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Bacterial communities in paddy soils changed by milk vetch as green manure: A study conducted across six provinces in South China

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Pedosphere 2021年第4期31卷 521-530页

作者： Songjuan GAO Weidong CAO Guopeng ZHOU Robert M.REES College of Resources and Environmental Sciences Nanjing Agricultural UniversityNanjing 210095(China) Key Laboratory of Plant Nutrition and Fertilizer Ministry of Agriculture and Rural Affairs/Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081(China) Scotland’s Rural College(SRUC) West Mains RoadEdinburgh EH93JG(UK)

The use of green manures contributes to sustainable soil and nutrient management in agriculture;however, the responses of soil microbial communities to different fertilization regimes at the regional scale are uncertain. A study was undertaken across multiple sites and years in Hunan, Jiangxi, Anhui, Henan,Hubei, and Fujian provinces of South China to investigate the effects of green manuring on the structure and function of soil bacterial communities in rice-green manure cropping systems. The study included four treatments: winter fallow with no chemical fertilizer as a control(NF), milk vetch as green manure without chemical fertilizer(GM), winter fallow and chemical fertilizer(CF), and a combination of chemical fertilizer and milk vetch(GMCF).Significant differences were found in the responses of soil microbial communities at different sites, with sampling sites explaining 72.33%(F = 36.59,P = 0.001) of the community composition variation. The bacterial communities in the soils from Anhui, Henan, and Hubei were broadly similar, while those from Hunan were distinctly different from other locations. The analysis of Weighted UniFrac distances showed that milk vetch changed soil microbial communities compared with winter fallow. Proteobacteria and Chloroflexi predominated in these paddy soils;however, the application of green manures increased the relative abundance of Actinobacteria. There was evidence showing that the functional microbes which play important roles in the cycling of soil carbon, nitrogen(N), and sulfur(S) changed after several years of milk vetch utilization(linear discriminant analysis score > 2). The abundance of methane-oxidizing bacteria and S-reducing bacteria increased, and microbes involved in N fixation, nitrification, and denitrification also increased in some provinces. We concluded that the application of milk vetch changed the bacterial community structure and affected the functional groups related to nutrient transformation in soils at

关键词： alpha diversity bacterial composition functional group operational taxonomic unit soil fertility Weighted UniFrac distance

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Patterns of grassland community composition and structure along an elevational gradient on the Qinghai–Tibet Plateau

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Journal of Plant Ecology 2022年第4期15卷 808-817页

作者： Xin Wang Jiangling Zhu Shitao Peng Tianli Zheng Zhaoyu Qi Jianbo Hu Chengjun Ji State Key Laboratory of Grassland Agro-ecosystems College of Pastoral Agricultural Science and TechnologyLanzhou UniversityLanzhou 730020China Department of Ecology College of Urban and Environmental ScienceKey Laboratory for Earth Surface Processes of the Ministry of EducationPeking UniversityBeijing 100871China Environmental Science and Technology Research Center Tianjin Research Institute for Water Transport EngineeringM.O.T.Tianjin 300456China

Grasslands in the Qinghai–Tibet Plateau play an important role in preserving ecological security and high biodiversity in this ***,the distribution of the composition and structure of plant community and the mechanism by which it maintains itself in this region are still poorly ***,we designed 195 grassland plots in 39 grassland sites along an approximately 1700 m elevation gradient on the Northeastern Qinghai–Tibet *** found that the grassland community height decreased significantly with increasing elevation,whereas community coverage did not significantly *** increasing elevation,plant species richness(αdiversity)increased significantly,but the community variability(βdiversity)decreased *** constrained clustering analysis suggested that theα-andβ-diversity in the grasslands transformed gradually with elevation,and that three discontinuous points(based on community structure)were observed at elevation of 3640,4252 and 4333 *** equation modeling(SEM)indicated that the increase in precipitation and the decrease in temperature significantly positively influencedαdiversity,which was negatively correlated withβ*** results demonstrate a quantitative-to-qualitative change in the community composition and structure along this elevational gradient on the Qinghai–Tibet Plateau.

