K03494T).

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Three novel species of the genus Flavobacterium, Flavobacterium odoriferum sp. nov., Flavobacterium fragile sp. nov. and Flavobacterium luminosum sp. nov., isolated from activated sludge
Qi Ran, Xinran Du, Lin Han, Jingjing Wang, Yue-zhong Li
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Ten Novel Species Belonging to the Genus Flavobacterium, Isolated from Freshwater Environments: F. praedii sp. nov., F. marginilacus sp. nov., F. aestivum sp. nov., F. flavigenum sp. nov., F. luteolum sp. nov., F. gelatinilyticum sp. nov., F. aquiphilum s
Hyunyoung Jo, Miri S. Park, Yeonjung Lim, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2023; 61(5): 495. CrossRef
Description of Flavobacterium cyclinae sp. nov. and Flavobacterium channae sp. nov., isolated from the intestines of Cyclina sinensis (Corb shell) and Channa argus (Northern snakehead)
Seomin Kang, Jae-Yun Lee, Jeong Eun Han, Yun-Seok Jeong, Do-Hun Gim, Jin-Woo Bae
Journal of Microbiology.2022; 60(9): 890. CrossRef
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Neak Muhammad, Ho Le Han, Yong-Jae Lee, Jaeho Ko, Tra T. H. Nguyen, Song-Gun Kim
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Flavobacterium salilacus sp. nov., isolated from surface water of a hypersaline lake, and descriptions of Flavobacterium salilacus subsp. altitudinum subsp. nov. and Flavobacterium salilacus subsp. salilacus subsp. nov.
Sanjit Chandra Debnath, Can Chen, Ishrat Khan, Wen-Jie Wang, Dao-Qiong Zheng, Jin-Zhong Xu, Pin-Mei Wang
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4250. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(3): 1443. CrossRef
Flavobacterium phycosphaerae sp. nov. isolated from the phycosphere of Microcystis aeruginosa
Minkyung Kim, Byoung-Hee Lee, Ki-Eun Lee, Woojun Park
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Trichoderma biodiversity in major ecological systems of China: Kai Dou , Jinxin Gao , Chulong Zhang , Hetong Yang , Xiliang Jiang , Jishun Li , Yaqian Li , Wei Wang , Hongquan Xian , Shigui Li , Yan Liu , Jindong Hu , Jie Chen; J. Microbiol. 2019;57(8):668-675. Published online May 23, 2019; DOI: https://doi.org/10.1007/s12275-019-8357-7

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Abstract

An investigation of Trichoderma biodiversity involving a large-scale environmental gradient was conducted to understand the Trichoderma distribution in China. A total of 3,999 isolates were isolated from forestry, grassland, wetland and agriculture ecosystems, and 50 species were identified based on morphological characteristics and sequence analysis of genetic markers. Trichoderma harzianum showed the largest proportion of isolates and the most extensive distribution. Hypocrea semiorbis, T. epimyces, T. konilangbra, T. piluliferum, T. pleurotum, T. pubescens, T. strictipilis, T. hunua, T. oblongisporum and an unidentified species, Trichoderma sp. MA 3642, were first reported in China. Most Trichoderma species were distributed in Jilin and Heilongjiang Provinces in northeast China and the fewest were distributed in Qinghai Province. Based on the division of ecological and geographic factors, forestry ecosystems and low-altitude regions have the greatest species biodiversity of Trichoderma.

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Journal of Fungi.2024; 10(10): 697. CrossRef
Trichoderma Diversity in Mexico: A Systematic Review and Meta-Analysis
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Screening of the Biocontrol Efficacy of Potent Trichoderma Strains against Fusarium oxysporum f.sp. ciceri and Scelrotium rolfsii Causing Wilt and Collar Rot in Chickpea
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Jing Han, Zhantong Lu, Huifang Zhang, Shida Ji, Bin Liu, Ning Kong, Yongfeng Yang, Baoyue Xing, Zhihua Liu
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Weifang Xu, Tao Sun, Jiahui Du, Shuqing Jin, Ying Zhang, Guofa Bai, Wanyu Li, Dengke Yin
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Beneficial and biocontrol effects of Trichoderma atroviride, a dominant species in white birch rhizosphere soil
Kuo Liu, Yu-Zhou Zhang, Hua-Ying Du, Zhi-Ying Wang, Pei-Wen Gu, Zhi-Hua Liu, Ze-Yang Yu
Frontiers in Microbiology.2023;[Epub] CrossRef
Three new species of Trichoderma (Hypocreales, Hypocreaceae) from soils in China
Rui Zhao, Li-Juan Mao, Chu-Long Zhang
MycoKeys.2023; 97: 21. CrossRef
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Haiping Ni, Yuxia Wu, Rui Zong, Shiai Ren, Deng Pan, Lei Yu, Jianwei Li, Zhuling Qu, Qiyao Wang, Gengxing Zhao, Jianzhong Zhao, Lumin Liu, Tao Li, Youming Zhang, Qiang Tu
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Microbiological Research.2021; 242: 126596. CrossRef
Trichoderma harzianum-Mediated ZnO Nanoparticles: A Green Tool for Controlling Soil-Borne Pathogens in Cotton
Shimaa A. Zaki, Salama A. Ouf, Fawziah M. Albarakaty, Marian M. Habeb, Aly A. Aly, Kamel A. Abd-Elsalam
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How Do Trichoderma Genus Fungi Win a Nutritional Competition Battle against Soft Fruit Pathogens? A Report on Niche Overlap Nutritional Potentiates
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Microbiological Research.2020; 235: 126445. CrossRef

