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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 birds.Microbiota extracted from feces has been widely used as a proxy for gut microbiota.Although several methods have been developed for microbial DNA extraction,their performances in the bird feces have not been systematacially evaluated yet.Methods: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 guild.Results:Bead method was the best on the performance of both DNA yield and DNA integrity regardless of dietary guild.In granivore,microbial relative abundance at both species and phylum levels,alpha diversity and cell lysis capacity were comparable among all methods.In omnivore,Qiagen had the best performance on alpha diversity,fol-lowed by Bead and MoBio.There were small variations on microbial relative abundance at both species and phylum levels among different extraction methods.MoBio exhibited the best performance on cell lysis capacity.In carnivore,considerable variations were found on microbial relative abundance at both species and phylum levels.Qiagen had the best performance on alpha diversity,followed by MoBio and Bead.MoBio had the highest cell lysis capacity.Conclusions:DNA yield and integrity have no obvious impact on microbial composition,alpha diversity or cell lysis capacity.The 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 birds.Either method could be used in granivore microbiota studies.For omnivores and carnivores,we recommend Qiagen method when the research purpose is microbial diversity and MoBi

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

Integrated tool for microsatellite isolation and validation from the reference genome and their application in the study of breeding turnover in an endangered avian population

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Integrative Zoology 2018年第5期13卷 553-568页

作者： Xian HOU Pengwei XU Zhenzhen LIN Josephine D’URBAN-JACKSON AndrewDIXON Batbayar BOLD Jiliang XU xiangjiang zhan Key Laboratory of Animal Ecology and Conservation Biology Institute of ZoologyChinese Academy of SciencesBeijingChina School of Nature Conservation Beijing Forestry UniversityBeijingChina BGI-Tech BGI-ShenzhenShenzhenChina Milner Centre for Evolution Department of Biology and BiochemistryUniversity of BathBathUK Emirates Falconers’Club Abu DhabiUnited Arab Emirates Cardiff University-Institute of Zoology Joint Laboratory for Biocomplexity Research BeijingChina Wildlife Science and Conservation Center UlaanbaatarMongolia Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunmingChina

Accurate individual identification is required to estimate survival rates in avian populations.For endangered species,non-invasive methods of obtaining individual identification,such as using molted feathers as a source of DNA for microsatellite markers,are preferred because of less disturbance,easy sample preparation and high efficiency.With the availability of many avian genomes,a few pipelines isolating genome-wide microsatellites have been published,but it is still a challenge to isolate microsatellites from the reference genome efficiently.Here,we have developed an integrated tool comprising a bioinformatic pipeline and experimental procedures for microsatellite isolation and validation based on the reference genome.We have identified over 95000 microsatellite loci and established a system comprising 10 highly polymorphic markers(PIC value:0.49–0.93,mean:0.79)for an endangered species,saker falcon(Falco cherrug).These markers(except 1)were successfully amplified in 126 molted feathers,exhibiting high amplification success rates(83.9–99.7%),high quality index(0.90–0.97)and low allelic dropout rates(1–9.5%).To further assess the efficiency of this marker system in a population study,we identified individual sakers using these molted feathers(adult)and 146 plucked feathers(offspring).The use of parent and offspring samples enabled us to infer the genotype of missing samples(N=28),and all adult genotypes were used to ascertain that breeding turnover is a useful proxy for survival estimation in sakers.Our study presents a cost-effective tool for microsatellite isolation based on publicly available reference genomes and demonstrates the power of this tool in estimating key parameters of avian population dynamics.

关键词： breeding turnover Falco cherrug feather microsatellite isolation parentage analysis reference genome saker falcon

Correction to:Performance comparison of different microbial DNA extraction methods on bird feces

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Avian Research 2021年第2期12卷 255-256页

Following publication of the original article(Hou et al.2021),the authors identified an error in Fig.1.The cor-rect figure is given below.The original article(Hou et al.2021)has been updated.

关键词： comparison figure updated

Wildlife conservation and management in China: achievements,challenges and perspectives

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National Science Review 2021年第7期8卷 26-30页

作者： Guangping Huang Xiaoge Ping Weihua Xu Yibo Hu Jiang Chang Ronald R.Swaisgood Jiang Zhou xiangjiang zhan Zejun zhang Yonggang Nie Jie Cui Michael Bruford Zhihe zhang Baoguo Li Li zhang Zhi Lv Fuwen Wei CAS Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences State Key Laboratory of Environmental Criteria and Risk Assessment Chinese Research Academy of Environmental Sciences School of Karst Sciences Guizhou Normal University Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education) China West Normal University Center for Nature and Society College of Life Sciences Peking University

Dramatic global changes to the environment have wrought unprecedented reductions in biodiversity, with>28%species assessed by the International Union for Conservation of Nature(IUCN) under the threat of extinction[1].... 详细信息

关键词： BIODIVERSITY SCIENCE

Mitochondrial complex I bridges a connection between regulation of carbon flexibility and gastrointestinal commensalism in the human fungal pathogen Candida albicans

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Mitochondrial complex I bridges a connection between regulat...

