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Plant–Microbe Interactions for Sustainable Agriculture
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Plant–Microbe Interactions for Sustainable Agriculture

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

Deadline for manuscript submissions: closed (20 November 2023) | Viewed by 18801

Special Issue Editor

Prof. Dr. Mario De Andrade Lira Junior

E-Mail Website
Guest Editor
Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Rua Dom Manuel de Medeiros, s/n, Dois Irmãos, Recife 52171-900, PE, Brazil
Interests: soil biology and biochemistry

Special Issue Information

Dear Colleagues,

The plant microbiome is a highly diverse environment, with several very important biosystems, ranging from pathogenic to plant growth promoting, all of which involve both plant and microorganism interactions, but the effect of other biotic and abiotic environmental conditions on these interactions. These interactions are a major research field from several different research fronts and have a major potential to help reduce some of the environmental constraints agriculture faces due to the predicted climate change. This special issue will highlight new research and critical reviews on these interactions, from a wide ranging of point of views, covering plant pathogens and growth promoters, from the microbiological and plant point of views.

Prof. Dr. Mario De Andrade Lira Junior
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

  • microbiome
  • plant-growth-promoting bacteria
  • plant pathogen
  • rhizobia
  • endophytic bacteria
  • endophytic fungi
  • mycorrhiza

Published Papers (7 papers)

