The impact of agricultural practices on microbial spatiotemporal dynamics and contributions to soil health

Progress report for GNC21-332

Project Type: Graduate Student
Funds awarded in 2021: $14,883.00
Projected End Date: 08/31/2023
Grant Recipient: North Dakota State University
Region: North Central
State: North Dakota
Graduate Student:
Faculty Advisor:
Samiran Banerjee
North Dakota State University
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Project Information


Growing global population demands for the increment on the food production on the same rate the population is increasing. Various agricultural production practices these days to attain these demands are threat for the food security of the future generation and for the balance of agroecosystems. The physical, chemical, and biological wellness of soil is important for the ecosystem balance and food production. Soil microbes play a pivotal role on the agroecosystem by facilitating number of processes incurring. Despite this, the role of microbial communities on the improvement of soil health has not been studied to optimize these benefits for the food production. This gap exists because of the inadequate understanding about the microbial communities and how they can be manipulated for sustainable agricultural practices that the future is seeking for. The clear definition and understanding of soil health and the role of soil microbiome on maintaining better soil health is still not vivid among the producers. The proposed research aims to investigate how microbial communities contribute to soil health and how agricultural practices have an impact on microbial spatiotemporal dynamics. In this project, I will use the North Dakota Agriculture Microbiome project as the baseline and extend it to conduct field surveys and manipulative experiments to understand the contribution of microbiomes to soil health and agricultural practices affect that contribution. I will perform the latest molecular sequencing approaches to analyze the assembly, recruitment and functioning of microbial communities under various agricultural practices. I will also test findings in a long-term field trial to further assess the consistency of field data. By combining the crop yield and management information from farmlands and the long-term field trial, I will create statistical models illustrating the contribution of microbial parameters to soil health under different scenarios. The knowledge on the importance of soil microbes and soil health improvement is growing among the producers of North Dakota. I will facilitate the deepening of this understanding by reaching the producers through existing extension activities. I will prepare the extension materials focusing the impact of the intensive agricultural practices have on the microbial communities and sustainable practices that can be adapted to promote these communities. The project aims to disseminate information about the microbial communities, their impact on plant and soil health, and the effects that agricultural practices have on these communities.

Project Objectives:

The project aims at exploring the impact various agricultural practices have on the spatiotemporal dynamics of microbes which includes their functioning, assembly, recruitment, and relationship within the microbiome. As an outcome, the project aims at an increased understanding of the producers of North Dakota about the soil health and roles of microbial communities in soil health. Further, the project aims to engage the producers in surveys so that they can learn how different agricultural practices shape microbiomes with subsequent impact on soil health. In addition, the project aims at preparing and publishing various extension materials which would help the producers gather knowledge on microbial communities at their agricultural lands. With this knowledge the project intends to help farmers adapt farming practices which would promote the soil health and adapt the sustainable approaches of farming as per the recommendations made. The project aims to increase awareness among the producers about the sustainable farming approaches that harness the soil microbes and improve overall physical, chemical, and biological qualities of soil. The project also aims to publish the scientific publications and impart them to the extension specialists of North Dakota, who acknowledge the producers about the production sustainability and soil wellness. Thus, the project aims to promote sustainable farming and climate-resilient agroecosystems in North Dakota.




Materials and methods:

Bulk Soil and Plant Sampling
In August 2021 and August 2022, soil and plant samples were gathered from agricultural lands spanning North Dakota and Minnesota. In the first year, samples were taken from a total of 61 farms, including 31 conventional and 30 organic ones. Similarly, in the second year, samples were collected from 57 of the same farms, with 30 being conventional and 27 organics. USDA (United States Department of Agriculture) defines organic farming as a method that utilizes cultural, biological, and mechanical techniques to maintain on-farm resources, preserve the environment, and protect the variety of living organisms enhancing the ecosystem. ( Conventional farms apply resources like fertilizer, water for irrigation, amendments, and pesticides evenly, without considering the natural variations in soil and crop conditions between and within fields. This leads to an uneven distribution of resources, with some areas receiving too much and others too little (Corwin & Scudiero, 2019). To prevent potential edge effects, the sampling was conducted at 25 meters from the edges. To ensure that the samples represented the entire farm, the sampling locations were chosen randomly. 5 soil cores (15 cm deep) were collected from the area around randomly chosen 5 plants resulting in a total of 25 soil cores from each of the 61 farms using a 1” diameter soil step probe. In 2021, 5 fully matured corn plants were uprooted from each farm using a shovel, and the same process was repeated in 2022 for the crop that was present at that time. The soil cores from each farm were collected in one-gallon Ziploc© bags which were then stored on ice packs in coolers during transportation to the laboratory. Once in the lab, plant particles and macro-organisms were removed from the soil and the soil cores were broken up and homogenized by sieving with a 2 mm sieve, and then divided into two 15 ml conical tubes. One of the tubes and the remaining soil in Ziplock bags were stored at -20°C for soil analysis, and the other was stored at -80°C for long-term storage for molecular analysis. In the field, the roots of the plants were clipped off at the root-shoot junction using sterilized secateurs, and 5 roots were collected and stored in a Ziplock bag and placed in coolers with ice packs during transportation to the laboratory. Once in the lab, the roots were washed with tap water to remove the soil. They were then washed in 95% EtOH for a minute and disinfected with a 10% bleach solution for a minute. Roots were again washed with 95% EtOH for 30 seconds and then rinsed with sterile water for 2 minutes. Excess water was removed using paper towels out of the processed roots. The roots were then cut into approximately 1cm pieces using scalpels, with about 40% of the cut roots from each plot stored in a 15 ml conical tube at -80°C for molecular analysis. Thinner roots were selected for mycorrhizal slide preparation and were placed in 15 ml conical tubes with 70% ethyl alcohol for longer storage. To measure the weight of fresh plants, they were wrapped and taped individually before being weighed. The collected plants were placed in brown paper bags and stored on ice packs for transporting to the lab. The plants were then dried in an oven at 40°C for approximately for 5 days to measure dry biomass.

