生态系统中微生物群落基因组特征的变异。

Peter F Chuckran, Bruce A Hungate, Egbert Schwartz, Paul Dijkstra
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引用次数: 7

摘要

在营养有限的环境中自由生活的细菌通常表现出一些可以降低繁殖成本的特性,如基因组大小较小、GC含量低、sigma (σ)因子和16S rRNA基因拷贝数较少。尽管这些特征在检测微生物群落和生态系统尺度特性之间的关系方面具有潜在的效用,但很少有研究在群落尺度上评估这些特征。在这里,我们分析了来自海洋、土壤、宿主相关和嗜热群落的公开元基因组的这些特征。在海洋和嗜热群落中,基因组大小和GC含量平行下降,与基因组流线型一致,嗜热群落的GC含量普遍高于海洋系统。相比之下,平均较小基因组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的不同而不同。在海洋中,控制鞭毛生物合成的σ-因子fliA丰度与群落平均基因组大小正相关,反映了已知的营养保存和趋化性之间的权衡。在土壤中,高丰度的应力响应σ因子基因rpoS与较小的平均基因组大小相关,并且通常位于恶劣和/或碳限制的环境中,这一结果与在培养中观察到的特征一致,表明在营养贫乏的土壤中应力响应能力增强。这项工作显示了生态系统特异性限制如何与微生物群落中嵌入细菌基因组特征的权衡相关联,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。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Variation in genomic traits of microbial communities among ecosystems.

Variation in genomic traits of microbial communities among ecosystems.

Variation in genomic traits of microbial communities among ecosystems.

Variation in genomic traits of microbial communities among ecosystems.

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 fliA, 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 rpoS 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.

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CiteScore
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