Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster

Abstract

Drosophila melanogaster is one of the most widely used model systems in biology. However, little is known about its associated bacterial community. As a first step towards understanding these communities, we compared bacterial 16S rRNA gene sequence libraries recovered from 11 natural populations of adult D. melanogaster. Bacteria from these sequence libraries were grouped into 74 distinct taxa, spanning the phyla Proteobacteria, Bacteroidetes, and Firmicutes, which were unevenly spread across host populations. Summed across populations, the distribution of abundance of genera was closely fit by a power law. We observed differences among host population locations both in bacterial community richness and in composition. Despite this significant spatial variation, no relationship was observed between species richness and a variety of abiotic factors, such as temperature and latitude. Overall, bacterial communities associated with adult D. melanogaster hosts are diverse and differ across host populations.

FIG. 1.

Unrooted phylogenetic tree of Wolbachia sequences based on 16S rRNA gene sequences showing the positions of members of the six Wolbachia supergroups (A to F), as described previously (44), and the 10 Wolbachia OTUs isolated from the 11 D. melanogaster host populations. Letters in parentheses to the right of the OTUs represent the populations where the OTUs were observed. Populations corresponding to each letter are presented in Table 1. The neighbor-joining tree is the result of 10,000 bootstrap replicates, using 1,313 nucleotides. Bootstrap values of ≥50% are posted above the branches at the nodes. Branch lengths with more than zero nucleotide substitutions per site are indicated below the corresponding branches. Scientific names correspond to the invertebrate host species where the Wolbachia sequences are found and are followed by GenBank accession numbers. Letters to the right of the phylogeny represent Wolbachia supergroup designations (44).

FIG. 2.

Phylogenetic trees representing the taxonomic positions of proteobacterial OTUs isolated from 11 D. melanogaster host populations. (a) Alphaproteobacteria; (b) Betaproteobacteria; (c) Epsilonproteobacteria; (d) Gammaproteobacteria. Phylogenies were inferred using the neighbor-joining method and were bootstrapped for 10,000 replicates. The number of bases used for analysis was (a) 670, (b) 427, (c) 253, and (d) 690. Numbers above branch points represent bootstrap values of ≥50%. Numbers below branches indicate branch lengths (nucleotide substitutions per site) of greater than zero. Trees are rooted with the 16S rRNA gene sequence for Synechococcus elongata (AF132930), a member of the phylum Cyanobacteria. Letters in parentheses to the right of each OTU indicate the D. melanogaster host populations where that OTU was observed. A key for these letters is presented in Table 1.

FIG. 3.

Phylogenetic trees representing the taxonomic positions of Firmicutes OTUs isolated from 11 D. melanogaster host populations. Phylogenies were inferred using the neighbor-joining method, using 371 bases, and were bootstrapped for 10,000 replicates. Numbers above branch points represent bootstrap values of ≥50%. Numbers below branches indicate branch lengths (nucleotide substitutions per site) of greater than zero. Trees are rooted with the 16S rRNA gene sequence for Synechococcus elongata (AF132930), a member of the phylum Cyanobacteria. Letters in parentheses to the right of each OTU indicate the D. melanogaster host populations where that OTU was observed. A key for these letters is presented in Table 1.

FIG. 4.

Phylogenetic trees representing the taxonomic positions of Bacteroidetes OTUs isolated from 11 D. melanogaster host populations. Phylogenies were inferred using the neighbor-joining method, using 808 bases, and were bootstrapped for 10,000 replicates. Numbers above branch points represent bootstrap values of ≥50%. Numbers below branches indicate branch lengths (nucleotide substitutions per site) of greater than zero. Trees are rooted with the 16S rRNA gene sequence for Synechococcus elongata (AF132930), a member of the phylum Cyanobacteria. Letters in parentheses to the right of each OTU indicate the D. melanogaster host populations where that OTU was observed. A key for these letters is presented in Table 1.

FIG. 5.

Rarefaction analysis of bacterial 16S rRNA gene clone libraries recovered from 11 D. melanogaster host populations. Populations are labeled A through K. A key to the population labels is presented in Table 1. The predicted number of OTUs was calculated from the number of clones analyzed at the 3% level of sequence divergence. The slope of each curve indicates whether the diverse populations were completely sampled (zero or low slope) or whether new taxa are predicted if additional clones are analyzed (steep slope).