Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, the Netherlands.
Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, Texel, the Netherlands.
Nat Ecol Evol. 2023 May;7(5):768-781. doi: 10.1038/s41559-023-02027-7. Epub 2023 Apr 3.
Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microorganisms because it depends on an objective definition of the environment. Here, by defining the environment of a microorganism as the community it resides in, we integrated information from over 22,000 environmental sequencing samples to derive a quantitative measure of the niche, which we call social niche breadth. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, whereas social specialists are stable but low in abundance. Social generalists have a more diverse and open pan-genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, whereby specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies.
通才可以在许多环境中生存，而专家则局限于单一环境。尽管这是生态学中的一个经典概念，但由于它依赖于对环境的客观定义，微生物的生态位宽度一直难以量化。在这里，我们将微生物的环境定义为其所在的群落，从而整合了来自超过 22000 个环境测序样本的信息，得出了一种定量的生态位测度，我们称之为社会生态位宽度。在属的水平上，我们在整个原核生物生命树中探索了生态位范围策略。我们发现，社会通才包括随机占据当地群落的机会主义者，而社会专家则稳定但数量较少。社会通才的泛基因组比社会专家更具多样性和开放性，但我们没有发现社会生态位宽度与基因组大小之间存在全局相关性。相反，我们观察到两种截然不同的进化策略，即专家在本地多样性较低的栖息地中具有相对较小的基因组，但在本地多样性较高的栖息地中具有相对较大的基因组。总的来说，我们的分析为微生物生态位范围策略提供了数据驱动的新视角。
