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

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.


Anaplasma
Anaplasma-001, the only OTU in this data set assigned to the Anaplasma genus, is identical to V4 16S rRNA reference sequences of Anaplasma phagocytophilum (formerly Ehrlichia phagocytophilum) and several unspecified Ehrlichia sp. sequences. Table S1: Similarity, expressed as a percentage, and coverage (in parentheses) of the OTU Anaplasma-001 compared to a selection of reference strains of Anaplasma phagocytophilum and unspecified Ehrlicia. Sequences were compared using the blastn search tool.

Bordetella
The seed sequence of Bordetella-001, the most prevalent of the 11 Bordetella OTUs in the data set, is identical to V4 16S rRNA reference sequences of Bordetella parapertussis and B. bronchiseptica. The seed sequence of Bordetella-003, the second-most prevalent 40 Bordetella OTU, differs from these two reference sequences by 4 base-pairs. The remaining Bordetella OTU seed sequences differ from reference sequences by at least 4 base-pairs and do not show strong affinities with any of the reference sequences.  Figure S4: Variable base-pair positions within the V4 region of the 16S rRNA bacterial gene of a selection of reference Bordetella sequences and Bordetella OTU seed sequences (numbered) obtained from Arvicola terrestris in Franche-Comté, France. Tile colour indicates the base pair in each sequence at each position. Sequences were clustered using complete linkage of raw distances (ie. no assumptions were made about evolution rates). Black crossed tiles (N) indicate ambiguous base pairs in the sequence.  Figure S5: nMDS ordination of differences between Bordetella OTU seed sequences (numbered, coloured to indicate frequency of detection within the animals sampled) and reference Bordetella sp. sequences (red).

Borelliela
The seed sequence of Borrelliela-001, the only Borrelliela OTU in this data set, is iden-45 tical to reference sequences of Borelliella (Borellia) burgdorferi as well as an unspecified Borelliela strain.

Rickettsia
Only one OTU in this data set was assigned to Rickettsia; the seed sequences is most similar to several members of the tick-borne spotted fever group.

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Table S10: Similarity, expressed as a percentage, and coverage (in parentheses) of the OTU Rickettsia-001 compared to a selection of reference strains of Rickettsia sp. Sequences were compared using the blastn search tool.

Yersinia
Only one OTU in this data set was assigned to Yersinia; the seed sequence is identical to a number of species in this genus, as well as the type sequence for Serratia liquefaciens.