2023 年 2 巻 p. 58-74
Microbiomes play a pivotal role in mediating essential ecosystem functions, yet understanding the relationship between microbiome composition and ecosystem function rates remains challenging. Directly manipulating microbiome composition proves difficult due to the impracticality of identifying key functional taxa beforehand, and microbiomes’ strong covariance with environmental drivers of function. To tackle these challenges, we conducted artificial selection on whole soil ecosystems over multiple generations to enrich microbial communities exhibiting high CH4 oxidation rates. This biologically “agnostic” approach minimizes assumptions about crucial taxa and weakens microbe-environment covariance through repeated passaging with fresh substrate. In response to selection, we observed a significant 50.7% increase in CH4 oxidation rate per passage compared to a randomly selected control. While 31.5% of the CH4 oxidation rate variation in soils could be attributed to microbiome variation (not statistically significant), the selection did not enrich for known CH4 oxidizers. Instead, 12 families not previously associated with CH4 oxidation, such as Fimbriimonadaceae, Cytophagaceae, and Diplorickettsiaceae, were enriched. This finding challenges the conventional assumption that ecosystem function rates are limited by the final step in the microbial pathway. Our study underscores that microbiome composition can independently influence ecosystem function rates, regardless of the environment, and that such rates may not always be constrained by the final pathway step. Consequently, directly manipulating microbiome composition without altering the environment emerges as a viable strategy for managing ecosystem functions.
