Beyond the snapshot: identification of the timeless, enduring indicator microbiome informing soil fertility and crop production in alkaline soils

Zhang, Jianwei, Dolfing, Jan, Liu, Wenjing, Chen, Ruirui, Zhang, Jiabao, Lin, Xiangui and Feng, Youzhi (2022) Beyond the snapshot: identification of the timeless, enduring indicator microbiome informing soil fertility and crop production in alkaline soils. Environmental Microbiomes, 17 (1). p. 25. ISSN 2524-6372

s40793-022-00420-6.pdf - Published Version
Available under License Creative Commons Attribution 4.0.

Download (3MB) | Preview
Official URL:


Microorganisms are known to be important drivers of biogeochemical cycling in soil and hence could act as a proxy informing on soil conditions in ecosystems. Identifying microbiomes indicative for soil fertility and crop production is important for the development of the next generation of sustainable agriculture. Earlier researches based on one-time sampling have revealed various indicator microbiomes for distinct agroecosystems and agricultural practices as well as their importance in supporting sustainable productivity. However, these microbiomes were based on a mere snapshot of a dynamic microbial community which is subject to significant changes over time. Currently true indicator microbiomes based on long-term, multi-annual monitoring are not available.

Here, using samples from a continuous 20-year field study encompassing seven fertilization strategies, we identified the indicator microbiomes ecophysiologically informing on soil fertility and crop production in the main agricultural production base in China. Among a total of 29,184 phylotypes in 588 samples, we retrieved a streamlined consortium including 2% of phylotypes that were ubiquitously present in alkaline soils while contributing up to half of the whole community; many of them were associated with carbon and nutrient cycling. Furthermore, these phylotypes formed two opposite microbiomes. One indicator microbiome dominated by Bacillus asahii, characterized by specific functional traits related to organic matter decomposition, was mainly observed in organic farming and closely associated with higher soil fertility and crop production. The counter microbiome, characterized by known nitrifiers (e.g., Nitrosospira multiformis) as well as plant pathogens (e.g., Bacillus anthracis) was observed in nutrient-deficit chemical fertilizations. Both microbiomes are expected to be valuable indictors in informing crop yield and soil fertility, regulated by agricultural management.

Our findings based on this more than 2-decade long field study demonstrate the exciting potential of employing microorganisms and maximizing their functions in future agroecosystems. Our results report a “most-wanted” or “most-unwanted” list of microbial phylotypes that are ready candidates to guide the development of sustainable agriculture in alkaline soils.

Item Type: Article
Additional Information: Funding information: This work is supported by the National Natural Science Foundation of China (Project No. 41771294), National Key R&D Program (2019YFC1520700) and the Youth Innovation Promotion Association, CAS (Member No. 2014271).
Uncontrolled Keywords: Fertilization, Soil fertility, Soil Microorganisms, Sustainable Agroecosystem, Archived Soils
Subjects: C700 Molecular Biology, Biophysics and Biochemistry
F200 Materials Science
Department: Faculties > Engineering and Environment > Mechanical and Construction Engineering
Depositing User: Rachel Branson
Date Deposited: 14 Jun 2022 10:48
Last Modified: 14 Jun 2022 11:00

Actions (login required)

View Item View Item


Downloads per month over past year

View more statistics