A long‐standing dilemma for soil microbial assays is how best to store soil samples between sampling and analysis. We studied the effects of sample handling and storage on methods used to determine soil microbial biomass, structure, and function. For this study, one forest soil (Gilpin), and two agricultural soils (Granby and Hoytville) were selected with five commonly used sample pretreatments: (i) fresh soil; (ii) air drying for 14 d followed by rewetting (65% water‐holding capacity) and incubation (25°C) for 14 d (D/R); (iii) 28 d at 4°C; (iv) 28 d at −20°C; and (v) 28 d at −80°C. Immediately after pretreatments, soils were analyzed for fatty acid methyl esters (FAMEs), total DNA (tDNA), seven enzyme activities, microbial biomass C, and respiration. Drying and rewetting significantly reduced microbial biomass, respiration, most enzyme activities, tDNA, and total FAME concentrations compared with fresh soil in all three soils. The percentage of fungal FAME markers and two enzyme assays were unaffected by 4°C storage in all soils, and microbial biomass C was unchanged in Hoytville and Gilpin soil at −20 and −80°C. Total DNA was unchanged in the Granby soil at −80°C, and in the Hoytville soil at both −20 and −80°C compared with fresh soil. Total FAME was reduced by all storage treatments in all three soils. We concluded that storage should be avoided whenever possible, particularly for extraction of FAME and total DNA, but that 4 or −20°C is the best storage method for FAME analysis, and −80°C is preferable for DNA analysis. Microbial biomass C and enzyme activities were least affected when stored at 4 or −20°C. The D/R treatment was the least desirable soil preparation method for microbial analyses, and we recommend that this pretreatment be avoided.
Glyphosate is one of the most widely used herbicides in agriculture with predictions that 1.35 million metric tons will be used annually by 2017. With the advent of glyphosate tolerant (GT) cropping more than 10 years ago, there is now concern for non-target effects on soil microbial communities that has potential to negatively affect soil functions, plant health, and crop productivity. Although extensive research has been done on short-term response to glyphosate, relatively little information is available on long-term effects. Therefore, the overall objective was to investigate shifts in the rhizosphere bacterial community following long-term glyphosate application on GT corn and soybean in the greenhouse. In this study, rhizosphere soil was sampled from rhizoboxes following 4 growth periods, and bacterial community composition was compared between glyphosate treated and untreated rhizospheres using next-generation barcoded sequencing. In the presence or absence of glyphosate, corn and soybean rhizospheres were dominated by members of the phyla Proteobacteria, Acidobacteria, and Actinobacteria. Proteobacteria (particularly gammaproteobacteria) increased in relative abundance for both crops following glyphosate exposure, and the relative abundance of Acidobacteria decreased in response to glyphosate exposure. Given that some members of the Acidobacteria are involved in biogeochemical processes, a decrease in their abundance could lead to significant changes in nutrient status of the rhizosphere. Our results also highlight the need for applying culture-independent approaches in studying the effects of pesticides on the soil and rhizosphere microbial community.
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