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Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats
Li, Shuzhen; Deng, Ye; Du, Xiongfeng; Feng, Kai; Wu, Yueni; He, Qing; Wang, Zhujun; Liu, Yangying; Wang, Danrui; Peng, Xi; Zhang, Zhaojing; Escalas, Arthur; Qu, Yuanyuan
2021-05-01
Source PublicationSCIENCE OF THE TOTAL ENVIRONMENT
ISSN0048-9697
Volume767Pages:-
AbstractDue to the massive quantity and broad phylogeny, an accurate measurement of microbial diversity is highly challenging in soil ecosystems. Initially, the deviation caused by sampling should be adequately considered. Here, we attempted to uncover the effect of different sampling strategies on a diversity measurement of soil prokaryotes. Four 1 m(2) sampling quadrats in a typical grassland were thoroughly surveyed through deep 16S rRNA gene sequencing (over 11 million reads per quadrat) with numerous replicates (33 soil sampling cores with total 141 replicates per quadrat). We found the difference in diversity was relatively small when pooling soil cores before and after DNA extraction and sequencing, but they were both superior to a non-pooling strategy. Pooling a small number of soil cores (i.e., 5 or 9) combined with several technical replicates is sufficient to estimate diversities for soil prokaryotes, and there is great flexibility in pooling original samples or data at different experimental steps. Additionally, the distribution of local alpha diversity varies with sampling core number, sequencing depth, and abundance distribution of the community, especially for high orders of Hill diversity index (Le., Shannon entropy and inverse Simpson index). For each grassland soil quadrat (1 m(2)), retaining 100,000 reads after taxonomic dustering might be a realistic option, as these number of reads can efficiently cover the majority of common species in this area. Our findings provide important guidance for soil sampling strategy, and the general results can serve as a basis for further studies. (C) 2021 Elsevier B.V. All rights reserved.
Department中国科学院环境生物技术重点实验室
KeywordSampling strategy alpha diversity Pooling Biological replicate Common species Hill number
WOS Research AreaEnvironmental Sciences
Document Type期刊论文
Identifierhttps://ir.rcees.ac.cn/handle/311016/46152
Collection中国科学院环境生物技术重点实验室
Affiliation1.Chinese Acad Sci, Res Ctr Ecoenvironm Sci, CAS Key Lab Environm Biotechnol, Beijing 100085, Peoples R China
2.Dalian Univ Technol, Sch Environm Sci & Technol, Minist Educ, Key Lab Ind Ecol & Environm Engn, Dalian 116024, Liaoning, Peoples R China
3.Univ Chinese Acad Sci, Coll Resources & Environm, Beijing 100049, Peoples R China
4.Shandong Univ, Inst Marine Sci & Technol, Qingdao, Peoples R China
5.Univ Montpellier, MARBEC, CNRS, IRD,IFREMER, F-34090 Montpellier 5, France
Recommended Citation
GB/T 7714
Li, Shuzhen,Deng, Ye,Du, Xiongfeng,et al. Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats[J]. SCIENCE OF THE TOTAL ENVIRONMENT,2021,767:-.
APA Li, Shuzhen.,Deng, Ye.,Du, Xiongfeng.,Feng, Kai.,Wu, Yueni.,...&Qu, Yuanyuan.(2021).Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats.SCIENCE OF THE TOTAL ENVIRONMENT,767,-.
MLA Li, Shuzhen,et al."Sampling cores and sequencing depths affected the measurement of microbial diversity in soil quadrats".SCIENCE OF THE TOTAL ENVIRONMENT 767(2021):-.
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