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Bacteria
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Harnessing of Soil Microbiome for Sustainable Agriculture
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Harnessing of Soil Microbiome for Sustainable Agriculture

A special issue of Bacteria (ISSN 2674-1334).

Deadline for manuscript submissions: 30 June 2025 | Viewed by 3514

Special Issue Editors

Dr. Debasis Mitra

E-Mail Website1 Website2
Guest Editor
Department of Microbiology, Graphic Era (Deemed to be University), Dehradun 248002, Uttarakhand, India
Interests: plant microbe interactions; soil microbiology; arbuscular mycorrhizal fungi; environmental microbiology; microbial diversity; plant growth-promoting microbes; biocontrol; strigolactone
Special Issues, Collections and Topics in MDPI journals
Dr. Marika Pellegrini

E-Mail Website
Guest Editor
Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy
Interests: plant–soil–microbe interactions; sustainable agriculture; plant growth-promoting bacteria; bio stimulants; biocontrol agents; bioactive compounds
Special Issues, Collections and Topics in MDPI journals
Dr. Leonard Koolman

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Guest Editor
UCD-Centre for Food Safety, University College Dublin, 4 Dublin, Ireland; School of Biological Sciences, Technological University Dublin, Dublin, Ireland
Interests: antimicrobial resistance; plastisphere; biofilms; one health in agriculture; carbon dots; electromicrobiology; horizontal gene transfer

Special Issue Information

Dear Colleagues,

Soil microorganisms such as bacteria, fungi, protozoa and archaea, collectively known as the soil microbiome, play a vital role in plant health and crop productivity. By incorporating microbial inoculants, biofertilizers and biopesticides into agricultural practices, farmers can enhance soil health, promote resilience to climate change and reduce environmental impacts. Biofertilizers and soil inoculants containing beneficial microorganisms can increase nutrient availability and plant uptake. The use of diverse microbial communities over single strains can lead to more effective and resilient agricultural systems. Certain microorganisms can act as natural enemies of pests, reducing the need for synthetic pesticides in integrated pest management strategies. Soil microorganisms also contribute to carbon cycling, storing atmospheric carbon dioxide in soil organic matter, which can mitigate climate change by sequestering carbon in agricultural soils. Microbial bioremediation techniques can clean up contaminated soils by using microorganisms to break down pollutants. Advances in soil microbiome research and biotechnology are crucial for promoting sustainable agriculture. Technologies such as metagenomics and microbial ecology provide insights into soil microbial communities in agroecosystems. This Special Issue emphasizes the potential of the soil microbiome to improve agricultural sustainability, increase crop yields and reduce environmental damage, thereby supporting food security and ecosystem stability for future generations.

Dr. Debasis Mitra
Dr. Marika Pellegrini
Dr. Leonard Koolman
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. Bacteria 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

  • microorganisms
  • soil microbiome
  • plant growth-promoting rhizobacteria (PGPR)
  • arbuscular mycorrhizal fungi
  • plant microbe interaction
  • rhizospheric microenvironment
  • environmental impacts
  • climate change
  • soil nutrient
  • nutrient uptake
  • microbial inoculants
  • pest management 
  • bioremediation
  • soil organic matter
  • metagenomics
  • biocontrol
  • microbial ecology 
  • food security
  • sustainable agriculture

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Published Papers (2 papers)

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Research

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16 pages, 1457 KiB  
Article
New Insights on the Glyphosate-Degrading Enzymes C-P Lyase and Glyphosate Oxidoreductase Based on Bioinformatics
by Marina Giannakara and Vassiliki Lila Koumandou
Bacteria 2024, 3(4), 314-329; https://doi.org/10.3390/bacteria3040021 - 2 Oct 2024
Viewed by 1150
Abstract
Bioremediation, the degradation of environmental pollutants by living organisms, has immense potential to lead to a greener planet. Bioinformatics analysis can contribute to the identification of novel microorganisms, which biodegrade contaminants, or of participating proteins and enzymes, and the elucidation of the complex [...] Read more.
Bioremediation, the degradation of environmental pollutants by living organisms, has immense potential to lead to a greener planet. Bioinformatics analysis can contribute to the identification of novel microorganisms, which biodegrade contaminants, or of participating proteins and enzymes, and the elucidation of the complex metabolic pathways involved. In this study, we focus on C-P lyase and glyphosate oxidoreductase (Gox), two enzymes which degrade glyphosate, a widely used pesticide. Amino acid sequences of the two enzymes were collected from a broad range of microorganisms using the KEGG database and BLAST. Based on this, we identified additional lineages, with putative glyphosate-degrading activity, for which no glyphosate-degrading species have been reported yet. The conserved residues in each enzyme were identified via multiple alignments and mapped onto the 3D structures of the enzymes, using PyMOL, leading to novel insights into their function. As the experimental structure of Gox is still unknown, we created structural models based on three different programs and compared the results. This approach can be used to yield insights into the characteristics of potential glyphosate-degrading enzymes. Given the limited information available, such a step is important to gain further knowledge about them, which can contribute to their application in bioremediation in the future. Full article
(This article belongs to the Special Issue Harnessing of Soil Microbiome for Sustainable Agriculture)
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Review

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16 pages, 320 KiB  
Review
Application of Biofertilizers for Enhancing Beneficial Microbiomes in Push–Pull Cropping Systems: A Review
by Admire R. Dzvene and Cornelius Chiduza
Bacteria 2024, 3(4), 271-286; https://doi.org/10.3390/bacteria3040018 - 25 Sep 2024
Viewed by 1214
Abstract
The need for sustainable farming practices has brought attention to biofertilizers to improve soil quality and boost crop yield while minimizing environmental impacts. This study explores the potential integration of biofertilizers within push–pull cropping systems, an agroecological approach that utilizes companion cropping to [...] Read more.
The need for sustainable farming practices has brought attention to biofertilizers to improve soil quality and boost crop yield while minimizing environmental impacts. This study explores the potential integration of biofertilizers within push–pull cropping systems, an agroecological approach that utilizes companion cropping to repel and attract pests. This review focuses on how biofertilizers could optimize plant–microbe interactions, promoting nutrient uptake, pest control, and soil health. Key biofertilizers, including nitrogen-fixing, phosphate-solubilizing, and potassium-solubilizing bacteria, improve nutrient availability, which leads to higher crop yields and resilience. They also enhance soil water retention and drought tolerance, which are crucial under changing climate conditions. Biofertilizers support beneficial microbial communities, reducing reliance on synthetic fertilizers and pesticides while fostering disease suppression and stress tolerance in crops. Their effectiveness can be significantly increased when biofertilizers are integrated with push–pull technology (PPT). However, challenges remain, such as inconsistent biofertilizer performance and the complexity of microbial interactions. Overcoming these challenges necessitates a multidisciplinary approach to refining production and application techniques. This study emphasizes the need to investigate biofertilizer-mediated plant–microbiome dynamics further to unlock their full potential. It concludes that future research should focus on the synergies between biofertilizers and agroecological systems to enhance food security and environmental sustainability. This work advances our understanding of optimizing biofertilizers in sustainable farming practices, particularly within the PPT framework. Full article
(This article belongs to the Special Issue Harnessing of Soil Microbiome for Sustainable Agriculture)
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