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Plant-Microbiome Interactions
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Plant-Microbiome Interactions

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Protection and Biotic Interactions".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 4517

Special Issue Editor

Dr. Waqar Islam

E-Mail Website
Guest Editor
Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
Interests: plant–soil microbiome interactions; plant protection; plant stress tolerance; plant defense mechanisms

Special Issue Information

Dear Colleagues,

Plant–microbiome interactions are instrumental in shaping plant performance, stress tolerance, and nutrient acquisition. The study of mutualistic and pathogenic interactions, as well as the impact of environmental factors on these associations, has broad relevance in the context of sustainable agriculture, biotechnology, and ecosystem restoration. This Special Issue aims to consolidate research contributions from diverse geographical regions and ecological contexts, fostering a holistic view of plant–microbiome interactions.

We encourage contributions covering a wide range of topics related to plant–microbiome interactions, including, but not limited to, the following:

  1. Beneficial plant–microbe interactions.
  2. Pathogenic interactions and plant defense mechanisms.
  3. Microbial communities in the plant rhizosphere and phyllosphere.
  4. Impact of abiotic and biotic stressors on plant–microbiome interactions.
  5. Methodological advances in studying plant–microbiome dynamics.

Authors are invited to submit original research articles, reviews, and methodological papers. All submissions will undergo a rigorous peer-review process to ensure the highest scientific quality.

Dr. Waqar Islam
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • plant–microbiome interactions
  • rhizosphere microbiota
  • phyllosphere microbes
  • symbiotic relationships
  • pathogenic interactions
  • microbial diversity
  • plant health
  • nutrient cycling
  • biostimulants
  • plant defence mechanisms
  • abiotic stress tolerance
  • microbiome manipulation
  • soil microbiota
  • ecological restoration
  • microbiome engineering

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (4 papers)

