Journal of Microbiology

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Roseovarius tibetensis sp. nov., a halophilic bacterium isolated from Lake LongmuCo on Tibetan Plateau: Hui-bin Lu , Xiao-feng Xue , Dorji Phurbu , Peng Xing , Qing-long Wu; J. Microbiol. 2018;56(11):783-789. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8178-0

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Two Gram-stain negative halophilic strains, designated as LM2T and LM4, were isolated from Lake LongmuCo on Tibetan Plateau. These two strains were aerobic, catalaseand oxidase- positive, nonmotile and rod-shaped organisms. Phylogenetic analysis based on 16S rRNA gene sequences indicated that LM2T and LM4 belong to the genus Roseovarius, with Roseovarius tolerans EL-172T (97.3% and 97.4% 16S rRNA gene sequence similarity, respectively) and Roseovarius azorensis SSW084T (95.5% and 95.6% 16S rRNA gene sequence similarity, respectively) as their closest neighbors. Q-10 was the sole respiratory quinone of these two strains. The major fatty acids were C18:1 ω7c/C18:1 ω6c, C16:0, C19:0 cyclo ω8c, and 11-methyl C18:1 ω7c. The polar lipids included phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phospholipid of unknown structure containing glucosamine, and unidentified aminolipid. The DNA G + C content was between 64.2 and 64.5 mol%. DNA-DNA hybridization showed 96.7% relatedness between LM2T and LM4, 24.9% relatedness between LM2T and R. tolerans EL-172T, and 36.3% relatedness between LM4 and R. tolerans EL-172T. Based on phylogenetic analysis, DNA-DNA hybridization, a range of physiological and biochemical characteristics, LM2T and LM4 belong to the same species and were clearly distinguished from the type strains of the genus Roseovarius. It was evident that LM2T and LM4 could be classified as a novel species of the genus Roseovarius, for which the name Roseovarius tibetensis sp. nov. is proposed. The type strain is LM2T (= CGMCC 1.16230T = KCTC 62028T).

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Lithoautotrophic lifestyle of the widespread genusRoseovariusrevealed by physiological and genomic characterization ofRoseovarius autotrophicussp. nov
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Hui-Bin Lu, Zhi-Peng Cai, Yong-Gang Yang, Mei-Ying Xu
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Hui-Bin Lu, Tong-Chu Deng, Mei-Ying Xu
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Halomonas rituensis sp. nov. and Halomonas zhuhanensis sp. nov., isolated from natural salt marsh sediment on the Tibetan Plateau
Peixin Gao, Huibin Lu, Peng Xing, Qinglong L. Wu
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Roseovarius spongiae sp. nov., a bacterium isolated from marine sponge
Lingping Zhuang, Lianzhong Luo
International Journal of Systematic and Evolutionary Microbiology .2020; 70(1): 274. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
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Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone: Dan Xue , Huai Chen , Xiaolin Luo , Jiuqiang Guan , Yixin He , Xinquan Zhao; J. Microbiol. 2018;56(10):734-743. Published online August 22, 2018; DOI: https://doi.org/10.1007/s12275-018-8133-0

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Abstract

The ruminant digestive system harbors a complex gut microbiome, which is poorly understood in the case of the four stomach compartments of yak. High-throughput sequencing and quantitative PCR were used to analyse microbial communities in the rumen, reticulum, omasum, and abomasum of six domesticated yak. The diversity of prokaryotes was higher in reticulum and omasum than in rumen and abomasum. Bacteroidetes predominated in the four stomach compartments, with abundance gradually decreasing in the trend rumen > reticulum > omasum > abomasum. Microorganism composition was different among the four compartments, all of which contained high levels of bacteria, methanogens, protozoa and anaerobic fungi. Some prokaryotic genera were associated with volatile fatty acids and pH. This study provides the first insights into the microorganism composition of four stomach compartments in yak, and may provide a foundation for future studies in this area.

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Halomonas tibetensis sp. nov., isolated from saline lakes on Tibetan Plateau: Hui-bin Lu , Peng Xing , Lei Zhai , Dorji Phurbu , Qian Tang , Qing-long Wu; J. Microbiol. 2018;56(7):493-499. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8076-5

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Abstract

Strains pyc13T and ZGT13 were isolated from Lake Pengyan and Lake Zigetang on Tibetan Plateau, respectively. Both strains were Gram-negative, catalase- and oxidase-positive, aerobic, rod-shaped, nonmotile, and nonflagellated bacteria. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains pyc13T and ZGT13 belong to the genus Halomonas, with Halomonas alkalicola 56-L4-10aEnT as their closest neighbor, showing 97.4% 16S rRNA gene sequence similarity. The predominant respiratory quinone of both strains was Q-9, with Q-8 as a minor component. The major fatty acids of both strains were C18:1 ω6c/C18:1 ω7c, C16:1 ω6c/C16:1 ω7c, C16:0, and C12:0 3OH. The polar lipids of both strains consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, glycolipid, phospholipids of unknown structure containing glucosamine, and unidentified phospholipids. The DNA G + C content of pyc13T and ZGT13 were 62.6 and 63.4 mol%, respectively. The DNA-DNA hybridization values of strain pyc13T were 34, 41, 61, 35, and 35% with the reference strains H. alkalicola 56-L4-10aEnT, H. sediminicola CPS11T, H. mongoliensis Z-7009T, H. ventosae Al12T, and H. fontilapidosi 5CRT, respectively. Phenotypic, biochemical, genotypic, and DNA-DNA hybridization data showed that strains pyc13T and ZGT13 represent a new species within the genus Halomonas, for which the name H. tibetensis sp. nov. is proposed. The type strain is pyc13T (= CGMCC 1.15949T = KCTC 52660T).

