Provorov Nikolay A, Andronov Evgeny E, Kimeklis Anastasiia K, Onishchuk Olga P, Igolkina Anna A, Karasev Evgeny S
Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia.
Laboratory of Soil Biology and Biochemistry, V.V. Dokuchaev Soil Science Institute, Moscow, Russia.
Front Plant Sci. 2022 Oct 25;13:1026943. doi: 10.3389/fpls.2022.1026943. eCollection 2022.
Nodule bacteria (rhizobia), N-fixing symbionts of leguminous plants, represent an excellent model to study the fundamental issues of evolutionary biology, including the tradeoff between microevolution, speciation, and macroevolution, which remains poorly understood for free-living organisms. Taxonomically, rhizobia are extremely diverse: they are represented by nearly a dozen families of α-proteobacteria (Rhizobiales) and by some β-proteobacteria. Their genomes are composed of core parts, including house-keeping genes (), and of accessory parts, including symbiotically specialized () genes. In multipartite genomes of evolutionary advanced fast-growing species (Rhizobiaceae), genes are clustered on extra-chromosomal replicons (megaplasmids, chromids), facilitating gene transfer in plant-associated microbial communities. In this review, we demonstrate that in rhizobia, microevolution and speciation involve different genomic and ecological mechanisms: the first one is based on the diversification of genes occurring under the impacts of host-induced natural selection (including its disruptive, frequency-dependent and group forms); the second one-on the diversification of s under the impacts of unknown factors. By contrast, macroevolution represents the polyphyletic origin of super-species taxa, which are dependent on the transfer of genes from rhizobia to various soil-borne bacteria. Since the expression of newly acquired genes on foreign genomic backgrounds is usually restricted, conversion of resulted recombinants into the novel rhizobia species involves post-transfer genetic changes. They are presumably supported by host-induced selective processes resulting in the sequential derepression of genes responsible for nodulation and of / genes responsible for symbiotic N fixation.
根瘤菌（豆科植物的固氮共生体）是研究进化生物学基本问题的优秀模型，包括微观进化、物种形成和宏观进化之间的权衡，而对于自由生活的生物体来说，这一点仍知之甚少。在分类学上，根瘤菌极其多样：它们由近十二个α-变形菌科（根瘤菌目）和一些β-变形菌代表。它们的基因组由核心部分（包括看家基因）和辅助部分（包括共生特化基因）组成。在进化上较高级的快速生长物种（根瘤菌科）的多分体基因组中，基因聚集在染色体外复制子（大质粒、染色体质粒）上，便于在与植物相关的微生物群落中进行基因转移。在这篇综述中，我们证明在根瘤菌中，微观进化和物种形成涉及不同的基因组和生态机制：前者基于在宿主诱导的自然选择（包括其破坏性、频率依赖性和群体形式）影响下发生的基因多样化；后者基于在未知因素影响下的基因多样化。相比之下，宏观进化代表超级物种分类群的多系起源，这依赖于从根瘤菌到各种土壤细菌的基因转移。由于新获得的基因在外国基因组背景上的表达通常受到限制，将产生的重组体转化为新的根瘤菌物种涉及转移后的遗传变化。它们可能受到宿主诱导的选择过程的支持，导致负责结瘤的基因和负责共生固氮的基因/基因的顺序去抑制。
