Frequency of taxa identified corresponding to each taxon analysed with the mini-COI barcodes.

<p>Generated by 454 pyrosequencing, the table displays the taxonomic rank, the frequencies of samples and the corresponding sample size in brackets, and the number of sequences corresponding to taxa identified by barcoding and belonging to the same order of the taxa analysed. A frequency of 100% means that all samples of the taxa analysed had at least two sequences of the taxa identified by barcoding (BLAST+ with E-value = 10⁻²⁰, FASTA with 85% similarity threshold, and Nearest Neighbour algorithm for the final identification).</p

Transcriptome-guided assembly pipeline.

<p>We present the pipeline for transcriptome assembly and contig assignment. (A) The transcriptome-guided assembly <i>per se</i> (green background) combines a <b>read assignment step</b> based on blastn, making use of a local database merging the related reference transcriptome and <i>de novo</i> assembly of the query transcriptome. (B) The <i>de novo</i> assembly (red background) with a blastn annotation of generated contigs to obtain a <i>de novo</i> assembly for the inferred transcriptome. Cylinders represent the database, rectangles represent analytical steps in the processes, and parallelograms correspond to results. Note that the dashed lines represent optional steps in the pipelines.</p

Positive controls, feeding trials, and negative controls.

<p>Positive controls (rows 1–3 in the table) were designed to estimate the number of sequences recovered as a function of the quantity of <i>C. sordidus</i> material assayed, which was varied by processing different numbers of <i>C. sordidus</i> eggs. The feeding trial (rows 4–6 in the table) was designed to determine whether <i>C. sordidus</i> DNA could be detected in the gut contents of a predator (<i>O. baurii</i> in this case) that had consumed one <i>C. sordidus</i> egg (in related treatments, the predator had not consumed a <i>C. sordidus</i> egg or was processed with one egg that it had not consumed). Negative controls (rows 7 and 8 in the table) consisted of ultra-pure HPLC grade water.</p

Bipartite food webs of predator-prey interactions on (A) bare soil, and (B) cover cropped banana plantation.

<p>For each web, lower bars represent relative abundance of consumed prey, and upper bars represent relative abundance of positive ground-dwelling predators, each drawn at different scale. The width of links between ground-dwelling predators and prey represents the frequency of consumption. Numbers in grey indicate unlinked taxa. Visualization was performed with the R package “bipartite” <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0093740#pone.0093740-Dormann1" target="_blank">[50]</a>. 1: <i>Anopheles claviger.</i> 2: <i>Anopheles nimbus.</i> 3: <i>Baetis rhodani.</i> 4: <i>Blatella germanica.</i> 5: <i>Calliphora vomitoria.</i> 6: <i>Carabidae</i> spp. 7: <i>Codophila varia</i>. 8: <i>Coridius chinensis</i>. <i>9</i>: <i>Cosmopolites sordidus</i>. 10: Diptera. 11: <i>Drosophila anceps</i>. 12: <i>Drosophila melanica</i>. 13: <i>Drosophila montana</i>. 14: <i>Gryllus</i>. 15: Hemiptera. 16: <i>Jalysus spinosus</i>. 17: <i>Nebria chinensis</i>. 18: <i>Neoneides muticus</i>. 19: <i>Nezara viridula</i>. 20: Oniscidae. 21: <i>Ophyra spinigera</i>. 22: <i>Periplaneta americana</i>. 23: <i>Podisus serieventris</i>. 24: <i>Polytus mellerborgi</i>. 25: <i>Resseliella yagoi</i>. 26: <i>Sarcophila</i>. 27: <i>Scolopendra</i>. 28: <i>Scolopendra mutilans</i>. 29: <i>Stephensioniella sterrei</i>. 30: Lycosidae. 31: <i>Camponotus sexguttatus</i>. 32: <i>Euborellia caraibea</i>. 33: <i>Odontomachus baurii</i>. 34: Scolopendridae. 35: <i>Solenopsis geminata</i>. 36: Staphilinidae. 37: <i>Wasmannia auropunctata.</i></p

Diversity of the faecal and oral microbiota of the great tit.

<p>Alpha diversity was measured as Chao1, number of observed OTUs and Shannon diversity. To account for uneven sequencing depths, alpha diversities were calculated based on rarefied OTU tables.</p

Heatmap for OTUs, whose abundance varied between the oral and faecal microbiota of the great tit.

<p>OTUs were identified according to permutations-based LMEs. Cell colours indicate OTU abundances in individual samples (log10 scaled values). Column annotations indicate GIT regions, whereas row annotations show Phylum-level assignations and if the OTU was overrepresented in oral or faecal samples (+oral or +faecal). OTUs are ordered according to their phylogeny (i.e. FastTree-based phylogeny for representative sequences).</p

Efficiency and performance of <i>de novo</i> and transcriptome-guided assembly based on Blastn by read length and divergence level.

<p>(A) Number of identified genes; (B) completeness; (C) contiguity. Divergence between target and reference transcriptomes is described in the figure legend.</p

Differences in the composition between the oral and faecal microbiota of the great tit.

<p>PCoA was performed for four dissimilarity indexes. Sex is indicated by different plotting symbols.</p

Predicted recovery rate (rr) using the mixed logistic model as a function of gene length (rr), read length and divergence between target and reference transcriptomes: red lines denote 0% divergence; green 5%; blue 15% & purple 30%.

<p>Solid lines correspond to the median of predictions, conditioned on random variation among genes, with 80% prediction intervals indicated by dashed lines. Read length increases downward, and panels to the right represent a magnified view of the upper 5th quantile of rr scores to better visualize differences between low divergent sequences: 100 base reads (A & B); 150 bases (C & D); 200 bases (E & F); 350 bases (G & H).</p

Diet changes of ground-dwelling predators between bare soil plot and cover cropped plot.

<p>The bar charts display the difference of frequencies of consumption for each prey calculated between the two plots, with the bare soil plot as a reference. The significance of the difference of frequencies of consumption observed between plots was assessed with a Fisher’s exact test. (***: <i>p</i>-value<0.0001; **: <i>p</i>-value<0.001; *: <i>p</i>-value<0.01). Black crosses above bar charts indicate that the prey was not detected in both treatments.</p