Department of Microbiology, Key Lab of Microbiology for Agricultural Environment, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
Newe Ya'ar Research Center, Agricultural Research Organization, P.O. Box 1021, Ramat Yishay, 30095, Israel.
ISME J. 2019 Feb;13(2):494-508. doi: 10.1038/s41396-018-0288-5. Epub 2018 Oct 5.
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine-a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.
微生物群落在生物地球化学循环中起着至关重要的作用，使各种污染物得以生物降解。群落的组成和成员之间的相互作用会影响降解速度，并决定最终产物的身份。在这里，我们展示了测序技术和代谢建模方法在增强莠去津（一种造成环境污染的除草剂）生物降解方面的应用。对莠去津处理的农业土壤进行的研究表明，它会引起群落结构和功能性能的显著变化。为莠去津的降解菌节杆菌和其他四种非莠去津降解菌构建了基因组规模的代谢模型，这些菌的相对丰度在接触除草剂后发生了变化。通过对群落功能进行建模，我们表明包括直接降解菌和非降解菌在内的差异丰度物种的共生体比单独的节杆菌表现得更好。模拟预测，通过群落成员之间的代谢交换，实现了生长/降解增强。基于模拟，我们设计了用于增强降解的内源性共生体，在体外进行了验证，并在盆栽实验中测试了生物刺激策略。总的来说，我们的分析表明，从更广泛的角度（不仅仅是直接降解菌的角度）理解群落功能，有助于设计生物刺激策略。
