Bacterial diversity at different stages of the composting process

Abstract

Background: Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA.

Results: Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts.

Conclusions: Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants.

Figure 1

Process characteristics. a) The full-scale process samples were taken from the feeding material, the feeding and unloading ends of the drum and from the tunnel. b) Pilot scale process samples were taken from the drum feeding and the unloading end. The polygons indicate the sites of sampling.

Figure 2

Bacterial sequence clustering. Composition of bacterial communities in a) the full-scale process and b) in the pilot-scale process at different composting stages. Similarity of > 99% was used. The number of clones used in the analysis is in parenthesis after the sample number on the x-axis. "Uncultured" denotes sequences similar to bacteria that were reported in the EMBL database as uncultured bacteria. "Other" denotes bacterial sequences with similarity to classes other than the six major bacterial classes or genera used here in the classification. "Unclassified" denotes bacterial sequences with no close similarity to sequences in the nucleotide database.

Figure 3

Sample clustering. An UPGMA tree showing the clustering of the samples based on the UniFrac analysis. Weighted classification was used. The scale bar shows the distance between clusters in UniFrac units: a distance of 0 means that two environments are identical and a distance of 1 means that two environments contain mutually exclusive lineages. Shading was used to differentiate the three nodes representing different stages of the process.