中国土壤微生物多样性监测的现状和思考

doi:10.17520/biods.2015345

生物多样性 ›› 2016, Vol. 24 ›› Issue (11): 1240-1248. DOI: 10.17520/biods.2015345 cstr: 32101.14.biods.2015345

所属专题：生物多样性与生态系统功能；土壤生物与土壤健康

• 中国生物多样性监测与研究网络专题 • 上一篇下一篇

中国土壤微生物多样性监测的现状和思考

李香真^1,,A;^*, 郭良栋², 李家宝¹, 姚敏杰¹

1.中国科学院成都生物研究所环境与应用重点实验室, 环境微生物四川省重点实验室, 成都 610041
2 .中国科学院微生物研究所真菌学国家重点实验室, 北京 100101

收稿日期:2015-12-07 接受日期:2016-03-29 出版日期:2016-11-20 发布日期:2016-12-14
通讯作者: 李香真
基金资助:
国家自然科学基金(41371268, 31400458)、中国生物多样性监测与研究网络(Sino BON)和中国科学院科学数据库项目(XXH12504-3-18)

Soil microbial diversity observation in China: current situation and future consideration

Xiangzhen Li^1,^*, Liangdong Guo², Jiabao Li¹, Minjie Yao¹

1 Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041
2 State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101

Received:2015-12-07 Accepted:2016-03-29 Online:2016-11-20 Published:2016-12-14
Contact: Li Xiangzhen

摘要/Abstract

摘要：

土壤微生物多样性研究是整个生态系统研究中最薄弱的环节之一。高通量测序技术和生物信息学方法的快速发展极大地促进了土壤微生物多样性监测研究的深度和广度。目前世界范围内已经开展了一些综合的微生物多样性研究计划, 如地球微生物计划。这些计划存在的主要问题是缺少动态的监测、研究方法不统一、数据整合困难等。中国土壤微生物多样性监测网(Soil Microbial Observation Network, SMON)是中国生物多样性监测与研究网络(Chinese Biodiversity Monitoring and Research Network, Sino BON)的重要组成部分, 本文中我们对该监测网的建设提出了一些思考。在监测布局上建议选择我国南北水热梯度下的森林生态系统、东西降雨梯度下的草原生态系统、典型湿地生态系统及重要农田生态系统, 同时依托现已建成的生物多样性监测网络观测点或大样地, 布设监测样点, 利用现代环境基因组学和生物信息学技术, 重点围绕土壤微生物群落和功能基因组的组成与多样性, 开展长期定点的动态监测。监测的结果将以名录、数据集或图鉴的形式发布, 包括中国典型生态系统中土壤细菌、古菌、真菌与地衣、土壤宏基因组和重要功能基因的组成和多样性等数据, 同时建设土壤生物大数据平台, 达到监测数据的储存、查询、分析、下载、成图的功能。通过土壤微生物多样性监测, 将阐明我国重要森林、草地、湿地、农田生态系统中土壤微生物组成、多样性、功能基因的时空变化特征和驱动机制, 建立土壤微生物多样性变化与生态系统功能的关系及相关的模型, 预测全球环境条件变化下土壤微生物的演变规律, 为土壤微生物多样性资源的保护和利用提供科学依据。

关键词: 土壤微生物群落, 多样性, 监测网, 环境基因组, 生态系统功能

Abstract

Soil microbial diversity has not been extensively observed due to technique limitations. With the development of the high-throughput sequencing technique and bioinformatics, much progress has been made in observations of microbial diversity. Currently, international microbiome initiatives have been founded (including the Earth Microbial Project). However, problems in these projects include a lack of dynamic observations, differences in observational methods, and data integration. The soil microbial observation network (SMON) is an important part of the Chinese Biodiversity Monitoring and Research Network (Sino BON). The observational network initially selected field observation sites in forest ecosystems along a temperature and precipitation gradient from south to north, in grassland ecosystems along a precipitation transect from east to west, and in typical wetland and agricultural ecosystems in China. Field ecological observation stations have been established in these selected ecosystems. Key tasks for the SMON are to observe spatial and temporal dynamics of soil microbial communities and functional genes in various ecosystems, including bacteria, archaea, fungi, and lichens. Observational data will be published periodically in the format of database, annals, and illustrated handbooks. Key methods used in the SMON are high- throughput sequencing, metagenomics, and bioinformatics. A soil biota database is currently being constructed to store observational data for public inquiry and analysis. Through the efforts of SMON, we plan to explore the driving mechanisms of spatial and temporal variations of soil microbial communities and their functional genes, and understand the relationships between microbial diversity and ecosystem function, in order to predict microbial dynamics under global environmental change scenarios, and to design strategies to protect soil microbial diversity and properly utilize microbial resources.

