Soil grinding increases the relative abundance of eukaryotic phospholipid fatty acids

Pretreatment of soil samples, such as grinding and sample size, can potentially affect phospholipid fatty acid (PLFA) extraction efficiencies. The objective of this study was to determine how soil pretreatment affects PLFA analysis and interpretation. Two grinding (ground and control) and five soil sample sizes (0.125-5 g) in factorial combinations were applied to restored or remnant prairie soils. In the restored soil, the smaller soil aliquots were more likely to result in outlying values of community composition, suggesting small-scale heterogeneity in microbial community distribution. Grinding reduced this variability in community composition, with no outliers, even with the lowest size in ground soils. However, grinding increased the abundance of eukaryotic relative to prokaryotic PLFAs, and we hypothesize that grinding exposed root cells and the interior of fungal hyphae to extraction. We suggest that in soils with high root densities, soils should not be ground as grinding may obscure changes in the microbial community by exaggerating the eukaryotic signal from roots. However, in soils with low rooting densities, grinding will reduce heterogeneity and ensure that eukaryotic biomarkers are not underestimated.