Biodiversity Science ›› 2016, Vol. 24 ›› Issue (11): 1240-1248.doi: 10.17520/biods.2015345


• Orginal Article • Previous Article     Next Article

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

Xiangzhen Li1, *, Liangdong Guo2, Jiabao Li1, Minjie Yao1   

  1. 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:2016-12-14
  • Li Xiangzhen

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

Fig. 1

General scientific goals and outline of soil microbial observation network"

Table 1

Observation items, approaches and main aims of soil microbial diversity"

Observation items
Main aims
Ecological and geographic information collection
Field observation, data collection
Geographic coordinate, climate parameters (temperature, precipitation), plant composition and biomass, land use types
Soil microbial community composition and diversity (fungi, bacteria, archaea)
High-throughput sequencing (Hiseq, Miseq), bioinformatics analysis
Revealing soil microbial community composition and diversity
Soil genomic composition and diversity
High-throughput sequencing,
quantitative PCR
Revealing soil microbial functional gene composition and diversity
Observation of macrofungi in typical forest ecosystems
Field study, morphology observation, physiology study
Revealing soil macrofungal composition, diversity and physiological characteristics
Observation of microbial processes
Field measurement
Revealing the processes related to greenhouse gas flux and nutrient cycling
Isolation, purification and
characteristics of soil microorganisms
Microbial isolation and culturing techniques
Isolating and identifying important microorganisms

Fig. 2

General technique route used in the soil microbial observation network"

