Tag: dna

Picture – RhizeBio.com (Decoding Nutrient Availability with DNA Soil Testing for Agriculture)

In recent years, scientific advances in DNA sequencing have allowed us to delve deeper into the hidden world of soil microbiomes—complex ecosystems of bacteria, fungi, and other microorganisms that play a crucial role in soil health. For certified organic farms, where soil vitality is central to crop productivity, DNA testing has become a powerful tool to track the rejuvenation of soil microbial life. Here are several case studies and research examples showing how organic practices can bring “dead” or degraded soils back to life, backed by peer-reviewed studies and long-term trials.

1. Rodale Institute’s Farming Systems Trial (FST)

The Rodale Institute’s Farming Systems Trial (FST) in Pennsylvania, one of the longest-running studies of its kind, has provided compelling evidence on how organic practices restore microbial life in soils. Comparing conventional and organic farming systems, the trial found that organic soils had higher microbial diversity and biomass, which supported better nutrient cycling, drought resilience, and overall soil health. This microbial community improvement was observed within just a few years of organic management.

• Supporting Study: Rodale Institute. (2021). Rodale Institute Farming Systems Trial: 40-Year Report. Retrieved from: https://rodaleinstitute.org/science/farming-systems-trial/
• Seufert, V., Ramankutty, N., & Foley, J. A. (2012). Comparing the yields of organic and conventional agriculture. Nature, 485(7397), 229-232. doi:10.1038/nature11069

2. University of California, Davis – Russell Ranch Sustainable Agriculture Facility

At the Russell Ranch Sustainable Agriculture Facility, part of UC Davis, researchers compared organic and conventional farming systems to understand their impact on soil health. DNA sequencing revealed that organic plots contained a significantly higher abundance of beneficial microbes, such as Actinobacteria and Proteobacteria, which are essential for decomposing organic matter and supplying nutrients to plants. Improvements in microbial diversity were observed within three years, showing how quickly organic management can enhance soil life.

• Supporting Study: Bowles, T. M., Acosta-Martínez, V., Calderón, F., & Jackson, L. E. (2014). Soil enzyme activities, microbial communities, and carbon and nitrogen availability in organic agroecosystems across an intensively managed agricultural landscape. Soil Biology and Biochemistry, 68, 252-262. doi:10.1016/j.soilbio.2013.10.004
• University of California, Davis. Russell Ranch Sustainable Agriculture Facility. Retrieved from: https://russellranch.ucdavis.edu

3. USDA-ARS Study on Organic Transition in Salinas Valley, California

In California’s Salinas Valley, a USDA-ARS study focused on soil health during the transition from conventional to organic practices. DNA analysis was used to track microbial changes over time, showing that organic practices led to increased populations of beneficial organisms like Pseudomonas (known for disease suppression) and mycorrhizal fungi (which assist in nutrient uptake). Even heavily degraded fields showed signs of microbial recovery within three to five years under organic management.

The graph below illustrates how microbial diversity increased over several years under organic management, similar to what was observed in the USDA-ARS study in the Salinas Valley.

• Supporting Study: Schmidt, J. E., Gaudin, A. C. M., & Scow, K. M. (2018). Cover cropping and no-till increase diversity and symbiotrophratios of soil fungal communities. Soil Biology and Biochemistry, 129, 99-109. doi:10.1016/j.soilbio.2018.10.010
• USDA Agricultural Research Service (ARS). Organic Agriculture Research and Extension Initiative (OREI). Retrieved from: https://www.ars.usda.gov

4. The DOK Trial in Switzerland (FiBL – Research Institute of Organic Agriculture)

The DOK trial in Switzerland, a long-term study by the Research Institute of Organic Agriculture (FiBL), compares biodynamic, organic, and conventional systems. DNA sequencing and microbial analysis have shown that the organic and biodynamic plots consistently feature higher microbial diversity and functionality. Within the first few years, these systems already showed greater resilience and microbial activity compared to conventional plots, highlighting the role of organic practices in fostering a healthy, living soil ecosystem.

• Supporting Study: Mäder, P., Fließbach, A., Dubois, D., Gunst, L., Fried, P., & Niggli, U. (2002). Soil fertility and biodiversity in organic farming. Science, 296(5573), 1694-1697. doi:10.1126/science.1071148
• FiBL – Research Institute of Organic Agriculture. DOK Trial: Long-Term Farming Systems Comparison in Switzerland. Retrieved from: https://www.fibl.org

5. Organic Almond and Grape Vineyards in California

In California, several almond and grape vineyards that transitioned to organic practices have used DNA analysis to monitor soil microbial changes. Within a few years, they reported a rise in beneficial mycorrhizal fungi and reduced pathogen levels, signaling a healthier, more resilient soil system. DNA sequencing tracked these positive shifts, confirming that organic management can replace harmful microbes with beneficial ones in soil over time.

