A comparison among EL-FAME, PLFA, and quantitative PCR methods to detect changes in the abundance of soil bacteria and fungi

EL-FAME (ester-linked fatty acid methyl ester), PLFA (phospholipid fatty acid), and qPCR (quantitative PCR) of ribosomal genes are three of the most common methods used to quantify soil microbial communities due to their versatility. The reliability of these three methods has not been simultaneously compared in situations of rapid (in the frame of days and weeks) changes in soil microbial abundances. For this purpose, we (i) incubated badland, cropland, and forest soils with nutrients or antibiotics for 2, 7, 14, and 28 days, (ii) quantified total, bacterial, and fungal abundances through EL-FAME, PLFA, and qPCR methods, and (iii) measured soil basal respiration (as indicator of living biomass). The general dynamic patterns of the three soil microbial fractions in response to soil addition of nutrients and antibiotics were captured by the three methods, which led to strong and positive associations between the abundances of total microorganisms, bacteria, and fungi measured by the three procedures. However, these relationships were stronger between the EL-FAME and PLFA results. Further, soil basal respiration was associated to a higher extent with total, bacterial, and fungal abundances captured by EL-FAME and PLFA analyses than with those measured by qPCR, which suggests that the first two methods are most closely related to the soil living microbial community. In general, dynamics in the abundance of total and bacterial communities were better captured than those of fungi by the three methods. The PLFA analysis seems to perform better than the EL-FAME method in forest soil and in detecting the small antibiotic-induced decreases in microbial abundances. Since the EL-FAME method is cheaper and allows a much faster processing of samples than the PLFA method, and the reliability of both methods is similar in detecting rapid changes of soil microbial abundances, choosing EL-FAME over PLFA may be advantageous in most cases.