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Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms

Citation

Goffredi, Shana; Brzechffa, Camille (2020), Contrasting influences on bacterial symbiont specificity by co-occurring deep-sea mussels and tubeworms, Dryad, Dataset, https://doi.org/10.5061/dryad.7pvmcvdqt

Abstract

Relationships between deep-sea invertebrates and bacterial symbionts, fueled by sulfide and methane, are well known, yet factors influencing symbiont specificity remain cryptic. For animals that obtain their symbionts from the environment, both host identity and geographic location can impact the ultimate symbiont partner. Bacterial symbionts were analyzed for 3 co-occurring species each of Bathymodiolus mussels and vestimentiferan tubeworms, from three deep methane seeps off the west coast of Costa Rica. The bacterial internal transcribed spacer gene was analyzed via direct and barcoded amplicon sequencing to reveal fine-scale symbiont diversity. Each of the three mussel species (B. earlougheri, B. billschneideri and B. nancyschneideri) hosted genetically-distinct thiotrophic endosymbionts, despite living nearly side-by-side in their habitat, suggesting that host identity is influential in driving symbiont specificity. The dominant thiotrophic symbiont of co-occurring tubeworms Escarpia spicata and Lamellibrachia (L. barhami and L. donwalshi), on the other hand, was identical regardless of host species or sample location, suggesting lack of influence by either factor on symbiont selectivity in this group of animals. These findings highlight the specific, yet distinct, influences on the environmental acquisition of symbionts in two foundational invertebrates with similar lifestyles, and provide a rapid and precise method of examining symbiont identities.

Methods

Three co-occurring mussel species (B. earlougheri, B. billschneideri and B. nancyschneideri) and co-occurring vestimentiferans, Escarpia spicata and two species of Lamellibrachia (L. barhami and L. donwalshi), were sampled from three methane seep sites in 2017 and 2018 ranging from 990m-1742 m depth off the west coast of Costa Rica (Quepos Seep, Mound 12, Jaco Scar). Mound 12 (8° 55.794N / 84° 18.780W), Jaco Scar (9° 7.071N / 84° 50.445W), and Quepos Seep (9° 1.904N / 84° 37.294W). 

Total genomic DNA was extracted from symbiont-bearing tissues using the Qiagen DNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. A ~400bp region of the ITS gene was amplified using primers with Illumina adapters on the 5′ end Sym-ITS-1322F (5′- TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGGTTGGAATCGCTAGTAATCG-3′) and Sym-ITS-356R (5′-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACCAGGCCGACAACGCAGT-3′; according to Won et al. 2003), and an annealing temperature of 54°C for 25 cycles, and further following the details in Goffredi et al. 2020. Data was processed in Quantitative Insights Into Microbial Ecology (v1.8.0)

Direct 16S rRNA sequencing was accomplished using the 27F-1492R primer pair. Direct ITS sequencing was accomplished using the Sym-ITS-1322F / Sym-ITS-356R primer pair without the Illumina adapters (underlined above).

Funding

Southern California Academy of Sciences