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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

2012 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:
Analysis of samples from a series of soil incubation experiments was continued. These experiments were designed to test the effects of fundamental soil properties (water potential, temperature, pH, texture, and organic matter) on soil microbial communities. A DNA-based approach, multiplex terminal restriction fragment length profiling, was used to profile the community structure of bacteria, fungi, and archaebacteria. Preliminary analysis indicates that bacteria and archaebacteria were affected by soil type and experimental conditions, but fungal community structure was almost entirely controlled by soil type with little effect of experimental conditions. We have received soil samples from different cover cropping systems in different locations across the United States. We have analyzed these samples by phospholipid fatty acid analysis which measures both the mass of microorganisms present (biomass) and the microbial community composition. Preliminary data analysis indicates that microbial community composition is controlled primarily by the location of the field experiment rather than the cover cropping system used.


4.Accomplishments
1. ARS scientists at Beltsville, MD, in collaboration with scientists at MIDI Inc., developed a high-throughput method for phospholipid fatty acid (PLFA) analysis of soils. PLFA analysis is widely used to measure microbial biomass and community composition, but is somewhat slow, expensive, and difficult to run on large numbers of samples at one time. We adapted the method to run 96 samples simultaneously, and created a faster gas chromatographic method for use with the analysis. During FY2012 we transferred this technology to commercial testing laboratories in the United States, India, and Australia, as well as to research laboratories in the United States, Europe, Asia, and South America.


Review Publications
Franzluebbers, A.J., Endale, D.M., Buyer, J.S., Stuedemann, J.A. 2012. Tall fescue management in the Piedmont: Sequestration of soil organic and total nitrogen. Soil Science Society of America Journal. 76:1016-1026.

Lehman, R.M., Taheri, W.I., Osborne, S.L., Buyer, J.S., Douds, D.D. 2012. Fall cover cropping can increase arbuscular mycorrhizae in soils supporting intensive agricultural production. Applied Soil Ecology. 61:300-304. doi:10.1016/j.apsoil.2011.11.008.

Last Modified: 10/21/2014
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