Metagenomic analysis of a tropical composting operation at the São Paulo Zoo Park reveals diversity of biomass degradation functions and organisms.

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 Sao 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.FAPESP 2009/52030-5RCNPqCAPE

454 GS FLX Titanium pyrosequencing and Newbler assembly metrics of two metagenomic DNA samples from São Paulo Zoo composting.

<p>454 GS FLX Titanium pyrosequencing and Newbler assembly metrics of two metagenomic DNA samples from São Paulo Zoo composting.</p

ZC1 large contig encoding pectin degradation enzymes.

<p>ZC1 sequences assembled into a 27,919 bp contig encoding the following proteins: 1. Beta-xylosidase (376 aa, COG3507); 2. Dehydrogenases (280 aa, COG1028); 3. hypothetical protein (379 aa); 4. hypothetical protein (283 aa); 5. 5-keto 4-deoxyuronate isomerase (280 aa, COG3717); 6. Dehydrogenases (267 aa, COG1028);7. hypothetical protein (1799 aa); 8. SusD family protein (606 aa, pfam07980); 9. TonB-linked outer membrane protein (1068 aa, COG4771); 10. Pectate lyase (518 aa, COG3866); 11. Predicted unsaturated glucuronyl hydrolase (398 aa, COG4225); 12. Pectin methylesterase (568 aa, COG4677); 13. Endopolygalacturonase (523 aa, COG5434); 14. Nucleoside-diphosphate-sugar epimerase (326 aa, COG0451); 15. Nucleoside-diphosphate-sugar pyrophosphorylase (249 aa, pfam00483); 16. Galactokinase (377 aa, COG0153); 17. Soluble lytic murein transglycosylase (347 aa, COG0741); 18. hypothetical protein (235 aa); 19. Predicted UDP-glucose 6-dehydrogenase (283 aa, COG1004).</p

Microbial Community Composition of ZC1 and ZC2 metagenomes.

<p>Unassembled reads annotated on MG-RAST were analyzed using the classification tool based on RDP (98% identity; e-value cutoff of 10⁻³⁰) and M5NR (60% identity; e-value cutoff of 10⁻⁵) with minimum alignment length of 50 bp. The figure displays the taxonomic distribution for the 10 most abundant orders.</p

Relative abundance of COG functional categories for ZC1 and ZC2 and seven public metagenomes.

<p>Assembled sequence reads were classified into the 25 COG categories designated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061928#pone-0061928-g005" target="_blank">Figure 5</a> and their relative abundances for each metagenome were estimated considering the respective total number of protein coding sequences with function prediction. The public metagenomes included in the comparison are benzene-degrading bioreactor, biofuel reactor, compost minireactor, termite hindgut, poplar biomass bioreactor, lake sediment and soil rain forest, whose features are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061928#pone.0061928.s008" target="_blank">Table S5</a>. Asterisks indicate statistically significant values.</p

Relative abundance of COG functional categories for ZC1 and ZC2 metagenomes.

<p>Assembled sequence reads were classified into the 25 COG functional categories, and their relative abundances for ZC1 and ZC2 metagenomes were estimated considering the total number of protein coding sequences with function prediction. Designations of functional categories: A: RNA processing and modification, B: Chromatin structure and dynamics, C: Energy production and conversion, D: Cell cycle control, cell division, chromosome partitioning, E: Amino acid transport and metabolism, F: Nucleotide transport and metabolism, G: Carbohydrate transport and metabolism, H: Coenzyme transport and metabolism, I: Lipid transport and metabolism, J: Translation, ribosomal structure and biogenesis, K: Transcription, L: Replication, recombination and repair, M: Cell wall/membrane/envelope biogenesis, N: Cell motility, O: Posttranslational modification, protein turnover, chaperones, P: Inorganic ion transport and metabolism, Q: Secondary metabolites biosynthesis, transport and catabolism, R: General function prediction only, S: Function unknown, T: Signal transduction mechanisms, U: Intracellular trafficking, secretion, and vesicular transport, V: Defense mechanisms, W: Extracellular structures, Y: Nuclear structure, Z: Cytoskeleton.</p

Top 30 (by sequence count) COG functions represented among ZC1 and ZC2 metagenomic assembled sequences.

<p>793758 and 680461 annotated assembled sequences of ZC1 and ZC2 metagenomes were respectively classified in 4529 and 4872 COGs and ranked according to their abundance. Sequence count and ranking for COGs outside the top 30 list are indicated in numbers with smaller font.</p