Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis

Sumit Mukherjee, Zhuoran Kuang, Samrat Ghosh, Rajesh Detroja, Gon Carmi, Sucheta Tripathy, Danny Barash, Milana Frenkel-Morgenstern, Eviatar Nevo, Kexin Li

Research output: Contribution to journalArticlepeer-review


Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.

Original languageEnglish
Article number1110
Issue number8
StatePublished - 26 Jul 2022

Bibliographical note

Funding Information:
This project was supported by the National Natural Science Foundation of China (32071487), National Key Research and Development Programs of China (2021YFD1200901), Science Fund for Creative Research Groups of Gansu Province (21JR7RA533), Lanzhou University’s “Double First-Class” Guided Project-Team Building Funding-Research Startup Fee for Kexin Li, Chang Jiang Scholars Program, The Fundamental Research Funds for Central Universities, LZU (lzujbky-2021-ey17), a grant from State Key Laboratory of Grassland Agro-Ecosystems (Lanzhou University) (Grant Number: SKLGAE-202001, 202009 and 202010), and constant financial support for the Spalax research Program by Ancell-Teicher Research Foundation for Genetic and Molecular Evolution. We received support for computational work from the Big Data Computing Platform for Western Ecological Environment and Regional Development and Supercomputing Center of Lanzhou University.

Funding Information:
The authors would like to thank the Cooperativa de Crédito Livre Admissão Sul Serrana do Espírito Santo—Sicoob (23186000886201801), the Coordination for the Improvement of Higher Education Personnel (CAPES), the National Council for Scientific and Technological Development (CNPq), the Fundação o Apoio à Research and Innovation of Espírito Santo (FAPES), to the Federal Institute of Espírito Santo through PRPPG nº. 10/2019, the Federal University of Viçosa (UFV), the Federal University of Espírito Santo (UFES) and the Federal University of Lavras.

Publisher Copyright:
© 2022 by the authors.


  • evolution plateau
  • genetic divergence
  • metagenomics
  • riboswitches
  • structured non-coding RNA
  • sympatric speciation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (all)
  • Immunology and Microbiology (all)
  • Agricultural and Biological Sciences (all)


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