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Microorganisms
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Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion,...
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Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion, 3rd Edition

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Plant Microbe Interactions".

Deadline for manuscript submissions: 31 March 2025 | Viewed by 3029

Special Issue Editor

Dr. José David Flores-Félix

E-Mail Website
Guest Editor
Lab 237, Edif Departamental de Biología, Universidad de Salamanca, 37007 Salamanca, Spain
Interests: microbiology; rhizobium; PGPB
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, based on the knowledge about plant bacterial communities, it is evident that an important bacterial diversity is present in the environment, where plants are able to model these populations. The development of next-generation sequencing (NGS) and transcriptomics techniques has allowed us to delve into bacterial diversity, contributing to a complete view of culturable and nonculturable plant-associated bacteria. It should also be noted that, in recent years, the study of bacterial populations associated with plants has allowed the identification of a high number of new species, and genome sequencing has revealed a more complete view of the metabolism and the relationship of bacteria that inhabit these environments. These bacteria will have a key role in the development of efficient agricultural strategies to achieve higher crop production and better crop adaptation to future climatic conditions. In this way, some bacteria present a high biotechnological profile due to their ability to produce a plant growth-promoting mechanism, which has a positive effect on the development and health of plants. For this reason, the integration between metagenomic and culturomic techniques is essential to achieve a global vision that allows knowing the population dynamics and their biotechnological applications in modern agriculture.

This Special Issue will focus on providing the current view of the diversity and importance of bacterial populations associated with plants through culturomic, metagenomic, and molecular approaches, the relationship between community members, their relationship with their hosts, and their importance in plant nutrition.

Dr. José David Flores-Félix
Guest Editor

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Keywords

  • rhizobacteria
  • endophytes
  • epiphytes
  • rhizosphere
  • phyllosphere
  • plant growth-promoting bacteria
  • plant microbiome
  • plant–microbe transcriptomic
  • plant–microbe interactions
  • culturomic microbiote
  • quorum sensing

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Published Papers (3 papers)