关键词： alpha diversity beta diversity elevational gradient Qinghai–Tibet Plateau discontinuous points

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How many species of Apodemus and Rattus occur in China？ A survey based on mitochondrial cyt b and morphological analyses

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Zoological Research 2018年第5期39卷 309-320页

作者： Shao-Ying Liu Kai He Shun-De Chen Wei Jin Robert W.Murphy Ming-Kun Tang Rui Liao Feng-Jun Li Sichuan Academy of Forestry Chengdu Sichuan 610081 China Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China College of Life Sciences Sichuan Normal University Chengdu Sichuan 610066 China Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto M5S 2C6 Canada

Apodemus （mice） and Rattus （rats） are the top rodent reservoirs for zoonoses in China,yet little is known about their *** reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in *** also tested whether species could be identified using external and craniodental measurements *** from 147 specimens of Apodemus and 233 specimens of Rattus were used for morphological *** analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic *** demonstrated that nine species of Apodemus and seven species of Rattus,plus a new subspecies of Rattus nitidus,are distributed in *** component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized *** occurrence of Rattus pyctoris in China remains uncertain.

关键词： alpha diversity Apodemus DNA-barcoding Rattus Taxonomy Phylogenies New subspecies

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Performance comparison of different microbial DNA extraction methods on bird feces

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Avian Research 2021年第2期12卷 247-254页

作者： Xian Hou Shengkai Pan Zhenzhen Lin Jiliang Xu Xiangjiang Zhan School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China Key Lab of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Cardiff University-Institute of Zoology Joint Laboratory for Biocomplex-ity Research Chinese Academy of SciencesBeijing 100101China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sci-encesKunming 650223China

Background:As an important player during food digestion,gut microbiota has attracted much attention in diet adaptation studies in *** extracted from feces has been widely used as a proxy for gut *** several methods have been developed for microbial DNA extraction,their performances in the bird feces have not been systematacially evaluated ***:In this study,we applied three DNA extraction methods(Qiagen,MoBio and Bead)to extract DNA from feces of three avian dietary guilds(granivore,omnivore and carnivore),sequenced V4 region of 16S rRNA gene for each extract and evaluated the performances of DNA yield,DNA integrity,microbial composition,cell lysis capacity and alpha diversity for the three methods on each dietary ***:Bead method was the best on the performance of both DNA yield and DNA integrity regardless of dietary *** granivore,microbial relative abundance at both species and phylum levels,alpha diversity and cell lysis capacity were comparable among all *** omnivore,Qiagen had the best performance on alpha diversity,fol-lowed by Bead and *** were small variations on microbial relative abundance at both species and phylum levels among different extraction *** exhibited the best performance on cell lysis *** carnivore,considerable variations were found on microbial relative abundance at both species and phylum *** had the best performance on alpha diversity,followed by MoBio and *** had the highest cell lysis ***:DNA yield and integrity have no obvious impact on microbial composition,alpha diversity or cell lysis *** microbiota results(e.g.,microbial composition,cell lysis capacity,alpha diversity)obtained from differ-ent methods are comparable in granivorous avian species but not in omnivorous or carnivorous *** method could be used in granivore microbiota *** omnivores and carnivores,we recommend Qiagen method when the

关键词： 16S rRNA alpha diversity Avian Dietary guild Feces DNA extraction method Microbial relative abundance

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High‑throughput sequencing view on the magnitude of global fungal diversity

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Fungal diversity 2022年第3期114卷 539-547页

作者： Petr Baldrian TomášVětrovský Clémentine Lepinay Petr Kohout Laboratory of Environmental Microbiology Institute of Microbiology of the Czech Academy of SciencesVídeňská108314220 Prague 4Czech Republic

