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Microorganisms
Special Issues
Microbiomes in Crop Yield and Stress Biology
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Microbiomes in Crop Yield and Stress Biology

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

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 7265

Special Issue Editor

Dr. M. Shahid Mukhtar

E-Mail Website
Guest Editor
Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Interests: systems biology; network science; functional genomics; bioinformatics; deep/machine learning using animal and plant models
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Over the next two decades, the world is predicted to experience an unprecedented global food crisis due to the rapidly growing world population, a food security issue further compounded by global climate change. It is a well-known fact that human activities are undoubtedly driving up the global temperature and fundamentally changing the world around us. Global climate change has far-reaching consequences on plant life and agriculture as a whole. Diverse environmental stresses, including plant pathogens, droughts, flooding, salinity, soil acidification, cold and heat, directly limit crop production. By identifying beneficial microorganisms, crops may be more resilient to such unfavorable stressors, thus, de-escalating the food security problem. In this Special Issue, we aim to focus on plant metagenomics, with articles presenting the functional characterization of novel microbes capable of helping plants thrive in both biotic and abiotic stress conditions.

Dr. M. Shahid Mukhtar
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. Microorganisms 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 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

  • metagenomics
  • bioinformatics
  • microbiome
  • model plant systems
  • agronomically important crops
  • functional genomics
  • climate change
  • crop production
  • plant pathogens
  • abiotic stresses

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Published Papers (3 papers)

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9 pages, 2107 KiB  
Article
Bacterial Communities Associated with the Leaves and the Roots of Salt Marsh Plants of Bayfront Beach, Mobile, Alabama, USA
by Aqsa Majeed, Jinbao Liu, Adelle J. Knight, Karolina M. Pajerowska-Mukhtar and M. Shahid Mukhtar
Microorganisms 2024, 12(8), 1595; https://doi.org/10.3390/microorganisms12081595 - 6 Aug 2024
Viewed by 1042
Abstract
Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located [...] Read more.
Salt marshes are highly dynamic and biologically diverse ecosystems that serve as natural habitats for numerous salt-tolerant plants (halophytes). We investigated the bacterial communities associated with the roots and leaves of plants growing in the coastal salt marshes of the Bayfront Beach, located in Mobile, Alabama, United States. We compared external (epiphytic) and internal (endophytic) communities of both leaf and root plant organs. Using 16S rDNA amplicon sequencing methods, we identified 10 bacterial phyla and 59 different amplicon sequence variants (ASVs) at the genus level. Bacterial strains belonging to the phyla Proteobacteria, Bacteroidetes, and Firmicutes were highly abundant in both leaf and root samples. At the genus level, sequences of the genus Pseudomonas were common across all four sample types, with the highest abundance found in the leaf endophytic community. Additionally, Pantoea was found to be dominant in leaf tissue compared to roots. Our study revealed that plant habitat (internal vs. external for leaves and roots) was a determinant of the bacterial community structure. Co-occurrence network analyses enabled us to discern the intricate characteristics of bacterial taxa. Our network analysis revealed varied levels of ASV complexity in the epiphytic networks of roots and leaves compared to the endophytic networks. Overall, this study advances our understanding of the intricate composition of the bacterial microbiota in habitats (epiphytic and endophytic) and organs (leaf and root) of coastal salt marsh plants and suggests that plants might recruit habitat- and organ-specific bacteria to enhance their tolerance to salt stress. Full article
(This article belongs to the Special Issue Microbiomes in Crop Yield and Stress Biology)
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19 pages, 4149 KiB  
Article
Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System
by Carolina N. Resendiz-Nava, Fernando Alonso-Onofre, Hilda V. Silva-Rojas, Angel Rebollar-Alviter, Dulce M. Rivera-Pastrana, Matthew J. Stasiewicz, Gerardo M. Nava and Edmundo M. Mercado-Silva
Microorganisms 2023, 11(7), 1633; https://doi.org/10.3390/microorganisms11071633 - 22 Jun 2023
Cited by 7 | Viewed by 3835
Abstract
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and [...] Read more.
Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs. Full article
(This article belongs to the Special Issue Microbiomes in Crop Yield and Stress Biology)
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15 pages, 3628 KiB  
Article
Biocontrol Potential of Some Rhizospheric Soil Bacterial Strains against Fusarium culmorum and Subsequent Effect on Growth of Two Tunisian Wheat Cultivars
by Habiba Kouki, Mouna Souihi, Ilhem Saadouli, Sabrine Balti, Amira Ayed, Nihed Majdoub, Amor Mosbah, Ismail Amri and Yassine Mabrouk
Microorganisms 2023, 11(5), 1165; https://doi.org/10.3390/microorganisms11051165 - 29 Apr 2023
Cited by 1 | Viewed by 1751
Abstract
PGPR (Plant Growth Promoting Rhizobacteria) are used as biofertilizers and biological control agents against fungi. The objective of this work was to evaluate the antagonistic activities of some bacterial strains isolated from soil against four phytopathogenic fungal strains (Fusarium graminearum, F. [...] Read more.
PGPR (Plant Growth Promoting Rhizobacteria) are used as biofertilizers and biological control agents against fungi. The objective of this work was to evaluate the antagonistic activities of some bacterial strains isolated from soil against four phytopathogenic fungal strains (Fusarium graminearum, F. culmorum, Phytophthora sp. and Verticillium dahlia). Two strains having an antagonist effect on fungi and displaying the maximum of plant growth promoting (PGP) traits were selected for further study and identified as Bacillus subtilis and B. amyloliquefaciens respectively. In planta assays demonstrated that the two Bacillus strains are able to enhance plant growth of two wheat cultivars in absence of nitrogen and protect them against F. culmorum. Pot experiments performed in a greenhouse showed that wheat plants inoculation with two bacterial strains reduce F. culmorum disease severity correlated with the accumulation of phenolic compounds and chlorophyll content. These could partly explain the effectiveness of these bacteria in protecting Tunisian durum wheat cultivars against F. culmorum. Application B. amyloliquefaciens, showed better protection than B. subtilis although the last one enhanced more the plant growth of two wheat cultivars in absence of fungus. Hence, combination of two bacterial strains could be a strategic approach to enhance plant growth and control plant diseases. Full article
(This article belongs to the Special Issue Microbiomes in Crop Yield and Stress Biology)
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