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microbial diversity and structure in the gastrointestinal tracts of two stranded short-finned pilot whales(Globicephala macrorhynchus)and a pygmy sperm whale(Kogia breviceps)

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Integrative Zoology 2021年第3期16卷 324-335页

作者： Shijie BAI Peijun ZHANG Mingli LIN Wenzhi LIN Zixin YANG Songhai LI Institute of Deep-sea Science and Engineering Chinese Academy of SciencesSanyaChina

Information on the gut microbiome composition of different mammals could provide novel insights into the evolution of mammals and succession of microbial communities in different ***,there is limited information on the gut microbiome composition of marine mammals,especially cetaceans because of sampling *** this study,we investigated the diversity and composition of microbial communities in the stomach,midgut,and hindgut of 2 stranded short-finned pilot whales(Globicephala macrorhynchus)and hindgut of a stranded pygmy sperm whale(Kogia breviceps)by using 16S rRNA gene amplicon sequencing *** the basis of the 50 most abundant operational taxonomic units,principal coordinate analysis,and non-metric multidimensional scaling analysis,we confirmed that the gut microbial communities of the 3 whales were *** results revealed that the gut microbiome of 1 stranded short-finned pilot whale GM16 was dominated by Firmicutes(mainly Clostridium)and Fusobacteria;whereas that of the other pilot whale GM19 was composed of Gammaproteobacteria and Bacteroidetes(mainly Vibrio and Bacteroides,respectively),probably caused by intestinal disease and antibiotic *** gut microbiome of the pygmy sperm whale was dominated by Firmicutes and ***,different gastrointestinal tract regions harbored different microbial community *** our knowledge,this is the first report of the gut microbiome of short-finned pilot whales,and our findings will expand our current knowledge on microbial diversity and composition in the gastrointestinal tract of cetaceans.

关键词： gastrointestinal tract gut microbiome microbial diversity pygmy sperm whale(Kogia breviceps) short-finned pilot whale(Globicephala macrorhynchus)

microbial diversity of sediments from an inactive hydrothermal vent field,Southwest Indian Ridge

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Marine Life Science & Technology 2020年第1期2卷 73-86页

作者： Zhifeng Yang Xiang Xiao Yu Zhang School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of Ocean Engineering Shanghai Jiao Tong UniversityShanghai 200240China State Key Laboratory of microbial Metabolism and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China

The Southwest Indian Ridge,which is the slowest-spreading of the main ridges,separates the African and Antarctic *** slow expanding rate is associated with less density of hydrothermal vent fields,shorter longevity of hydrothermal activity,cold mantle temperatures and thick ***,the microbial communities adapting to such specific characteristics of this area have remained largely *** study the microbial diversity at the Southwest Indian Ridge,we sampled three sediment cores in a newly found inactive vent field,the Tianzuo field,and used high-throughput sequencing of 16S rRNA genes to reveal the microbial *** communities of three sampling sites were very similar at the surface,and underwent a gradient change along ***,namely Alteromonadaceae,Nitrosococcus and the JTB255 marine benthic group,were the most dominant bacterial *** Group I was the dominant archaeal taxon in our *** addition,microbial populations capable of ammonia oxidation,nitrite oxidation,sulfur oxidation and manganese oxidation were detected to be the main *** enrichment of sulfur-oxidizing and manganese-oxidizing bacteria was observed in deep *** compared with other vent fields along different ocean ridges,the Tianzuo field showed distinct composition in both archaeal and bacterial *** results provide the first view of microbial communities of the Tianzuo field at the Southwest Indian Ridge,and give a better understanding of metabolic potential possessed by the microbial populations.

关键词： Hydrothermal microbial diversity High-throughput sequencing Deep-sea sediments Ultraslow-spreading ridge

microbial diversity in cold seep sediments from the northern South China Sea

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Geoscience Frontiers 2012年第3期3卷 301-316页

作者： Yong Zhang Xin Su Fang Chen Yuanyuan Wang Lu Jiao Hailiang Dong Yongyang Huang Hongchen Jiang State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesBeijing 100083China School of Ocean Sciences China University of GeosciencesBeijing 100083China Guangzhou Marine Geology Survey Guangzhou 510075China Department of Geology Miami UniversityOxfordOH 45056USA Geomicrobiology Laboratory Science InstituteChina University of GeosciencesBeijing 100083China

