Hu Ang, Ren Minglei, Wang Jianjun
College of Resources and Environment, Hunan Agricultural University, Changsha, 410128, China.
State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, 210008, China.
Ecology. 2021 Jul;102(7):e03382. doi: 10.1002/ecy.3382. Epub 2021 Jun 1.
How microbial species performance indicators, such as growth rate and carbon assimilation rate, respond to environmental changes is a challenging question, especially for complex communities. This limits our ability to understand how species performance responses to environmental changes (that is, species environmental responses) of microbes could be linked to genomic traits and nutrient availability. Based on stable isotope labeling of DNA, we propose a new approach with effect-size metrics to quantify the species environmental responses of microbes by comparing the species performance between defined control and treatment groups. The species performance within microbial communities of the natural or altered environments could be quantitatively determined with quantitative stable isotope probing (qSIP). We further apply this approach, namely effect-size qSIP, to measure species environmental responses upon carbon and nitrogen additions for soil bacteria on mountainsides and to understand their responses from the perspective of genomic traits. Towards high elevations, there is a stronger nitrogen limitation that is indicated by the higher aggregated responses, measured as community-weighted means, of bacterial growth rate upon nitrogen additions. The aggregated responses are further explained by genomic traits, which show higher percentages of significant Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues (KOs) and more diverse KEGG pathways under nutrient additions including nitrogen, and further improve the explanatory power of microbial environmental responses. Nitrogen-induced responses at the species level show the strongest associations with essential KOs for rare species, whereas carbon-induced responses show the strongest associations for dominant species. We conclude that, in addition to environmental determinants such as nitrogen limitation, genomic traits are extremely important for predicting microbial environmental responses at both the community and species levels. Taking advantage of this new approach at the species level, we reveal that rare and dominant species differentially respond to nutrient enrichment via their metabolic traits. The approach and findings can lead to a more holistic understanding of microbial environmental responses in natural habitats, which will be essential for predicting microbial community responses to global environmental changes.
微生物物种的性能指标，如生长速率和碳同化率，如何响应环境变化是一个具有挑战性的问题，尤其是对于复杂的群落而言。这限制了我们理解微生物的物种性能对环境变化的响应（即物种环境响应）如何与基因组特征和养分可用性相关联的能力。基于DNA的稳定同位素标记，我们提出了一种新方法，即效应量指标法，通过比较定义的对照组和处理组之间的物种性能来量化微生物的物种环境响应。自然或改变环境中微生物群落内的物种性能可以通过定量稳定同位素探测（qSIP）来定量确定。我们进一步应用这种方法，即效应量qSIP，来测量山坡土壤细菌在添加碳和氮后物种的环境响应，并从基因组特征的角度理解它们的响应。随着海拔升高，氮限制更强，这通过添加氮后细菌生长速率的更高聚集响应（以群落加权平均值衡量）表明。基因组特征进一步解释了这些聚集响应，在包括氮在内的养分添加情况下，基因组特征显示出更高比例的京都基因与基因组百科全书（KEGG）直系同源物（KOs）和更多样化的KEGG途径，并进一步提高了微生物环境响应的解释力。在物种水平上，氮诱导的响应与稀有物种的必需KOs关联最强，而碳诱导的响应与优势物种关联最强。我们得出结论，除了氮限制等环境决定因素外，基因组特征对于预测群落和物种水平上的微生物环境响应极为重要。利用这种在物种水平上的新方法，我们揭示了稀有物种和优势物种通过其代谢特征对养分富集的不同响应。该方法和研究结果可以使我们对自然栖息地中微生物的环境响应有更全面的理解，这对于预测微生物群落对全球环境变化的响应至关重要。
