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.

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微生物物种对环境变化的性能响应：基因组特征和营养可用性

微生物物种的性能指标，如增长率和碳同化率，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。这限制了我们理解微生物对环境变化的物种表现反应（即物种环境反应）如何与基因组特征和营养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，通过比较定义的对照组和处理组之间的物种表现来量化微生物的物种环境响应。自然或改变环境的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) 进行定量测定。我们进一步应用这种方法，即效应大小的 qSIP，以测量物种环境对山腰土壤细菌碳和氮添加的响应，并从基因组特征的角度了解它们的响应。对于高海拔，氮限制更强，这表明添加氮时细菌生长率的较高聚合反应（以社区加权平均值衡量）。基因组特征进一步解释了聚合反应，这表明京都基因和基因组百科全书 (KEGG) 直系同源物 (KOs) 的比例更高，并且在添加营养物（包括氮）下更多样化的 KEGG 途径，并进一步提高了微生物环境反应的解释力. 物种水平的氮诱导反应显示与稀有物种的基本 KOs 的最强关联，而碳诱导反应显示与优势物种的最强关联。我们得出的结论是，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的微生物环境反应也极为重要。在物种水平上利用这种新方法，我们揭示了稀有物种和优势物种通过其代谢特征对营养丰富的反应不同。该方法和发现可以更全面地了解自然栖息地中的微生物环境响应，这对于预测微生物群落对全球环境变化的响应至关重要。而碳诱导的反应显示出与优势物种的最强关联。我们得出的结论是，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的微生物环境反应也极为重要。在物种水平上利用这种新方法，我们揭示了稀有物种和优势物种通过其代谢特征对营养丰富的反应不同。该方法和发现可以更全面地了解自然栖息地中的微生物环境响应，这对于预测微生物群落对全球环境变化的响应至关重要。而碳诱导的反应显示出与优势物种的最强关联。我们得出的结论是，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的微生物环境反应也极为重要。在物种水平上利用这种新方法，我们揭示了稀有物种和优势物种通过其代谢特征对营养丰富的反应不同。该方法和发现可以更全面地了解自然栖息地中的微生物环境响应，这对于预测微生物群落对全球环境变化的响应至关重要。基因组特征对于预测群落和物种水平的微生物环境反应极为重要。在物种水平上利用这种新方法，我们揭示了稀有物种和优势物种通过其代谢特征对营养丰富的反应不同。该方法和发现可以更全面地了解自然栖息地中的微生物环境响应，这对于预测微生物群落对全球环境变化的响应至关重要。基因组特征对于预测群落和物种水平的微生物环境反应极为重要。在物种水平上利用这种新方法，我们揭示了稀有物种和优势物种通过其代谢特征对营养丰富的反应不同。该方法和发现可以更全面地了解自然栖息地中的微生物环境响应，这对于预测微生物群落对全球环境变化的响应至关重要。