Testing for adaptive divergence in the microbiome under warming conditions: the case of sticklebacks from geothernal habitats

All animals are microbial ecosystems, but with individuals differing in the composition and function of their resident microbiota1. Microbial communities can include commensal, symbiotic, and pathogenic microorganisms that are major players for determining inter-individual variation in metabolism, digestion, feeding behaviour, development, growth, and overall performance2. But how might these processes be influenced by a warming world?
Climate change may alter the available communities of microbiota contracted by organisms3. This could have important downstream effects mediated by microbiota such as the stimulation of gut and intestine development. Further, relationships between mitochondrial activity, ATP synthesis, and microbes could be altered to change energy use and efficiency. Studies on non-mammalian models such as fish are needed to provide insights into these potential responses in natural populations, and for understanding how microbiota are impacted by the environment4.
Temperature influences the composition and abundance of microbiota. This could significantly alter biodiversity at multiple scales beyond the microbiome. Therefore, using unique systems of stickleback fish (Gasterosteus aculeatus) from Iceland that inhabit geothermally-warmed habitats this project will address the following three questions:
1) How does the microbiome of stickleback vary in relation to thermal habitat?
2) Does thermally-related microbiome variation influence the development and function of the gut?
3) Do temperature associated differences in the microbiome influence mitochondrial activity, energy use efficiency, and the production of ATP?

Findings should provide fundamental insights into how ectotherms will respond to climate change. The study system is extremely powerful due to the close proximity of long-term naturally-warmed populations to comparable ambient temperature populations. These sticklebacks are also highly amenable to being kept in the lab which affords a great deal of experimental flexibility. The studentship should appeal to individuals with an interest in evolution, ecology, microbiomes, developmental biology and conservation


Approaches would involve field work in Iceland combined with a series of complementary lab experiments. Question 1 would involve the collection of wild sticklebacks from multiple sites. Material from these specimens would be preserved and returned to Glasgow University for processing and microbiome profiling. Briefly, this would involve the use of high throughput targeted amplicon sequencing of the 16S ribosomal RNA (rRNA) subunit encoded by 16S rDNA. These data would provide a means for assessing both the diversity and abundance of microbiota and provide a means to assess differences between fish residing in warmed and ambient habitats.

To address questions 2 and 3 fish would be exposed to experimental manipulations of their microbiome. This would allow for the effects of the microbiome including its interaction with a fish host to be assessed. Therefore, following established protocols germ-free stickleback4,5 would be generated and reciprocally inoculated with microbiota from geothermal and ambient habitats. Inoculation would be assessed with further 16S sequencing and confirmation would provide a basis for comparison among treatment groups. Specifically, for question 2 embryos would be collected during periods of gut and intestine development for histological examination. Gene expression for gut-related genes would also be examined using in situ hybridization and qPCR.

If the composition of the microbiome is adaptive for sticklebacks and promotes coevolution6 we can predict that fish inoculated with native biota will perform better than those inoculated with non-native biota. For question 3 inoculated fish would again be used to examine metabolic activity in the stomach, muscle and liver. Specifically, extracted live tissue would be used for high resolution respirometry which enables the examination of mitochondrial activity, ATP production, and oxygen use.

Project Timeline

Year 1

– collection of wild sticklebacks from Iceland
– establishment of 16S protocols and sequencing
– analysis of differences between populations

Year 2

– lab crosses of sticklebacks
– establishment of inoculation procedures
– collection of embyros for in situ and qPCR
– analysis of gene expression data
– initial assessment of metabolic phenotypes

Year 3

– continued assessment of metabolic phenotypes
– lab work to assess ATP production and efficiency
– completion of data collection
– final analysis of data and writing of chapters

Year 3.5

– final editing and write up

& Skills

The candidate will learn a broad range of transferable skills that will enhance their prospects and prepare them for a career in academia or industry. These skills include genomic sequencing, microbiological sampling, fish husbandry, high-resolution respirometry, data management and manipulation, molecular and developmental biology. In addition, the field work component will provide the experience of international fieldwork and the interaction with a team in Iceland. We will take advantage of the close proximity of the supervisors to ensure frequent meetings, and the candidate will also profit from exposure to the extended networks of the collaborating team.

References & further reading

1) Youngblut ND,Reischer GH,Walters W, Schuster N, et al. 2019. Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades Nature Communications 10: 2200.
2) Robinson CD, Klein HS, Murphy KD, Parthasarathy R, Guillemin K, Bohannan BJM (2018) Experimental bacterial adaptation to the zebrafish gut reveals a primary role for immigration. PLoS Biology 16: e2006893.
3) Cavicchioli R, Ripple WJ, Timmis KN, Azam F,Bakken LR,Baylis M et al. 2019. Scientists’ warning to humanity: microorganisms and climate change. Nature Reviews Microbiology 17: 569-586.
4) Small CM, Milligan-Myhre K, Bassham S, Guillemin K, Cresko WA. 2017. Host genotype and microbiota contribute asymmetrically to transcriptional variation in the threespine stickleback gut. Genome Biology and Evolution 9: 504-520.
5) Kathryn Milligan-Myhre, Clayton M. Small, Erika K. Mittge, Meghna Agarwal, Mark Currey, William A. Cresko, Karen Guillemin 2016. Innate immune responses to gut microbiota differ between oceanic and freshwater threespine stickleback populations
Disease Models & Mechanisms 9: 187-198
6) Bolnick DI, Snowberg LK, Hirsch PE, Lauber CL, Knight R, et al. 2014 Individuals’ diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch). Ecology Letters 17:979-987.

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