Biome Makers Blog

How DNA Soil Testing Can Enhance Citrus Farming: Lessons from a Case Study



The world of agriculture is rapidly evolving. One of the most significant developments in recent years has been the study of soil microbes and their crucial role in plant growth and health. This has led to the emergence of regenerative agriculture, a practice that focuses on promoting soil health through the use of diverse cover crops and other techniques that support the growth of soil microorganisms.

Biome Makers recently hosted a webinar, "Microbial Nutrition in Citrus Agriculture: Using DNA Soil Testing in Real-Life Case Study," which did a deep dive into soil microbes, their interaction with citrus trees, and their impact on crop health and yield. The webinar featured three industry experts: Herb Young, a regenerative citrus grower and owner of Squeeze Citrus LLC, Meri Mullins, and Gus Plamann, team members at Biome Makers.

In this blog, we explore answers to some of the questions asked during the webinar and provide even further insights into Herb Young's experience as a regenerative citrus grower in GA.

The Importance of Microbial Nutrition in Citrus Agriculture

Soil microbes facilitate nutrient cycling and uptake, improve soil structure and water-holding capacity, and help protect plants from diseases and pests. In citrus agriculture, a healthy microbial community can lead to improved yield, fruit quality, and tree health.

Citrus growers face various challenges, including water scarcity, soil degradation, and spreading diseases like citrus greening. A healthy microbial community can help citrus growers reduce their reliance on synthetic fertilizers and pesticides, reducing input costs and environmental impact. A healthy soil ecosystem can improve soil resiliency and help plants withstand environmental stresses such as drought and extreme temperatures.

By focusing on building a healthy soil ecosystem through practices such as cover cropping, reduced tillage, and microbial amendments, growers can improve soil health and plant resilience, thereby overcoming these challenges. In addition, new technologies such as DNA soil testing can help growers better understand the microbial communities in their soil, enabling them to make more informed decisions about nutrient management and other farming practices.

Real-Life Case Study: Regenerative Citrus Farming

The case study presented in the webinar, "Microbial Nutrition in Citrus Agriculture: Using DNA Soil Testing in Real-Life Case Study," features a citrus farm in Georgia owned by Herb Young. He is currently devoted to cultivating his citrus in an environmentally-friendly manner that honors the earth's natural processes. Herb's experience and insights could offer valuable guidance to growers and crop advisors interested in adopting similar practices. 

How DNA Soil Testing Can Enhance Citrus Farming1

In conventional citrus farming, the emphasis is placed on maximizing yields by using synthetic fertilizers and pesticides. However, this approach can have negative consequences on the health of the trees and the soil. Herb realized that the conventional approach was not sustainable in the long term. He split his farm into three main areas based on different management practices: conventional, indigenous, and regenerative. On his farm, Herb Young grows Shiranui (“Sumo”) X Poncirus trifoliata. He has 15 trees per plot in single rows  (135 trees). Tree spacing 8’ X 21’ with 3 replications randomized. He uses microjet irrigation on each tree.

For the conventional area, he used RU, fertilizer, and pesticides. For the indigenous area, he implemented organic practices like cover cropping. For the regenerative area, he used organic practices and added beneficial microbes. His goals were to improve tree health, High BRIX, tight internodes, low insect diseases, 5 flushes/year, implement microbe feed trees, and nutrient-dense fruit. To measure his success, he used four parameters: trunk growth, canopy volume, Soil DNA Testing, and BRIX.

Herb incorporated cover crops and used organic soil amendments. Cover crops for winter included: Clovers (Crimson, White, Arrowleaf, Balansa), Hairy Vetch, Austrian Winter Pea, Buckwheat, Diakon Radish, Annual Ryegrass, and Black Oats. For summer, cover crops included: Brown Top millet, Oats, Clovers, Sunn Hemp, Buckwheat, and Spring pea.

