Abstract
Calanoid copepods, abundant crustacean zooplankton, play crucial roles in oceanic food webs and carbon fluxes. Copepod microbiomes could impact host health and ecosystem function, but their sources, localization, residence time, and susceptibility to climate change are poorly understood. Acartia tonsa copepod microbiomes were studied by 16S rRNA gene amplicon sequencing from a 3-year climate change experiment and a 2-year seasonal time series from the coastal Northwestern Atlantic Ocean. Taxon Richness and Shannon diversity significantly increased under high temperature but Proteobacterial proportional contribution to overall Richness decreased under high temperature and/or CO2, suggesting Phylum-level differences in microbiome susceptibility to climate change. The majority of total microbiome community was attributed to gut, forming up to 75% of the community, while diet-originated and epibiotic communities contributed up to 28% and 45%, respectively. A core microbiome of 11 taxa formed up to 70% of voided-gut copepod microbiome community, supporting the idea of a stable majority while transient taxa constituted a smaller community proportion. Representative phyla of Vibrio, Enterovibrio, and Crocinitomix were strongly enriched under climate change, while two core taxa were depleted, demonstrating that climate change alters potentially important stable communities. A core taxon Thiothrix, a novel gammaproteobacterial phylotype, formed a large portion (7.5-31.5%) of the cultured copepod microbiome, but its relative abundances were not significantly altered by increased temperature and/or CO2. Thiothrix may play a symbiotic role by detoxifying sulfur waste products accumulating from copepods. Field-collected copepod microbiomes contained four core taxa identified in the culture experiments, with the core Thiothrix phylotype at up to 23% relative abundance. The relative abundances of core taxa fluctuated seasonally, but observations indicate they play long-term roles in natural A. tonsa populations. Copepods from both the transgenerational experiments and from the field demonstrated microbiome flexibility and response to changing conditions. Despite the dynamic composition of the microbiomes, stable taxa persisted in both populations, suggesting host-specific microbiome components are an element of copepod biology.