South China Sea （SCS） is the largest Western Pacific marginal sea. However, microbial studies have never been performed in the cold seep sediments in the SCS. In 2004, ＂SONNE＂ 177 cruise found two cold seep areas with different water depth in the northern SCS. Haiyang 4 area, where the water depth is around 3000 m, has already been confirmed for active seeping on the seafloor, such as microbial mats, authigenic carbonate crusts and bivalves. We investigated microbial abundance and diver- sity in a 5.55-m sediment core collected from this cold seep area. An integrated approach was employed including geochemistry and 16S rRNA gene phylogenetic analyses. Here, we show that microbial abun- dance and diversity along with geochemistry profiles of the sediment core revealed a coupled reaction between sulphate reduction and methane oxidation. Acridine orange direct count results showed that microbial abundance ranges from 105 to 106 cells/g sediment （wet weight）. The depth-related variation of the abundance showed the same trend as the methane concentration profile. Phylogenetic analysis indicated the presence of sulphate-reducing bacteria and anaerobic methane-oxidizing archaea. The diver- sity was much higher at the surface, but decreased sharply with depth in response to changes in the geochemical conditions of the sediments, such as methane, sulphate concentration and total organic carbon. Marine Benthic Group B, Chloroflexi and JS1 were predominant phylotypes of the archaeal and bacterial libraries, respectively.

关键词： 16S rRNA microbial diversity Cold seep Marine sediments Northern South China Sea

microbial diversity in two cold springs on the Qinghai-Tibetan Plateau

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Geoscience Frontiers 2012年第3期3卷 317-325页

作者： Gaoyuan Li Hongchen Jiang Weiguo Hou Shang Wang Liuqin Huang Huilei Ren Shicai Deng Hailiang Dong State Key Laboratory of Biogeology and Environmental Geology China University of GeosciencesBeijing 100083China AE&E Geomicrobial Technologies Inc.Beijing 102200China Department of Geology and Environmental Earth Science Miami UniversityOxfordOH 45056USA

The microbial diversity in Wuli Area, Qinghai-Tibetan Plateau was investigated using 16S rRNA gene phylogenetic analyses. A total of 117 bacterial and 66 archaeal 16S rRNA gene clones were obtained from the Wuli cold springs, The bacterial clones could be classified into Proteobacteria, Acid- obacteria, Deinococci, Sphingobacteria, Flavobacteria, Nitrospirae, Actinobacteria, Gemmatimona- detes, and unclassified-bacteria; and the archaeal clones could be classified into Crenarchaeota and Thaumarchaeota. Among the major groups, Proteobacteria and Crenarchaeota were dominant in the bacterial and archaeal 16S rRNA gene clone libraries, respectively. The clone sequences obtained in Wuli cold springs were closely related to those from cold habitats, such as snow/ice/soils on high mountains or at high latitude. Especially, the microbial community composition of Wuli Area was more similar to that in Tibetan glaciers than cold environments of other locations. The data presented in this study have impli- cations for a better understanding of microbial diversity in cold springs on the Qinghai-Tibetan Plateau.

关键词： Cold spring microbial diversity Qinghai-Tibetan Plateau

microbial diversity in lake sediments detected by PCR-DGGE

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Frontiers in Biology 2008年第3期3卷 293-299页

作者： Xinqing ZHAO Liuyan YANG Can CHEN Lin XIAO Lijuan JIANG Zhe MA Haowei ZHU Zhenyang YU Daqiang YIN State Key Laboratory of Pollution Control and Resource Reuse School of the EnvironmentNanjing UniversityNanjing 210093China

