Transforming Agriculture through Soil Microbiota: Pathways to a Sustainable Future
Reconciling the need for both higher yields and environmental preservation is a challenge for agriculture. With growing demand for food and climate change, innovative and sustainable solutions become vital. One of the most promising approaches in this area lies in being able to understand and manipulate soil microorganisms, which play essential roles in plant health, soil fertility and mitigation of environmental stresses.
It is important to study soil microorganisms because protecting biodiversity, proper soil management and efficient water use are key strategies to mitigate impacts of climate change on agriculture. Global warming is one of the clearest impacts of climate change, causing prolonged droughts, intense heat waves and changes in the distribution of rainfall, all of which directly affect agricultural activity.
In addition, climate change in agriculture can increase the incidence of pests and diseases in crops. As global warming and changes in rainfall patterns create more favorable conditions for the proliferation of harmful pathogens and insects, farmers must cope with more pests and diseases, with negative impacts on yields.
Soil microorganisms, known as soil microbiota, help supply, cycle and absorb nutrients in plants, decompose organic matter, store carbon, and make sustainable use of the soil as part of new management solutions for restoration processes. This is giving rise to the Agro 4.0 phenomenon, encompassing multidisciplinary solutions such as the use of biology, remote sensing, biotechnology and technological systems.
The main soil microorganisms are bacteria, fungi, algae, archaea, protozoa and microfauna. The rapid evolution of microorganisms, especially in plant-microbiota interactions, plays a critical role in keeping agricultural ecosystems functional and can significantly alter the ecology of soils, with direct impacts on how plants grow and develop.
Understanding these interactions is vital for the development of evolutionarily stable biofertilizers and pathogen control strategies to promote more sustainable agriculture. Microbial evolution is therefore not just a natural phenomenon, but a potentially powerful resource for agricultural innovation. Among beneficial microorganisms, Plant Growth Promoting Bacteria (PGPB) are one of the most promising tools for sustainable agriculture. These bacteria benefit plants by producing hormones, solubilizing nutrients, inducing defense mechanisms, improving their hosts' physical and biochemical characteristics and general resilience, as well as helping plants manage biotic and abiotic stress. The main BPCPs used in agriculture include species of Bacillus, Azospirillum, Burkholderia, Bradyrhizobium, Streptomyces, Rhizobium and Acetobacter, for example.
Besides this beneficial symbiotic relationship with their host, BPCP communities also help reduce the use of agricultural inputs such as fertilizers, which may boost yields, but have negative environmental impacts. One prime example is the use of Bradyrhizobium in soy crops, enabling both higher yields and lower greenhouse gas emissions. This is just one of many organisms used in agriculture to stimulate plants, deliver nutrients or control pests.
These bacterias’ variable effectiveness in different environments and conditions, however, is still a challenge. More research is needed to better understand interactions between BPCPs, plants and the environment, and to develop practical applications suitable for large-scale adoption in agriculture.
Other innovative strategies, such as using a mixture of microorganisms like Bacillus, Trichoderma and Purpureocillium, offer several advantages over the application or use of products with a single microorganism. This approach not only makes biological control of pathogens more effective, but also improves plant and soil health.
Each microorganism in the blend has specific mechanisms to suppress soil pathogens, promote plant growth and increase soil fertility. For example, B. subtilis and T. harzianum produce plant hormones and improve nutrient absorption, while P. lilacinum makes plants more resistant to biotic and abiotic stress.
Using a mixture of microorganisms reduces dependence on chemical inputs and enhances a farm's sustainability and efficiency. This synergism is especially important given growing concerns over environmental sustainability and soil health.
Maximizing the benefits of microbiology in the field requires investments in soil microbiome analysis. Understanding microbial composition and diversity allows farmers to adjust management practices for optimal soil health and crop yields. In addition, ongoing monitoring of microbiomes can reveal how agricultural practices affect the ecological balance of the soil, shedding valuable insights for more sustainable management. Various technologies can be used to identify these microbes, but the recent use of genomics in particular offers a more assertive identification of microorganisms at genus and species levels, which other conventional microbiology techniques cannot achieve.
After sequencing, databases identify DNA sequences from microorganisms with genomes already on file. This technique can find beneficial microorganisms, such as the aforementioned BPCPs, as well as pathogens such as Fusarium, Rhizoctonia, Sclerotinia, Colletotricum, Phoma, Cercospora, and others, which can cause disease in different crops. An in-depth, metagenomic study of soil microorganisms can generate results on the complete genomes in those communities, and record specific genes and metabolites. It is also possible to select microorganisms with potential agricultural characteristics and even discover new organisms that have never been identified before.
The same technique for identifying soil microorganisms through DNA sequencing can be used in crop areas to find microorganisms of agronomic interest; in native forest areas, to understand the microbial dynamics of this harmonious environment; or in degraded soil situations. Studies have now correlated microbial diversity and abundance in different soils, crop types and biomes in Brazil. However, many more specific databases for samples from throughout the country, along with other technologies for soil and climate analysis, still need to be developed.
Knowing which microorganisms are present in the soil, or in other parts of the plant – such as the root, stem, leaf, flower, fruit and seed – is also extremely important for other approaches, opening doors to more demanding markets and ensuring farmers' satisfaction, especially as we consider developing and validating new bio-inputs and maintaining harmonious ecosystems in the soil. Microbiome analysis, coupled with the use of artificial intelligence, can revolutionize agriculture by bringing biodiversity indices to the field, enabling more assertive, data-based decisions.
Integrating solutions based on microorganisms into agriculture is a promising way to pursue sustainability and productivity, by understanding which microorganisms are present in each biome and in specific climatic conditions. Innovations in the field not only benefit agricultural production, but also contribute to environmental preservation, fostering a more sustainable future for generations to come. With sustainable practices, agribusiness can find its place on the environmental agenda, ensuring benefits for both sectors and building a more promising and ecologically balanced future for agriculture.
* Stela Virgilio is owner and CEO of the Startup ByMyCell, B.S. in Biotechnology, M.S and PhD in Biotechnology and Executive MBA in Business Management.
References:
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Hungria, M.; Nogueira, M.; Araujo, R. (2015) Soybean Seed Co-Inoculation with Bradyrhizobium spp. and Azospirillum brasilense: A New Biotechnological Tool to Improve Yield and Sustainability. American Journal of Plant Sciences, 6, 811-817. doi: 10.4236/ajps.2015.66087
Ordine, J.V.W.; de Souza, G.M.; Tamasco, G.; Virgilio, S.; Fernandes, A.F.T.; Silva-Rocha, R.; Guazzaroni, M.E. (2023) Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil. Antibiotics, 12, 334. https://doi.org/10.3390/antibiotics12020334
Szoboszlay. M.; Schramm, L.; Pinzauti, D.; Scerri, J.; Sandionigi, A.; Biazzo M. (2023) Nanopore Is Preferable over Illumina for 16S Amplicon Sequencing of the Gut Microbiota When Species-Level Taxonomic Classification, Accurate Estimation of Richness, or Focus on Rare Taxa Is Required. Microorganisms, 11(3), 804. doi: 10.3390/microorganisms11030804