Bacterial Diversity in Livestock Manure Composts as Characterized by Terminal Restriction Fragment Length Polymorphisms (T-RFLP) of PCR-amplified 16s rRNA Gene Sequences

Abstract

Composts contain a large and diverse community of microorganisms that play a central role in the decomposition of organic matter during the composting process. However, microbial communities active in composts have not been well described in the past. In the present study, the phylogenetic diversity of bacterial communities in livestock manure compost was determined based on terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes. This technique uses a PCR in which one of the primers is fluorescently labeled. After amplification, the PCR product is then digested with restriction enzymes such as HhaI, MspI, and RsaI to generate T-RFLP fingerprints of bacterial communities. In the present study, a mixture of dairy and horse manure (dairy+horse manure; 1:1 ratio w/w) was composted in windrows and in-vessel to investigate compost bacterial diversity. The DNA was isolated from the feedstocks (day 0) and after 21 and 104 days of in-vessel and windrow composting, respectively, for T-RFLP analysis. A variety of techniques were then used to analyze T-RFLP data to gain insights about the structure of the bacterial community from these compost samples. Results of the T-RFLP analysis revealed high species diversity in the feedstocks sample As many as 27 to 39 different terminal restriction fragments (T-RFs) were found in these samples, revealing high diversity in the livestock manure composts. After composting, an increase in the T-RFLP-based Shannon diversity index was observed in the in-vessel compost, while a decrease was found in the windrow compost. Differences in chemical properties were also observed in the windrow and in-vessel composts. The windrow compost had lower water, organic matter (OM) and C contents and higher C and OM loss than the in-vessel compost.