Research Support, Non-U.S. Gov'ts

Bacterial Diversity in the Mountains of South-West China: Climate Dominates Over Soil Parameters: Dharmesh Singh , Lingling Shi , Jonathan M. Adams; J. Microbiol. 2013;51(4):439-447. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-2446-9

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Abstract: Certain patterns in soil bacterial diversity and community composition have become evident from metagenomics studies on a range of scales, from various parts of the world. For example, soil pH has generally been seen as dominating variation in bacterial diversity, above all other soil and climate parameters. It is important however to test the generality of these relationships by studying previously unsampled areas. We compared soil bacterial diversity and community composition under a wide range of climatic and edaphic conditions in mountainous Yunnan Province, SW China. Soil samples were taken from a range of primary forest types and altitudes, reflecting the great variation of forest environments in this region. From each soil sample, DNA was extracted and pyrosequenced for bacterial 16S rRNA gene identification. In contrast to other recent studies from other parts of the world, pH was a weaker predictor of bacterial community composition and diversity than exchangeable Ca2+ concentration, and also the more poorly defined >environmental parameter of elevation. Samples from within each forest type clustered strongly, showing the distinctive pattern of their microbial communities on a regional scale. It is clear that on a regional scale in a very heterogeneous environment, additional factors beyond pH can emerge as more important in determining bacterial diversity.

Highland Macrolichen Flora of Northwestern Yunnan, China: Jae-Seoun Hur , Li-Song Wang , Soon-Ok Oh , Gyoung Hee Kim , Kwang-Mi Lim , Jae-Sung Jung , Young Jin Koh; J. Microbiol. 2005;43(3):228-236.; DOI: https://doi.org/2222 [pii]

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Abstract: Fifty-six species in 36 genera of macrolichens are reported from the Zhongdian area, northwest Yunnan, China during the lichenological expedition for highland macrolichen survey in June, 2004. More than 60% of these species have not been reported in South Korea. All of the 182 collected specimens are deposited in the Korean Lichen Research Institute (KoLRI) at Sunchon National University in Korea, and some of them are duplicated in the lichen herbarium, Crytogamic Herbarium, Kunming Institute of Botany, Academia Sinica (KUN-L) in China. This is the first report on the macrolichen flora in the visited areas.

High Prevalence of the China 1 Strain of Epstein-Barr Virus in Korea as Determined by Sequence Polymorphisms in the Carboxy-Terminal Tail of LMP1: Sung-Gyu Cho , Won-Keun Lee; J. Microbiol. 2003;41(2):129-136.

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Abstract: The Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMP1) exhibits considerable sequence heterogeneity among EBV isolates. Seven distinct EBV strains have been defined based on sequence polymorphisms in the LMP1 gene, which are designated China 1, China 2, China 3, Alaskan, Mediterranean, NC, and the B95-8 strains. In this study, we analyzed a 30-bp deletion and sequence variations in the carboxy-terminal region of the LMP1 gene in 12 EBV isolates from spontaneous lymphoblastoid cell lines derived from individuals with non-EBV associated cancers in Korea. Eleven of the 12 isolates showed a 30-bp deletion spanning LMP1 amino acids 342 to 353, suggesting a high prevalence of the LMP1 30-bp deletion variant among EBV isolates in Korea. In addition, all 12 isolates had a 15-bp common deletion in the 33-bp repeat region and multiple base-pair changes relative to the prototype B95-8 EBV strain along with variations in the number of the 33-bp repeats. The bp changes at positions 168746, 168694, 168687, 168395, 168357, 168355, 168631, 168320, 168308, 168295, and 168225 were highly conserved among the isolates. Comparative analysis of sequence change patterns in the LMP1 carboxy-terminal coding region identified nine 30-bp deletion variants as China 1, two deletion variants as a possible interstrain between the Alaskan and China 1 strains, and a single undeleted variant as a possible variant of the Alaskan strain. These results suggest the predominance of the China 1 EBV strain in the Korean population.

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