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Research

20 pages, 3582 KiB  
Article
Diversity and Plant Growth-Promoting Properties of Rhodiola rosea Root Endophytic Bacteria
by Inga Tamošiūnė, Muhammad Fahad Hakim, Odeta Buzaitė, Vidmantas Stanys, Jurgita Vinskienė, Elena Andriūnaitė and Danas Baniulis
Microorganisms 2025, 13(1), 13; https://doi.org/10.3390/microorganisms13010013 - 25 Dec 2024
Viewed by 577
Abstract
Plants inhabiting environments with suboptimal growth conditions often have a more pronounced capacity to attract and sustain microbial communities that improve nutrient absorption and expand abiotic stress tolerance. Rhodiola rosea L. is a succulent plant of the Crassulaceae family adapted to survive in [...] Read more.
Plants inhabiting environments with suboptimal growth conditions often have a more pronounced capacity to attract and sustain microbial communities that improve nutrient absorption and expand abiotic stress tolerance. Rhodiola rosea L. is a succulent plant of the Crassulaceae family adapted to survive in sandy or rocky soils or dry tundra. The aim of the present study was to investigate the diversity and plant growth-stimulating potential of R. rosea endophytic microbiota. Metataxonomic analysis of the bacterial diversity in the rhizome of R. rosea revealed 108 families. Among these, three families were found exclusively in the core microbiome of 1-year-old plants, while nine families were unique to the core microbiome of mature plants grown in the field for more than 4 years. Seventy-three endophytic bacteria isolates were obtained from the rhizome of R. rosea plants and were assigned into 14 distinct bacterial genera of Firmicutes (26%) or Proteobacteria (74%) phyla. Screening for functional genes related to the nitrogen cycle, phosphorus mineralisation or dissolution, and traits associated with nitrogen fixation (56% of isolates), siderophore production (40%), inorganic phosphorus solubilisation (30%), and production of indole-related compounds (51%) led to the classification of the isolates into 16 distinct clusters. Co-cultivation of 45 selected isolates with germinating Arabidopsis seedlings revealed 18 and 5 isolates that resulted in more than a 20% increase in root or shoot growth, respectively. The study results established the complexity of the succulent R. rosea endophytic microbiome and identified isolates for potential plant growth-stimulating applications. Full article
(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion, 3rd Edition)
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13 pages, 4195 KiB  
Article
Impact of Transgenic Maize Ruifeng125 on Diversity and Dynamics of Bacterial Community in Rhizosphere Soil
by Chaofeng Hao, Xinyao Xia, Chao Xu, Hongwei Sun, Fan Li, Shuke Yang, Xiaohui Xu and Xingbo Lu
Microorganisms 2024, 12(9), 1763; https://doi.org/10.3390/microorganisms12091763 - 25 Aug 2024
Viewed by 945
Abstract
With the development of commercialized planting of genetically modified crops, their ecological security risks remain a key topic of public concern. Insect-resistant genetically modified maize, Ruifeng125, which expresses a fusion Bt protein (Cry1Ab-Cry2Aj), has obtained the application safety certificate issued by the Chinese [...] Read more.
With the development of commercialized planting of genetically modified crops, their ecological security risks remain a key topic of public concern. Insect-resistant genetically modified maize, Ruifeng125, which expresses a fusion Bt protein (Cry1Ab-Cry2Aj), has obtained the application safety certificate issued by the Chinese government. To determine the effects of Ruifeng125 on the diversity and dynamics of bacterial communities, the accumulation and degradation pattern of the fusion Bt protein in the rhizosphere soil of transgenic maize were detected. Results showed that the contents of Bt protein varied significantly at different developmental stages, but after straw was returned to the field, over 97% of Bt proteins were degraded quickly at the early stages (≤10 d) and then they were degraded at a relatively slow rate. In addition, the variations in bacterial community diversity in the rhizosphere soil were detected by 16S ribosomal RNA (Rrna) high-throughput sequencing technology. A total of 44 phyla, 435 families, and 842 genera were obtained by 16S rRNA sequencing, among which Proteobacteria, Actinobacia, Acidobacter Acidobacterium, and Chloroflexi were the dominant taxa. At the same developmental stage, no significant differences in soil bacterial diversity were detected between Ruifeng125 and its non-transgenic control variety. Further analysis revealed that developmental stage, rather than the transgenic event, made the greatest contribution to the changes in soil microbial diversity. This research provides important information for evaluating the impacts of Bt crops on the soil microbiome and establishes a theoretical foundation for their environmental safety assessment. Full article
(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion, 3rd Edition)
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21 pages, 5907 KiB  
Article
A Comparative Analysis of Bacterial and Fungal Communities in Coastal and Inland Pecan Plantations
by Shijie Zhang, Ting Chen, Yu Chen, Shucheng Li, Wu Wang, Yuqiang Zhao and Cancan Zhu
Microorganisms 2024, 12(7), 1313; https://doi.org/10.3390/microorganisms12071313 - 27 Jun 2024
Viewed by 993
Abstract
Pecan forests (Carya illinoinensis) are significant contributors to both food and oil production, and thrive in diverse soil environments, including coastal regions. However, the interplay between soil microbes and pecan forest health in coastal environments remains understudied. Therefore, we investigated soil [...] Read more.
Pecan forests (Carya illinoinensis) are significant contributors to both food and oil production, and thrive in diverse soil environments, including coastal regions. However, the interplay between soil microbes and pecan forest health in coastal environments remains understudied. Therefore, we investigated soil bacterial and fungal diversity in coastal (Dafeng, DF) and inland (Guomei, GM) pecan plantations using high-throughput sequencing. The results revealed a higher microbial diversity in the DF plantation than in the GM plantation, significantly influenced by pH and edaphic factors. The dominant bacterial phyla were Proteobacteria, Acidobacteriota and Bacteroidota in the DF plantation, and Acidobacteriota, Proteobacteria, and Verrucomicrobiota in the GM plantation. Bacillus, Nitrospira and UTCFX1 were significantly more abundant bacterial genera in DF soil, whereas Candidatus Udaeobacter, HSB_OF53-F07 and ADurbBin063-1 were more prevalent in GM soil. Basidiomycota dominated fungal sequences in the GM plantation, with a higher relative abundance of Ascomycota in the DF plantation. Significant differences in fungal genus composition were observed between plantations, with Scleroderma, Hebeloma, and Naucoria being more abundant in DF soil, and Clavulina, Russula, and Inocybe in GM soil. A functional analysis revealed greater carbohydrate metabolism potential in GM plantation bacteria and a higher ectomycorrhizal fungi abundance in DF soil. Significantly positive correlations were detected between certain bacterial and fungal genera and pH and total soluble salt content, suggesting their role in pecan adaptation to coastal environments and saline–alkali stress mitigation. These findings enhance our understanding of soil microbiomes in coastal pecan plantations, and are anticipated to foster ecologically sustainable agroforestry practices and contribute to coastal marshland ecosystem management. Full article
(This article belongs to the Special Issue Bacterial Plant Communities: Diversity, Molecular Interactions, and Plant Growth Promotion, 3rd Edition)
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