Spatial variation in diet–microbe associations across populations of a generalist North American carnivore

Abstract

Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population‐level characteristics. In the present study, we assessed spatial variation in diet characteristics, gut microbiome and associations between these two ecological traits across populations of coyotes Canis latrans. We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations. We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ13C) and nitrogen (δ15N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values. Although consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ15N was highest where coyotes were the apex predator and lowest where coyotes co‐occurred with grey wolves Canis lupus. The gut microbial community exhibited marked spatial variation across populations with the lowest operational taxonomic units diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ13C and microbial community attributes. However, positive associations between δ15N and specific microbial genera increased as coyotes ascended trophic levels. Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide‐ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology and alterations in behaviour.

Downtown Diet: a global meta-analysis of urbanization on consumption patterns of vertebrate predators

“…The inclusion of stable isotopes in future urban-rural diet analyses would fill important information gaps to couple trophic and urban ecology, as these data capture a crucial dimension of niche space at a broader trophic level. Recent work has demonstrated variation in dietary niche and trophic position for urban versus rural coyotes using stable isotopes (Colborn et al, 2020). To conclude, we provide the first quantification of predator diets in a comparative urban versus rural or wildland framework for multiple predator taxa at a global multi-city scale and revealed that urbanization enriches predator diets with carbon but does not inherently relax predation.…”

“…Carbon and nitrogen isotopic ratios present in scat, hair, and vibrissae allow researchers to assess individual heterogeneity in the trophic niche space (Ben-David, & Flaherty, 2012;Colborn et al, 2020). Higher δ 13 C IR reflect consumption of plants with C4 photosynthetic pathways such as corn and sugarcane, which are common in anthropogenic food sources, in contrast to lower values associated with C3 plants found in rural or wildland habitat (Galetti et al, 2016).…”

Michigan ZoomIN: validating crowd-sourcing to identify mammals from camera surveys

“…Majority, yielded completion of 10%, and majority plus gold standard < 1% of images. To underscore the importance of considering multiple consensus thresholds, we evaluated results for coyotes ( Canis latrans ) as a case study, given understanding their placement is valuable to wildlife managers, their dynamic role within the carnivore community and are commonly mistaken for other canid species (Prugh et al 2009, Hilton et al 2015, Colborn et al 2020). There were 520 classifications of coyotes by users, of which 265 reached consensus.…”

“…To underscore the importance of considering multiple consensus thresholds, we evaluated results for coyotes as a case study, given their dynamic role within the carnivore community and because they are commonly mistaken for other canid species (Prugh et al 2009, Colborn et al 2020). There were 520 classifications of coyotes by users, of which 265 were classified through one of our consensus criteria.…”

Effect of Geography and Captivity on Scat Bacterial Communities in the Imperiled Channel Island Fox

“…Broadly, geographic isolation of populations can lead to divergence in microbiota over time due to drift and/or local adaptation. While geography has been shown to play a role in shaping the gut microbiome in a number of taxa [19][20][21][22], few studies have looked at these effects in intraspecific island populations. Relative to interspecific comparisons, intraspecific comparisons can be expected to minimize differences in host factors such as physiology, behavior and ecology, and therefore allow better resolution of factors such as host sex and condition, as well as the effects of geography.…”