{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,5]],"date-time":"2026-09-05T05:16:55Z","timestamp":1788585415550,"version":"build-2803163510"},"reference-count":59,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012190","name":"Ministry of Science and Higher Education of the Russian Federation","doi-asserted-by":"crossref","award":["075-15-2025-473"],"award-info":[{"award-number":["075-15-2025-473"]}],"id":[{"id":"10.13039\/501100012190","id-type":"DOI","asserted-by":"crossref"}]},{"award":["075-15-2025-473"],"award-info":[{"award-number":["075-15-2025-473"]}],"id":[{"id":"https:\/\/ror.org\/00ghqgy32","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Int. J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Plant growth-promoting bacteria (PGPB) are increasingly deployed as biofertilizers, yet the link between an inoculant\u2019s genomic potential and its realized effect on the plant is rarely assessed within an integrative framework that jointly captures the rhizosphere microbiome, plant phenotype, and strain genome. Two Bacillus strains\u2014B. halotolerans 1453 and B. pumilus 630\u2014were applied to wheat and soybean in a factorial pot experiment (2 strains \u00d7 2 application methods \u00d7 3 frequencies + control, 3\u20134 replicates). Rhizosphere samples (n = 67 after filtering) were profiled by 16S rRNA sequencing with PICRUSt2 functional prediction and compositional validation (Aitchison PERMANOVA, ALDEx2, ANCOM-BC2). The PGPB gene repertoire was characterized by genome mining (481 marker genes, 14 categories). Wheat phenotype (six traits) and soybean height were analyzed with models appropriate for count data (Negative Binomial and binomial GLMs) for treatment-vs.-control comparisons, and with factorial ANOVA for decomposition into main effects and interactions. Crop identity was the dominant factor shaping both microbiome structure and function (PERMANOVA R2 = 14.7% taxonomically and R2 = 7.8% functionally, both p &lt; 0.001), with biologically meaningful taxonomic differences between wheat and soybean; strain, application count and method had no significant effect on community composition (R2 &lt; 4% each), and co-occurrence networks showed no reliable differences between crops once read depth and sample size were controlled for. Despite this neutrality at the microbiome level, inoculation significantly increased wheat spike count (NB-GLM, all 12 treatments vs. control, padj 0.0002\u20130.031), ear weight, and stem count, with application count the strongest source of variability and a pronounced strain \u00d7 application count. Strain 1453 outperformed 630 in spike count (+23.1%, p = 0.012) and ear weight (+20.4%, p = 0.023); we hypothesize that this may be related to its more complete DNRA pathway (narGHI + nirB-nirD) and biocontrol genes (bacE, srfAA). Strain 630 produced a less pronounced effect than strain 1453 but was subject to smaller fluctuations across replicates (CV \u2248 16\u201321% vs. \u224824\u201326% for 1453), which may reflect better resilience to environmental fluctuations, possibly due to its confirmed rsbV\/rsbW stress-tolerance regulon. Rhizosphere microbiome composition differed clearly by crop (wheat vs. soybean) but showed no detectable response to strain, application method, or application count. Despite this lack of a microbiome signal, inoculation significantly increased wheat spike count and ear weight, with the magnitude and stability of this effect differing by strain. We hypothesize that this strain-dependent difference relates to underlying genomic differences\u2014particularly in nitrogen metabolism (DNRA pathway) and stress-tolerance genes\u2014though this link has not been tested directly and remains a hypothesis for future work.<\/jats:p>","DOI":"10.3390\/ijms27177873","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T10:10:33Z","timestamp":1788430233000},"page":"7873","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Two Bacillus PGPB Strains in Wheat and Soybean: Wheat Growth Promotion Without Detectable Rhizosphere Microbiome Restructuring"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3405-6980","authenticated-orcid":false,"given":"Elena Nikolaevna","family":"Voronina","sequence":"first","affiliation":[{"name":"V. A. Knorre Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4852-5661","authenticated-orcid":false,"given":"Ekaterina Alexeevna","family":"Sokolova","sequence":"additional","affiliation":[{"name":"V. A. Knorre Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Irina Nikolaevna","family":"Tromenschleger","sequence":"additional","affiliation":[{"name":"V. A. Knorre Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Olga Viktorovna","family":"Mishukova","sequence":"additional","affiliation":[{"name":"V. A. Knorre Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2070-6332","authenticated-orcid":false,"given":"Valeria Aleksandrovna","family":"Fedorets","sequence":"additional","affiliation":[{"name":"V. A. Knorre Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inna Viktorovna","family":"Khlistun","sequence":"additional","affiliation":[{"name":"V. A. Knorre Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9088-285X","authenticated-orcid":false,"given":"Oleg Aleksandrovich","family":"Savenkov","sequence":"additional","affiliation":[{"name":"Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2906-7199","authenticated-orcid":false,"given":"Oleg Igorevich","family":"Saprikin","sequence":"additional","affiliation":[{"name":"Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"given":"Maria Dmitrievna","family":"Buyanova","sequence":"additional","affiliation":[{"name":"Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Irina Mikhailovna","family":"Filippova","sequence":"additional","affiliation":[{"name":"Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Marina Andreevna","family":"Glukhova","sequence":"additional","affiliation":[{"name":"Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Evgeny Ivanovich","family":"Rogaev","sequence":"additional","affiliation":[{"name":"Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sirius Federal Territory, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4391-7068","authenticated-orcid":false,"given":"Lada Vladimirovna","family":"Zhohova","sequence":"additional","affiliation":[{"name":"Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sirius Federal Territory, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Andrey Dmitrievich","family":"Manakhov","sequence":"additional","affiliation":[{"name":"Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sirius Federal Territory, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"}]},{"given":"Natalya Valentinovna","family":"Smirnova","sequence":"additional","affiliation":[{"name":"Institute of Soil Science and Agrochemistry, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.tplants.2017.09.003","article-title":"Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?","volume":"23","author":"Sasse","year":"2018","journal-title":"Trends Plant Sci."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/s41564-018-0129-3","article-title":"Dynamic Root Exudate Chemistry and Microbial Substrate Preferences Drive Patterns in Rhizosphere Microbial Community Assembly","volume":"3","author":"Zhalnina","year":"2018","journal-title":"Nat. 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