Metagenomic Analysis of a Tropical Composting Operation at the São Paulo Zoo Park Reveals Diversity of Biomass Degradation Functions and Organisms

Abstract

Composting operations are a rich source for prospection of biomass degradation enzymes. We have analyzed the microbiomes of two composting samples collected in a facility inside the São Paulo Zoo Park, in Brazil. All organic waste produced in the park is processed in this facility, at a rate of four tons/day. Total DNA was extracted and sequenced with Roche/454 technology, generating about 3 million reads per sample. To our knowledge this work is the first report of a composting whole-microbial community using high-throughput sequencing and analysis. The phylogenetic profiles of the two microbiomes analyzed are quite different, with a clear dominance of members of the Lactobacillus genus in one of them. We found a general agreement of the distribution of functional categories in the Zoo compost metagenomes compared with seven selected public metagenomes of biomass deconstruction environments, indicating the potential for different bacterial communities to provide alternative mechanisms for the same functional purposes. Our results indicate that biomass degradation in this composting process, including deconstruction of recalcitrant lignocellulose, is fully performed by bacterial enzymes, most likely by members of the Clostridiales and Actinomycetales orders.

Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia

“…Both consortia showed presence of phylotypes from the phylum Proteobacteria whose members are known for metabolic diversity48. Members of Bacteroidetes and Actinobacteria present in both communities have been linked to degradation of complex polymers in compost16 and have been reported in composting piles previously4950. Interestingly, MM community was enriched in phylotypes including known and characterized genera such as Cellulomonas, Paenibacillus and Cellvibrio .…”

Thermal analysis and 454 pyrosequencing to evaluate the performance and mechanisms for deep stabilization and reduction of high-solid anaerobically digested sludge using biodrying process

“…degraded cellulose under the thermophilic and anoxic conditions of a composting pile, especially in the initial stage of the composting process. Martins et al (2013) reported that Bacillales in compost could degrade cellulose and solubilize lignin and colonize substrates under conditions of low nutrient availability. Li et al (2013) showed that some Bacillus spp.…”

Freshwater quality of a stream in agricultural area where organic compost from animal and vegetable wastes is used

“…The bacterial populations of the compost were studied using a metagenomic approach (Martins et al, 2013). This work showed high bacterial diversity in compost that can fully account for the observed biomass degradation.…”

“…Martins et al (2013), in their study of the microbial diversity of the organic compost used in the vegetable garden of the FPZSP, found a low relative abundance of organisms belonging to the family Enterobacteriaceae. However, we cannot determine whether this microbial contamination occurred through leaching from the vegetable garden because there are other factors that could also explain the observed bacteria, such as the presence of wild animals near the site.…”