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Research Support, Non-U.S. Gov't

A Survey of the Geographic Distribution of Ophiocordyceps sinensis: Yi Li , Xiao-Liang Wang , Lei Jiao , Yi Jiang , Hui Li , Si-Ping Jiang , Ngarong Lhosumtseiring , Shen-Zhan Fu , Cai-Hong Dong , Yu Zhan , Yi-Jian Yao; J. Microbiol. 2011;49(6):913-919. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1193-z

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Abstract

Ophiocordyceps sinensis is one of the best known fungi in Traditional Chinese Medicine. Many efforts have been devoted to locating the production areas of this species resulting in various reports; however, its geographic distribution remains incompletely understood. Distribution of O. sinensis at the county level is clarified in this work based on both a literature search and fieldwork. More than 3600 publications related to O. sinensis were investigated, including scientific papers, books, and online information. Herbarium specimens of O. sinensis and field collections made by this research group during the years 2000-2010 were examined to verify the distribution sites. A total of 203 localities for O. sinensis have been found, of which 106 are considered as confirmed distribution sites, 65 as possible distribution sites, 29 as excluded distribution sites and three as suspicious distribution sites. The results show that O. sinensis is confined to the Tibetan Plateau and its surrounding regions, including Tibet, Gansu, Qinghai, Sichuan, and Yunnan provinces in China and in certain areas of the southern flank of the Himalayas, in the countries of Bhutan, India and Nepal, with 3,000 m as the lowest altitude for the distribution. The fungus is distributed from the southernmost site in Yulong Naxi Autonomous County in northwestern Yunnan Province to the northernmost site in the Qilian Mountains in Qilian County, Qinghai Province, and from the east edge of the Tibetan Plateau in Wudu County, Gansu Province to the westernmost site in Uttarakhand, India. The clarification of the geographic distribution of O. sinensis will lay the foundation for conservation and sustainable use of the species.

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The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species
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Genomic analyses reveal evolutionary and geologic context for the plateau fungus Ophiocordyceps sinensis
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Composition and predictive functional analysis of bacterial communities inhabiting Chinese Cordyceps insight into conserved core microbiome
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Characterization of Humic Substances in the Soils of Ophiocordyceps sinensis Habitats in the Sejila Mountain, Tibet: Implication for the Food Source of Thitarodes Larvae
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Complete mitochondrial genome of two Thitarodes species (Lepidoptera, Hepialidae), the host moths of Ophiocordyceps sinensis and phylogenetic implications
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Morphological Observations and Fatty Acid Composition of Indoor-Cultivated Cordyceps sinensis at a High-Altitude Laboratory on Sejila Mountain, Tibet
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Fungal Biology.2014; 118(4): 359. CrossRef
Chasing Chinese Caterpillar Fungus (Ophiocordyceps sinensis) Harvesters in the Himalayas: Harvesting Practice and Its Conservation Implications in Western Nepal
Uttam Babu Shrestha, Sujata Shrestha, Shivaraj Ghimire, Kamal Nepali, Bharat Babu Shrestha
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Journal of Functional Foods.2014; 6: 33. CrossRef
Evaluation of nutritional and physical stress conditions during vegetative growth on conidial production and germination inOphiocordyceps sinensis
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DNA barcoding the commercial Chinese caterpillar fungus
Li Xiang, Jingyuan Song, Tianyi Xin, Yingjie Zhu, Linchun Shi, Xiaolan Xu, Xiaohui Pang, Hui Yao, Wenjia Li, Shilin Chen
FEMS Microbiology Letters.2013; : n/a. CrossRef
Detection ofOphiocordyceps sinensisin soil by quantitative real-time PCR
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Canadian Journal of Microbiology.2013; 59(3): 204. CrossRef
On the reliability of DNA sequences ofOphiocordyceps sinensisin public databases
Shu Zhang, Yong-Jie Zhang, Xing-Zhong Liu, Hong Zhang, Dian-Sheng Liu
Journal of Industrial Microbiology and Biotechnology.2013; 40(3-4): 365. CrossRef
A Systematic Review of the Mysterious Caterpillar Fungus Ophiocordyceps sinensis in DongChongXiaCao (冬蟲夏草 Dōng Chóng Xià Cǎo) and Related Bioactive Ingredients
Hui-Chen Lo, Chienyan Hsieh, Fang-Yi Lin, Tai-Hao Hsu
Journal of Traditional and Complementary Medicine.2013; 3(1): 16. CrossRef
Systematic analyses of Ophiocordyceps lanpingensis sp. nov., a new species of Ophiocordyceps in China
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Development of conventional and nested PCR assays for the detection of Ophiocordyceps sinensis
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