Determination of microbial biomass and fungal and bacterial distribution in cattle faeces

As an important component of organic fertilizers, animal faeces require methods for determining diet effects on their microbial quality to improve nutrient use efficiency in soil and to decrease gaseous greenhouse emissions to the environment. The objectives of the present study were (i) to apply the chloroform fumigation extraction (CFE) method for determining microbial biomass in cattle faeces, (ii) to determine the fungal cell-membrane component ergosterol, and (iii) to measure the cell-wall components fungal glucosamine and bacterial muramic acid as indices for the microbial community structure. Additionally, ergosterol and amino sugar data provide independent control values for the reliability of the microbial biomass range obtained by the CFE method. A variety of extractant solutions were tested for the CFE method to obtain stable extracts and reproducible microbial biomass C and N values, leading to the replacement of the original 0.5 M K2SO4 extractant for 0.05 M CuSO4. The plausibility of the data was assessed in a 28-day incubation study at 25 °C with cattle faeces of one heifer, where microbial biomass C and N were repeatedly measured together with ergosterol. Here, the microbial biomass indices showed dynamic characteristics and possible shifts in the microbial community. In faeces of five different heifers, the mean microbial biomass C/N ratio was 5.6, the mean microbial biomass to organic C ratio was 2.2%, and the mean ergosterol to microbial biomass C ratio was 1.1‰. Ergosterol and amino sugar analysis revealed a significant contribution of fungi, with a percentage of more than 40% to the microbial community. All three methods are expected to be suitable tools for analysing the quality of cattle faeces.

► The replacement of 0.5 M K2SO4 by 0.05 M CuSO4 results in reliable microbial biomass estimates by the CFE method in pasty cattle faeces.
► Amino sugar analysis revealed that fungi contribute more than 40% to the microbial community in cattle faeces.
► The different methodological approaches give results on a similar level in cattle faeces.