基于DNA条形码技术构建王朗国家级自然保护区陆生脊椎动物遗传资源数据库及物种鉴定

中国菌物学会第七届全国会员代表大会暨2017年学术年会

作者： Xinhua Huang Xiaoqing Chen Yongmin He Xiaoyu Yu Shanshan Li Ning Gao Lida Niu Yinhe Mao Yuanyuan Wang Xianwei Wu Wenjuan Wu Jianhua Wu Dongsheng Zhou xiangjiang zhan Changbin Chen Unit of Pathogenic Fungal Infection & Host Immunity CAS Key Laboratory of Molecular Virology &Immunology Institut Pasteur of Shanghai Chinese Academy of Sciences College of Life Science Shanghai University Department of Laboratory Medicine Shanghai East Hospital Tongji University School of medicine College of Life Science Shanghai Normal University Department of Dermatology Shanghai Changhai Hospital Second Military Medical University State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Key Laboratory of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences

Efficient assimilation of alternative carbon sources in glucose-limited host niches is critical for colonization of Candida albicans, a commensal yeast that frequently causes opportunistic infection in human. C. albicans evolved mechanistically to regulate alternative carbon assimilation for the promotion of fungal growth and commensalism in mammalian hosts. However, this highly adaptive mechanism that C. albicans employs to cope with alternative carbon assimilation has yet to be clearly understood. Here we identified a novel role of C. albicans mitochondrial complex I（CI） in regulating assimilation of alternative carbon sources such as mannitol. Our data demonstrate that CI dysfunction by deleting the subunit Nuo2 decreases the level of NAD+, downregulates the NAD+-dependent mannitol dehydrogenase activity, and consequently inhibits hyphal growth and biofilm formation in conditions when the carbon source is mannitol, but not fermentative sugars like glucose. Mannitoldependent morphogenesis is controlled by a ROS-induced signaling pathway involving Hog1 activation and Brg1 repression. In vivo studies show that nuo2Δ/Δ mutant cells are severely compromised in gastrointestinal colonization and the defect can be rescued by a glucose-rich diet. Thus,our findings unravel a mechanism by which C. albicans regulates carbon flexibility and commensalism.Alternative carbon assimilation might represent a fitness advantage for commensal fungi in successful colonization of host niches.

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生物多样性 2023年第7期31卷 83-95页

作者：邢超林依周智强赵联军蒋仕伟林蓁蓁徐基良詹祥江北京林业大学生态与自然保护学院北京100083 中国科学院动物研究所动物生态与保护生物学重点实验室北京100101 中国科学院大学北京100049 四川王朗国家级自然保护区管理局四川平武622550 平武县林业和草原局四川平武622550

DNA条形码(DNA barcode)是基因组中较短的、种内变异相对稳定的基因序列,已经成为生物多样性保护研究中物种鉴定、生物多样性评估的有力手段之一。四川王朗国家级自然保护区地处青藏高原东缘,属于世界生物多样性热点地区,具有丰富的生... 详细信息

DNA条形码(DNA barcode)是基因组中较短的、种内变异相对稳定的基因序列,已经成为生物多样性保护研究中物种鉴定、生物多样性评估的有力手段之一。四川王朗国家级自然保护区地处青藏高原东缘,属于世界生物多样性热点地区,具有丰富的生物资源,在我国珍稀动物保护领域具有重要地位。目前保护区已累积了大量的陆生脊椎动物监测数据,但缺乏遗传资源本底调查和基础的遗传资源数据库。本研究基于DNA条形码技术,以四川王朗国家级自然保护区为主要研究区域,基于样线法和博物馆标本调研,对所采集的314份样品进行DNA条形码分析,共鉴定兽类、鸟类、两栖类18目35科74种,首次获得了王朗齿突蟾(Scutigerwanglangensis)的线粒体基因(COI、12S-16S、16S、Cytb)及核基因(RAG1)的条形码序列信息,并通过比较不同监测方法说明了DNA条形码技术在动物多样性调查中的应用前景。本研究基于DNA条形码技术最终获得了216份DNA条形码数据,初步建立了保护区陆生脊椎动物遗传资源数据库,该数据库将为评估保护区生物多样性提供基础信息,为动物保护和管理工作提供技术支持。

