Effects of anthropogenic changes on nitrogen cycling microbes of coral holobionts

Abstract

Corals have co-evolved in symbiotic relationships with diverse eukaryotic and prokaryotic microbes, collectively termed “the coral holobiont”. The efficient nutrient exchange between the coral host and photosynthetic Symbiodiniaceae supports the high productivity of corals in oligotrophic waters, yet critically depends on nitrogen limitation within the holobiont. Nitrogen cycling prokaryotes (bacteria and archaea) are thus key players in the functioning of coral holobionts. Octocorals are important benthic reef organisms, yet little is known about their-associated nitrogen cycling prokaryotes under environmental change. Denitrifiers (i.e., prokaryotes capable of reducing nitrate/nitrite to N2) could help maintain nitrogen limitation in holobionts, yet their community structure and (a)biotic controls are still unknown. This thesis aims to extend the current knowledge of nitrogen cycling prokaryotes in coral holobionts by focusing on the following research objectives: 1) investigating the effects of dissolved organic carbon (DOC) and concomitant heat stress on the abundance of diazotrophs (i.e., prokaryotes capable of converting N2 into ammonia) and denitrifiers in two octocoral species with distinct trophic strategies: the more mixotrophic soft coral Xenia umbellata and the highly autotrophic gorgonian Pinnigorgia flava; 2) investigating the respective contributions of host and algal identities to the structuring of denitrifier communities in cnidarian holobionts; 3) characterizing denitrifier communities in cnidarian holobionts and identifying their driving factors. The experimental work consisted of a multidisciplinary approach combing physiological, molecular, and bioinformatical tools and executed over the course of two aquarium-based experiments: 1) a 45-day experiment consisting of 21 days of DOC enrichment at ambient 26 oC followed by 24 days of DOC enrichment under concomitant heat stress (32 oC) and 2) an experimental manipulation of algal communities in the coral model Aiptasia to generate distinct holobiont combinations of host and algal strains as well as aposymbiotic (i.e., algal-free) hosts. Our findings revealed that excess DOC alone had no effect on the diazotroph and denitrifier abundance in octocorals at ambient temperature. However, excess DOC and concomitant heat stress resulted in a contrasting microbiome response between diazotrophs (increased abundance) and denitrifiers (host-specific unaltered or decreased abundance) in octocorals. Such increased diazotroph abundance without equivalent increased denitrifier abundance in octocoral holobionts may disrupt the nitrogen limitation required for maintaining the symbiotic relationship. The presence of algal symbionts increased denitrifier abundance by up to 22-fold in Aiptasia holobionts. As increase of denitrifier abundances aligned with the superior photosynthetic performance of the inoculated algae and the identification of mostly heterotrophic denitrifiers in photosymbiotic Aiptasia, the photosynthetic carbon released by Symbiodiniaceae may be an important energy source for denitrifier communities. Thereby, I propose a positive feedback loop of photosynthetic Carbon, Denitrifier, Nitrogen limitation, and Symbiosis (PDNS) in the photosymbiotic holobiont, which may effectively contribute to maintaining the cnidarian-algal symbiosis in the unperturbed holobiont.

This thesis extends our understanding on the ecological significance of nitrogen cycling microbes in cnidarian holobionts and emphasizes the importance of algae-prokaryote interactions during this process. For a better understanding on the function of nitrogen cyclers underlying the cnidarian-algal symbiosis, future research should combine microbiome manipulations with functional gene knockouts in selected denitrifier isolates. At an ecological scale, comparing dynamics of nitrogen cycling prokaryotes in a range of marine cnidarian hosts, including octocorals, under environmental change may give new insights into the ecological drivers of novel reef ecosystems in which reef-building corals are largely replaced as dominant ecosystem engineers.