High-throughput DNA sequencing has dramatically transformed several areas of biodiversity research including *** limitations,high-throughput sequencing is nowadays a predominant method to characterize the alpha and beta diversity of fungal *** the papers utilizing high-throughput sequencing approaches to study natural habitats in terrestrial ecosystems worldwide,>200 studies published until 2019 have generated over 250 million sequences of the primary mycological metabarcoding marker,the nuclear ribosomal internal transcribed spacer 2(ITS2).Here we show that at a 97%sequence similarity threshold,the total richness of non-singleton fungal taxa across the studies published so far is 1.08 million,mostly Ascomycota(56.8%of the taxa)and Basidiomycota(36.7%of the taxa).The Chao-1 estimate of the total extant fungal diversity based on this dataset is 6.28 million taxa,representing a conservative estimate of global fungal species *** and litter represent the habitats with the highest alpha diversity of fungi followed by air,plant shoots,plant roots and deadwood with Chao-1 predictions,for samples containing 5000 sequences,of 1219,569,392,228,215 and 140 molecular species,*** on the high-throughput sequencing data,the highest proportion of unknown fungal species is associated with samples of lichen and plant *** considering the use of high-throughput sequenc-ing for the estimation of global fungal diversity,the limitations of the method have to be taken into account,some of which are sequencing platform-specific while others are inherent to the metabarcoding approaches of species *** this respect,high-throughput sequencing data can complement fungal diversity predictions based on methods of traditional mycology and increase our understanding of fungal biodiversity.

关键词： High-throughput sequencing Metabarcoding Internal transcribed spacer alpha diversity Meta-analysis

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Microbiome data analysis with applications to pre-clinical studies using QIIME2: Statistical considerations

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Genes & Diseases 2021年第2期8卷 215-223页

作者： Shesh N.Rai Chen Qian Jianmin Pan Jayesh P.Rai Ming Song Juhi Bagaitkar Michael Merchant Matthew Cave Nejat K.Egilmez Craig J.McClain Biostatistics and Bioinformatics Facility James Graham Brown Cancer CenterUniversity of LouisvilleLouisvilleKY40202USA Department of Biostatistics and Bioinformatics University of LouisvilleLouisvilleKY40202USA University of Louisville Alcohol Research Center University of LouisvilleLouisvilleKY40202USA University of Louisville Hepatobiology&Toxicology Center University of LouisvilleLouisvilleKY40202USA Department of Oral Immunology&Infectious Diseases University of LouisvilleLouisvilleKY40202USA Department of Medicine University of LouisvilleLouisvilleKY40202USA Robley Rex Louisville VAMC LouisvilleKY40206USA Department of Microbiology&Immunology University of LouisvilleLouisvilleKY40202USA

diversity analysis and taxonomic profiles can be generated from marker-gene sequence data with the help of many available computational *** Quantitative Insights into Microbial Ecology Version 2(QIIME2)has been widely used for 16S rRNA data *** many articles have demonstrated the use of QIIME2 with suitable datasets,the application to preclinical data has rarely been talked *** issues involved in the pre-clinical data include the low-quality score and small sample size that should be addressed properly during *** addition,there are few articles that discuss the detailed statistical methods behind those alpha and beta diversity significance tests that researchers are eager to *** the program without knowing the logic behind it is extremely *** this article,we first provide a guideline for analyzing 16S rRNA data using *** we will talk about issues in pre-clinical data,and how they could impact the ***,we provide brief explanations of statistical methods such as group significance tests and sample size calculation.

关键词： 16S rRNA gene alpha diversity ANOVA Beta diversity Bioinformatics Microbiome data QIIME Sample size calculation

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Climate Variability in Niger： Potential Impacts on Vegetation Distribution and Productivity

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Journal of Environmental Science and Engineering(A) 2012年第1期1卷 49-57页

作者： Ali Mahamane Boube Morou MaYnassara Zaman-Alia Mahamane Saadou Karim Saley Yacoubou Bakasso Issoufou Sama Wata Abdoulaye Amadou Oumani Sandrine Jauffret Department of Biology Faculty of SciencesUniversityA．MoumouniUAMNiamey10662Niger Faculty of Sconces University of MaradiMaracB465Niger National Center of Ecological and Environmental Surveillance CNSEE Ministry of Hydraulics the Environment and Fight Against the DesertificationNiamey 11874Niger NARGES Nature．Resources and Global Environmental Surveillance．Le Coulet Pred Engauri 04200 Les Omergues France

