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United States Department of Agriculture

Agricultural Research Service

Research Project: Controls on Microbial Community Structure and Function in Soil and Rhizosphere

Location: Sustainable Agricultural Systems Laboratory

2013 Annual Report


1a.Objectives (from AD-416):
Identify factors, such as soil properties and plant species, that influence microbial community structure and function in order to develop management systems that optimize ecosystem services and maximize sustainability.


1b.Approach (from AD-416):
A. Eight Maryland soils were chosen that varied in pH, texture, organic C, and land use. After collection soils were sieved and maintained at field moisture levels at 4 °C. Soil water potential curves were determined. Soils were incubated in Mason jars under controlled conditions to systematically vary soil moisture, soil temperature, soil pH, soil texture, and amendments with organic amendments. Soil samples are analyzed for microbial community structure by terminal restriction fragment length polymorphism (TRFLP) and phospholipid fatty acid (PLFA) analysis. B. Using the same soils as in (A), a variety of crop and weed seeds will be planted in each soil in pots, using 1 plant species per pot in a full factorial of plant species x soil with 6 replicates. Crop plant species will include cucumber (Cucumis sativus) and wheat (Triticum aestivum), while weed species will include smooth pigweed (Amaranthus hybridus), and giant foxtail (Setaria faberi). Soil and rhizosphere samples will be analyzed by TRFLP, PLFA, and pyrosequencing. C. We have a collection of 20 air-dried soils, collected in Maryland, that vary in pH, soil texture, and land use. Cucumber seeds will be planted in each soil and seedlings grown to select soils that will support cucumber growth with minimal disease. A subset of 8 soils will be chosen that maximize variation in pH and texture. Cucumber seeds will be planted in pots filled with these soils with and without prior seed inoculation with the biocontrol agent Pseudomonas fluorescens Pf-5. Colony forming units (CFU) of an antibiotic (rifampicin) resistant mutant of Pf5 will be determined by dilution-plating onto selective media containing rifampicin. As the cucumber plants grow rhizosphere soil samples (six replicates per treatment) will be taken and used directly to determine the population density of Pf-5 and frozen at -20 °C for analysis of rhizosphere community structure by TRFLP, PLFA, and pyrosequencing. D. We are collaborating with ARS scientists in a variety of locations, including Beltsville, MD; Watkinsville, Georgia; Brookings, South Dakota; Morris, MN; Prosser, WA; and Urbana, IL. They are using rye and/or vetch cover crops as part of their management systems. Bulk soil samples (0-15 cm depth) from three to four replicate plots, with treatments including rye, vetch, and bare soil, are being sent to us twice annually ( spring and fall) and being stored at -20 °C. Soil microbial community structure will be analyzed by TRFLP for Eubacteria, Archaea, and fungi, while soil enzyme assays will be used to measure community function.


3.Progress Report:
Soil microbial communities carry out important ecosystem services such as soil aggregation, pathogen suppression, and nutrient cycling. The factors that control soil microbial community composition and function are not understood. The objective of this project is to explore the soil, plant, and management factors that control soil microbial communities. A variety of soils under different environmental conditions were previously incubated in order to determine which conditions were most important in determining soil microbial community composition. Samples from these experiments have been analyzed by a simple DNA-based method that fingerprints the soil microbial community composition. Results indicate that imposed treatments of soil moisture, temperature, texture, and crop residue amendments had very little affect on soil microbial communities. Soil type had the largest effect, while time of incubation also had some effect. High-throughput sequencing of the soil DNA, a method with much higher resolution than the one previously used will be performed in order to confirm these results. Research has begun on the analysis of biologically available carbon compounds. Most soil carbon is bound up in highly stable polymeric compounds such as humic acids that are unavailable to microbial metabolism. Microbial activity and ecosystem services depend on available carbon compounds such as polysaccharides and proteins. Currently there are no methods to accurately analyze either the quantity or the composition of the available carbon. Currently being used are acid and base hydrolysis to quantify and identify compounds that should be susceptible to enzymatic hydrolysis, the first step in microbial metabolism of many compounds. Biocontrol agents including bacteria and fungi are used to reduce plant disease, but their effects on the indigenous microbial community have not been studied. Greenhouse experiments to test the effects of a bacterial biocontrol agent on the rhizosphere microbial community of cucumber were conducted. Technical difficulties with the selective medium used to measure the population of the biocontrol agent have limited progress. Soil microbial biomass and community composition have been analyzed under turfgrass in order to compare different fertilizer treatments in collaboration with a Cooperator. Analysis of the first year’s samples indicated that synthetic and organic fertilizers resulted in very similar soil microbial communities. This research will be continued for another year. In research on the effects of cover crops on soil microbial communities, it has been shown that hairy vetch and crimson clover suppress Fusarium wilt in watermelon by 21%. A quantitative PCR method has been developed to analyze the fungi that grow on decomposing cover crop residue on the soil surface. A multi-location program was initiated to study the effects of glyphosate on soil and root-associated microbial communities of corn and soybean. The study will also analyze the health of glyphosate-resistant corn and soybean grown with and without glyphosate application. Field trials are in place and sampling has begun.


4.Accomplishments
1. Effects of conventional and sustainable cacao management systems on soil health. Traditional cacao management systems are unsustainable due to destruction of soil resources and severe plant disease problems. In collaboration with scientists in the USDA-ARS Sustainable Perennial Crops Laboratory, Beltsville, MD, and the Instituto de Cultivos Tropicales, Peru, the soil microbial community under various cacao management systems has been analyzed. It has been found that alternative agroforestry systems have distinctly different microbial communities than conventional systems, with higher Gram-negative bacterial populations and higher arbuscular mycorrhizal populations. These increases are indicative of higher biologically available carbon and therefore a more active microbial community. These results suggest that soil health, and therefore sustainability, is improved in an agroforestry management system for cacao production.


Review Publications
Pimenta, R., Moreira Da Silva, J., Buyer, J.S., Janisiewicz, W.J. 2012. Endophytic fungi from plums (Prunus domestica) and their antifungal activity against Monilinia fructicola. Journal of Food Protection. 75(10):1883-1889.

Buyer, J.S., Sasser, M. 2012. High throughput phospholipid fatty acid analysis of soils. Soil Biology and Biochemistry. 61:127-130.

Last Modified: 10/21/2014
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