In this study,PCR-denaturing gradient gel electrophoresis(DGGE)was applied to analyze the microbial communities in lake sediments from Lake Xuanwu,Lake Mochou in Nanjing and Lake Taihu in *** samples from seven locations in three lakes were collected and their genomic DNAs were *** DNA yields of the sediments of Lake Xuanwu and Lake Mochou were high(10 mg/g),while that of sediments in Lake Taihu was relatively *** DNA purification,the 16S rDNA genes(V3 to V5 region)were amplified and the amplified DNA fragments were separated by parallel *** DGGE profiles showed that there were five common bands in all the lake sediment samples indicating that there were similarities among the populations of microorganisms in all the lake *** DGGE profiles of Lake Xuanwu and Lake Mochou were similar and about 20 types of micro-organisms were identified in the sediment samples of both *** results suggest that the sediment samples of these two city lakes(Xuanwu,Mochou)have similar microbial ***,the DGGE profiles of sediment samples in Lake Taihu were significantly different from these two ***,the DGGE profiles of sediment samples in different locations in Lake Taihu were also different,suggesting that the microbial communities in Lake Taihu are more diversified than those in Lake Xuanwu and Lake *** differences in microbial diversity may be caused by the different environmental conditions,such as redox potential,pH,and the concentrations of organic *** major bands of 16S rDNA genes fragments from the DGGE profiles of sediment samples were further reamplified and *** results of sequencing analysis indicate that five sequences shared 99%-100%homology with known sequences(Bacillus and Brevibacillus,uncultured bacteria),while the other two sequences shared 93%-96%homology with known sequences(Acinetobacter,and Bacillus).The study shows that the PCR-DGGE technique combined with sequenc

关键词： Sediment microbial diversity denaturing gradient gel electrophoresis(DGGE) 16S ribosome DNA(16S rDNA) sequence

Afforestation increases microbial diversity in low-carbon soils

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Journal of Forestry Research 2024年第2期35卷 14-22页

作者： Xuesen Pang Chuankuan Wang Chengjie Ren Zhenghu Zhou Center for Ecological Research Key Laboratory of Sustainable Forest Ecosystem Management‑Ministry of EducationNortheast Forestry UniversityHarbin 150040People’s Republic of China Northeast Asia Biodiversity Research Center Northeast Forestry UniversityHarbin 150040People’s Republic of China State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau Northwest A&F UniversityYangling 712100People’s Republic of China

Afforestation has an important role in biodiversity conservation and ecosystem function improvement.A meta-analysis was carried out in China,which has the largest plantation area globally,to quantify the effects of plantings on soil microbial *** results showed that the overall effect of afforestation on soil microbial diversity was positive across the *** forest algorithm suggested that soil carbon was the most important factor regulating microbial diversity and the positive response was only found with new plantings on low-carbon bare lands but not on high-carbon farmlands and *** addition,afforestation with broadleaved species increased microbial diversity,whereas planting with conifers had no effect on microbial *** study clarified the effects of plantings on soil microbial diversity,which has an important implication for establishing appropriate policies and practices to improve the multiple functionalities(e.g.,biodiversity conservation and climate change mitigation)during plantation establishment.

关键词： Afforestation microbial diversity Soil microbial communities Species-energy theory Plantations

Effects of viral infection and microbial diversity on patients with sepsis:A retrospective study based on metagenomic next-generation sequencing

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World Journal of Emergency Medicine 2021年第1期12卷 29-35页

作者： Li-wei Duan Jin-long Qu Jian Wan Yong-hua Xu Yi Shan Li-xue Wu Jin-hao Zheng Wei-wei Jiang Qi-tong Chen Yan Zhu Jian Zhou Wen-bo Yu Lei Pei Xi Song Wen-fang Li Zhao-fen Lin Department of Emergency and Critical Care Medicine Changzheng Hospitalthe Second Military Medical UniversityShanghai 200003China Department of Emergency and Critical Care Medicine Pudong New Area People’s HospitalShanghai 201299China

BACKGROUND: The study aims to investigate the performance of a metagenomic next-generationsequencing (NGS)-based diagnostic technique for the identifi cation of potential bacterial and viral infectionsand eff ects of concomitant viral infection on the survival rate of intensive care unit (ICU) sepsis ***: A total of 74 ICU patients with sepsis who were admitted to our institution from February1, 2018 to June 30, 2019 were enrolled. Separate blood samples were collected from patients for bloodcultures and metagenomic NGS when the patients’ body temperature was higher than 38 °C. Patients’demographic data, including gender, age, ICU duration, ICU scores, and laboratory results, were *** correlations between pathogen types and sepsis severity and survival rate were ***: NGS produced higher positive results (105 of 118;88.98%) than blood cultures(18 of 118;15.25%) over the whole study period. Concomitant viral infection correlated closelywith sepsis severity and had the negative effect on the survival of patients with sepsis. However,correlation analysis indicated that the bacterial variety did not correlate with the severity of ***: Concurrent viral load correlates closely with the severity of sepsis and thesurvival rate of the ICU sepsis patients. This suggests that prophylactic administration of antiviraldrugs combined with antibiotics may be benefi cial to ICU sepsis patients.