Since 2003, the sites of the national environmental monitoring system （DNSE） of Niger, set up by the long term ecological monitoring observatories network （ROSELT） with the support of the Sahel and Sahara Observatory （OSS）, were used to collect ecological data with harmonized methods for spatio-temporal comparisons purpose. Floristic and phytoecological data were collected using the phytosociological methodology of Braun-Blanquet （1932）. Ecosystem vital attributes used included the specific diversity, alpha diversity, equidistribution, biological types and herbaceous phytomass. At the whole system scale, the analysis revealed that the specific diversity, the alpha diversity and the phytomass values were higher in less disturbed biotopes of the north soudanian and south sahelian bioclimates where the rainfall rate is relatively high. Regarding the north sahelian and saharian bioclimates, the topography may play a critical role in the redistribution of this phytodiversity. Besides, the distribution of the biological types showed the prevalence of therophytes （56.8 ± 11%） regardless of the bioclimate and, to a lesser extent, the perennial species （26.5 ± 7.3%）, the later group showing higher values for the north soudanian bioclimate.

关键词： Ecological monitoring ecosystem vital attributes alpha diversity environmental gradient ROSELT-Niger.

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Local and regional richness and rarity of leaf-litter ants:An overview from spacial scale in neotropical region

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Open Journal of Animal Sciences 2013年第2期3卷 10-15页

作者： Manoel Fernando Demétrio Rogério Silvestre Programa de Pós Graduacao em Entomologia e Conservacao da Biodiversidade Universidade Federal da Grande DouradosDouradosMato Grosso do SulBrazil Laboratorio de Ecologia de Hymenoptera HECOLAB Faculdade de Ciencias Biologicas e Ambientais-UFGDCidade UniversitariaDouradosMato Grosso do SulBrazil

An unusual approach about richness and rarity of leaf-litter ant species is presented here from a dry forest reminiscent in Pantanal province (Chacoan subregion) suggesting the boundaries that defining local and regional scales for this particular ant community. We analysed the frequency of distribution of 170 ant species collected on 262 Winkler’s samples along Serra da Bodoquena National Park, Mato Grosso do Sul state, Brazil and described some ecological mechanisms that made the species richness estimates be highly influenced by species with low frequencies of records in an extent regional of a pristine dry forest. Bayesian inference was conducted to provide if the probability of latitudinal gradient was correlated with the species richness to define alpha diversity.

关键词： alpha diversity Formicidae Rarity Patterns Regional Scale

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Altitude is Associated with Human Oral Microbiomes

Altitude is Associated with Human Oral Microbiomes

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中国生物化学与分子生物学会2020全国学术在线会议

作者： Tian Liang Wenxue Dong Fang Liu Xu Yang Han Zhang Yaqiong Jiang Su Bai Lifeng Ma Longli Kang Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region School of MedicineXizang Minzu University Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region School of MedicineXizang Minzu University

Human oral microbes play a vital role in maintaining host metabolic *** Qinghai-Tibet Plateau is mainly characterized by high altitude,dry,cold,and *** oral microbiota is subject to selective pressure from the plateau environment,which affects the oral *** a few studies have focused on explored the characteristics of oral microbiota in high-altitude *** order to explore the relationship between high altitude environment and oral microbiota,we collected saliva samples from 167 Tibetans from four altitudes gradients(2800 to 4500 meters) in *** conduct two group(high altitude and ultra-high-altitude groups) analyses based on altitude,and adopt 16 S rRNA strategy for high-throughput *** study found that the alpha diversity of the decreased with the increasing in altitude,but the beta diversity increased with the increasing in *** analysis found that the oral microbial biomarker of highaltitude group(below 3650 meters) was Streptococcus;and the biomarker of ultra-high-altitude group(above 4000 meters)was *** relative abundance of Prevotella increased with the increasing in altitude,but the relative abundance of Streptococcus with the decrease in *** analysis found that the microbial network structure was more compact and complex,and the interaction between the bacteria genera were more intensive in the high-altitude *** function prediction results show that the amino acid and vitamin metabolic pathways in high altitude group were *** research shows that altitude was an important factor affecting the diversity and community structure of human oral microbiota.

关键词： Oral microbiota altitude Tibetans alpha diversity beta diversity

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