1 Amaral-Zettler LA, McCliment EA, Ducklow HW, Huse SM (2009) A method for studying protistan diversity using massively parallel sequencing of V9 hypervariable regions of small-subunit ribosomal RNA genes. PLoS ONE, 4, e6372.
2 Butterbach-Bahl K, Baggs EM, Dannenmann M, Kiese R, Zechmeister-Boltenstern S (2013) Nitrous oxide emissions from soils: how well do we understand the processes and their controls? Philosophical Transactions of the Royal Society B, 368. doi: 10.1098/rstb.2013.0122
3 Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335-336.
4 Dubilier N, McFall-Ngai M, Zhao LP (2015) Create a global microbiome effort. Nature, 526, 631-641.
5 Fierer N, Jackson RB (2006) The diversity and biogeography of soil bacterial communities. Proceedings of the National Academy of Sciences, USA, 103, 626-631.
6 Gao C, Shi NN, Liu YX, Peay KG, Zheng Y, Ding Q, Mi XC, Ma KP, Wubet T, Buscot F, Guo LD (2013) Host plant genus-level diversity is the best predictor of ectomycorrhizal fungal diversity in a Chinese subtropical forest. Molecular Ecology, 22, 3403-3414.
7 Gao C, Zhang Y, Shi NN, Zheng Y, Chen L, Wubet T, Bruelheide H, Both S, Buscot F, Ding Q, Erfmeier A, Kühn P, Nadrowski K, Scholten T, Guo LD (2015) Community assembly of ectomycorrhizal fungi along a subtropical secondary forest succession. New Phytologist, 205, 771-785.
8 Gilbert JA, Jansson JK, Knight R (2014) The Earth Micro- biome project: successes and aspirations. BMC Biology, 12, 69. doi: 10.1186/s12915-014-0069-1.
9 Gonzalez A, King A, Robeson II MS, Song S, Shade A, Metcalf JL, Knight R (2012) Characterizing microbial communities through space and time. Current Opinion in Biotechnology, 23, 431-436.
10 Jia ZJ (2016) 2015 Nobel Prize and soil microbiology—culture-dependent study warrants more attention. Acta Pedologica Sinica, 53, 12-15. (in Chinese with English abstract)
[贾仲君 (2016) 2015年诺贝尔生理学或医学奖的启示——土壤微生物分离培养推动了寄生虫病防治. 土壤学报, 53, 12-15.]
11 Lemanceau P (2011) EcoFINDERS: characterizing biodiversity and soil functioning in Europe. 23 partners from 10 European countries and China. Biofutur, 326, 56-58.
12 Liu C, Li JB, Rui JP, An JX, Li XZ (2015) The applications of the 16S rRNA gene in microbial ecology: current situation and problems. Acta Ecologica Sinica, 35, 1-9. (in Chinese with English abstract)
[刘驰, 李家宝, 芮俊鹏, 安家兴, 李香真 (2015) 16S rRNA 基因在微生物生态学中的应用: 现状和问题. 生态学报, 35, 1-9.]
13 Liu JJ, Sui YY, Yu ZH, Shi Y, Chu HY, Jin J, Liu XB, Wang GH (2014) High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China. Soil Biology and Biochemistry, 70, 113-122.
14 Liu JJ, Sui YY, Yu ZH, Shi Y, Chu HY, Jin J, Liu XB, Wang GH (2015) Soil carbon content drives the biogeographical distribution of fungal communities in the black soil zone of northeast China. Soil Biology and Biochemistry, 83, 29-39.
15 Lu YH, Fu SL, Chu HY, Yang YF, Liu ZF (2015) Recent advances in global change and soil biology. Science Foundation in China, 29(1), 19-24. (in Chinese with English abstract)
[陆雅海, 傅声雷, 褚海燕, 杨云锋, 刘占锋 (2015) 全球变化背景下的土壤生物学研究进展. 中国科学基金, 29(1), 19-24.]
16 Lynch JM, Benedetti A, Insam H, Nuti MP, Smalla K, Torsvik V, Nannipieri P (2004) Microbial diversity in soil: ecological theories, the contribution of molecular techniques and the impact of transgenic plants and transgenic microorganisms. Biology and Fertility of Soils, 40, 363-385.
17 Ma KP (2015) Biodiversity monitoring in China: from CForBio to Sino BON. Biodiversity Science, 23, 1-2.
[马克平 (2015) 中国生物多样性监测网络建设: 从CForBio到Sino BON. 生物多样性, 23, 1-2.]
18 Oberhardt MA, Zarecki R, Gronow S, Lang E, Klenk H, Gophna U, Ruppin E (2015) Harnessing the landscape of microbial culture media to predict new organism-media pairings. Nature Communications, 6, 8493.
19 Ohtonen R, Aikio S, Väre H (1997) Ecological theories in soil biology. Soil Biology and Biochemistry, 29, 1613-1619.
20 Orgiazzi A, Dunbar MB, Panagos P, de Groot GA, Lemanceau P (2015) Soil biodiversity and DNA barcodes: opportunities and challenges. Soil Biology and Biochemistry, 80, 244-250.
21 Rasche F, Knapp D, Kaiser C, Koranda M, Kitzler B, Zechmeister-Boltenstern S, Richter A, Sessitsch A (2011) Seasonality and resource availability control bacterial and archaeal communities in soils of a temperate beech forest. ISME Journal, 5, 389-402.
22 Rui JP, Li JB, Wang SP, An JX, Liu W-T, Lin QY, Yang YF, He ZL, Li XZ (2015) Responses of bacterial communities to simulated climate changes in alpine meadow soil of Qinghai-Tibet Plateau. Applied and Environmental Microbiology, 81, 6070-6077.
23 Shade A, Caporaso JG, Handelsman J, Knight R, Fierer N (2013) A meta-analysis of changes in bacterial and archaeal communities with time. ISME Journal, 7, 1493-1506.
24 Shen CC, Liang WJ, Shi Y, Lin XG, Zhang HY, Wu X, Xie G, Chain P, Grogan P, Chu HY (2014) Contrasting elevational diversity patterns between eukaryotic soil microbes and plants. Ecology, 95, 3190-3202.
25 Shen CC, Xiong JB, Zhang HY, Feng YZ, Lin XG, Li XY, Liang WJ, Chu HY (2013) Soil pH drives the spatial distribution of bacterial communities along elevation on Changbai Mountain. Soil Biology and Biochemistry, 57, 204-211.
