Rohwer Robin R, Kirkpatrick Mark, Garcia Sarahi L, Kellom Matthew, McMahon Katherine D, Baker Brett J
Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.
Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
Nat Microbiol. 2025 Jan;10(1):246-257. doi: 10.1038/s41564-024-01888-3. Epub 2025 Jan 3.
Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. These genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities.
生态学和进化被认为是在微生物群落的当代时间尺度上相互作用的不同过程。在这里，为了在自然系统中观察这些过程，我们从美国威斯康星州门多塔湖收集了一个长达二十年、包含471个宏基因组的时间序列。我们组装了2855个物种代表性基因组，发现基因组变化是常见且频繁的。通过追踪单核苷酸变异的菌株组成，我们在80%的物种中识别出周期性的季节性模式，在20%的物种中识别出十年期的变化。在占主导地位的淡水科纳米远洋科中，极端环境与菌株组成的变化以及氨基酸和核酸代谢基因的正选择相吻合。这些基因将有机氮化合物确定为淡水对全球变化响应的潜在驱动因素。季节性和长期的菌株动态可以被视为生态过程，或者等效地，视为进化变化。我们不是将其视为不同的相互作用过程，而是提出将生态学和进化概念化为一个连续体，以更好地描述微生物群落的变化。
