(In June 2013, I began a postdoctoral position at the California Academy of Sciences, please click here if you are interested in learning about that work)

Symbiotic microbial communities in animals play important roles in human health, the pest status of agricultural insects, and the evolutionary potential and diversification of animal lineages. Drosophila is a promising model for the study of these animal-associated microbial communities (collectively called the microbiota) because this system combines ecological diversity with genetic and experimental tractability. However, in order to understand the role of microbial symbionts in Drosophila physiology, ecology, and evolution, we first need to characterize the diversity of the Drosophila-associated microbiota and establish which factors, environmental or genetic, are most important in determining microbial community composition. My dissertation research addresses these questions and provides the basis for future interdisciplinary research programs that will use Drosophila as a model for investigating fundamental topics in symbiotic animal-microbe interactions.

Culture-independent identification of the bacterial communities of diverse Drosophila species

Microbial communities are notoriously difficult to characterize because many lineages are resistant to culturing. This work is the first to provide a culture-independent characterization of the bacterial communities associated with ecologically, phylogenetically and geographically, diverse Drosophila populations. Using a natural community survey in combination with controlled laboratory experiments, we showed that Drosophila-associated bacterial communities are dominated by a small number of abundant taxa (Figure 1A), that the same bacterial lineages are associated with different host species and populations (Figure 1B), and that host diet has a greater effect on the bacterial community composition than host species or location. Surprisingly, we found that the most common bacterial associate of wild flies is never used in laboratory studies and is a member of a novel bacterial genus that is resistant to standard culturing techniques. This comprehensive study lays the foundation for future experimental work investigating the role of different bacteria in shaping host fitness and how commensal bacteria evolve and persist within their hosts.

Chandler J.A., Morgan Lang J., Bhatnagar, S., Eisen J.A., and Kopp A. 2011. Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system. PLOS Genetics 7(9): e1002272. doi:10.1371/journal.pgen.1002272. PDF

What about other symbionts? A holistic approach to microbiota community composition

Although the bacterial communities associated with animals are undoubtedly important, it is clear that other symbiont groups play a vital part in animal ecology and evolution. Indeed, yeasts have a well-established role in insect, and especially Drosophila, physiology, behavior and fitness. Despite this, few studies, and none in Drosophila, look at multiple symbiont groups simultaneously and therefore our understanding of most host-microbe systems is far from complete. To gain a more comprehensive view of the Drosophila microbiota, we used next-generation sequencing to characterize the yeast communities associated with natural Drosophila populations. This work was performed on the same samples of flies for which the above bacterial work was done, allowing the unprecedented opportunity to compare the distribution and structure of the yeast and bacterial communities in the same host populations. Considering that these two symbiont groups are environmentally acquired and they are both interacting with the host immune system, community structure may be similar among them. Conversely, group-specific immunity or interactions between symbiont groups may create community structure differences between them. We find that, as with the bacterial symbionts, host diet is more important than host species in shaping Drosophila-associated yeast communities. However, we did not detect a significant correlation in community structure between these two symbiont groups (Figure 2). These results indicate that while diet shapes the structure of both symbiont communities, other factors, such as bacteria- or yeast-specific immunity, may also be important. We anticipate that this paper will prompt future Drosophila-microbe researchers, whether they are focused on genetics, metabolism, or evolution, and animal-microbe researchers in general, to take a similarly holistic view and consider all possible symbionts that are associated with a given host.

Chandler J.A., Eisen J.A., and Kopp A. 2012 Yeast communities of diverse Drosophila species: Comparison of two symbiont groups within the same hosts. Applied and Environmental Microbiology. vol. 78. no. 20. 7327-7337 PDF

Discovery of Trypanosomatids as common associates of Drosophila

In the course of analyzing the yeast dataset, we made a rather serendipitous discovery. Unbeknownst to anyone, a commonly used pair of “fungal-specific” primers will amplify genetic material from a wide range of eukaryotic taxa. Since we were the first to use these primers for culture-independent studies, their more ubiquitous nature was unknown to researchers. Consequently, in addition to yeasts, we soon realized that over two-thirds of the sampled Drosophila populations were associated with trypanosomatid parasites. Phylogenetic analysis shows that the discovered organisms are closely related to the insect-vectored human parasites Trypanosoma brucei, Trypanosoma cruzi, and Leishmania (the causative agents of African sleeping sickness, Chagas disease, and Leishmaniasis, respectively) and an economically important bumble bee parasite Crithidia bombi. Given that trypanosomatids are responsible for several clinically and economically important diseases and that Drosophila is the best developed system for studying the genetic and immunological interactions between insects and pathogens, this work may lead to Drosophila becoming a model for investigating how the insect immune system interacts with these important, but often neglected, parasites.

Chandler, J.A. and James, P.M. 2013. Discovery of trypanosomatid parasites in globally distributed Drosophila species. PloS ONE.  8(4):e61937.doi:10.1371/journal.pone.0061937 PDF

Not just “who is there” but “what are they doing”: Using bacterial genomics to reveal the metabolic potential of the Drosophila suzukii microbiota

It is hypothesized that animal intestinal microbial communities may help their hosts colonize novel environments and increase their realized niche. Females of Drosophila suzukii (commonly called spotted-wing Drosophila) have a serrated ovipositor that allows them to lay eggs in undamaged fruit. Larvae of this invasive pest are therefore exposed to a very different environment than larvae of the more common “fruit flies” which can only lay eggs in damaged, and therefore much older, fruits. Does the intestinal microbiota of D. suzukii assist with the breakdown and digestion of this novel habitat? While culture-independent microbial characterization can provide insight into the taxonomic and phylogenetic diversity of host-associated microbes, genomic data gives a more complete picture of its metabolic capability. I have isolated bacteria from D. suzukii larvae collected on undamaged cherries and I am currently preparing genomic libraries for whole-genome Illumina sequencing. By comparing the metabolic potential of larvae-associated bacteria to that of bacteria found on rotted and damaged fruit (publicly available data produced by the agricultural research community), it can be determined which metabolic pathways are potentially beneficial to larvae in this novel environment.

Beyond a single snapshot: Spatial and temporal dynamics of the Drosophila microbiota

Theory predicts that stability in microbial communities is needed for co-evolution between host and symbiont. However, many studies of the animal-associated microbiota are based upon a single collection per species or population with no replication across space or time. Because of this, I set out to understand the spatial and temporal dynamics of Drosophila-associated microbial communities. During summer 2011, as part of an NSF East Asia and Pacific Summer Institute (EAPSI) fellowship, I collected mushroom feeding flies from numerous sites across northern Taiwan. Mushrooms are a temporally stable food source for flies (as opposed to decaying fruits that are preferred by most species of Drosophila) and this selection of host diet allowed the repeated sampling of the same population of flies over an extended period of time. Since the same Drosophila species was collected at several sites and each population was present at each site for several weeks, the spatial and temporal dynamics of the microbial communities associated with these Drosophila could be determined. Unfortunately, these samples were confiscated by customs upon entry into the United States. I will not elaborate here, but if you are interested, I would be happy to tell you the story, preferably over a beer….

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