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The Molecular Research of Plant and Microbial Communities
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The Molecular Research of Plant and Microbial Communities

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 2365

Special Issue Editor

Prof. Dr. Anna Gałązka

E-Mail Website
Guest Editor
Department of Agricultural Microbiology, Institute of Soil Science and Plant Cultivation—State Research Institute, Czartoryskich 8, 24-100 Puławy, Poland
Interests: microbiome and mycobiome of soil and plant rhizosphere; endorhizosphere; next generation sequencing; soil and plant biodiversity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The aim of this Special Issue is to present the latest achievements in research in the field of plant and microbial communities (metagenomics, metataxonomics, metatranscriptomics, metabolomics, molecular biology, and interactions between micro- and macroorganisms in various environments). Metagenomic tools make it possible to test all populations of microorganisms found in a given environment and are inextricably linked with bioinformatics research and data analysis. The variety of microorganisms associated with plant roots is enormous, amounting to tens of thousands of species. This complex microbial community, also called the second plant genome, is essential for plant health and productivity. Over the last few years, there has been significant progress in research into the structure and dynamics of the microbial sphere of the rhizosphere. In general, rhizosphere microorganisms promote plant growth directly by providing plants with minerals such as nitrogen and phosphorus and by synthesizing growth regulators, as well as indirectly, by inhibiting the development of various plant pathogens. It allows for the transfer of knowledge and experience to each other, enables the establishment of comprehensive cooperation, and allows for a lively discussion on the most modern research methods.

This Special Issue intends to improve our understanding of the comprehensive diagnosis of the biodiversity of microorganisms. Submissions may consist of research on topics including, but not limited to:

  • Genetic diversity among soil microbial communities;
  • Metagenomics;
  • Metataxonomics;
  • Metatranscriptomics;
  • Metabolomics;
  • Molecular biology;
  • Interactions between micro- and macro-organisms in various environments.

We would like to take this opportunity to welcome the submission of research articles and reviews, as well as technical notes and communications, on these related topics.

Prof. Dr. Anna Gałązka
Guest Editor

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 100 words) can be sent to the Editorial Office for announcement on this website.

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-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • microbiome and mycobiome of soil and plant rhizosphere
  • mycorrhizal fungi
  • next-generation sequencing
  • soil biodiversity

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Published Papers (3 papers)

