Article Figures & Data
Figures
- Fig 1
Phylogenetic tree of bacteria associated with Cephalotes varians turtle ants and their GenBank relatives. Shown is a maximum likelihood phylogeny of the most prevalent OTUs as generated by 454 sequencing and by cloning. For each method, we clustered reads (454 sequencing) or sequences (cloning) at 97% similarity and selected the top clusters that accounted for 90% of reads or sequences, respectively. The branch color and inner circle refer to the source from which the bacteria were isolated, the middle circle refers to the bacterial order, and the outer circle refers to the method used to acquire the respective sequence. Colony CSM1323 was excluded from these analyses due to an infection with Entomoplasmatales bacteria. Please note the misplacement of Campylobacterales, which should group with other Proteobacteria.
- Fig 2
Comparison of bacterial communities in Cephalotes varians ants detected through 454 pyrosequencing (upper rows) and cloning (lower rows). Samples were prepared from dissected ant body parts or entire workers of Cephalotes varians. Sample names are given above pies and sample sizes below pies. The relative abundance of reads at the taxonomic level of bacterial orders is displayed. Orders that accounted for less than 1% in a sample are summarized in a category termed “other.” “Unclass. gamma” refers to an unclassified gammaproteobacterium that clustered with the Pseudomonadales bacteria.
- Fig 3
PCoA analysis of bacterial communities from samples that were subjected to 454 sequencing and cloning. Positions of the bacterial communities for each species along the two first principal coordinate axes are illustrated, along with the percentage of variation explained by each axis. Results based on 454 sequencing are displayed with no lines, while the same symbols with black outlines illustrate results obtained through cloning and Sanger sequencing. Note the distinct clustering of samples prepared from colony CSM1323 (gray symbols), which was infected by bacteria of the order Entomoplasmatales (Spiroplasma sp.), and also the clustering of the samples prepared from the hindguts of colony CSM1280 (1280 hind-2 and 1280 hind-3), as well as of the midguts of colony CSM1280 (1280 mid-2 and 1280 mid-3). “Hind” refers to the hindgut, “mid” refers to the midgut, and “wk” refers to samples prepared from whole worker extractions. Results are based on weighted UniFrac distances.
Tables
- Table 1
The most common OTUs (at 97% identity level) associated with Cephalotes varians ants as discovered by 454 sequencinga
Cluster no. Cluster size Cumulative % Bacterial order Three closest GenBank matches GenBank accession no. % identity Cloning Cultivation 01 1392 29.0 Rhizobiales Uncultured Rhizobiales FJ477551 96.0 Yes No Uncultured Rhizobiales FJ477647 93.4 Uncultured Rhizobiales FJ477654 91.3 02 963 49.0 Opitutales Uncultured Opitutus FJ477619 96.3 Yes No Uncultured Opitutus FJ477566 96.1 Uncultured Opitutus FJ477620 95.9 03 688 63.4 Pseudomonadales Uncultured bacterium FM996048 96.7 No No Uncultured bacterium FM996869 96.7 Uncultured bacterium FM996088 96.7 04 350 70.7 Campylobacterales Acrobacter sp. GU300768 95.1 Yes No Acrobacter sp. FN650333 95.1 Acrobacter sp. FN650332 95.1 05 197 74.8 Unclassified gammaproteobacterium Gammaproteobacterium FJ477677 99.0 Yes No Uncultured gammaproteobacterium FJ477626 99.0 Uncultured gammaproteobacterium FJ477606 98.8 06 196 78.9 Rhizobiales Uncultured Rhizobiales FJ477652 96.8 Yes No Uncultured Rhizobiales FJ477593 96.8 Uncultured Rhizobiales FJ477651 96.4 07 96 80.9 Burkholderiales Alcaligenaceae bacterium FJ477675 98.7 Yes No Uncultured Alcaligenaceae FJ477560 98.0 Uncultured betaproteobacterium AF507838 93.8 08 77 82.5 Xanthomonadales Uncultured Xanthomonadaceae FJ477622 96.9 Yes No Uncultured Xanthomonadaceae FJ477598 96.7 Uncultured Xanthomonadaceae FJ477621 96.7 09 69 83.9 Rhizobiales Uncultured Rhizobiales FJ477593 95.7 Yes No Uncultured Rhizobiales FJ477654 95.7 Uncultured Rhizobiales FJ477653 95.5 10 69 85.3 Xanthomonadales Uncultured Xanthomonadaceae FJ477618 98.3 Yes No Uncultured Xanthomonadaceae FJ477594 92.0 Uncultured Xanthomonadaceae FJ477554 91.8 11 53 86.4 Sphingobacteriales Uncultured bacterium FJ477607 97.1 No No Uncultured Bacteroidetes FJ477649 88.3 Uncultured bacterium GQ263639 83.8 12 47 87.4 Burkholderiales Uncultured Comamonadaceae FJ477610 99.0 No No Uncultured bacterium HQ728243 90.3 Uncultured bacterium AF390917 90.3 13 37 88.2 Flavobacteriales Flavobacterium terrae EF117329 90.3 Yes No Flavobacterium columnare AB015480 90.3 Flavobacterium columnare AZ842900 90.3 14 36 88.9 Burkholderiales Uncultured Alcaligenaceae FJ477612 94.5 Yes No Uncultured Alcaligenaceae FJ477592 93.9 Uncultured Alcaligenaceae FJ477590 93.7 15 33 89.6 Xanthomonadales Uncultured Xanthomonadaceae FJ477622 96.2 Yes No Uncultured Xanthomonadaceae FJ477603 96.1 Uncultured Xanthomonadaceae FJ477598 96.1 16 32 90.3 Opitutales Uncultured Opitutus FJ477608 98.3 Yes No Uncultured Opitutus FJ477619 98.0 Uncultured Opitutus FJ477620 97.5 ↵a A total of 400 reads were randomly selected for each of 13 C. varians samples. Colony CSM1323 was excluded, as it was infected with Enteroplasmatales bacteria, which strongly biased the data toward this group of bacteria alone. This table provides the cluster size, cumulative percentage, the three top BLAST hits, GenBank accession numbers, percent identity, and the detection of the same OTUs through cloning or cultivation. Sixteen OTUs accounted for about 90% of bacterial diversity. BLAST searches were performed against the NCBI GenBank database on 12 October 2011.
Supplemental material
Files in this Data Supplement:
- Supplemental file 1 -
Ant bacterial species richness rarefaction curves (Fig. S1).
PDF, 377K
- Supplemental file 2 -
Overview of culture-independent approaches of bacterial diversity (Fig. S2).
PDF, 8.6K
- Supplemental file 3 -
Comparison of bacterial communities associated with different body parts of Cephalotes varians ants detected through 454 pyrosequencing (Fig. S3).
PDF, 272K
- Supplemental file 4 -
Sample characteristics and alpha diversity measures for all samples subjected to 454 pyrosequencing and to Sanger sequencing of clone libraries (Table S1).
PDF, 360K
- Supplemental file 5 -
Information on the sequences utilized in this study (Table S2).
PDF, 574K
- Supplemental file 6 -
RDP library comparison results for 454 and clone libraries (Table S3).
PDF, 193K
- Supplemental file 1 -
