Pedosphere 30(1): 5--17, 2020
ISSN 1002-0160/CN 32-1315/P
©2020 Soil Science Society of China
Published by Elsevier B.V. and Science Press
Beyond microbial diversity for predicting soil functions: A mini review
Paolo NANNIPIERI1, Judith ASCHER-JENULL2, Maria Teresa CECCHERINI1, Giacomo PIETRAMELLARA1, Giancarlo RENELLA1, Michael SCHLOTER3
1Department of Agriculture, Food, Environment and Forestry, University of Firenze, P. le delle Cascine 28, Firenze 50144(Italy)
2Department of Microbiology, University of Innsbruck, Technikerstrasse 25 d, Innsbruck 6020(Austria)
3Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, Neuherberg 85764(Germany)
Corresponding Author:Paolo NANNIPIERI
ABSTRACT
      Since the advent of sequencing technologies, the determination of microbial diversity to predict microbial functions, which are the major determinants of soil functions, has become a major topic of interest, as evidenced by the 900 publications dealing with soil metagenome published up to 2017. However, the detection of a gene in soil does not mean that the relative function is expressed, and the presence of a particular taxon does not mean that the relative functions determined in pure culture also occur in the studied soil. Another critical step is to link microbial community composition or function to the product analyzed to determine flux rates. Indeed, flux rates might not only be highly dynamic, but several metabolites can depend on different reactions, which makes the link to one process of interest difficult or even impossible. This review also discusses biases caused by sampling, storage of samples, DNA extraction and purification, sequencing (amplicon-vs. metagenome sequencing), and bioinformatic data analysis. Insights and the limits of predicting microbial interactions by network inference methods are critically discussed, and finally, future directions for a better understanding of soil functions by using measurements of microbial diversity are presented.
Key Words:  cultivation-based approach,DNA-based approach,flux rate,network inference method,omics technology,rare biosphere,soil metagenome
Citation: Nannipieri P, Ascher-Jenull J, Ceccherini M T, Pietramellara G, Renella G, Schloter M. 2020. Beyond microbial diversity for predicting soil functions:A mini review. Pedosphere. 30(1):5-17.
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