关键词： Sepsis Metagenomic next-generation sequencing Viral infections Bacterial infections microbial diversity

Dynamics of microbial diversity during the composting of agricultural straw

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Journal of Integrative Agriculture 2021年第5期20卷 1121-1136页

作者： CHANG Hui-qing ZHU Xiao-hui WU Jie GUO Da-yong ZHANG Lian-he FENG Yao Henan University of Science and Technology Luoyang 471023P.R.China Institute of Agricultural Resources and Regional Planning Chinese Academy of Agricultural Sciences/Key Laboratory of Plant Nutrition and FertilizerMinistry of Agriculture and Rural AffairsBeijing 100081P.R.China

The dynamic changes in microbial diversity during the aerobic composting of agricultural crop straw with additives were evaluated using high-throughput sequencing at four phases of composting(mesophilic,thermophilic,cooling and maturation phases).In addition,the physicochemical parameters of the composting system were determined in this *** fermentation time of the thermophilic period was prolonged with the addition of urea or urea combined with a microbial *** ratio of C/N and germination index variation indicated that the additives were favorable for composting,because the additives directly changed the physicochemical properties of the compost and had effects on the diversity and abundance of bacteria and *** abundance of operational taxonomic units(OTUs),diversity index(Shannon)and richness index(Chao1)of fungi and bacteria were found to significantly increase when urea+microbial agents were added to straw in the thermophilic *** relative abundance of the predominant bacteria and fungi at the phylum and genus levels differed during different composting *** abundance of the phyla Firmicutes and Proteobacteria declined in the order of treatments SNW>SN>S(S is straw only compost;SN is straw+5 kg t^(–1) urea compost;and SNW is straw+5 kg t^(–1) urea+1 kg t^(–1) microbial agent compost)in the thermophilic *** abundance of the genera Staphylococcus,Bacillus and Thermobifida followed the same order in the mesophilic *** accounted for more than 92%of the total fungal *** the progression of the composting process,the abundance of Ascomycota decreased *** abundance of Ascomycota followed the order of S>SN>SNW during the thermophilic *** abundance of Aspergillus accounted for 4–59%of the total abundance of fungi and increased during the first two sampling *** abundance followed the order of SNW>SN>***,principal component analysis(PCA)revealed that the community compositi

关键词： crop straws microbial diversity community composition dynamic characteristics high-throughput sequencing

Fecal microbial diversity and putative function in captive western lowland gorillas(Gorilla gorilla gorilla),common chimpanzees(Pan troglodytes),Hamadryas baboons(Papio hamadryas)and binturongs(Arctictis binturong)

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Integrative Zoology 2014年第5期9卷 557-569页

作者： Erin A.McKENNEY Melissa ASHWELL Joanna E.LAMBERT Vivek FELLNER Department of Animal Sciences North Carolina State UniversityRaleighNorth CarolinaUSA Department of Anthropology The University of Texas at San AntonioTexasUSA

microbial populations in the gastrointestinal tract contribute to host health and *** gut microbial ecology is well studied in livestock and domestic animals,little is known of the endogenous populations inhabiting primates or *** characterized microbial populations in fecal cultures from gorillas(Gorilla gorilla gorilla),common chimpanzees(Pan troglodytes),Hamadryas baboons(Papio hamadryas)and binturongs(Arctictis binturong)to compare the microbiomes associated with different gastrointestinal morphologies and different omnivorous feeding *** species was fed a distinct standardized diet for 2 weeks prior to fecal *** diets were formulated to reflect the species’feeding strategies in *** fecal samples were pooled within species and used to inoculate in vitro batch ***,propionate,butyrate and valerate were measured after 24 h of *** DNA was extracted from individual fecal samples,pooled,and the cpn60 gene region was amplified and then sequenced to identify the major eubacterial constituents associated with each host *** chain fatty acids(Pdiversity with dietary fiber.

关键词： ecology fermentation gastrointestinal microbiota microbial diversity