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Microbiology Research
Special Issues
Rhizosphere Processes and Plant–Microbiome Interactions
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Rhizosphere Processes and Plant–Microbiome Interactions

A special issue of Microbiology Research (ISSN 2036-7481).

Deadline for manuscript submissions: 30 November 2026 | Viewed by 918

Editors

Dr. Ruibo Sun

E-Mail Website
Guest Editor
Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
Interests: microbial ecology; microbial N and P cycling; plant–microbe interaction mechanisms
Special Issues, Collections and Topics in MDPI journals
Dr. Da Tian

E-Mail Website
Guest Editor
Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention, Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
Interests: mineral–soil–microorganism interaction; development of microbial resources
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The rhizosphere is a dynamic and critical interface where plant roots, soil, and a diverse microbiome interact, shaping plant health, nutrient cycling, and ecosystem productivity. This Special Issue aims to explore the latest advances in understanding rhizosphere processes and the complex mechanisms of plant–microbiome interactions. We invite contributions that investigate the signaling, assembly, and functional dynamics of root-associated microbial communities, and their roles in nutrient acquisition, stress tolerance, and disease suppression. By integrating multidisciplinary approaches, this collection seeks to provide insights into harnessing the rhizosphere microbiome for sustainable agricultural practices. Original research and comprehensive reviews are welcome.

Dr. Ruibo Sun
Dr. Da Tian
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-anonymized peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microbiology Research is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • rhizosphere nutrients dynamics
  • plant–microbiome interactions
  • microbial community assembly in rhizosphere
  • plant nutrient acquisition
  • plant health and rhizosphere microbiome
  • principles and technologies for regulating rhizosphere microbial communities
  • sustainable agriculture

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Published Papers (2 papers)

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Research

15 pages, 12802 KB  
Article
Klebsiella variicola Alleviates Chromium-Induced Growth Inhibition in Chicory by Modulating the Rhizosphere Microecology
by Xuebing Han, Lingling Feng, Wenli Xin, Shanshan Lu, Jialian Li, Tao Zhang, Wencong Long, Ximeng Xiao, Jiafeng Li, Xianting Yin, Xi Wang and Hanyu Wang
Microbiol. Res. 2026, 17(6), 114; https://doi.org/10.3390/microbiolres17060114 - 10 Jun 2026
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Abstract
Chromium is an environmental pollutant with high toxicity and carcinogenicity. It can induce severe oxidative stress and DNA damage after entering the human body through the food chain. As a plant growth-promoting rhizobacterium (PGPR) with both heavy metal tolerance and plant growth-promoting properties, [...] Read more.
Chromium is an environmental pollutant with high toxicity and carcinogenicity. It can induce severe oxidative stress and DNA damage after entering the human body through the food chain. As a plant growth-promoting rhizobacterium (PGPR) with both heavy metal tolerance and plant growth-promoting properties, Klebsiella variicola has considerable potential for the remediation of chromium contamination. In this study, chicory served as the experimental plant to explore the mitigating impacts of K. variicola on stress induced by hexavalent chromium (Cr(VI)) at a concentration of 400 mg/kg. The results showed that chromium severely inhibited the growth of chicory. In contrast, K. variicola significantly reduced the soil chromium content. As the chromium content decreased, the activities of soil urease, sucrase, catalase, and alkaline phosphatase were restored, increasing by 32.60–53.69%. Accordingly, the contents of total phosphorus, available phosphorus, total nitrogen, available nitrogen, soil organic carbon, and available potassium also increased by 34.71–51.81%. In addition, K. variicola reversed the decline in microbial diversity induced by chromium stress, promoted the growth of beneficial bacteria such as Acidobacteriota and Chloroflexota, and enhanced the stability of soil ecosystem functions. Ultimately, the growth inhibition of chicory caused by chromium stress was alleviated, with fresh weight, root length, maximum leaf width, maximum leaf length, plant height, and stem diameter significantly increasing by 21.89–61.60%. This study enhances our comprehension of the various functions of PGPR when exposed to heavy metal stress, and provides support for the development of microbe–plant combined strategies in the remediation of chromium-contaminated soils. Full article
(This article belongs to the Special Issue Rhizosphere Processes and Plant–Microbiome Interactions)
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23 pages, 3393 KB  
Article
Exploratory Analysis of Rhizosphere Bacterial Communities in Two Brazilian Eucalyptus Plantation Systems Suggests Taxonomic Turnover with Conserved Functional Potential
by Paulo Roberto Dall Cortivo, Ueric José Borges de Souza, Talyta Galafassi Zarpelon, Norton Borges Junior, Evgeni Evgeniev Gabev, Fabrício Souza Campos and Roberto Lanna-Filho
Microbiol. Res. 2026, 17(6), 107; https://doi.org/10.3390/microbiolres17060107 - 30 May 2026
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Abstract
Soil microbiomes play a central role in nutrient cycling and ecosystem stability in forestry ecosystems. Here, we present an exploratory analysis of rhizosphere bacterial communities from eucalyptus plantations in two ecologically distinct Brazilian regions. Using 16S rRNA amplicon sequencing followed by ASV inference [...] Read more.
Soil microbiomes play a central role in nutrient cycling and ecosystem stability in forestry ecosystems. Here, we present an exploratory analysis of rhizosphere bacterial communities from eucalyptus plantations in two ecologically distinct Brazilian regions. Using 16S rRNA amplicon sequencing followed by ASV inference and phylogenetic reconstruction, we observed distinct taxonomic composition pattern between samples. Dominant phyla across both samples were Actinomycetota, Pseudomonadota, Acidobacteriota, and Bacillota, with Actinomycetota more abundant in TL (44.0%) than in ES (26.5%), and Acidobacteriota and Verrucomicrobiota more represented in ES. The family Streptomycetaceae and the genus Streptantibioticus were strongly enriched in ES (19.6% and 18.6%, respectively), whereas Solirubrobacteraceae, Pseudonocardiaceae, and Nocardiaceae were preferentially associated with TL. The Eldorado do Sul (ES) sample was characterized by higher observed richness and phylogenetic diversity, whereas Três Lagoas (TL) sample displayed relatively greater community evenness. Beta diversity metrics were consistent with high compositional dissimilarity between samples, with a limited fraction of ASVs forming a shared core microbiome. Despite this taxonomic variation, PICRUSt2-based predictions suggested a broadly conserved set of dominant metabolic pathways across samples. Predicted MetaCyc pathways were largely associated with central carbon metabolism, amino acid biosynthesis, and energy production. At the same time, variation in predicted metabolic profiles was observed between samples. The ES sample showed higher relative representation of pathways related to chitin degradation, purine metabolism, and nitrifier denitrification, whereas the TL sample displayed higher relative representation of pathways associated with alternative TCA variants, glyoxylate metabolism, menaquinol biosynthesis, and aromatic compound degradation. Overall, this exploratory analysis suggests that substantial taxonomic variation may coexist with a relatively conserved predicted functional framework across contrasting eucalyptus plantation systems. These observations should be interpreted as hypothesis-generating and highlight the need for future studies incorporating replicated sampling and direct functional measurements. Full article
(This article belongs to the Special Issue Rhizosphere Processes and Plant–Microbiome Interactions)
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