Zhang Jianwei, Dolfing Jan, Liu Wenjing, Chen Ruirui, Zhang Jiabao, Lin Xiangui, Feng Youzhi
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, People's Republic of China.
University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
Environ Microbiome. 2022 May 12;17(1):25. doi: 10.1186/s40793-022-00420-6.
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.
已知微生物是土壤中生物地球化学循环的重要驱动因素，因此可以作为了解生态系统土壤状况的一个指标。识别指示土壤肥力和作物产量的微生物群落对于下一代可持续农业的发展至关重要。早期基于一次性采样的研究已经揭示了不同农业生态系统和农业实践中的各种指示微生物群落，以及它们在支持可持续生产力方面的重要性。然而，这些微生物群落只是动态微生物群落的一个快照，随着时间的推移会发生显著变化。目前，基于长期、多年监测的真正指示微生物群落尚不存在。
在这里，我们使用了一项为期20年的连续田间研究的样本，该研究涵盖了七种施肥策略，我们在中国主要农业生产基地确定了从生态生理学角度指示土壤肥力和作物产量的指示微生物群落。在588个样本中的总共29184个系统发育型中，我们获得了一个精简的群落，其中包括2%的系统发育型，这些系统发育型普遍存在于碱性土壤中，同时占整个群落的一半；其中许多与碳和养分循环有关。此外，这些系统发育型形成了两个相反的微生物群落。一个以浅井芽孢杆菌为主导的指示微生物群落，其特征是与有机物分解相关的特定功能特性，主要出现在有机农业中，并且与较高的土壤肥力和作物产量密切相关。在营养缺乏的化肥施用中观察到了相反的微生物群落，其特征是已知的硝化细菌（如多形亚硝化单胞菌）以及植物病原体（如炭疽芽孢杆菌）。预计这两种微生物群落都是在农业管理调控下指示作物产量和土壤肥力的有价值指标。
我们基于这项长达20多年的田间研究的结果表明，在未来的农业生态系统中利用微生物并最大限度地发挥其功能具有令人兴奋的潜力。我们的结果报告了一份微生物系统发育型的“最需要”或“最不需要”清单，这些系统发育型是指导碱性土壤可持续农业发展的现成候选者。