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Research

20 pages, 6351 KiB  
Article
Endophytic Bacteria and Fungi Associated with Polygonum cuspidatum in the Russian Far East
by Olga A. Aleynova, Alexey A. Ananev, Nikolay N. Nityagovsky, Andrey R. Suprun, Nursaule Zh. Zhanbyrshina, Alina A. Beresh, Zlata V. Ogneva, Alexey P. Tyunin and Konstantin V. Kiselev
Plants 2024, 13(18), 2618; https://doi.org/10.3390/plants13182618 - 19 Sep 2024
Viewed by 476
Abstract
Polygonum cuspidatum, alternatively known as Fallopia japonica or Reynoutria japonica, is a perennial herb belonging to the Polygonaceae family. Commonly called Japanese knotweed or Asian knotweed, this plant is native to East Asia, particularly in regions such as Korea, China, and [...] Read more.
Polygonum cuspidatum, alternatively known as Fallopia japonica or Reynoutria japonica, is a perennial herb belonging to the Polygonaceae family. Commonly called Japanese knotweed or Asian knotweed, this plant is native to East Asia, particularly in regions such as Korea, China, and Japan. It has successfully adapted to a wide range of habitats, resulting in it being listed as a pest and invasive species in several countries in North America and Europe. This study focuses on analysing the composition of the bacterial and fungal endophytic communities associated with Japanese knotweed growing in the Russian Far East, employing next-generation sequencing (NGS) and a cultivation-based method (microbiological sowing). The NGS analysis showed that the dominant classes of endophytic bacteria were Alphaproteobacteria (28%) and Gammaproteobacteria (28%), Actinobacteria (20%), Bacteroidia (15%), and Bacilli (4%), and fungal classes were Agaricomycetes (40%), Dothideomycetes (24%), Leotiomycetes (10%), Tremellomycetes (9%), Pezizomycetes (5%), Sordariomycetes (3%), and Exobasidiomycetes (3%). The most common genera of endophytic bacteria were Burkholderia-Caballeronia-Parabukholderia, Sphingomonas, Hydrotalea, Methylobacterium-Metylorubrum, Cutibacterium, and Comamonadaceae, and genera of fungal endophytes were Marasmius, Tuber, Microcyclosporella, Schizothyrium, Alternaria, Parastagonospora, Vishniacozyma, and Cladosporium. The present data showed that the roots, leaves, and stems of P. cuspidatum have a greater number and diversity of endophytic bacteria and fungi compared to the flowers and seeds. Thus, the biodiversity of endophytic bacteria and fungi of P. cuspidatum was described and analysed for the first time in this study. Full article
(This article belongs to the Special Issue Plant-Microbiome Interactions)
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20 pages, 4749 KiB  
Article
Variation in Root-Associated Microbial Communities among Three Different Plant Species in Natural Desert Ecosystem
by Yulin Zhang, Yi Du, Zhihao Zhang, Waqar Islam and Fanjiang Zeng
Plants 2024, 13(17), 2468; https://doi.org/10.3390/plants13172468 - 3 Sep 2024
Viewed by 766
Abstract
The process and function that underlie the assembly of root-associated microbiomes may be strongly linked to the survival strategy of plants. However, the assembly and functional changes of root-associated microbial communities in different desert plants in natural desert ecosystems are still unclear. Thus, [...] Read more.
The process and function that underlie the assembly of root-associated microbiomes may be strongly linked to the survival strategy of plants. However, the assembly and functional changes of root-associated microbial communities in different desert plants in natural desert ecosystems are still unclear. Thus, we studied the microbial communities and diversity of root endosphere (RE), rhizosphere soil (RS), and bulk soil (BS) among three representative desert plants (Alhagi sparsifolia, Tamarix ramosissima, and Calligonum caput-medusae) in three Xinjiang desert regions {Taklimakan (CL), Gurbantünggüt (MSW), and Kumtag (TLF)} in China. This study found that the soil properties {electrical conductivity (EC), soil organic carbon (SOC), total nitrogen (TN) and phosphorus (TP), available nitrogen (AN) and phosphorus (AP)} of C. caput-medusae were significantly lower than those of A. sparsifolia and T. ramosissima, while the root nutrients (TN and TP) of A. sparsifolia were significantly higher compared to C. caput-medusae and T. ramosissima. The beta diversity of bacteria and fungi (RE) among the three desert plants was significantly different. The common OTU numbers of bacteria and fungi in three compartments (RE, RS, and BS) of the three desert plants were ranked as RS > BS > RE. The bacterial and fungal (RE) Shannon and Simpson indexes of C. caput-medusae were significantly lower as compared to those of A. sparsifolia and T. ramosissima. Additionally, bacterial and fungal (RE and RS) node numbers and average degree of C. caput-medusae were lower than those found in A. sparsifolia and T. ramosissima. Root and soil nutrients collectively contributed to the composition of root-associated bacterial (RE, 12.4%; RS, 10.6%; BS, 16.6%) and fungal communities (RE, 34.3%; RS, 1.5%; BS, 17.7%). These findings demonstrate variations in the bacterial and fungal populations across different plant species with distinct compartments (RE, RS, and BS) in arid environments. More importantly, the study highlights how much soil and plant nutrients contribute to root-associated microbial communities. Full article
(This article belongs to the Special Issue Plant-Microbiome Interactions)
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13 pages, 2439 KiB  
Article
Geographic Location Affects the Bacterial Community Composition and Diversity More than Species Identity for Tropical Tree Species
by Kepeng Ji, Yaqing Wei and Guoyu Lan
Plants 2024, 13(11), 1565; https://doi.org/10.3390/plants13111565 - 5 Jun 2024
Viewed by 1120
Abstract
Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as [...] Read more.
Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as well as how these communities respond to environmental changes. In this study, we aimed to elucidate the characteristics of bacterial community composition in association with two rare and endangered tropical tree species, Dacrydium pectinatum and Vatica mangachapoi, across various geographical locations on Hainan Island. Our findings can be summarized as follows: (1) Significant differences existed in the bacterial composition between D. pectinatum and V. mangachapoi, as observed in the diversity of bacterial populations within the root endosphere. Plant host-related variables, such as nitrogen content, emerged as key drivers influencing leaf bacterial community compositions, underscoring the substantial impact of plant identity on bacterial composition. (2) Environmental factors associated with geographical locations, including temperature and soil pH, predominantly drove changes in both leaf and root-associated bacterial community compositions. These findings underscored the influence of geographical locations on shaping plant-associated bacterial communities. (3) Further analysis revealed that geographical locations exerted a greater influence than tree species identity on bacterial community compositions and diversity. Overall, our study underscores that environmental variables tied to geographical location primarily dictate changes in plant bacterial community composition. These insights contribute to our understanding of microbial biogeography in tropical regions and carry significant implications for the conservation of rare and endangered tropical trees. Full article
(This article belongs to the Special Issue Plant-Microbiome Interactions)
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21 pages, 5816 KiB  
Article
The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field
by Yao Yao, Changxing Liu, Yu Zhang, Yang Lin, Tao Chen, Jiatao Xie, Haibin Chang, Yanping Fu, Jiasen Cheng, Bo Li, Xiao Yu, Xueliang Lyu, Yanbo Feng, Xuefeng Bian and Daohong Jiang
Plants 2024, 13(6), 912; https://doi.org/10.3390/plants13060912 - 21 Mar 2024
Cited by 1 | Viewed by 1415
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, [...] Read more.
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes. Full article
(This article belongs to the Special Issue Plant-Microbiome Interactions)
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