Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes,Environmental Microbiology

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Genome-resolved metagenomics reveals the effect of nutrient availability on bacterial genomic properties across 44 European freshwater lakes
Environmental Microbiology ( IF 4.3 ) Pub Date : 2024-06-17 , DOI: 10.1111/1462-2920.16634
Manan Shah _{1,

2,

3} , Till L V Bornemann _{2,

4} , Julia K Nuy _{2,

4} , Martin W Hahn ₅ , Alexander J Probst _{2,

4} , Daniela Beisser _{3,

4} , Jens Boenigk _{1,

4}

Affiliation

Understanding intricate microbial interactions in the environment is crucial. This is especially true for the relationships between nutrients and bacteria, as phosphorus, nitrogen and organic carbon availability are known to influence bacterial population dynamics. It has been suggested that low nutrient conditions prompt the evolutionary process of genome streamlining. This process helps conserve scarce nutrients and allows for proliferation. Genome streamlining is associated with genomic properties such as %GC content, genes encoding sigma factors, percent coding regions, gene redundancy, and functional shifts in processes like cell motility and ATP binding cassette transporters, among others. The current study aims to unveil the impact of nutrition on the genome size, %GC content, and functional properties of pelagic freshwater bacteria. We do this at finer taxonomic resolutions for many metagenomically characterized communities. Our study confirms the interplay of trophic level and genomic properties. It also highlights that different nutrient types, particularly phosphorus and nitrogen, impact these properties differently. We observed a covariation of functional traits with genome size. Larger genomes exhibit enriched pathways for motility, environmental interaction, and regulatory genes. ABC transporter genes reflect the availability of nutrients in the environment, with small genomes presumably relying more on metabolites from other organisms. We also discuss the distinct strategies different phyla adopt to adapt to oligotrophic environments. The findings contribute to our understanding of genomic adaptations within complex microbial communities.

中文翻译：

基因组解析的宏基因组学揭示了 44 个欧洲淡水湖中营养物质可用性对细菌基因组特性的影响

了解环境中复杂的微生物相互作用至关重要。对于营养物和细菌之间的关系尤其如此，因为已知磷、氮和有机碳的可用性会影响细菌种群动态。有人认为，低营养条件促进了基因组精简的进化过程。这个过程有助于保存稀缺的营养物质并允许增殖。基因组精简与基因组特性相关，例如 %GC 含量、编码 sigma 因子的基因、编码区百分比、基因冗余以及细胞运动和 ATP 结合盒转运蛋白等过程中的功能转变等。目前的研究旨在揭示营养对远洋淡水细菌基因组大小、GC 含量百分比和功能特性的影响。我们以更精细的分类分辨率为许多宏基因组特征的群落做到了这一点。我们的研究证实了营养水平和基因组特性的相互作用。它还强调，不同的营养类型，特别是磷和氮，对这些特性的影响不同。我们观察到功能性状与基因组大小的共变。更大的基因组表现出丰富的运动、环境相互作用和调控基因的途径。 ABC 转运蛋白基因反映了环境中营养物质的可用性，小基因组可能更多地依赖其他生物体的代谢物。我们还讨论了不同门为适应寡营养环境而采取的不同策略。这些发现有助于我们了解复杂微生物群落内的基因组适应。

更新日期：2024-06-18

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