vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-24-35vavilov-4144Research ArticleФИЛОГЕНЕТИКАPHYLOGENETICSФилогенетический и пангеномный анализ представителей семейства Micrococcaceae, родственных стимулирующей рост растений ризобактерии, изолированной из ризосферы картофеля (Solanum tuberosum L.)Phylogenetic and pangenomic analyses of members of the family Micrococcaceae related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (Solanum tuberosum L.)ЩеголевС. Ю.ShchyogolevS. Yu.

Саратов

Saratov

shegolev_s@ibppm.ruБурыгинГ. Л.BuryginG. L.

Саратов

Saratov

ДыкманЛ. А.DykmanL. A.

Саратов

Saratov

МатораЛ. Ю.MatoraL. Yu.

Саратов

Saratov

Институт биохимии и физиологии растений и микроорганизмов Федерального исследовательского центра «Саратовский научный центр Российской академии наук»РоссияInstitute of Biochemistry and Physiology of Plants and Microorganisms – Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of SciencesRussian FederationИнститут биохимии и физиологии растений и микроорганизмов Федерального исследовательского центра «Саратовский научный центр Российской академии наук»; Саратовский государственный университет генетики, биотехнологии и инженерии им. Н.И. ВавиловаРоссияInstitute of Biochemistry and Physiology of Plants and Microorganisms – Subdivision of the Saratov Federal Scientific Centre of the Russian Academy of Sciences; Saratov State Vavilov Agrarian UniversityRussian Federation202430052024283308316Copyright © Щеголев С.Ю., Бурыгин Г.Л., Дыкман Л.А., Матора Л.Ю., 20242024Щеголев С.Ю., Бурыгин Г.Л., Дыкман Л.А., Матора Л.Ю.Shchyogolev S.Y., Burygin G.L., Dykman L.A., Matora L.Y.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4144

Исследованы представители семейства Micrococcaceae, родственные, согласно тестам 16S рРНК, ITS1 (транскрибируемый межгенный спейсер), средней нуклеотидной идентичности (ANI) и средней аминокислотной идентичности (AAI), штамму RCAM04488 Kocuria rosea – стимулирующей рост растений ризобактерии (PGPR), изолированному из ризосферы картофеля (Solanum tuberosum L.) с использованием полногеномных филогенетических тестов и пангеномного анализа. Согласно критерию ANI > 95 %, ряд известных представителей видов K. salina, K. polaris и K. rosea (включая типовой штамм K. rosea ATCC 186T), наиболее близкородственных изоляту в тесте ITS1, должны быть приписаны к одному и тому же виду с соответствую щей верификацией штаммов. Однако указанные штаммы были выделены из весьма контрастных по экологии и географии мест обитания, что не могло не сказаться на их генотипе и фенотипе и должно быть так или иначе учтено в оценках их систематического положения. Данное противоречие проясняют результаты пангеномного анализа, продемонстрировавшие существенные различия в этих штаммах количества акцессорных и штамм-специфичных генов, определяющих их индивидуальность и, возможно, потенциал для адаптации к различным экологическим нишам с соответствующими фенотипическими признаками. Аналогичные результаты получены в тесте AAI в полномасштабном варианте его применения против базы данных UniProt (около 250 млн записей) с использованием программы AAI-profiler и протеома штамма K. rosea ATCC 186T в качестве запроса. Согласно критерию AAI > 65 %, в один и тот же род с Kocuria должны быть объединены представители рода Arthrobacter и некоторых других родов, относящихся к классу актиномицетов, с весьма широким географическим и экологическим спектром источников их выделения. В рамках парадигмы о вертикально наследуемых филогенетических маркерах это можно трактовать как сигнал для их последующей таксономической переквалификации. Важным фактором при этом может быть детализация генного состава штаммов и таксономических соотношений, получаемых в результате анализа пангеномов соответствующих клад.

We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.

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The authors declare that there are no conflicts of interest present.