Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA.
Department of Earth System Sciences, University of California, Irvine, California, USA.
Environ Microbiol. 2018 Nov;20(11):4112-4126. doi: 10.1111/1462-2920.14405. Epub 2018 Oct 5.
The high diversity of soil bacteria is attributed to the spatial complexity of soil systems, where habitat heterogeneity promotes niche partitioning among bacterial taxa. This premise remains challenging to test, however, as it requires quantifying the traits of closely related soil bacteria and relating these traits to bacterial abundances and geographic distributions. Here, we sought to investigate whether the widespread soil taxon Curtobacterium consists of multiple coexisting ecotypes with differential geographic distributions. We isolated Curtobacterium strains from six sites along a climate gradient and assayed four functional traits that may contribute to niche partitioning in leaf litter, the top layer of soil. Our results revealed that cultured isolates separated into fine-scale genetic clusters that reflected distinct suites of phenotypic traits, denoting the existence of multiple ecotypes. We then quantified the distribution of Curtobacterium by analysing metagenomic data collected across the gradient over 18 months. Six abundant ecotypes were observed with differential abundances along the gradient, suggesting fine-scale niche partitioning. However, we could not clearly explain observed geographic distributions of ecotypes by relating their traits to environmental variables. Thus, while we can resolve soil bacterial ecotypes, the traits delineating their distinct niches in the environment remain unclear.
土壤细菌的高度多样性归因于土壤系统的空间复杂性，其中生境异质性促进了细菌分类群之间的生态位划分。然而，这一前提仍然具有挑战性，因为它需要量化密切相关的土壤细菌的特征，并将这些特征与细菌丰度和地理分布联系起来。在这里，我们试图研究广泛存在的土壤分类单元短杆菌是否由具有不同地理分布的多个共存生态型组成。我们从气候梯度上的六个地点分离出短杆菌菌株，并检测了可能有助于叶凋落物（土壤顶层）中生态位划分的四个功能特征。我们的结果表明，培养的分离物分为精细的遗传聚类，反映出不同的表型特征组合，这表明存在多个生态型。然后，我们通过分析在 18 个月内沿梯度收集的宏基因组数据来量化 Curtobacterium 的分布。观察到六个丰富的生态型，它们在梯度上的丰度不同，表明存在精细的生态位划分。然而，我们无法通过将生态型的特征与环境变量联系起来来清楚地解释观察到的生态型的地理分布。因此，虽然我们可以解决土壤细菌生态型的问题，但仍不清楚界定它们在环境中不同生态位的特征。
