Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns

Nikolay A Provorov; Evgeny E Andronov; Anastasiia K Kimeklis; Olga P Onishchuk; Anna A Igolkina; Evgeny S Karasev

doi:10.3389/fpls.2022.1026943

Microevolution, speciation and macroevolution in rhizobia: Genomic mechanisms and selective patterns

Front Plant Sci. 2022 Oct 25:13:1026943. doi: 10.3389/fpls.2022.1026943. eCollection 2022.

Authors

Nikolay A Provorov¹, Evgeny E Andronov^{1

2}, Anastasiia K Kimeklis^{1

3}, Olga P Onishchuk¹, Anna A Igolkina⁴, Evgeny S Karasev¹

Affiliations

¹ Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia.
² Laboratory of Soil Biology and Biochemistry, V.V. Dokuchaev Soil Science Institute, Moscow, Russia.
³ Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia.
⁴ Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.

Abstract

Nodule bacteria (rhizobia), N₂-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 (hkg), and of accessory parts, including symbiotically specialized (sym) genes. In multipartite genomes of evolutionary advanced fast-growing species (Rhizobiaceae), sym 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 sym 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 hkgs under the impacts of unknown factors. By contrast, macroevolution represents the polyphyletic origin of super-species taxa, which are dependent on the transfer of sym genes from rhizobia to various soil-borne bacteria. Since the expression of newly acquired sym 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 nod genes responsible for nodulation and of nif/fix genes responsible for symbiotic N₂ fixation.

Keywords: evolutionary genomics; leguminous plants; micro- and macro-evolution; natural selection; plant–microbe symbioses; rhizobia; speciation; symbiotic N2 fixation.

Publication types

Review