Table 1.
454 GS FLX Titanium pyrosequencing and Newbler assembly metrics of two metagenomic DNA samples from São Paulo Zoo composting.
Figure 1.
Distribution of the GC content percentage for ZC1 and ZC2 compared with selected metagenomes.
Each position represents the percentage of sequences reads within a GC percentage range. Sources: ZC1 and ZC2 (this work); Luquillo Experimental Forest Soil at Puerto Rico [36]; termite gut [37] and cow rumen pooled planktonic [25] metagenomes were retrieved from MG-RAST.
Table 2.
Features of the composting metagenomes based on MG-RASTa and IMG/Mb annotations.
Figure 2.
Microbial Community Composition of ZC1 and ZC2 metagenomes.
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.
Figure 3.
Most abundant bacterial genera in ZC1 and ZC2 compost samples.
Unassembled reads annotated on MG-RAST were analyzed using the classification tool based on RDP (98% identity; e-value cutoff of 10−30; minimum alignment length of 50 bp). The figure displays the taxonomic distribution for the 20 most abundant bacterial genera.
Figure 4.
Rarefaction curves for ZC1 and ZC2 metagenomes.
rRNA-related sequences were retrieved from the whole metagenomic data set and classified on RDP to obtain rarefaction curves at genetic distance of 3%.
Figure 5.
Relative abundance of COG functional categories for ZC1 and ZC2 metagenomes.
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.
Table 3.
Top 30 (by sequence count) COG functions represented among ZC1 and ZC2 metagenomic assembled sequences.
Figure 6.
ZC1 large contig encoding pectin degradation enzymes.
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).
Figure 7.
Relative abundance of COG functional categories for ZC1 and ZC2 and seven public metagenomes.
Assembled sequence reads were classified into the 25 COG categories designated in Figure 5 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 Table S5. Asterisks indicate statistically significant values.
Figure 8.
Hierarchical clustering of functional gene groups of ZC1 and ZC2 and seven public metagenomes.
(A) Clustering based on COG functional categories; (B) clustering based on COG functions. Hierarchical trees were generated using the “Compare Genomes” tool in IMG/M. Branch lengths are shown.