Since the Neolithic Revolution, agriculture has fundamentally transformed human existence. By freeing people from the constant search for food, it has delivered two pivotal advantages: enhanced security and the gift of time. These changes enabled communities to settle, fostering the growth of cities and the pursuit of knowledge, innovation, and art (1). In this sense, agriculture stands as the cornerstone of civilization itself.
Low relief from the Baths of Diocletian in Rome (300 AD)
Yet, despite these monumental advances, modern agricultural practices now threaten the very foundations they helped build. Environmental degradation, risks to human and animal health, and climate instability challenge the sustainability of our societies.
Restoring the importance of biology in agriculture can help to solve this ironic and urgent paradox.
What are the Main Threats Posed by Modern Agriculture?
Agriculture lies at the heart of both local and global environmental and health challenges vividly illustrated by the planetary boundaries’ framework proposed by Rockström in 2009 (2).
At the local level, agricultural expansion disrupts biosphere integrity, directly threatening biodiversity by destroying habitats and disrupting the delicate interactions between species. The use of agricultural inputs further exacerbates these issues, releasing novel chemical entities into air, water, and soil (3). This diffuse pollution exposes both ecosystems and human populations to potentially harmful substances and complex mixtures, with unknown long-term health consequences.
Update of the planetary boundaries transgressed (2023). Image from Richardson et al. Sci Adv. 2023 Sep 15;9(37):eadh2458. doi: 10.1126/sciadv.adh2458. Epub 2023 Sep 13. PMID: 37703365; PMCID: PMC10499318.
These farming practices traps agriculture in a vicious cycle wherein intensive farming harnessing chemical prophylaxis, fertilization, and tillage degrade soil structure and fertility, necessitating even greater inputs of land and synthetic fertilizers to offset erosion and declining productivity.
On a global scale, agriculture’s environmental footprint is highly concerning. Deforestation, soil degradation, production of synthetic pesticides and fertilizers, livestocks and transport of crops and machines collectively account for an estimated 20% of human-induced CO₂ emissions, making agriculture a major driver of climate change (4).
How did We Reach this Tipping Point?
Over the past 10,000 years, humanity has transformed farming to sustain the dietary needs of 8 billion people. Looking back, this remarkable journey is marked by a constellation of empirical breakthroughs and scientific advancements, each contributing to the steady evolution of agriculture. From the domestication of plants and animals to the cutting-edge techniques of genetic breeding, every innovation has shaped the way we feed the world today.
Many of these pivotal discoveries including crop rotation, fallow land, composting, and selective breeding have gradually enhanced agricultural productivity, all associated with fundamental biological principles. Yet, since the mid-19th century, a profound shift has reshaped farming. Chemistry and mechanization have overtaken biology as the driving forces behind agricultural expansion and intensification (5).
The advent of synthetic fertilizers, the rise of conventional pesticides, and mechanized tilling have largely replaced farming practices. These innovations by propelling agriculture into the industrial era, enabled humanity to circumvent the biological constraints of sustainability, fundamentally altering our conception of farming, and transforming food from a natural resource into a commodity like any other.
Are We Able to Change?
Sustainable, resilient agriculture is a goal everyone supports, but can it be achieved without disrupting economic stability, reducing yields, or compromising food security? This is the defining challenge of our time. While the path is complex, there is reason for optimism. We can certainly make the bet that by democratizing knowledge, technology, and best practices, we can reconnect agriculture with biology and unlock transformative progress.
Take soil management as a prime example. Modern farming has largely overlooked and often damaged the soil microbiome, the rich community of microorganisms that underpin soil health. Yet, recent research reveals these microbes as indispensable allies.
They enhance crop growth, suppress plant diseases, and reduce the need for pesticides and synthetic fertilizers (6). Certain microbes even improve crop resilience to drought (7,8). Beyond the field, microbes preserve soil structure, prevent erosion, and help sequester carbon, directly contributing to climate change mitigation.
Microorganisms used in agriculture to support crop growth and protection. From left to right: Trichoderma, Penicillium, Bacillus, Pseudomonas
These discoveries are grounded in empirical discoveries that received in recent years a fantastic level of refinement stemming from recent scientific research and innovations. For instance, breakthroughs in DNA sequencing now allow us to analyze microbial biodiversity with remarkable precision, speed, and affordability thereby revolutionizing our understanding of how microbes interact with soil and plants, and how this is important for enhancement of farming practices (8).
The applications unfolding are vast and promising. Farmers will be enabled to access soil health diagnostics, manage microbial diversity, and make data-driven decisions by integrating microbiology to improve their practices, production quality and yields while spending less resources. By quantifying the status and functions of soil microbes, we can also create incentives for farmers to adopt practices that preserve soil health and reward stewardship fostering long-term sustainability.
From nature-inspired biopesticides (such as plant extracts and beneficial microbes) for eco-friendly crop protection (9), to precision genome editing (like CRISPR) for resilient, high-yield crops (10), and microbiome engineering to restore degraded soils (12), biotechnologies hold great promise. Together, they can address the critical challenges of fertilization, pest control, and yield maintenance as agriculture transitions toward greener practices.