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Research

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23 pages, 7382 KiB  
Article
Molecular Mechanisms of Phosphate Use Efficiency in Arabidopsis via Penicillium olsonii TLL1
by Valiya Nadakkakath Agisha, Erinjery Jose Suraby, Savitha Dhandapani, Yee Hwui Sng, Shi Hui Lim and Bong Soo Park
Int. J. Mol. Sci. 2024, 25(23), 12865; https://doi.org/10.3390/ijms252312865 - 29 Nov 2024
Viewed by 485
Abstract
Beneficial fungi are promising tools for enhancing plant growth and crop yield in stressful environments. Penicillium olsonii TLL1 (POT1) was identified as a potential biofertilizer enhancing plant growth and phosphate use efficiency especially under phosphate deficiency stress. Hence, we attempted to explore bioinformatic [...] Read more.
Beneficial fungi are promising tools for enhancing plant growth and crop yield in stressful environments. Penicillium olsonii TLL1 (POT1) was identified as a potential biofertilizer enhancing plant growth and phosphate use efficiency especially under phosphate deficiency stress. Hence, we attempted to explore bioinformatic insights into how POT1 enhances plant growth under phosphate starvation. In our study, wild-type Arabidopsis thaliana Columbia-0 roots and shoots cultivated with POT1 under phosphate-limiting conditions were employed for comparative analyses. By integrating transcriptomic and proteomic data, we identified key molecular pathways regulated by POT1 that influenced phosphate acquisition and plant stress tolerance. Comprehensive RNA-seq analysis revealed significant upregulation of genes involved in phosphate transport, root architecture, and stress-related pathways, while proteome profiling further highlighted proteins associated with lipid remodeling, phosphate metabolism, and phytohormone signaling. Bioinformatic analyses of differentially expressed genes (DEGs) and proteins (DEPs) elucidated the complex regulatory networks at both transcriptional and translational levels, with key contributions from auxin and ethylene signaling. Our study demonstrated that POT1-treated plants exhibited enhanced root development and nutrient uptake under phosphate-deficient conditions, driven by the coordinated regulation of phosphate solubilization genes and stress-responsive proteins. Our findings underscore the potential of multi-omics approaches in unraveling the molecular mechanisms behind plant–microbe interactions, with implications for improving sustainable agricultural practices. Full article
(This article belongs to the Special Issue The Molecular Research of Plant and Microbial Communities)
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22 pages, 2442 KiB  
Article
Unearthing Optimal Symbiotic Rhizobia Partners from the Main Production Area of Phaseolus vulgaris in Yunnan
by Junjie Zhang, Jingqi Wang, Yufeng Feng, Brigitte Brunel and Xuxiao Zong
Int. J. Mol. Sci. 2024, 25(15), 8511; https://doi.org/10.3390/ijms25158511 - 4 Aug 2024
Viewed by 907
Abstract
Phaseolus vulgaris is a globally important legume cash crop, which can carry out symbiotic nitrogen fixation with rhizobia. The presence of suitable rhizobia in cultivating soils is crucial for legume cropping, especially in areas beyond the plant-host native range, where soils may lack [...] Read more.
Phaseolus vulgaris is a globally important legume cash crop, which can carry out symbiotic nitrogen fixation with rhizobia. The presence of suitable rhizobia in cultivating soils is crucial for legume cropping, especially in areas beyond the plant-host native range, where soils may lack efficient symbiotic partners. We analyzed the distribution patterns and traits of native rhizobia associated with P. vulgaris in soils of Yunnan, where the common bean experienced a recent expansion. A total of 608 rhizobial isolates were tracked from soils of fifteen sampling sites using two local varieties of P. vulgaris. The isolates were discriminated into 43 genotypes as defined by IGS PCR-RFLP. Multiple locus sequence analysis based on recA, atpD and rpoB of representative strains placed them into 11 rhizobial species of Rhizobium involving Rhizobium sophorae, Rhizobium acidisoli, Rhizobium ecuadorense, Rhizobium hidalgonense, Rhizobium vallis, Rhizobium sophoriradicis, Rhizobium croatiense, Rhizobium anhuiense, Rhizobium phaseoli, Rhizobium chutanense and Rhizobium etli, and five unknown Rhizobium species; Rhizobium genosp. I~V. R. phaseoli and R. anhuiense were the dominant species (28.0% and 28.8%) most widely distributed, followed by R. croatiense (14.8%). The other rhizobial species were less numerous or site-specific. Phylogenies of nodC and nifH markers, were divided into two specific symbiovars, sv. phaseoli regardless of the species affiliation and sv. viciae associated with R. vallis. Through symbiotic effect assessment, all the tested strains nodulated both P. vulgaris varieties, often resulting with a significant greenness index (91–98%). However, about half of them exhibited better plant biomass performance, at least on one common bean variety, and two isolates (CYAH-6 and BLYH-15) showed a better symbiotic efficiency score. Representative strains revealed diverse abiotic stress tolerance to NaCl, acidity, alkalinity, temperature, drought and glyphosate. One strain efficient on both varieties and exhibiting stress abiotic tolerance (BLYH-15) belonged to R. genosp. IV sv. phaseoli, a species first found as a legume symbiont. Full article
(This article belongs to the Special Issue The Molecular Research of Plant and Microbial Communities)
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Review

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47 pages, 2520 KiB  
Review
Deciphering Molecular Mechanisms and Diversity of Plant Holobiont Bacteria: Microhabitats, Community Ecology, and Nutrient Acquisition
by Tomasz Grzyb and Justyna Szulc
Int. J. Mol. Sci. 2024, 25(24), 13601; https://doi.org/10.3390/ijms252413601 - 19 Dec 2024
Abstract
While gaining increasing attention, plant–microbiome–environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the [...] Read more.
While gaining increasing attention, plant–microbiome–environment interactions remain insufficiently understood, with many aspects still underexplored. This article explores bacterial biodiversity across plant compartments, including underexplored niches such as seeds and flowers. Furthermore, this study provides a systematic dataset on the taxonomic structure of the anthosphere microbiome, one of the most underexplored plant niches. This review examines ecological processes driving microbial community assembly and interactions, along with the discussion on mechanisms and diversity aspects of processes concerning the acquisition of nitrogen, phosphorus, potassium, and iron—elements essential in both molecular and ecological contexts. These insights are crucial for advancing molecular biology, microbial ecology, environmental studies, biogeochemistry, and applied studies. Moreover, the authors present the compilation of molecular markers for discussed processes, which will find application in (phylo)genetics, various (meta)omic approaches, strain screening, and monitoring. Such a review can be a valuable source of information for specialists in the fields concerned and for applied researchers, contributing to developments in sustainable agriculture, environmental protection, and conservation biology. Full article
(This article belongs to the Special Issue The Molecular Research of Plant and Microbial Communities)
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