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Research

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15 pages, 1499 KiB  
Article
Screening Digitaria eriantha cv. Suvernola Endophytic Bacteria for Maize Growth Promotion
by Michelle J. G. Alves, Johny Jesus Mendonça, Gisely Moreira Vitalino, José Paula Oliveira, Erix Xavier Carvalho, Felipe José Cury Fracetto, Giselle Gomes Monteiro Fracetto and Mario Andrade Lira Junior
Plants 2023, 12(14), 2589; https://doi.org/10.3390/plants12142589 - 08 Jul 2023
Viewed by 961
Abstract
The search for sustainable agriculture has increased interest in using endophytic bacteria to reduce fertilizer use and increase stress resilience. Stress-adapted plants are a potential source of these bacteria. Some species of these plants have not yet been evaluated for this, such as [...] Read more.
The search for sustainable agriculture has increased interest in using endophytic bacteria to reduce fertilizer use and increase stress resilience. Stress-adapted plants are a potential source of these bacteria. Some species of these plants have not yet been evaluated for this, such as pangolão grass, from which we considered endophytic bacteria as potential plant growth promoters. Bacteria from the root, colm, leaves, and rhizospheric soil were isolated, and 132 strains were evaluated for their in vitro biological nitrogen fixation, IAA and siderophores production, and phosphate solubilization. Each mechanism was also assessed under low N availability, water stress, and low-solubility Fe and P sources in maize greenhouse experiments. All strains synthesized IAA; 63 grew on N-free media, 114 synthesized siderophores, and 46 solubilized P, while 19 presented all four mechanisms. Overall, these strains had better performance than commercial inoculant in all experiments. Still, in vitro responses were not good predictors of in vivo effects, which indicates that the former should not be used for strain selection, since this could lead to not testing strains with good plant growth promotion potential. Their heterologous growth promotion in maize reinforces the potential of stress-adapted plant species as potential sources of strains for inoculants. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions for Sustainable Agriculture)
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14 pages, 2568 KiB  
Article
Growth Increase in the Herbaceous Plant Centella asiatica by the Plant Growth-Promoting Rhizobacteria Priestia megaterium HyangYak-01
by HyungWoo Jo, Kyeongmo Lim, Jerald Conrad Ibal, Min-Chul Kim, Hye-Been Kim, Chaeyun Baek, Young Mok Heo, Haeun Lee, Seunghyun Kang, Dong-Geol Lee and Jae-Ho Shin
Plants 2023, 12(13), 2398; https://doi.org/10.3390/plants12132398 - 21 Jun 2023
Cited by 1 | Viewed by 1614
Abstract
Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) [...] Read more.
Centella asiatica is a traditional herbaceous plant with numerous beneficial effects, widely known for its medicinal and cosmetic applications. Maximizing its growth can lead to beneficial effects, by focusing on the use of its active compounds. The use of plant growth-promoting rhizobacteria (PGPR) is known to be an alternative to chemical fertilizers. In this study, we used the PGPR Priestia megaterium HY-01 to increase the yield of C. asiatica. In vitro assays showed that HY-01 exhibited plant growth-promoting activities (IAA production, denitrification, phosphate solubilization, and urease activity). Genomic analyses also showed that the strain has plant growth-promoting-related genes that corroborate with the different PGP activities found in the assays. This strain was subsequently used in field experiments to test its effectiveness on the growth of C. asiatica. After four months of application, leaf and root samples were collected to measure the plant growth rate. Moreover, we checked the rhizosphere microbiome between the treated and non-treated plots. Our results suggest that treatment with Hyang-yak-01 not only improved the growth of C. asiatica (leaf length, leaf weight, leaf width, root length, root width, and chlorophyll content) but also influenced the rhizosphere microbiome. Biodiversity was higher in the treated group, and the bacterial composition was also different from the control group. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions for Sustainable Agriculture)
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21 pages, 1656 KiB  
Article
Characterization of a Disease-Suppressive Isolate of Lysobacter enzymogenes with Broad Antagonistic Activity against Bacterial, Oomycetal and Fungal Pathogens in Different Crops
by Christian Drenker, Doris El Mazouar, Gerrit Bücker, Sonja Weißhaupt, Eveline Wienke, Eckhard Koch, Stefan Kunz, Annette Reineke, Yvonne Rondot and Ada Linkies
Plants 2023, 12(3), 682; https://doi.org/10.3390/plants12030682 - 03 Feb 2023
Cited by 5 | Viewed by 1671
Abstract
Although synthetic pesticides play a major role in plant protection, their application needs to be reduced because of their negative impact on the environment. This applies also to copper preparations, which are used in organic farming. For this reason, alternatives with less impact [...] Read more.
Although synthetic pesticides play a major role in plant protection, their application needs to be reduced because of their negative impact on the environment. This applies also to copper preparations, which are used in organic farming. For this reason, alternatives with less impact on the environment are urgently needed. In this context, we evaluated eight isolates of the genus Lysobacter (mainly Lysobacter enzymogenes) for their activity against plant pathogens. In vitro, the investigated Lysobacter isolates showed broad antagonistic activity against several phytopathogenic fungi, oomycetes and bacteria. Enzyme assays revealed diverse activities for the tested isolates. The most promising L. enzymogenes isolate (LEC) was used for further detailed analyses of its efficacy and effective working concentrations. The experiments included in vitro spore and sporangia germination tests and leaf disc assays as well as ad planta growth chamber trials against Alternaria solani and Phytophthora infestans on tomato plants, Pseudoperonospora cubensis on cucumbers and Venturia inaequalis on young potted apple trees. When applied on leaves, dilutions of a culture suspension of LEC had a concentration-dependent, protective effect against the tested pathogens. In all pathosystems tested, the effective concentrations were in the range of 2.5–5% and similarly efficacious to common plant protection agents containing copper hydroxide, wettable sulphur or fenhexamid. Thus, the isolate of L. enzymogenes identified in this study exhibits a broad activity against common plant pathogens and is therefore a promising candidate for the development of a microbial biocontrol agent. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions for Sustainable Agriculture)
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12 pages, 3549 KiB  
Article
Changes in Microbial Community Structure in Response to Gummosis in Peach Tree Bark
