Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats

Abstract

As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. ‘Omics techniques show promise in quantifying key components of reef ecosystems, dissolved metabolites and microorganisms, that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies, and contributing to nutrient cycling and signaling on reefs. Here we applied four ‘omics techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics and untargeted metabolomics) to waters overlying Florida’s Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite ‘omics approaches both differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.

Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs

“…While we did not detect significant changes in organic nitrogen or carbon, perhaps microorganisms efficiently remineralized it, maintaining the lower levels of organic matter. Enriched reef water ammonium coincident with a high prevalence of SCTLD was also found in Florida (Becker et al, 2023).…”

Advancing Reef Monitoring Techniques through Exometabolomics: Quantification of Labile Dissolved Organic Metabolites on Coral Reefs

“…To determine the advantages and complementarity of incorporating pre-extraction benzoyl-chloride derivatization into the marine metabolomics workflow, we assessed the overlap of identified metabolites across coral reef benthic communities from four previously published PPL-SPE extracted reef water targeted metabolomics datasets (Fiore et al 2017, 28 Weber et al 2020, 18 Weber et al 2022, 22 and Becker et al 2023 27 ) and the current study (Figure 4). A total of 85 distinct metabolites were identified across the five studies.…”

“…15,28,50,51 Previous work by Becker et al 2023 further demonstrated the significant impact of disease state on targeted coral exometabolomes. 27…”

“…Comparisons between the metabolites observed in this study using the BC derivatization method and four independent, targeted benthic exometabolomics datasets that did not employ BC derivatization were investigated. Studies were selected due to their quantitative measurements of exometabolites on coral reefs allowing for valid comparisons, and included reef seawater samples collected in Cuba 18 and along the coast of Florida, 27 a U.S. Virgin Islands coral reef seawater incubation experiment, 22 and Florida field-collected sponge inhalant and exhalant seawater samples. 28 All four studies utilized PPL SPE extraction (without derivatization), the most common methodology employed for characterizing DOM by LC-MS described by Dittmar et al 7 Metabolite names from each study were downloaded from each manuscript’s publicly available metadata.…”

“…Although reef did not significantly structure metabolite composition, it explained 33% of the variance in the metabolite data. Reef habitat components and biogeography are known to influence reef water metabolite composition 22,27,49 , and further sampling across US Virgin Islands reefs in the future is needed to confirm these initial trends.…”