Spatio-temporal trends in richness and persistence of bacterial communities in decline-phase water vole populations

Abstract

Understanding the driving forces that control vole population dynamics requires identifying bacterial parasites hosted by the voles and describing their dynamics at the community level. To this end, we used high-throughput DNA sequencing to identify bacterial parasites in cyclic populations of montane water voles that exhibited a population outbreak and decline in 2014-2018. An unexpectedly large number of 155 Operational Taxonomic Units (OTUs) representing at least 13 genera in 11 families was detected. Individual bacterial richness was higher during declines, and vole body condition was lower. Richness as estimated by Chao2 at the local population scale did not exhibit clear seasonal or cycle phase-related patterns, but at the vole meta-population scale, exhibited seasonal and phase-related patterns. Moreover, bacterial OTUs that were detected in the low density phase were geographically widespread and detected earlier in the outbreak; some were associated with each other. Our results demonstrate the complexity of bacterial community patterns with regard to host density variations, and indicate that investigations about how parasites interact with host populations must be conducted at several temporal and spatial scales: multiple times per year over multiple years, and at both local and long-distance dispersal scales for the host(s) under consideration. Rodents are the most diverse mammal group in the world, with an estimated 2,277 species 1 , a global distribution that includes every continent, except Antarctica, and terrestrial habitats ranging from arid deserts to swamps and rainforest 2. Generally characterized by fast life histories and large reproductive capacities, rodents are keystone species or ecosystem engineers in many of the ecosystems in which they are found 3,4 , but also frequently come into conflict with humans, causing significant loses in agricultural systems globally (see Singleton et al. 5 for an overview). They also act as reservoirs for many socially and economically burdensome zoonoses (e.g. 6,7), a pattern which is predicted to increase 8. Of particular interest to population ecologists for more than 100 years is the phenomenon of the rodent outbreak, in which the population in question exhibits dramatic multi-annual fluctuations in abundance, often with such a degree of regularity that these outbreaks are considered cycles, with four distinct phases. The increase phase is defined as a period of large increase in abundance from one spring to the next, and is followed by the peak phase, in which abundance is stable but high 9. The peak phase can range in duration from mere weeks to a year, and is followed by the decline phase, in which abundance drops over as brief a period as months but can also take up to two years. The following low phase is characterized by stable but low population abundance. The study of these systems has generated a large body of research 10 , but a consensus regarding the underlying demographic mechanisms of these outbreaks and their intrinsic or extrinsic driver...

Pathogen community composition and co-infection patterns in a wild community of rodents

“…Moreover, both the 16S metabarcoding approach and serological antibody tests can only be interpreted in terms of presence/absence of exposure to pathogens, although co-infection may rather impact parasite abundance (e.g., (Thumbi et al, 2013;Gorsich et al, 2014)). Other extrinsic factors, such as seasonal variation in pathogen community composition, could also impact both interpretation and year-round generality of our results due to adherence to autumn sampling dates (Maurice et al, 2015;Villette et al, 2020). Lastly, we also acknowledge several caveats to consider with our methods.…”

Modeling Microbial Community Networks: Methods and Tools

“…A probabilistic approach to define the type of association between pairs ( i , j ) has been used by Veech et al [ 74 ] and implemented in the R package cooccur [ 75 ]. Although this method is not originally developed for metagenomic data, there are studies that use it to analyze association patterns also in 16 rDNA-seq field [ 76 , 77 ]. Observed co-occurrence between i and j is defined as the number of co-presences among all samples ( Q obs ).…”

Population density does not affect seasonal regulation of reproductive physiology in male water voles

“…Regarding the population dynamics of the water vole, several studies have notably examined predation, landscape influence, agricultural practices, parasitism and pathogen-induced stress [6,[11][12][13][14][15][16]. However, the impact of vole population density on reproductive physiology is still poorly documented.…”