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Thermostable Keystone Bacteria Maintain the Functional Diversity of the Ixodes scapularis Microbiome Under Heat Stress

  • Invertebrate Microbiology
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Abstract

Variations in the composition and diversity of tick microbiome due to high temperatures may influence the hierarchy of community members as a response to environmental change. Modifications in the community structure are hypothesized to drive alterations in the presence and/or abundance of functional pathways in the bacterial metagenome. In this study, this hypothesis was tested by using published 16S rRNA datasets of Ixodes scapularis males incubated at different temperatures (i.e., 4, 20, 30, and 37 °C) in a laboratory setting. Changes in community structure and functional profiles in response to temperature shifts were measured using co-occurrence networks and metagenome inference. Results from laboratory-reared ticks were then compared with those of field-collected ticks. The results from laboratory-reared ticks showed that high temperature altered the structure of the microbial community and decreased the number of keystone taxa. Notably, four taxa were identified as keystone in all the temperatures, and the functional diversity of the tick microbiome was contained in the four thermostable keystone their associated bacterial taxa. Three of the thermostable keystone taxa were also found in free-living ticks collected in Massachusetts. Moreover, the comparison of functional profiles of laboratory-reared and field-collected ticks revealed the existence of an important set of metabolic pathways that were common among the different datasets. Similar to the laboratory-reared ticks, the keystone taxa identified in field-collected ticks alongside their consortia (co-occurring taxa) were sufficient to retain the majority of the metabolic pathways in the functional profile. These results suggest that keystone taxa are essential in the stability and the functional resiliency of the tick microbiome under heat stress.

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Acknowledgements

UMR BIPAR is supported by the French Government's Investissement d'Avenir program, Laboratoire d'Excellence “Integrative Biology of Emerging Infectious Diseases” (grant no. ANR-10-LABX-62-IBEID). Alejandra Wu-Chuang is supported by Programa Nacional de Becas de Postgrado en el Exterior “Don Carlos Antonio López” (grant no. 205/2018).

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Authors and Affiliations

  1. Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France

    Alejandra Wu-Chuang & Alejandro Cabezas-Cruz

  2. School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada

    Dasiel Obregon

  3. Faculty of Veterinary Medicine, University of Zaragoza, Zaragoza, Spain

    Agustín Estrada-Peña

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  1. Alejandra Wu-Chuang
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  4. Alejandro Cabezas-Cruz
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Contributions

A.C.C. and D.O. conceived the study. A.W.C., D.O., and A.E.P. performed the analyses. A.W.C. prepared the figures and drafted the manuscript. All authors revised and accepted the last version of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Alejandro Cabezas-Cruz.

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Supplementary Information

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Supplementary Figure S1

Effects of different temperatures on microbial diversity. ASV richness of microbial communities of I. scapularis incubated at 4, 20, 30 and 37°C. Statistical comparisons were carried out with pairwise Kruskal-Wallis (* p < 0.05, ** p < 0.01, *** p < 0.001).

Supplementary Figure S2

Correlation between bacterial taxa abundance and changes in temperature. Heatmap representing the center log ratio (clr) values of bacteria genera that change significantly (Kruskal-Wallis, p < 0.05) among the four temperatures. Different days of incubation for each tick, in the different temperatures, are represented above the heatmap. Spearman correlation coefficient (ρ) calculated between each bacterial taxa and the temperature are represented as barplots at the right side of the heatmap. Statistical comparisons were carried out with Spearman rank correlation (* p < 0.05, ** p < 0.01, *** p < 0.001). The heatmap was constructed in R studio using heatmap.2 function. (PDF 563 KB)

Supplementary Figure S3

Functional contribution of thermostable keystone taxa and their positively associated neighbors. The number of metabolic pathways contributed by the subnetwork composed of the thermostable keystone taxa and their positively co-occurred bacterial neighbors compared to the total of hypothetical functions for the whole microbial community at different temperatures is displayed as a Venn diagram. (PDF 126 KB)

Supplementary Table 1

Type of connection between persistent neighbor and thermostable keystone taxa in the four temperatures (XLSX 11 KB)

Supplementary Table 2

Predicted pathways shared between the total community of bacteria and the subnetwork, composed of the keystone taxa and their direct neighbor, from ticks incubated at different temperatures. (XLSX 62 KB)

Supplementary Table 3

Predicted pathways shared between the total community of bacteria and the subnetwork, composed of the keystone taxa and their direct, positively associated neighbor, from ticks incubated at different temperatures. (XLSX 78 KB)

Supplementary Table 4

Predicted pathways shared between the total community of bacteria and the subnetwork, composed of the keystone taxa and their direct neighbor, from field-collected ticks. (XLSX 34 KB)

Supplementary Table 5

Predicted pathways shared between laboratory-reared and field collected ticks. (XLSX 27 KB)

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Wu-Chuang, A., Obregon, D., Estrada-Peña, A. et al. Thermostable Keystone Bacteria Maintain the Functional Diversity of the Ixodes scapularis Microbiome Under Heat Stress. Microb Ecol 84, 1224–1235 (2022). https://doi.org/10.1007/s00248-021-01929-y

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