26 Song CQ, Wu JS, Lu YH, Shen QR, He JZ, Huang QY, Jia ZJ, Leng SY, Zhu YG (2013) Advances of soil microbiology in the last decade in China. Advances in Earth Science, 28, 1087-1105. (in Chinese with English abstract)
[宋长青, 吴金水, 陆雅海, 沈其荣, 贺纪正, 黄巧云, 贾仲君, 冷疏影, 朱永官 (2013) 中国土壤微生物学研究十年回顾. 地球科学进展, 28, 1087-1105.]
27 Tedersoo L, Bahram M, Põlme S, Kõljalg U, Yorou NS, Wijesundera R, Ruiz LV, Vasco-Palacios AM, Thu PQ, Suija A, Smith ME, Sharp C, Saluveer E, Saitta A, Rosas M, Riit T, Ratkowsky D, Pritsch K, Põldmaa K, Piepenbring M, Phosri C, Peterson M, Parts K, Pärtel K, Otsing E, Nouhra E, Njouonkou AL, Nilsson RH, Morgado LN, Mayor J, May TW, Majuakim L, Lodge DJ, Lee SS, Larsson K, Kohout P, Hosaka K, Hiiesalu I, Henkel TW, Harend H, Guo LD, Greslebin A, Grelet G, Geml J, Gates G, Dunstan W, Dunk C, Drenkhan R, Dearnaley J, Kesel AD, Dang T, Chen X, Buegger F, Brearley FQ, Bonito G, Anslan S, Abell S, Abarenkov K (2014) Global diversity and geography of soil fungi. Science, 346, 1256688.
28 Torsvik V, Øvreås L (2002) Microbial diversity and function in soil: from genes to ecosystems. Current Opinion in Microbiology, 5, 240-245.
29 Veresoglou SD, Halley JM, Rillig MC (2015) Extinction risk of soil biota. Nature Communications, 6, 8862.
30 Wang XB, Van Nostrand JD, Deng Y, Lu XT, Wang C, Zhou JJ, Han XG (2015) Scale-dependent effects of climate and geographic distance on bacterial diversity patterns across northern China’s grasslands. FEMS Microbiology Ecology, 91. doi: 10.1093/femsec/fiv133.
31 Yao MJ, Rui JP, Li JB, Dai YM, Bai YF, Heděnec P, Wang JM, Zhang SH, Pei KQ, Liu C, Wang YF, He ZL, Frouz J, Li XZ (2014) Rate-specific responses of prokaryotic diversity and structure to nitrogen deposition in the Leymus chinensis steppe. Soil Biology and Biochemistry, 79, 81-90.
[1] Yi Li Zhiyao Tang Yujing Yan Ke Wang Lei Cai Jinsheng He Song Gu Yijian Yao. (2020) Incorporating species distribution modelling into the red list assessment and conservation of macrofungi: A case study with Ophiocordyceps sinensis . Biodiv Sci, 28(1): 0-0.
[2] Wenying Zhuang Yi Li Huandi Zheng Zhaoqing Zeng Xincun Wang. (2020) Threat status of macro-ascomycetes in China and analysis of its threatening factors . Biodiv Sci, 28(1): 0-0.
[3] Shun Li, Liang Zou, Yinan Gong, Haitao Yang, Tianming Wang, Limin Feng, Jianping Ge. (2019) Advances in LiDAR technology in the field of animal ecology . Biodiv Sci, 27(9): 1021-1031.
[4] Rui Yang, Qinyi Peng, Yue Cao, Le Zhong, Shuyu Hou, Zhicong Zhao, Cheng Huang. (2019) Transformative changes and paths toward biodiversity conservation in China . Biodiv Sci, 27(9): 1032-1040.
[5] FANG Wen-Jing,CAI Qiong,ZHU Jiang-Ling,JI Cheng-Jun,YUE Ming,GUO Wei-Hua,ZHANG Feng,GAO Xian-Ming,TANG Zhi-Yao,FANG Jing-Yun. (2019) Distribution, community structures and species diversity of larch forests in North China . Chin J Plant Ecol, 43(9): 742-752.
[6] Yongmin Li, Xiaobing Wu. (2019) A revised species list of amphibians and reptiles in the Anhui Province . Biodiv Sci, 27(9): 1002-1011.
[7] XU Jin-Shi,CHAI Yong-Fu,LIU Xiao,YUE Ming,GUO Yao-Xin,KANG Mu-Yi,LIU Quan-Ru,ZHENG Cheng-Yang,JI Cheng-Jun,YAN Ming,ZHANG Feng,GAO Xian-Ming,WANG Ren-Qing,SHI Fu-Chen,ZHANG Qin-Di,WANG Mao. (2019) Community assembly, diversity patterns and distributions of broad-leaved forests in North China . Chin J Plant Ecol, 43(9): 732-741.
[8] TANG Li-Li,YANG Tong,LIU Hong-Yan,KANG Mu-Yi,WANG Ren-Qing,ZHANG Feng,GAO Xian-Ming,YUE Ming,ZHANG Mei,ZHENG Pu-Fan,SHI Fu-Chen. (2019) Distribution and species diversity patterns of Vitex negundo var. heterophylla shrublands in North China . Chin J Plant Ecol, 43(9): 825-833.
[9] SHI Jing-Jing,ZHAO Ming-Fei,WANG Yu-Hang,XUE Feng,KANG Mu-Yi,JIANG Yuan. (2019) Community assembly of herbaceous layer of the planted forests in the central Loess Plateau, China . Chin J Plant Ecol, 43(9): 834-842.
[10] QIN Hao,ZHANG Yin-Bo,DONG Gang,ZHANG Feng. (2019) Altitudinal patterns of taxonomic, phylogenetic and functional diversity of forest communities in Mount Guandi, Shanxi, China . Chin J Plant Ecol, 43(9): 762-773.
[11] Zihong Chen, Yuanbing Wang, Yongdong Dai, Kai Chen, Ling Xu, Qingcheng He. (2019) Species diversity and seasonal fluctuation of entomogenous fungi of Ascomycota in Taibaoshan Forest Park in western Yunnan . Biodiv Sci, 27(9): 993-1001.
[12] Yibo Tan, Wenhui Shen, Zi Fu, Wei Zheng, Zhiyang Ou, Zhangqiang Tan, Yuhua Peng, Shilong Pang, Qinfei He, Xiaorong Huang, Feng He. (2019) Effect of environmental factors on understory species diversity in Southwest Guangxi Excentrodendron tonkinense forests . Biodiv Sci, 27(9): 970-983.
[13] Jun Liu, Ning Wang, Daizong Cui, Lei Lu, Min Zhao. (2019) Community structure and diversity of soil bacteria in different habitats of Da Liangzihe National Forest Park in the Lesser Khinggan Mountains . Biodiv Sci, 27(8): 911-918.
[14] Meilin Lü, Ze Liu, Zhen Song, Yaning Wang, Xiaoyong Liu. (2019) Diversity and distribution of culturable Mucoromycota fungi in the Greater Khinggan Mountains, China . Biodiv Sci, 27(8): 821-832.
[15] Jun Liu, Ning Wang, Daizong Cui, Lei Lu, Min Zhao. (2019) Diversity of bacterial resources in the Greater and Lesser Khinggan Mountains . Biodiv Sci, 27(8): 903-910.
Full text