Chuckran Peter F, Hungate Bruce A, Schwartz Egbert, Dijkstra Paul
Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America.
FEMS Microbes. 2021 Dec 1;2:xtab020. doi: 10.1093/femsmc/xtab020. eCollection 2021.
Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of , a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size-reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene was associated with smaller average genome size and often located in harsh and/or carbon-limited environments-a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.
在营养有限的环境中，自由生活的细菌通常表现出可能降低繁殖成本的特征，例如较小的基因组大小、低GC含量以及较少的σ因子和16S rRNA基因拷贝。尽管这些特征在检测微生物群落与生态系统尺度属性之间的关系方面具有潜在用途，但很少有研究在群落尺度上评估这些特征。在这里，我们从公开可用的宏基因组中分析了这些特征，这些宏基因组来自海洋、土壤、宿主相关和嗜热群落。在海洋和嗜热群落中，基因组大小和GC含量并行下降，这与基因组精简一致，嗜热群落中的GC含量通常高于海洋系统。相比之下，平均基因组较小的土壤群落具有较高的GC含量，并且通常来自低碳环境，这表明土壤细菌存在独特的选择压力。特定σ因子的丰度随平均基因组大小和生态系统类型而变化。在海洋中，控制鞭毛生物合成的σ因子的丰度与群落平均基因组大小呈正相关，这反映了营养保存和趋化性之间已知的权衡。在土壤中，应激反应σ因子基因的高丰度与较小的平均基因组大小相关，并且通常位于恶劣和/或碳限制环境中——这一结果与在培养中观察到的特征相符，表明贫营养土壤中应激反应能力增强。这项工作展示了生态系统特定的限制如何与权衡相关联，这些权衡体现在微生物群落中细菌的基因组特征中，并且可以在群落水平上检测到，突出了基因组特征在微生物群落分析中的重要性。