Key words: soil microbial community, diversity, monitoring network, metagenomics, ecosystem function

李香真, 郭良栋, 李家宝, 姚敏杰 (2016) 中国土壤微生物多样性监测的现状和思考. 生物多样性, 24, 1240-1248. DOI: 10.17520/biods.2015345.

Xiangzhen Li, Liangdong Guo, Jiabao Li, Minjie Yao (2016) Soil microbial diversity observation in China: current situation and future consideration. Biodiversity Science, 24, 1240-1248. DOI: 10.17520/biods.2015345.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2015345

https://www.biodiversity-science.net/CN/Y2016/V24/I11/1240

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监测内容 Observation items	监测方法 Approaches	主要指标 Main aims
监测点的基本生态、地理信息数据采集 Ecological and geographic information collection	野外直接测量、数据收集等 Field observation, data collection	地理坐标、气候参数(温度、降雨等)、植被组成、生物量、土地利用类型等 Geographic coordinate, climate parameters (temperature, precipitation), plant composition and biomass, land use types
土壤微生物的群落组成和多样性(真菌、细菌、古菌等) Soil microbial community composition and diversity (fungi, bacteria, archaea)	高通量测序(Hiseq、Miseq)、生物信息学分析 High-throughput sequencing (Hiseq, Miseq), bioinformatics analysis	鉴定出微生物的系统组成和多样性 Revealing soil microbial community composition and diversity
土壤基因组的组成和多样性 Soil genomic composition and diversity	高通量测序(Hiseq)、定量PCR High-throughput sequencing, quantitative PCR	鉴定出土壤微生物群落的功能基因组成和多样性 Revealing soil microbial functional gene composition and diversity
重点森林样地大型真菌监测 Observation of macrofungi in typical forest ecosystems	野外样线调查、形态观察、生理特征检测等 Field study, morphology observation, physiology study	完成重点森林样地的大型真菌组成和多样性调查及生理生态特征描述 Revealing soil macrofungal composition, diversity and physiological characteristics
土壤微生物过程监测 Observation of microbial processes	野外直接测定 Field measurement	重点监测与温室气体排放、养分循环相关的过程 Revealing the processes related to greenhouse gas flux and nutrient cycling
土壤微生物的分离、纯化和生理鉴定 Isolation, purification and characteristics of soil microorganisms	微生物分离培养技术 Microbial isolation and culturing techniques	分离纯化鉴定重要的微生物菌种资源 Isolating and identifying important microorganisms

监测内容 Observation items	监测方法 Approaches	主要指标 Main aims
监测点的基本生态、地理信息数据采集 Ecological and geographic information collection	野外直接测量、数据收集等 Field observation, data collection	地理坐标、气候参数(温度、降雨等)、植被组成、生物量、土地利用类型等 Geographic coordinate, climate parameters (temperature, precipitation), plant composition and biomass, land use types
土壤微生物的群落组成和多样性(真菌、细菌、古菌等) Soil microbial community composition and diversity (fungi, bacteria, archaea)	高通量测序(Hiseq、Miseq)、生物信息学分析 High-throughput sequencing (Hiseq, Miseq), bioinformatics analysis	鉴定出微生物的系统组成和多样性 Revealing soil microbial community composition and diversity
土壤基因组的组成和多样性 Soil genomic composition and diversity	高通量测序(Hiseq)、定量PCR High-throughput sequencing, quantitative PCR	鉴定出土壤微生物群落的功能基因组成和多样性 Revealing soil microbial functional gene composition and diversity
重点森林样地大型真菌监测 Observation of macrofungi in typical forest ecosystems	野外样线调查、形态观察、生理特征检测等 Field study, morphology observation, physiology study	完成重点森林样地的大型真菌组成和多样性调查及生理生态特征描述 Revealing soil macrofungal composition, diversity and physiological characteristics
土壤微生物过程监测 Observation of microbial processes	野外直接测定 Field measurement	重点监测与温室气体排放、养分循环相关的过程 Revealing the processes related to greenhouse gas flux and nutrient cycling
土壤微生物的分离、纯化和生理鉴定 Isolation, purification and characteristics of soil microorganisms	微生物分离培养技术 Microbial isolation and culturing techniques	分离纯化鉴定重要的微生物菌种资源 Isolating and identifying important microorganisms

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中国土壤微生物多样性监测的现状和思考

Soil microbial diversity observation in China: current situation and future consideration

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