摘要：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 signifcant changes over time. Currently true indicator microbiomes based on long-term, multi-annual monitoring are not available. Results: Here, using samples from a continuous 20-year feld study encompassing seven fertilization strategies, we identifed 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 specifc 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 nitrifers (e.g., Nitrosospira multiformis) as well as plant pathogens (e.g., Bacillus anthracis) was observed in nutrientdefcit chemical fertilizations. Both microbiomes are expected to be valuable indictors in informing crop yield and soil fertility, regulated by agricultural management. Conclusions: Our fndings based on this more than 2-decade long feld study demonstrate the exciting potential of employing microorganisms and maximizing their functions in future agroecosystems. Our results report a “mostwanted” or “most-unwanted” list of microbial phylotypes that are ready candidates to guide the development of sustainable agriculture in alkaline soils.
