Sinorhizobium meliloti: chromosomal types and genomic islands

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Abstract

Background. Polymorphism analysis was done for the core genome sequences of nodule bacteria of S. meliloti species in order to identify chromosomal types and to evaluate the occurrence of accessory elements (genomic islands) in them.

Materials and methods. Chromosomal studied loci were: betBC (marker M-I) and SMc04407-SMc04881 (marker M-II) both are related to metabolic processes and stress tolerance, and 16S-23S intergenic sequences (marker M-III) to search phylogenetical distance at intraspecies level.

Results. Significant differences between the occurrence of alleles of gene-markers M-I/M-II and MIII were determined between strains related to tested the 5 typical groups and 9 subgroups of strains differing by geographical region/source (nodule, soil) of isolation, as well as by salt tolerance. Four chromosomal types were identified among tested S. meliloti native isolates and a preference occurence of one of the three islands Rm1021 in links with particular chromosomal type was shown. The significant prevalence of strains with particular chromosomal type was shown for S. meliloti populations native to centers of alfalfa diversity at the NE of Caucasus, as well as at NE of Kazakhstan (Aral sea related region), as well as in agrocenoses. Conclusion. It was predicted that strains inherited altered markers M-I/M-II may belong to divergent clonal lines occured in both centers of alfalfa diversity, while strains with altered sequences of all three markers could be a representatives of a new S. meliloti biovar(s), the formation of which is occurred much more intensively at the modern center of the introgressive hybridization of alfalfa at NE of Kazakhstan.

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About the authors

Mariia E. Cherkasova

Federal State Budget Scientific Institution All-Russian Research Institute for Agricultural Microbiology

Email: mariiacherkasova@mail.ru
ORCID iD: 0000-0003-1873-9674
SPIN-code: 5341-5736
Scopus Author ID: 57191569585
ResearcherId: C-9626-2017

Research Engineer, Laboratory of Genetics and Breeding of Microorganisms

Russian Federation,  196608, Saint-Petersburg, Pushkin-8, sh. Podbelskogo 3

Victoria S. Muntyan

Federal State Budget Scientific Institution All-Russian Research Institute for Agricultural Microbiology

Email: vucovar@yandex.ru
ORCID iD: 0000-0002-1979-0853
SPIN-code: 7138-6763
Scopus Author ID: 56149831800
ResearcherId: K-5378-2013

Junior Researcher, Laboratory of Genetics and Breeding of Microorganisms

Russian Federation, 196608, Saint-Petersburg, Pushkin-8, sh. Podbelskogo 3

Alla S. Saksaganskaia

Federal State Budget Scientific Institution All-Russian Research Institute for Agricultural Microbiology

Email: allasaksaganskaya@mail.ru
ORCID iD: 0000-0002-8547-4904
SPIN-code: 5832-1676
Scopus Author ID: 57196477431
ResearcherId: H-8830-2017

Research Engineer, Laboratory of Genetics and Breeding of Microorganisms

Russian Federation, 196608, Saint-Petersburg, Pushkin-8, sh. Podbelskogo 3

Boris V. Simarov

Federal State Budget Scientific Institution All-Russian Research Institute for Agricultural Microbiology

Email: genet@yandex.ru
ORCID iD: 0000-0002-6893-557X
SPIN-code: 6859-1141
Scopus Author ID: 7003687173
ResearcherId: H-8898-2017

Doctor of Biology, Professor, Principal Researcher, Laboratory of Genetics and Breeding of Microorganisms

Russian Federation, 196608, Saint-Petersburg, Pushkin-8, sh. Podbelskogo 3

Marina L. Roumiantseva

Federal State Budget Scientific Institution All-Russian Research Institute for Agricultural Microbiology

Author for correspondence.
Email: mroumiantseva@yandex.ru
ORCID iD: 0000-0001-5582-6473
SPIN-code: 5470-9527
Scopus Author ID: 6506571716
ResearcherId: G-3628-2016

PhD (Candidate of Biology), Leading Researcher, Head of the Laboratory, Laboratory of Genetics and Breeding of Microorganisms

196608, Saint-Petersburg, Pushkin-8, sh. Podbelskogo 3

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