Understanding the biotic drivers of diversity is a major goal of microbial ecology. One approach toward tackling this issue is to interrogate relatively simple communities that are easy to observe and perturb. Figs (syconia) of the genus Ficus represent such a system. Here, we describe the microbial communities of Ficus septica figs, which are associated with the nematode Caenorhabditis inopinata (the sister species of the C. elegans genetic model system). In 2019, 38 Ficus septica figs (across 12 plants in Taiwan) were dissected, and metadata, such as foundress wasp number and nematode occupancy, were collected for each fig. Suspensions derived from interior fig material and fig surface washes were prepared for 16S microbial metabarcoding. Over 2,000 ASVs were detected, and microbial communities were dominated by members of Proteobacteria, Bacteroidota, and Actinobacteriota. Although microbial communities of fig exteriors and interiors can be distinguished, levels of microbial alpha diversity were comparable across these areas of the fig. A joint analysis of fig and previously published C. elegans substrate microbiomes revealed similarities and differences among the biotic environments of these nematode sister species. Fig microbial community composition was driven in large part by variation among individual plants. Conversely, nematodes had no detectable impact on microbial community composition or alpha diversity. A handful of ASVs (associated with the genera Ochrobactrum and Stenotrophomonas) revealed potential differential abundance among figs varying in nematode occupancy. Additionally, foundress wasp number was negatively correlated with microbial alpha diversity. These findings set the stage for future studies that directly test the role of nematode and wasp occupancy on microbial communities, as well as investigations that probe nematode-microbe interactions through laboratory experiments. Taken together, these results constitute a fundamental step in characterizing the natural microbial communities of figs and Caenorhabditis nematodes.IMPORTANCEUnraveling why different species live in different places is a longstanding open question in ecology. It is clear that interspecific interactions among species are a major contributor to species distributions. Ficus figs are a useful system for ecological studies because they are relatively simple microcosms where characterizing animal community composition of multiple samples is straightforward. Additionally, Caenorhabditis inopinata, a close relative of the C. elegans genetic model system, thrives in Ficus septica figs. Here, we tie 16S microbial metabarcoding to nematode and wasp occupancy data to understand the causes of bacterial community composition in F. septica figs. We found that microbial composition, but not total diversity, varies among fig surface and interiors. Additionally, microbial diversity is driven in large part by individual plant of origin. Likewise, we found that nematode occupancy does not appear to impact microbial composition. Moreover, we show that as the number of foundress wasps increases, the microbial α-diversity decreases. Finally, we identified ASVs that are potentially associated with nematode occupancy. Taken together, these results represent a key step in describing a community wherein ecological genetic hypotheses can be tested, as well as one that can potentially reveal the roles of uncharacterized genes in established model systems.
Woodruff et al. (Mon,) studied this question.