by YoungJae Jo, Da-Ryung Jung, Tae-Hyung Park, Dokyung Lee, Min-Kyu Park, Kyeongmo Lim and Jae-Ho Shin
Plants 2022, 11(21), 2834; https://doi.org/10.3390/plants11212834 - 25 Oct 2022
Cited by 4 | Viewed by 1581
Abstract
Peach gummosis disease has been identified as a serious challenge in Korean agriculture and has developed to become a major cause of agricultural productivity losses. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this [...] Read more.
Peach gummosis disease has been identified as a serious challenge in Korean agriculture and has developed to become a major cause of agricultural productivity losses. However, treatments for gummosis have not been systemically established and studies of the microbiome closely related to this plant disease are lacking. Therefore, we analyzed the bacterial and fungal communities in the bark and rhizosphere soil of healthy peach trees and those with gummosis. Through high-throughput sequencing, we obtained unprecedented insights into the bacterial and fungal dynamics of each group, including their diversity and taxonomic classification, as well as network analyses. We found that the presence of gummosis drives a significantly higher alpha diversity in the bark bacterial community. Peach gummosis bark mycobiomes included greater numbers of opportunistic pathogens such as Ascochyta, Botryosphaeria, Saccharomyces, Nectriaceae_NA, Trametes, and Valsaceae_NA. However, the microbiome also included bacteria beneficial to plant growth and the production of polysaccharides—namely, 1174-901-12, Catenibacterium, Cutibacterium, Friedmanniella, Methylobacterium-Methylorubrum, Pseudomonas, Rhodobacter, and Sphingomonas. Furthermore, we confirmed that gummosis induced a more complex structure in the bark microbiome network. We conclude that the findings of this study provide a valuable aid in profiling the overall peach tree microbial ecosystem, which can be utilized to develop precise biomarkers for the early diagnosis of gummosis. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions for Sustainable Agriculture)
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18 pages, 1586 KiB  
Article
Role of Nodulation-Enhancing Rhizobacteria in the Promotion of Medicago sativa Development in Nutrient-Poor Soils
by Noris J. Flores-Duarte, Enrique Mateos-Naranjo, Susana Redondo-Gómez, Eloísa Pajuelo, Ignacio D. Rodriguez-Llorente and Salvadora Navarro-Torre
Plants 2022, 11(9), 1164; https://doi.org/10.3390/plants11091164 - 26 Apr 2022
Cited by 10 | Viewed by 2548
Abstract
Legumes are usually used as cover crops to improve soil quality due to the biological nitrogen fixation that occurs due to the interaction of legumes and rhizobia. This symbiosis can be used to recover degraded soils using legumes as pioneer plants. In this [...] Read more.
Legumes are usually used as cover crops to improve soil quality due to the biological nitrogen fixation that occurs due to the interaction of legumes and rhizobia. This symbiosis can be used to recover degraded soils using legumes as pioneer plants. In this work, we screened for bacteria that improve the legume–rhizobia interaction in nutrient-poor soils. Fourteen phosphate solubilizer-strains were isolated, showing at least three out of the five tested plant growth promoting properties. Furthermore, cellulase, protease, pectinase, and chitinase activities were detected in three of the isolated strains. Pseudomonas sp. L1, Chryseobacterium soli L2, and Priestia megaterium L3 were selected to inoculate seeds and plants of Medicago sativa using a nutrient-poor soil as substrate under greenhouse conditions. The effects of the three bacteria individually and in consortium showed more vigorous plants with increased numbers of nodules and a higher nitrogen content than non-inoculated plants. Moreover, bacterial inoculation increased plants’ antioxidant activities and improved their development in nutrient-poor soils, suggesting an important role in the stress mechanisms of plants. In conclusion, the selected strains are nodulation-enhancing rhizobacteria that improve leguminous plants growth and nodulation in nutrient-poor soils and could be used by sustainable agriculture to promote plants’ development in degraded soils. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions for Sustainable Agriculture)
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9 pages, 1189 KiB  
Article
Plant Genotype Shapes the Bacterial Microbiome of Fruits, Leaves, and Soil in Olive Plants
by Antonino Malacrinò, Saveria Mosca, Maria Giulia Li Destri Nicosia, Giovanni E. Agosteo and Leonardo Schena
Plants 2022, 11(5), 613; https://doi.org/10.3390/plants11050613 - 24 Feb 2022
Cited by 12 | Viewed by 3020
Abstract
The plant microbiome plays an important role in plant biology, ecology, and evolution. While recent technological developments enabled the characterization of plant-associated microbiota, we still know little about the impact of different biotic and abiotic factors on the diversity and structures of these [...] Read more.
The plant microbiome plays an important role in plant biology, ecology, and evolution. While recent technological developments enabled the characterization of plant-associated microbiota, we still know little about the impact of different biotic and abiotic factors on the diversity and structures of these microbial communities. Here, we characterized the structure of bacterial microbiomes of fruits, leaves, and soil collected from two olive genotypes (Sinopolese and Ottobratica), testing the hypothesis that plant genotype would impact each compartment with a different magnitude. Results show that plant genotype differently influenced the diversity, structure, composition, and co-occurence network at each compartment (fruits, leaves, soil), with a stronger effect on fruits compared to leaves and soil. Thus, plant genotype seems to be an important factor in shaping the structure of plant microbiomes in our system, and can be further explored to gain functional insights leading to improvements in plant productivity, nutrition, and defenses. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions for Sustainable Agriculture)
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Review

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25 pages, 1158 KiB  
Review
The Microbial Connection to Sustainable Agriculture
by Kalaivani Nadarajah and Nur Sabrina Natasha Abdul Rahman
Plants 2023, 12(12), 2307; https://doi.org/10.3390/plants12122307 - 14 Jun 2023
Cited by 9 | Viewed by 6278
Abstract
Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants’ growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within [...] Read more.
Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants’ growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant–soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome’s diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant–soil microbiome. These initiatives are important to the advancement of green technologies in agriculture. Full article
(This article belongs to the Special Issue Plant–Microbe Interactions for Sustainable Agriculture)
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