• Supporting Study: Steenwerth, K. L., & Belina, K. M. (2008). Cover crops enhance soil organic matter, carbon dynamics and microbiological function in a vineyard agroecosystem. Applied Soil Ecology, 40(2), 359-369. doi:10.1016/j.apsoil.2008.06.006
• Hannula, S. E., & van Veen, J. A. (2016). The role of AM fungi in organic agriculture. Applied Soil Ecology, 96, 64-72. doi:10.1016/j.apsoil.2015.05.011

The Role of DNA Analysis in Understanding Soil Revival

DNA analysis has been a game-changer in soil science, allowing researchers to observe the specific microbial changes that occur when fields transition from conventional to organic management. By tracking shifts in microbial diversity and function, DNA testing provides clear, measurable evidence of how organic practices promote a healthy, balanced soil microbiome.

These studies illustrate that soil health restoration is achievable within a relatively short time under organic practices. While soils subjected to long-term conventional management may initially appear “dead” or lacking in microbial diversity, the examples above demonstrate that organic farming can foster microbial resilience and diversity, creating a foundation for sustainable, productive agriculture.

Organic farming practices have been shown to significantly improve soil health and microbial diversity compared to conventional farming methods. This article on recent DNA studies provides compelling evidence for the benefits of organic practices on soil ecosystems (eOrganic, 2023).

Increased Microbial Diversity and Abundance

Organic farming leads to greater microbial diversity and abundance in soils. Research in the Netherlands found that organically managed soils had higher numbers and more diverse populations of beneficial soil organisms compared to conventionally managed soils (Hartmann et al., 2015). Similar results were observed in banana plantation soils in Taiwan, with organic soils showing greater microbial diversity (Lehman et al., 2015). This increased microbial diversity is crucial for soil health, as it improves nutrient cycling, water retention, and disease suppression.

Enhanced Bacterial Communities

DNA studies reveal specific changes in soil bacterial communities under organic management. Organic systems show higher abundance of beneficial bacterial phyla like Acidobacteria, Firmicutes, Nitrospirae, and Rokubacteria (Hartmann et al., 2015). These bacterial groups correlate with improved soil biochemical properties and increased crop yields in organic systems (Lehman et al., 2015).

Improved Fungal Associations

Organic practices foster beneficial fungal relationships in the soil. Arbuscular mycorrhizal fungi (AMF) colonization is higher in organic soils (Hannula & van Veen, 2016). AMF extend plant root systems, improving water and nutrient uptake, especially in challenging conditions like drought or high soil salinity.

Soil Organic Matter and Carbon Sequestration

Organic farming significantly increases soil organic matter content. The National Soil Project found organic soils averaged 8.33% organic matter content versus 7.37% in conventional soils (National Soil Project). Organic soils showed higher levels of sequestered carbon (4.1% vs 2.85%) and a greater percentage of organic matter in stable forms (57.3% vs 45%). This increased organic matter improves soil structure, water retention, and carbon sequestration potential.

Nitrogen Fixation and Nutrient Cycling

Organic practices enhance natural nutrient cycling processes. Research suggests organic soybean plants may develop more extensive fine root systems and nitrogen-fixing nodules compared to conventional crops (Lehman et al., 2015). The diverse microbial communities in organic soils contribute to more efficient nutrient cycling and availability for plants (Hartmann et al., 2015).

Soil Enzyme Activity

Organic management boosts soil enzymatic activity. Higher levels of alkaline phosphatase and β-glucosidase activity are observed in organic systems (Bowles et al., 2014). These enzymes play crucial roles in organic matter decomposition and nutrient release.

In conclusion, DNA studies provide strong evidence that organic farming practices revitalize soil health by fostering diverse and abundant microbial communities, improving soil structure, enhancing nutrient cycling, and increasing carbon sequestration. These benefits create a more resilient and sustainable agricultural ecosystem.

Sources for Further Reading:

Hartmann, M., Frey, B., Mayer, J., Mäder, P., & Widmer, F. (2015). Distinct soil microbial diversity under long-term organic and conventional farming. The ISME Journal, 9(5), 1177-1194. doi:10.1038/ismej.2014.210

Lehman, R. M., Cambardella, C. A., Stott, D. E., Acosta-Martínez, V., Manter, D. K., Buyer, J. S., … & Halvorson, J. J. (2015). Understanding and enhancing soil biological health: The solution for reversing soil degradation. Sustainability, 7(1), 988-1027. doi:10.3390/su7010988

These resources provide additional insights into how soil biology supports agriculture and the role of organic practices in enhancing microbial diversity.