Ecological theory suggests that habitat disturbance differentially influences distributions of habitat generalist and specialist species. While well-established for macroorganisms, this theory has rarely been explored for microorganisms. Here we tested these principles in permeable (sandy) sediments, ecosystems with much spatiotemporal variation in resource availability and physicochemical conditions. Microbial community composition and function were profiled in intertidal and subtidal sediments using 16S rRNA gene amplicon sequencing and metagenomics, yielding 135 metagenome-assembled genomes. Community composition and metabolic traits modestly varied with sediment depth and sampling date. Several taxa were highly abundant and prevalent in all samples, including within the orders Woeseiales and Flavobacteriales, and classified as habitat generalists; genome reconstructions indicate these taxa are highly metabolically flexible facultative anaerobes and adapt to resource variability by using different electron donors and acceptors. In contrast, obligately anaerobic taxa such as sulfate reducers and candidate lineage MBNT15 were less abundant overall and only thrived in more stable deeper sediments. We substantiated these findings by measuring three metabolic processes in these sediments; whereas the habitat generalist-associated processes of sulfide oxidation and fermentation occurred rapidly at all depths, the specialist-associated process of sulfate reduction was restricted to deeper sediments. A manipulative experiment also confirmed habitat generalists outcompete specialist taxa during simulated habitat disturbance. Together, these findings show metabolically flexible habitat generalists become dominant in highly dynamic environments, whereas metabolically constrained specialists are restricted to narrower niches. Thus, an ecological theory describing distribution patterns for macroorganisms likely extends to microorganisms. Such findings have broad ecological and biogeochemical ramifications.

生态理论表明，栖息地干扰对栖息地普通物种和特殊物种的分布有不同的影响。虽然这一理论对于宏观生物体来说已经很成熟，但很少有人对微生物进行探索。在这里，我们在可渗透（沙质）沉积物、资源可用性和物理化学条件时空变化很大的生态系统中测试了这些原理。使用 16S rRNA 基因扩增子测序和宏基因组学对潮间带和潮下沉积物中的微生物群落组成和功能进行了分析，产生了 135 个宏基因组组装的基因组。群落组成和代谢特征随沉积物深度和采样日期略有变化。一些分类单元在所有样本中都非常丰富和普遍，包括Woeseiales和Flavobacteriales，并被归类为生境通才；基因组重建表明这些类群是代谢高度灵活的兼性厌氧菌，并通过使用不同的电子供体和受体来适应资源变异性。相比之下，硫酸盐还原剂和候选谱系 MBNT15 等专性厌氧类群总体上丰度较低，并且仅在更稳定的深层沉积物中繁衍生息。我们通过测量这些沉积物中的三个代谢过程证实了这些发现；与栖息地通才相关的硫化物氧化和发酵过程在所有深度都迅速发生，而与专家相关的硫酸盐还原过程仅限于较深的沉积物。一项操纵实验还证实，在模拟栖息地干扰期间，栖息地通才胜过专业类群。 总之，这些发现表明，代谢灵活的栖息地通才在高度动态的环境中占据主导地位，而代谢受限的专家则仅限于较狭窄的生态位。因此，描述宏观生物分布模式的生态理论很可能延伸到微生物。这些发现具有广泛的生态和生物地球化学影响。