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Progress in Multi-omics and Bioinformatics Approaches: Seed Microbiome and Metagenome
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Progress in Multi-omics and Bioinformatics Approaches: Seed Microbiome and Metagenome

A special issue of Seeds (ISSN 2674-1024).

Deadline for manuscript submissions: 20 February 2025 | Viewed by 2036

Special Issue Editors

Dr. Aria Dolatabadian

E-Mail Website
Guest Editor
School of Biological Sciences, The University of Western Australia, Crawley 6009 WA, Australia
Interests: genetics and genomics; plant microbe interaction; seed physiology
Dr. Mohammad Sayari

E-Mail Website
Guest Editor
Department of Plant Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
Interests: resistance genes; fungal pathogens; genomics and transcriptomics; bioinformatics; seed borne diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue explores the dynamic field of seed microbiome research, leveraging advanced multi-omics and bioinformatics methodologies. Historically, understanding the microbial communities associated with seeds has been pivotal in agriculture, influencing seed health, plant growth, and overall crop productivity. Traditional culture-based techniques have given way to high-throughput sequencing and bioinformatics tools, allowing for comprehensive analyses of the microbial diversity, community structure, and functional interactions of seeds.

The aim of this Special Issue is to showcase recent advancements in multi-omics (genomics, metagenomics, transcriptomics, proteomics, metabolomics) and bioinformatics approaches when applied to seed microbiomes. We aim to collate cutting-edge research that highlights innovative methodologies, novel findings on seeds’ microbial composition and function, insights into plant–microbe interactions, and advancements in understanding microbial contributions to seed health and crop performance.

We are inviting original research articles, reviews, reports, communications, and perspectives that address key aspects of seed microbiome and metagenome research. Topics of interest include but are not limited to microbial diversity across different seed types, the functional roles of seed-associated microbes, environmental influences on seed microbiomes, technological innovations in multi-omics analyses, and implications for sustainable agriculture and food security.

Overall, this Special Issue aims to foster interdisciplinary discussions, provide a platform for sharing state-of-the-art research, and drive future directions in leveraging seed microbiomes for agricultural improvement and environmental sustainability.

Dr. Aria Dolatabadian
Dr. Mohammad Sayari
Guest Editors

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. Seeds is an international peer-reviewed open access quarterly 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 1000 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

  • multi-omics
  • bioinformatics
  • seed microbiome
  • metagenomics
  • microbial ecology
  • functional diversity
  • plant–microbe interactions
  • community analysis
  • microbiota composition
  • environmental adaptation

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Published Papers (2 papers)

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19 pages, 2542 KiB  
Article
Prevalence of Seed-Borne Fungi on Soybean (Glycine max L. Merr.) Seeds Stored Under Medium-Term Cold Room Facilities: Implications for Genebanks
by Abdul J Shango, Sognigbé N’Danikou, Shebati Ramadhani, Saphina Sumaye, Jonas Nickas and Michael L Daud
Seeds 2024, 3(4), 589-607; https://doi.org/10.3390/seeds3040040 - 5 Nov 2024
Viewed by 532
Abstract
This study examined the prevalence of seed-borne fungi in polyethylene plastic-packaged soybean seeds stored in a genebank and identified factors influencing their incidence. Twenty-four seed lots were sampled from the collection stored at 10 °C in the World Vegetable Center genebank in Arusha, [...] Read more.
This study examined the prevalence of seed-borne fungi in polyethylene plastic-packaged soybean seeds stored in a genebank and identified factors influencing their incidence. Twenty-four seed lots were sampled from the collection stored at 10 °C in the World Vegetable Center genebank in Arusha, Tanzania. The seeds used were those regenerated and harvested in 2015, 2016, and 2017. A seed health test was conducted for sterilized seeds on potato dextrose agar, sterilized seeds on top of the paper, and unsterilized seeds on top of the paper. Seven-year-old sterilized seeds plated on top of the paper exhibited the highest germination percentage (74 ± 7.09%) and lowest fungal incidence (7.00 ± 4.41%). Conversely, seven-year-old unsterilized seeds plated on top of the paper had the lowest germination (22.00 ± 6.97%) and highest fungal incidence (79.00 ± 8.31%). Older seed lots showed significantly higher equilibrium seed moisture content (Eqmc), though seed age had no significant influence on germination percentage or fungal incidence. Seed germination percentage showed a significant negative relationship with Eqmc, though Eqmc had no significant effect on fungal incidence. Meanwhile, germination percentage showed a significant negative relationship with fungal incidence. Six fungi isolates were identified using their morphological features from soybean seed samples: Absidia glauca, Aspergillus niger, Fusarium spp., Mucor hiemalis, Pestalotiopsis versicolor, and Sordaria macrospora. It is concluded that high fungal incidence negatively affects seed germination but is not significantly correlated with seed moisture content. The dry and cold storage conditions in the genebank, while effective in extending seed longevity, can unintentionally allow seed-borne mycoflora to persist. Although fungi may not actively proliferate under these conditions, they may do so when favorable conditions are restored, such as during germination tests, and consequently may compromise seed viability. Therefore, this study emphasizes the importance of increased systematic seed health checks before storage in genebanks to ensure optimal seed quality, and the replacement of all polyethylene plastic bags to aluminium foil packaging. Full article
(This article belongs to the Special Issue Progress in Multi-omics and Bioinformatics Approaches: Seed Microbiome and Metagenome)
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12 pages, 1481 KiB  
Article
Comparative Metagenomic Profiling of Seed-Borne Microbiomes in a Landrace and a Hybrid Maize Variety
by Sarah Henaut-Jacobs, Beatriz Elisa Barcelos Cyríaco, Francisnei Pedrosa-Silva, Fabio Lopes Olivares and Thiago Motta Venancio
Seeds 2024, 3(4), 528-539; https://doi.org/10.3390/seeds3040035 - 26 Sep 2024
Viewed by 851
Abstract
The plant seed-borne microbiome comprises microorganisms vertically inherited from the mother plant. This microbiome is often linked to early-life protection and seedling growth promotion. Herein, we compare the seed-borne bacteriomes of a commercial hybrid (Santa Helena) and a landrace maize variety (Sol da [...] Read more.
The plant seed-borne microbiome comprises microorganisms vertically inherited from the mother plant. This microbiome is often linked to early-life protection and seedling growth promotion. Herein, we compare the seed-borne bacteriomes of a commercial hybrid (Santa Helena) and a landrace maize variety (Sol da Manhã). The landrace variety displays a more diverse seed-borne microbiome, featuring a variety of taxa across samples with an average Shannon’s diversity index of 1.12 compared to 0.45 in the hybrid variety. The landrace variety also showed a greater alpha diversity of 165.8, in contrast to 144.1 in the hybrid. Although both microbiomes lack a functional nitrogen fixation apparatus, we found a remarkably distinct presence of genes associated with phytohormone production and phosphate solubilization, particularly in the landrace variety. In addition, we recovered 18 metagenome-assembled genomes (MAGs), including four from potentially novel species. Collectively, our results allow for a better understanding of the contrasting diversity between maize varieties. The higher potential for phytohormone production in landraces, the absence of nif genes in both varieties, and the identification of core microbiome taxa offer valuable insights into how microbial communities impact plant health and development. This knowledge could pave the way for more sustainable and innovative agricultural practices in crop management. Full article
(This article belongs to the Special Issue Progress in Multi-omics and Bioinformatics Approaches: Seed Microbiome and Metagenome)
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