Table 1.
Description of all the metagenomes used in this study.
Figure 1.
Chitinase activity and 16S-rRNA qPCR quantification during microcosm enrichment.
Panel A displays chitinase assays performed with synthetic substrates on soil aqueous extracts. Activity was measured by quantification of the fluorescence release by the 4-Methylumbelliferon (4 MU) after specific cleavage of exo- and endochitinases. Enzyme activity is expressed in chitinase unity detected per gram of soil during incubation time (1 U = 1 µmole 4 MU released per minute). Panel B shows 16S-rRNA gene copies detected by qPCR per gram of soil. Results were normalized with obtained DNA yields and expressed per gram of soil. The enrichment kinetic is represented in days. In both panels, chitin concentration is represented by darker gray nuance: light grey (low chitin dose 1×), dark grey (high chitin dose 10×) and white (control 0×). The error bars are representing the standard deviation observed in the 3 microcosm replicates (SD).
Figure 2.
Relative abundance of major prokaryote groups detected on phylochips.
Stacked bar chart represents the percentage of total fluorescence signal detected in each group, based on probe hybridizations. The number of identified genera per condition (n) is indicated in white in the chart. Clusters analysis was performed on taxonomical profiles of each sample at the genus level, and exposed to bootstrap simulation (n = 10000). Approximately unbiased bootstrap p-value are expressed in percentage and indicated at each nod. The grouping was done with the Ward method based on variance analysis, and distances are calculated according a correlation algorithm (the complement 1−r of Pearson’s r correlation). Dendrogram scale is representing the similarity based on the Euclidean distance.
Table 2.
Counts of genera detected on phylochip for each condition.
Figure 3.
Hierarchical classification of metagenomes used in this study.
The dendrogram was established based on taxonomical annotation of reads on M5NR through MG-RAST at the genus level. Clusters were exposed to bootstrap simulation (n = 10000) and bootstrap p-value are indicated at each nod. The grouping was done with the Ward method based on variance analysis, and distances are calculated based on a correlation algorithm (the complement 1−r of Pearson’s r correlation). Dendrogram scale is representing the similarity based on the Euclidean distance. The letters are indicating the 4 main metagenomic clusters (A: indirect extraction cluster; B: direct extraction cluster; C: microcosm incubation cluster; D: untreated control soil).
Figure 4.
Major taxonomical changes in the soil bacterial community after incubation and chitin enrichment.
The graphics represent the abundance of different bacterial groups in percentage of sequences in metagenomes. Grey nuances represent the different conditions and the number of metagenome used is given in brackets. In the case of 0×20, 1×20 and 10×20, the error bars are representing the minimum and maximum observed for each of the two replicates.
Figure 5.
Major functional changes in the soil bacterial community after incubation and chitin enrichment.
The graphics represent the abundance of different functional subsystems in percentage of sequences in metagenomes (SEED subsystems classification). Grey nuances represent the different conditions and the number of metagenome used is given in brackets. In the case of 0×20, 1×20 and 10×20, the error bars are representing the minimum and maximum observed for each of the two replicates.
Figure 6.
Bacterial genera enriched by chitin treatment.
The graphic displays the number of genera belonging to each bacterial group that were increased in abundance in metagenomic datasets after low chitin treatment 1×(blue color nuances), high chitin treatment 10×(orange color nuances), or in both concentration (green nuances). Lighter color nuances indicate the count of genera with known representative species with chitin degrading genes in CAZy (CDG), while darker nuances are representing the ones with no references yet in CAZy (No CDG).