Selection for oligotrophy among bacteria inhabiting host microbiomes.
Selection for oligotrophy among bacteria inhabiting host microbiomes.
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作者：
宿主微生物组是机体健康、生理和生态的重要调节因子。微生物组通过缓冲宿主免受外部环境施加的波动条件和压力源的全面影响来促进宿主的健康。宿主是否反过来充当其相关微生物抵御外部环境变化的缓冲器尚不清楚。在这里，我们测试宿主微生物组中的细菌是否局部适应周围外部环境的营养水平。我们使用的系统中，浮游植物铜绿微囊藻的宿主具有适应低营养和高营养湖泊的局部菌株。通过评估属于宿主微生物组内异养细菌四个分类群的 40 个宏基因组组装基因组，我们发现源自低营养和高营养环境的菌株之间存在一致的系统发育差异。与从低营养湖泊获得的低营养宿主基因型相关的细菌证明了基因组精简，包括基因组大小减小和西格玛因子减少。这些细菌基因组具有促进低营养湖泊生存的特征，包括（i）更多对于磷获取至关重要的碱性磷酸酶基因，以及（ii）参与磷代谢的基因内的正选择。总体而言，我们的结果表明，尽管与宿主生物体密切相关，但微生物组内的细菌可能已经进化并经历了对其宿主外部压力源的环境选择，表现出与自由生活细菌中可能出现的适应模式相似的适应模式。了解自然选择在历史上如何塑造了宿主微生物组的微生物种群的特征，将有助于预测这些微生物的功能如何随着空间和时间的推移而继续进化。人们发现许多与宿主相关的微生物能够适应宿主，有时成为专性共生体，而自由生活的微生物则最能适应周围环境。我们的研究评估了宿主环境和周围外部环境在塑造宿主相关细菌的功能潜力方面的选择压力。尽管存在于宿主资源丰富的微生物组中，但我们证明，宿主相关的异养细菌显示出与其更广泛的周围环境的营养可用性相匹配的性状选择的证据。这些发现说明了选择压力的复杂组合，可能塑造了宿主微生物组中细菌的当前功能。我们的研究有助于深入了解随着时间的推移环境波动可能发生的功能变化。
Host microbiomes are important regulators of organismal fitness, physiology, and ecology. Microbiomes promote the fitness of their host in part by buffering the host from the full effects of fluctuating conditions and stressors imposed by the external environment. Whether the host conversely serves as a buffer for their associated microbes against variation in the external environment is less clear. Here, we test if bacteria inhabiting the microbiome of a host are locally adapted to nutrient levels in their surrounding external environment. We used a system in which the host, the phytoplankter Microcystis aeruginosa, has strains that are locally adapted to low-nutrient versus high-nutrient lakes. Assessing 40 metagenome-assembled genomes belonging to four taxonomic groups of heterotrophic bacteria residing within the host microbiome, we found consistent phylogenetic divergence between strains originating from low-nutrient versus high-nutrient environments. Bacteria found in association with low-nutrient host genotypes obtained from low-nutrient lakes demonstrated genome streamlining, including reduced genome size and fewer sigma factors. These bacterial genomes have features that would facilitate survival in low-nutrient lakes, including (i) greater number of alkaline phosphatase genes that are essential for phosphorus acquisition and (ii) positive selection within genes involved in phosphorus metabolism. Overall, our results demonstrate that despite living in close association with host organisms, bacteria residing within microbiomes may have evolved and undergone environmental selection to stressors external to their host, demonstrating similar patterns of adaptation to those that might be expected to develop among free-living bacteria. Understanding how natural selection has historically shaped the traits of microbial populations comprising host microbiomes would help predict how the functions of these microbes may continue to evolve over space and time. Numerous host-associated microbes have been found to adapt to their host, sometimes becoming obligate symbionts, whereas free-living microbes are best known to adapt to their surrounding environment. Our study assessed the selective pressures of both the host environment and the surrounding external environment in shaping the functional potential of host-associated bacteria. Despite residing within the resource-rich microbiome of their hosts, we demonstrate that host-associated heterotrophic bacteria show evidence of trait selection that matches the nutrient availability of their broader surrounding environment. These findings illustrate the complex mix of selective pressures that likely shape the present-day function of bacteria found inhabiting host microbiomes. Our study lends insight into the shifts in function that may occur as environments fluctuate over time.
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影响因子：
5.2
作者：
Coleman-Derr D;Tringe SG
通讯作者：
Tringe SG
DOI：
10.1038/nrg3182
发表时间：
2012-03-13
期刊：
Nature reviews. Genetics
影响因子：
--
作者：
通讯作者：
--
影响因子：
16.6
作者：
Henry LP;Bruijning M;Forsberg SKG;Ayroles JF
通讯作者：
Ayroles JF
DOI：
10.1073/pnas.1202319109
发表时间：
2012-08-28
影响因子：
11.1
作者：
Lau, Jennifer A.;Lennon, Jay T.
通讯作者：
Lennon, Jay T.
影响因子：
6.6
作者：
Nakagawa, Shinichi;Schielzeth, Holger
通讯作者：
Schielzeth, Holger