“For cover crops, germination in the summertime is difficult with irrigation over my entire orchard. I have had excellent luck with Brown top millet and Sunn Hemp. Buckwheat and spring pea can grow well. The challenge is 'ground-to-seed' exposure. I have been much more successful pulling a drag with 3" tines to get some soil exposure in the drive middles." shares Herb Young. "But around the trees, I don't want any disturbance, and seeds tend to fall into the winter residue and germinate. There are a few clovers that last into the summer, and I allow them to go as long as they can. Particularly Balansa Clover (used by pecan growers in the SE),” 

He also introduced beneficial microbes to his soil to improve soil health and plant nutrition. “Increasing diversity continues to be my goal. I benefited greatly from introducing 'foreign' microbes (non-indigenous), but I have a goal to increase locally adapted species,” states Young. “I have begun trying to develop compost on-farm and will use it to make compost tea to intensify the microbe populations. I am surrounded by wooded areas and have tried once to acquire native microbes (using a Korean Natural Farming - rice capture).”

Young also saw major differences in the areas with conventional practices vs. the areas with cover crops and added microbes. "A penetrometer pushed into 200psi goes about 3” in conventional soil or in row middles.  Anywhere in the tree row that has had: cover crops, mulch, microbe inoculum goes 9” to 24” deep.  The ground is 'fluffy,' actually 'spongy' when you walk across it.  The ground is 2’-3” higher."

To monitor the microbial community in his soil, Herb uses DNA soil testing. This technology allows him to identify the abundance of microbial populations in his soil and their functions and track their changes over time. He conducted a BeCrop Test pre-transplant in February 2021, October 2021, and June 2022, and he will conduct another sample in April 2023.

“This year, I will conduct replicated trials with multiple compost sources and some rigorous testing to see which is most adapted. I was amazed at the Biome Makers’ BeCrop Test results that showed adding supplemental microbes had huge advantages over just allowing 'Ingidenous' species to flourish.” Young adds.

Herb's DNA soil testing results have shown that his regenerative treatments doubled the microbial species and increased the total quantity of fungal soil biology 6x more than the conventional treatment. Young shares, “I do research on the 10 major bacteria and fungal species that I get. The new BeCrop Portal Explorer tool quickly shows what is dominant. Even as a Pathologist, I was taught to assume most things are 'pathogens.' I am learning otherwise. New research shows that the species we have always considered pathogenic in a healthy plant environment can be innocuous, endophytic, and even beneficial.”

Screen Shot 2023-03-23 at 3.28.04 PM

PHOTO: Sample screen share of the BeCrop Explorer Tool. Please note: this is not the actual results from Herb Young's Case Study.

"Also, both treatments of soil treatment, EnSoil Algae, caused carbon to increase...The nitrogen was fascinating. It was reduced... and the Haney Test [showed that] all of the nitrate and most of the ammonium in the soil applied with EnSoil was converted to organic nitrogen. By putting all of these tests together... we see that we've got microbes being activated by the algae... consuming all of the nitrate and ammonium, and actually producing amino acids and proteins, providing that to the trees. And then we get this explosive growth." adds Young.

BeCrop® enabled Herb Young to measure the effectiveness of the regenerative practices in his orchard operations at Squeeze Citrus. 

You can learn more about the case study and results here >> 

DNA Soil Testing: Understanding the Process and Benefits

DNA soil testing analyzes the abundance of microbial communities in soil and what functions they provide. The DNA is extracted and then sequenced using high-throughput sequencing. The sequence data is analyzed using various bioinformatics tools to identify the species present in the sample and their abundance.

The species present in the sample can be identified by comparing the DNA sequences obtained from the soil sample to Biome Makers’ taxonomic reference database. Their abundance can be estimated based on the amount of DNA detected. This allows for the quantification of different microbial species in the soil sample. BeCrop technology allows for a more comprehensive and accurate soil microbiome analysis than traditional soil testing methods.