关键词： DNA条形码王朗国家级自然保护区陆生脊椎动物生物多样性条形码数据库

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性别分配及鸟类子代性比研究进展

中国科学：生命科学 2019年第4期49卷 392-402页

作者：刘洋唐丹妮詹祥江中国科学院动物研究所中国科学院动物生态与保护生物学重点实验室北京100101 中国科学院大学生命科学学院北京100049 北京市第八中学怡海分校北京100070

性别分配涉及物种生存策略、个体适合度以及种群动态等多方面因素影响,一直受到研究人员的广泛关注.鸟类是性别分配研究的理想对象.当前,有关鸟类性别分配已有较多研究,其中,子代性比作为性别分配最直接的观测指标受到研究者的普遍关注... 详细信息

性别分配涉及物种生存策略、个体适合度以及种群动态等多方面因素影响,一直受到研究人员的广泛关注.鸟类是性别分配研究的理想对象.当前,有关鸟类性别分配已有较多研究,其中,子代性比作为性别分配最直接的观测指标受到研究者的普遍关注,其影响因素对于性别分配问题的研究具有指向性的意义,也因此成为该领域的一个研究热点.有关子代性比影响因素的研究主要集中在环境、亲代和子代三大方面,但是目前对于关键影响因素缺乏一般性结论,亲鸟对子代性比的控制能力及其内在作用机制也尚不明确,相关问题仍需不断探索.本文以性别分配研究得以发展的4个重要观点作为基础,对鸟类子代性比的相关研究及其进展进行了评述.

关键词：性别分配鸟类子代性比环境因素亲代因素子代因素

用物种分布模型和距离抽样估计三江源藏野驴、藏原羚和藏羚羊的数量

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中国科学：生命科学 2019年第2期49卷 151-162页

作者：李欣海郜二虎李百度詹祥江中国科学院动物研究所动物生态与保护生物学院重点实验室北京100101 中国科学院大学北京100049 国家林业和草原局调查规划设计院北京100714 中国人民大学附属中学北京100030

三江源国家公园成立后,人们需要了解该区域关键有蹄类物种如藏野驴(Equus kiang)、藏原羚(Procaprapicticaudata)和藏羚羊(Pantholops hodgsonii)等物种的分布和数量,以便制定相应的保护规划.我们于2014～2017年夏季在三江源53.8×10~4k... 详细信息

三江源国家公园成立后,人们需要了解该区域关键有蹄类物种如藏野驴(Equus kiang)、藏原羚(Procaprapicticaudata)和藏羚羊(Pantholops hodgsonii)等物种的分布和数量,以便制定相应的保护规划.我们于2014～2017年夏季在三江源53.8×10~4km^2的范围内进行了样线调查,考察行程总计14597.8 km,记录到藏野驴3711头,藏原羚1187只,藏羚羊423只.为了准确估计有蹄类的数量,我们用随机森林模型量化了物种分布与22个环境变量的关系,预测了三大有蹄类在整个区域的分布和数量,并通过样线调查的数据进行校正,得到藏野驴、藏原羚和藏羚羊在三江源研究区域的总数分别为44240头、13162只和2390只.四年来三大有蹄类数量稳定.我们应用距离抽样的探测函数、随机森林模型中环境变量对物种数量的解释程度以及调查结果和模型结果的匹配程度进行不确定性分析,计算了动物估计数量的置信区间.我们建立了新的动物数量估计方法,适合于动物分布与环境变量关系密切并有样线调查结果的情况.

关键词：三江源国家公园野生动物数量估计物种分布模型距离抽样有蹄类

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大熊猫保护区的生态系统服务价值

科学新闻 2019年第2期 120-120页

作者：魏辅文 Robert Costanza Qiang Dai Natalie Stoeckl Xiaodong Gu Stephen Farber Yonggang Nie Ida Kubiszewski Yibo Hu Ronald Swaisgood Xuyu Yang Michael Bruford Youping Chen Alexey Voinov Dunwu Qi Megan Owen Li Yan Daniel C.Kenny Zejun zhang Rong Hou Shiwei Jiang Hongbo Liu xiangjiang zhan Li zhang Biao Yang Lianjun Zhao Xiaoguang Zheng Wenliang Zhou Yali Wen Heran Gao Wen zhang 中国科学院中国科学院动物研究所

文章简介全球生态系统服务价值估计每年为125万亿美元,相似的国家和区域层面的评估也显示生态系统服务价值足以支撑我们的生活。所有的生态系统服务价值评估都肯定了生物多样性的重要作用,尽管全球的生物多样性

关键词：大熊猫保护区生态系统服务价值生物多样性