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ARS Home » Midwest Area » Columbia, Missouri » Cropping Systems and Water Quality Research » Research » Publications at this Location » Publication #358204

Research Project: Sustainable Intensification of Grain and Biomass Cropping Systems using a Landscape-Based GxExM Approach

Location: Cropping Systems and Water Quality Research

Title: Phospholipid fatty acid profiles of soils under variable handling and storage conditions

item Veum, Kristen
item LORENZ, TODD - University Of Missouri
item KREMER, ROBERT - University Of Missouri

Submitted to: Agronomy Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/31/2019
Publication Date: 2/5/2019
Publication URL:
Citation: Veum, K.S., Lorenz, T.E., Kremer, R.J. 2019. Phospholipid fatty acid profiles of soils under variable handling and storage conditions. Agronomy Journal. 111(3):1090-1096.

Interpretive Summary: Phospholipid fatty acid (PLFA) analysis provides an estimate of the microbial biomass and microbial diversity in soil and has become a popular method for assessment of the biological component of soil health. The utility and feasibility of PLFA analysis for large-scale producer assessments is partially dependent on the robustness of the analysis under various soil processing and handling conditions, yet the effects of typical handling procedures are not well understood. Currently, the recommended protocol is to freeze-dry fresh, field moist soil, which may not be practical or feasible for producers. In this study, near-surface soil samples were collected from two Missouri prairies and subjected to multiple sample handling and storage conditions prior to PLFA analysis. Room-temperature storage, under air-dry and field-moist conditions, resulted in an 11 – 16% reduction in the estimate of total microbial biomass and a 13 – 56% decline in the fungal markers. Oven-drying had the greatest effect, dramatically reducing the total microbial biomass estimate by 38% and the fungal biomarkers by 86% compared to freeze-drying. Overall, improper handling of PLFA samples resulted in an underestimate of the total microbial biomass and resulted in a significant shift in the microbial group ratios that are used to interpret PLFA data for soil health assessment. This study emphasizes the importance of proper handling of soil samples for PLFA analysis and will benefit producers and stakeholders interested in the application and utility of biological measurements in soil health assessment.

Technical Abstract: Phospholipid fatty acid (PLFA) analysis is an increasingly popular method for estimating microbial biomass and assessing microbial community structure in soils. In contrast to nucleic acid based methods, PLFA biomarkers reflect the living microbial biomass and are sensitive to rapid shifts in microbial community structure. In particular, there is a strong interest in the use of PLFA microbial group ratios as benchmarks for soil health assessment and interpretation. Due to the sensitivity of PLFA biomarkers, the recommended procedure for sample handling involves immediate freeze-drying of fresh, field-moist soil. This protocol may not be practical under all circumstances, yet the effects of handling and storage conditions, and the implications for interpretation of PLFA biomarkers, are not fully understood. The primary objective of this study was to evaluate the effects of multiple sample handling and storage conditions on quantification and interpretation of PLFA biomarkers. For this study, tallgrass prairie soils, known for their high microbial biomass and diversity, were selected. In March 2015, 18 soil samples were collected across landscape positions from the 0-5 cm depth layer at the Golden Prairie Natural Area and the Stark Family Prairie in Missouri, USA. A suite of traditional soil characterization and soil health indicators were measured, including PLFA analysis. Multiple processing and handling procedures were evaluated by splitting the soil samples and comparing PLFA profiles from 1) fresh, freeze-dried soil, 2) soil stored air-dry for 7 and 14 days, 2) soil stored field-moist at room temperature for 7 and 14 days, and 3) soil oven-dried for 48 hr at 105ºC. All handling and storage procedures resulted in significant losses of PLFA biomarkers relative to fresh, freeze-dried samples. Further, microbial groups were disproportionately affected, leading to significant shifts in biomarker ratios. Air-dry and field-moist storage resulted in an 11 – 15% reduction in total PLFA biomarkers and a 13 – 56% decline in fungal biomarkers (AMF and saprophytic fungi). This led to significant shifts in the bacteria to fungi ratio as well as the ratio of AMF to saprophytic fungi. Storage conditions also favored Gram-positive (G+) over Gram-negative (G-) bacteria, shifting the G+ to G- ratio. Oven-drying had the most dramatic effect on PLFA biomarkers, resulting in a 38%, 86%, and 52% reduction in total PLFA, saprophytic fungi, and AMF biomarkers, respectively. Overall, this study highlights the sensitivity of PLFA biomarkers, the importance of proper sample handling for PLFA analysis, and the potential for error and misinterpretation of PLFA data.