Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

Abstract

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L−1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.

Distinct Bacterial Microbiomes Associate with the Deep-Sea Coral Eguchipsammia fistula from the Red Sea and from Aquaria Settings

“…The deep Red Sea with low oxygen (1-2 mg O 2 L −1 ) and limited nutrient availability due to warm temperatures (>20 • C) features markedly different conditions than otherwise common for deep-sea coral habitats . In line with other studies, Röthig et al (2017) showed that these coral microbiomes were species-specific and suggested functional adaptation to their environment. These adaptations include in particular the presence of anaerobe bacterial taxa and potential hydrocarbon degraders.…”

“…About 90 min later upon retrieval, samples were rinsed with sterile-filtered seawater, crushed on liquid nitrogen, and stored at −80 • C. To assess the in situ microbiome 3 of the 4 E. fistula samples described in Röthig et al (2017) were used in this study. To ensure an evenly distributed sample set and a high sequencing depth, one in situ sample from Röthig et al (2017) presenting the lowest coverage was disregarded. Further, a water sample from the corals' direct vicinity was taken using Niskin bottles.…”

“…As described in Röthig et al (2017), coral samples used to assess the native microbiome (in situ) were collected from between 314 and 320 m depth (N22 • 17.837, E38 • 53.811) with a custom-made scoop, transferred into a specifically designed twocompartment container, and preserved in RNAlater at depth. About 90 min later upon retrieval, samples were rinsed with sterile-filtered seawater, crushed on liquid nitrogen, and stored at −80 • C. To assess the in situ microbiome 3 of the 4 E. fistula samples described in Röthig et al (2017) were used in this study.…”

“…Findings include species-specific microbiomes, but also considerable spatial and temporal variations. Only very recently, the microbiomes of three further scleractinian corals (i.e., Eguchipsammia fistula, Dendrophyllia sp., and Rhizotrochus typus) from the Red Sea have been characterized (Röthig et al, 2017). The deep Red Sea with low oxygen (1-2 mg O 2 L −1 ) and limited nutrient availability due to warm temperatures (>20 • C) features markedly different conditions than otherwise common for deep-sea coral habitats .…”

Rapid adaptive responses to climate change in corals

“…For example, transplantation of corals to a warmer environment resulted in shifts in the associated bacterial community that correlated with increased holobiont thermotolerance 87 . Additionally, higher bacterial diversity in deep compared to shallow water corals 88,89 suggests that some deep habitat-specific microbes may be involved in nutrient cycling specific to the low-irradiance environments. Both genetic and epigenetic processes contribute to high phenotypic plasticity and rapid evolution in bacteria 90 .…”