Host species and environmental effects on bacterial communities associated with Drosophila in the laboratory and in the natural environment

Abstract

The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila-associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates.

Figure 1. Rarefaction curves of 97% identity OTUs (A) for adult male flies.

Figure 2. Relative abundance of bacterial taxa as assessed by 16S rRNA gene sequences.

Wolbachia sequences were excluded. (A) The five most abundant bacterial families associated with Drosophila across all samples in the study. (B) Relative abundance of bacterial genera. Genera present at levels less than 5% were grouped into “others” category. (C) Relative abundance of bacterial genera for individual samples. Each vertical bar represents one sample of five pooled male flies. Bacterial genera of abundance <3% have been removed for clarity. D. melanogaster sample names start with m., D. simulans with s.. In wild-caught samples the sample names include an abbreviation for the substrate they were collected from: ora = orange, str = strawberry, app = apple, pea = peach, com = compost. Names of flies from the Petrov lab contain “pet” instead. Samples names ending with “_l” mark larval samples.

Figure 3

(A) Segregating sites of the 16S rRNA gene alignment of the highly abundant Providencia sequence from D. melanogaster (grey background) collected from strawberries (m.str) to Providencia species from . Sequences are sorted by virulence as determined by . Note that Galac and Lazzaro determined virulence of a different but closely related P. alcalifaciens strain. (B) Heatmap of the 10 most abundant 97% identity OTUs across all samples. OTUs are sorted by average relative abundance across all samples from left to right with the most abundant OTU to the left. Grey shades indicate the relative abundance of each OTU for a given sample. Numbers in brackets are OTU identifiers.

Figure 4. PCoA of Jaccard distances based on 97% identity OTUs.

(A) All samples in this study. Colors are according to origin. (B) Wild-caught samples. Colors are according to food-substrate (C) Wild-caught samples PCo3. D. melanogaster and D. simulans differ significantly for PCo3 (P = 0.0011). Colors are according to food-substrate.