Gios Emilie, Mosley Olivia E, Takeuchi Nobuto, Handley Kim M
School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
mSystems. 2025 Aug 15:e0004625. doi: 10.1128/msystems.00046-25.
Bacterial genomes are highly dynamic entities, mostly due to horizontal gene transfer (HGT). HGT is thought to be the main driver of genetic variation and adaptation to the local environment in bacteria. However, little is known about the modalities of HGT within natural microbial communities, especially the implications of genetic exchange for streamlined microorganisms such as Patescibacteria (Candidate Phyla Radiation). We searched for evidence of genetic exchange in 125 Patescibacteria genomes recovered from aquifer environments and detected the presence of hundreds of genomic islands, individually transferred genes, and prophages combined, with up to 13% of genome length attributed to HGT. Results show that most individual gene transfer events occurred between Patescibacteria, although putative donors included phylogenetically diverse groundwater microorganisms. For example, results indicate exchange of a transcriptional regulator gene between Omnitrophota and Patescibacteria taxa with highly similar relative abundance patterns across 16 groundwater samples. Overall, results indicate a wide variety of metabolic functions were introduced into Patescibacteria genomes by HGT, including transcription, translation, and DNA replication, recombination and repair. This study illustrates the evolutionarily dynamic nature of Patescibacteria genomes despite the constraints of streamlining and that HGT in these organisms is also mediated via viral infection.
Genomic fluidity and diversity in bacteria are mainly governed by horizontal gene transfer (HGT), leading to a variety of genome structures and physiological diversity. The predominantly uncultivated Patescibacteria comprise highly diverse bacteria that consistently exhibit small cell and genome sizes. Despite strong pressures to reduce genetic content, we predict that these ultra-small bacteria use HGT to the same extent as other bacteria and that HGT may help facilitate recovery and maintenance of critical metabolic functions, niche exploitation, and putative symbiont-host interactions. Here, we determine the contribution of gene exchange to the evolution and diversification of Patescibacteria, despite the constraints of streamlining. We provide evidence of gene gains in Patescibacteria genomes recovered from aquifer environments and describe the large extent to which ultra-small bacterial genomes are subjected to HGT. Results suggest distinct metabolic functions acquired by Patescibacteria compared to general groundwater communities, suggesting specific evolutionary pressures on gene transfer dynamics occurring in ultra-small prokaryotes.
细菌基因组是高度动态的实体，主要归因于水平基因转移（HGT）。HGT被认为是细菌遗传变异和适应当地环境的主要驱动力。然而，对于自然微生物群落中HGT的方式，尤其是基因交换对诸如Patescibacteria（候选门辐射）等简化微生物的影响，我们知之甚少。我们在从含水层环境中回收的125个Patescibacteria基因组中寻找基因交换的证据，并检测到数百个基因组岛、单个转移基因和噬菌体的存在，综合起来，高达13%的基因组长度归因于HGT。结果表明，大多数单个基因转移事件发生在Patescibacteria之间，尽管推定的供体包括系统发育上不同的地下水微生物。例如，结果表明，在16个地下水样本中，Omnitrophota和Patescibacteria分类群之间交换了一个转录调节基因，它们具有高度相似的相对丰度模式。总体而言，结果表明HGT将多种代谢功能引入了Patescibacteria基因组，包括转录、翻译以及DNA复制、重组和修复。这项研究说明了尽管受到简化的限制，但Patescibacteria基因组在进化上具有动态性质，并且这些生物体中的HGT也通过病毒感染介导。
细菌中的基因组流动性和多样性主要由水平基因转移（HGT）控制，导致了各种基因组结构和生理多样性。主要未培养的Patescibacteria包括高度多样的细菌，它们始终表现出小的细胞和基因组大小。尽管有减少遗传内容的强大压力，但我们预测这些超小细菌与其他细菌一样广泛利用HGT，并且HGT可能有助于促进关键代谢功能的恢复和维持、生态位利用以及假定的共生体 - 宿主相互作用。在这里，尽管受到简化的限制，我们确定了基因交换对Patescibacteria进化和多样化的贡献。我们提供了从含水层环境中回收的Patescibacteria基因组中基因获得的证据，并描述了超小细菌基因组受HGT影响的程度。结果表明，与一般地下水群落相比Patescibacteria获得了不同的代谢功能，这表明超小原核生物中基因转移动态存在特定的进化压力。