Discover more about DNA soil testing with BeCrop Test >>

By analyzing the microbial community in soil, DNA soil testing provides a deeper understanding of the nutrient cycling pathways and nutrients available to the plants. This information can help growers make decisions about fertilization and soil amendments, leading to healthier crops and increased yields. DNA soil testing also helps identify beneficial microbes that can aid plant growth and disease resistance, allowing growers to implement targeted microbial management strategies.

Traditional soil testing methods, such as chemical analysis, can provide an incomplete picture of the soil’s health. These methods are often limited to measuring essential nutrients and do not account for the complex interactions between microbes in the soil. DNA soil testing complements traditional soil testing methods by comprehensively analyzing the soil microbiome.

The BeCrop Portal: Microbial Nutrition Analysis Tool

After a grower purchases a BeCrop Test, they receive the results in the form of a PDF called the BeCrop Report. The BeCrop Report includes detailed information on soil nutrient cycling, health, quality, and more. Growers can also utilize the BeCrop Portal to get further insights about the soil and use various tools to compare analyses between different plots. 

“The below-ground DNA testing confirms exactly what I saw above ground. We've got a little bit of an increase in the number of species in the soil. The real difference was… the overall soil quality rating bumped up on my injection treatment, and so did the biodiversity… N, P, and K increased dramatically with the foliar and with the soil treatment [of EnSoil Algae]," says Young. BeCrop provided Herb Young with the soil intelligence he needed to adjust his input management strategies.

BeCrop also detects disease risks that may appear in the soil that may not be visible to the human eye. That way, growers can take preventative measures before the disease manifests in the field. By providing detailed information on microbial nutrition and soil health, the BeCrop Portal and BeCrop Report can help growers make data-driven decisions that lead to improved yields, reduced costs, and a healthier environment.

Get a BeCrop Test Demo today

Q&A Session with the Speakers

During the webinar, the audience had the opportunity to ask questions related to microbial nutrition and DNA soil testing in citrus farming. Some of the questions were:

Question: Can DNA soil testing be used in organic agriculture? Yes, DNA soil testing can be used in both conventional and organic farming practices.

Question: How often should citrus growers conduct DNA soil testing? It is recommended to conduct DNA soil testing at least once a year to monitor microbial nutrition and make necessary adjustments to farming practices. However, the amount of soil testing depends on the objective of the grower. Depending on the project's extent, pre and post-seasonal soil testing could be effective.

Question: How does the BeCrop Report differ from other soil testing reports? Our experts translate this data into practical and simplified information describing what functions the microbes can perform and how they are expected to interact. The final result is a soil microbe functional profile in the form of a BeCrop Report.  The BeCrop Report provides simplified data describing the soil health functions performed by microbes and how they impact plant growth and health.

Question: How might our understanding of microorganisms as beneficial or not shift? Would it be unwise to call all microorganisms beneficial based on the complexity of ecosystems? Acknowledging the complexity and diversity of ecosystems and the microorganisms within them is important. Microorganisms can have both beneficial and harmful effects depending on the context, their interactions with other organisms, and the broader ecosystem dynamics. For example, some microorganisms can break down pollutants, decompose organic matter, and fix nitrogen, while others can cause disease or disrupt ecosystem balance.

Labeling all microorganisms as beneficial based on the complexity of ecosystems would be an oversimplification, as it doesn't account for the intricate relationships and dependencies that exist within these systems. Recognizing the context-specific nature of these relationships is essential to understanding the role of microorganisms in the ecosystem and developing regenerative strategies.


The importance of microbial nutrition in citrus agriculture cannot be overstated. A healthy microbial community in the soil can lead to better plant growth, disease resistance, and higher yield. DNA soil testing and the BeCrop Report offer an effective way to monitor microbial nutrition and make data-driven decisions to improve farming practices.

The case study of the regenerative citrus grower Herb Young showcased how DNA soil testing was pivotal in his decision-making process to adopt certain regenerative farming practices that can lead to significant benefits in terms of soil health, plant growth, and sustainability.

You can learn more about Herb Young's story here >>