Environmental effect
The avian gut microbiome frequently reflects the local environment (Hird et al. 2014; Hird et al. 2018; Cao et al. 2020). Cyanobacteria, found in marine and brackish waters (Sivonen 1996), was common in birds in The Bahamas but nearly absent from most individuals in Michigan. Cyanobacteria has previously been found in the gut microbiota of island birds (García-Amado et al. 2018) and is known to be acquired through food (Birrenkott et al. 2004). Kirtland’s Warblers may acquire environmentally derived Cyanobacteria in The Bahamas via food consumption, as most birds were captured within 2km of the ocean and much of the groundwater on the island is brackish. We detected two common environmental bacterial genera,Solirubrobacter and Nocardioides , as more abundant with birds in The Bahamas (Janssen 2006; Topp et al. 2000).
While local habitats exert a notable influence on the gut microbiota of birds, it is unknown if microbial diversity increases or decreases during active migration or timing of gut microbiota to acclimate to new habitats. During migration birds are exposed to varying environments at stopover sites where they could acquire novel microbes (Lewis et al. 2017), resulting in temporarily inflated diversity. In contrast, possible adaptations to long distance flight, such as relatively shorter intestinal length and atrophication of intestines during active migration, might result in decreased microbial diversity (McWilliams and Karasov 2005; Caviedes-Viral et al. 2007). Using the ability to determine what day individuals arrive in Michigan following migration, we observed a decrease in microbial diversity the first three days before slowly increasing over days four through nine. Birds may be spending the first few days at their breeding grounds shedding transient microbes acquired at stopover sites. This suggests that during spring migration microbial diversity increases due to exposure at stopover sites rather than decreases as an adaptation to long-distance flight. However, sample size per day is small and additional research with larger sample size is needed to further support these results.
Gut microbiota are dynamic, displaying influence of novel microbial pools within 24-48 hours of exposure (Lewis et al. 2017; Grondet al. 2019; Capunitan et al. 2020). Two of our findings further support rapid acclimation to local microbiota. First, we observed no significant variation in gut microbial diversity of the 12 birds we sampled early in Michigan that were not part of the individuals we sampled in The Bahamas, implying rapid turnover of microbiota sourced from the local Michigan habitat. Second, we observed significant variation in beta diversity between 2017 and 2018, as well as within each sampling period. Environmental microbes often exhibit high turnover over time (Faust et al. 2015). As such, our observations further support significant influence of local environment on the gut microbiome. This highlights the continued need for long term monitoring of microbiomes as community-wide differences between years are demonstrable within the same geographic regions.