Shifting the Balance
Biology behaves like a “wild beast” in the way that living organisms possess the remarkable ability to respond to diverse cues in myriad ways. This inherent complexity that makes biological systems less predictable than physical or chemical phenomena made biology an outlier in the era of industrial productivism. Yet, today, we stand at a turning point where advances in scientific expertise and technology allow us to understand biology at every scale, macroscopic, microscopic, and molecular level, with unprecedented depth. Coupled with the power of machine and deep learning to process large datasets, we are equipped to address most intricate biological challenges.
This convergence creates transformative opportunities to refine, sustain, and optimize the integration of biology into agroecological practices. But seizing these opportunities demands more than just capability. It requires courage stepping beyond the established frameworks of industrial agriculture, embracing trial and error, and sharing between all the actors the risks that come with innovation.
Success will also hinge on collaboration. Farmers, researchers, and other stakeholders including consumers and politics must work together, co-creating knowledge and productive framework through participatory research. By confronting both the scientific and socio-economic complexities of this challenge, we can forge the legacy of a sustainable agriculture more extensively rooted in biology and ensure prosperity for future generations.
About the Author
This article was written by Dr. Patrick Gonzalez, PhD, Assistant Professor at SupBiotech Engineering School of Biotechnology, WP3 Research & Innovation Co-coordinator.
Author’s research focuses on mechanisms of action and impacts of cytotoxic molecules from diverse origins (animal, plant, and microbial) and their biotechnological applications in the fields of health and environment.
He is member of the LRPIA lab at SupBiotech. The LRPIA is drawing on its expertise in microbiology, cell biology, and meta-genomics to develop biocontrol solutions in agro-ecology, with the aim of reducing the use of phytosanitary inputs.
Current projects focus on the use of a crop resource considered to be waste, rich in antimicrobial compounds, to combat fungal diseases. It seeks to characterize the mechanisms of action, efficacy, and impact of these compounds on soil health, in collaboration with farmers, and academic and industrial partners. This project is supported by the Normandy region and the European Union via FEADER funds.
Bibliography
- Carey J. Unearthing the origins of agriculture. Proc Natl Acad Sci U S A. 2023 Apr 11;120(15):e2304407120. doi: 10.1073/pnas.2304407120. Epub 2023 Apr 5. PMID: 37018195; PMCID: PMC10104519.
- Rockström J et al. A safe operating space for humanity. Nature. 2009 Sep 24;461(7263):472-5. doi: 10.1038/461472a. PMID: 19779433.
- Froger C, et al. Pesticide Residues in French Soils: Occurrence, Risks, and Persistence. Environ Sci Technol. 2023 May 23;57(20):7818-7827. doi: 10.1021/acs.est.2c09591. Epub 2023 May 12. PMID: 37172312; PMCID: PMC10210535.
- For a Low-carbon, Resilient, and prosperous agriculture Shift Project Report 2024 November https://theshiftproject.org/app/uploads/2025/10/Final-report-Agriculture_2024_Shift-Project.pdf
- Angus C. Chu et al. Agricultural revolution and industrialization, Journal of Development Economics, 2022, Volume 158, 102887, ISSN 0304-3878, doi.org/10.1016/j.jdeveco.2022.102887.
- Taglialegna A. Microbial allies in plant defence against drought. Nat Rev Microbiol. 2025 Aug;23(8):471. doi: 10.1038/s41579-025-01204-8. PMID: 40500385.
- Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018 May;16(5):263-276. doi: 10.1038/nrmicro.2018.9. Epub 2018 Feb 5. PMID: 29398704.
- Stein LY. Agritech to Tame the Nitrogen Cycle. Cold Spring Harb Perspect Biol. 2024 Mar 1;16(3):a041668. doi: 10.1101/cshperspect.a041668. PMID: 37788889; PMCID: PMC10910340.
- Garg D et al. Cutting edge tools in the field of soil microbiology. Curr Res Microb Sci. 2024 Feb 21;6:100226. doi: 10.1016/j.crmicr.2024.100226. PMID: 38425506; PMCID: PMC10904168.
- Woo SL, et al. Trichoderma: a multipurpose, plant-beneficial microorganism for eco-sustainable agriculture. Nat Rev Microbiol. 2023 May;21(5):312-326. doi: 10.1038/s41579-022-00819-5. Epub 2022 Nov 22. PMID: 36414835.
- Tuncel A, et al. CRISPR-Cas applications in agriculture and plant research. Nat Rev Mol Cell Biol. 2025 Jun;26(6):419-441. doi: 10.1038/s41580-025-00834-3. Epub 2025 Mar 7. PMID: 40055491.
Pictures credits
- Trichoderma: US Department of Agriculture’s Mycology lab at Wikipedia
- Penicillium: Gerald Holmes, Strawberry Center, Cal Poly San Luis Obispo, Bugwood.org
- Bacillus: Katherine Ogando at Wikipedia
- Pseudomonas: pseudomonas.com