Measurement of Soil and Plant Properties
100gm of bulk soil was measured from the soil samples held in Ziplock bags and placed in sealable bags provided by soil and plant biomass analyzing facility “AgVise Laboratories” located at Grand Forks, North Dakota for the analysis of the physiochemical properties of the soil. 50 gm of dried plant biomass was grinded and sent off to " AgVise Laboratories" for plant physiochemical properties analysis. 

Mycorrhizal Colonization Assessment
Processed roots were further washed using one ml of a one M solution of (NaPO3)6, to remove any excess soil that remained. Approximately 15 root pieces were removed from each 15 ml conical tubes and kept into a 1.5 ml microcentrifuge tube. Labeling was done accordingly. (NaPO3)6 was added to each 1.5 ml microcentrifuge tubes, and the closed tubes were shaken for two hours. After two hours, the roots were removed and washed in deionized water. A 40% w/v KOH solution was added to the roots, and the mixture were incubated at 80°C for 30-40 minutes. After that, the roots were again rinsed with deionized water. Then, a 5% ink-vinegar solution was added to the roots and kept for 30-40 minutes at 80°C for staining. For the ink-vinegar stock solution, 50 ml ink (black from Parker Quink) was mixed with 950 ml of household vinegar (5% acetic acid). After the staining, the roots were rinsed with tap water and a drop of vinegar (Vierheilig et al., 1998). The stained roots were aligned parallel to the long axis of a microscopy slide. On each slide, there were five rows of roots- each having two to three pieces. Roots were fixed into place using 50% glycerol and a cover slip. The edges of the cover slips were securely sealed with coats of clear nail polish. The arbuscular mycorrhizal colonization was observed under a compound microscope at a magnification of 40X. The spot on the root surface where the center of the horizontal and vertical crosshairs entered through the side of the root was taken as the point of intersection. All intersections between the roots and the vertical crosshair were taken into consideration. Several categories were made to count the intersections: ‘arbuscules’, ‘vesicles’, ‘arbuscules and vesicles’, ‘only hyphae’, and ‘none’ i.e., there is no fungal material present in the root. To assess each intersection, the plane of focus was moved completely through the root. If the vertical crosshair cut one or more arbuscules or vesicles or hyphae, the appropriate category was incremented by one. For the arbuscular and vesicular colonization, the sum of the corresponding category was divided by the total number of intersections studied. The hyphal colonization was estimated as the ratio of non-negative intersections. One hundred intersections were calculated per sample to get the representative numbers (McGonigle et al., 1990b).

Microbiome analysis

The soil and root samples were frozen at -20°C until DNA extraction. To extract the DNA, 200 mg of soil was used for each bulk soil sample. For each root sample, 350 mg of root pieces were used. We utilized the Qiagen DNeasy Power Soil Pro kit and Qiagen DNeasy Plant Pro kit (Qiagen Inc., Valencia, CA) to extract the DNA, following the manufacturer’s instructions. We assessed the quality, quantity, and yield of the DNA using a NanoDrop ND-1000 spectrophotometer. After quantification, each DNA sample was normalized using nuclease-free water to a final volume of 50 µl at a concentration of 5 ng/µl. Standardized DNA samples have been sent to the University of Minnesota Genomics Center for amplicon sequencing for further microbiome analysis. 


Research results and discussion:

Corn Project Results

The results we have received so far are preliminary. However, we still need to conduct an extensive analysis using the microbiome data we are looking forward to.

Participation Summary
31 Farmers participating in research

Educational & Outreach Activities

3 Consultations
1 Curricula, factsheets or educational tools
1 Webinars / talks / presentations

Participation Summary:

31 Farmers participated
Education/outreach description:


Last year, I participated in a NCB ASM (North Central Branch American Society of Microbiological Sciences) meeting where I presented preliminary results and progress of the project. As the project is ongoing for four years, we anticipate discovering fascinating results in the future.

Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.