Lipidomics of Environmental Microbial Communities. I: Visualization of Component Distributions Using Untargeted Analysis of High-Resolution Mass Spectrometry Data

<jats:p>Lipids, as one of the main building blocks of cells, can provide valuable information on microorganisms in the environment. Traditionally, gas or liquid chromatography coupled to mass spectrometry (MS) has been used to analyze environmental lipids. The resulting spectra were then processed through individual peak identification and comparison with previously published mass spectra. Here, we present an untargeted analysis of MS<jats:sup>1</jats:sup> spectral data generated by ultra-high-pressure liquid chromatography coupled with high-resolution mass spectrometry of environmental microbial communities. Rather than attempting to relate each mass spectrum to a specific compound, we have treated each mass spectrum as a component, which can be clustered together with other components based on similarity in their abundance depth profiles through the water column. We present this untargeted data visualization method on lipids of suspended particles from the water column of the Black Sea, which included >14,000 components. These components form clusters that correspond with distinct microbial communities driven by the highly stratified water column. The clusters include both known and unknown compounds, predominantly lipids, demonstrating the value of this rapid approach to visualize component distributions and identify novel lipid biomarkers.</jats:p&gt

Coral thermal stress and bleaching enrich and restructure reef microbial communities via altered organic matter exudation

Abstract Coral bleaching is a well-documented and increasingly widespread phenomenon in reefs across the globe, yet there has been relatively little research on the implications for reef water column microbiology and biogeochemistry. A mesocosm heating experiment and bottle incubation compared how unbleached and bleached corals alter dissolved organic matter (DOM) exudation in response to thermal stress and subsequent effects on microbial growth and community structure in the water column. Thermal stress of healthy corals tripled DOM flux relative to ambient corals. DOM exudates from stressed corals (heated and/or previously bleached) were compositionally distinct from healthy corals and significantly increased growth of bacterioplankton, enriching copiotrophs and putative pathogens. Together these results demonstrate how the impacts of both short-term thermal stress and long-term bleaching may extend into the water column, with altered coral DOM exudation driving microbial feedbacks that influence how coral reefs respond to and recover from mass bleaching events

DataSheet_3_Sponges on shifting reefs: holobionts show similar molecular and physiological responses to coral versus macroalgal food.pdf

IntroductionMany coral reefs witness an ongoing coral-to-algae phase shift. Corals and algae release large quantities of (in)organic nutrients daily, of which a large part is utilized by sponges. In turn, sponges are important cyclers of precious resources to other inhabitants on reefs residing in oligotrophic waters. Here, we investigated whether sponge holobionts (i.e., host and prokaryotic symbionts) adapt their physiology to food released by coral- versus macroalgae.MethodsThereto, two sponge species, Plakortis angulospiculatus and Halisarca caerulea (high and low microbial abundance, respectively), were continuously exposed for 12 days to coral and macroalgal exudates in running seawater aquaria. Transcript expression of host and prokaryotic symbionts, changes in prokaryotic community composition, and holobiont physiological responses (i.e., respiratory demand, fluxes of carbon and nitrogen) were investigated after coral- versus macroalgae dominated treatments and compared to a seawater only control treatment.ResultsIn both sponge holobionts differential transcript expression between the coral and macroalgae treatments was very low (DiscussionAfter 12 days of exposure sponges appear to opportunistically feed on different food sources without having to adjust their metabolic pathways or associated prokaryotic communities. This suggests that sponges could be well-adapted to predicted changes in food source availability due to coral-to-algal phase shifts on many coral reefs.</p

DataSheet_2_Sponges on shifting reefs: holobionts show similar molecular and physiological responses to coral versus macroalgal food.xlsx

IntroductionMany coral reefs witness an ongoing coral-to-algae phase shift. Corals and algae release large quantities of (in)organic nutrients daily, of which a large part is utilized by sponges. In turn, sponges are important cyclers of precious resources to other inhabitants on reefs residing in oligotrophic waters. Here, we investigated whether sponge holobionts (i.e., host and prokaryotic symbionts) adapt their physiology to food released by coral- versus macroalgae.MethodsThereto, two sponge species, Plakortis angulospiculatus and Halisarca caerulea (high and low microbial abundance, respectively), were continuously exposed for 12 days to coral and macroalgal exudates in running seawater aquaria. Transcript expression of host and prokaryotic symbionts, changes in prokaryotic community composition, and holobiont physiological responses (i.e., respiratory demand, fluxes of carbon and nitrogen) were investigated after coral- versus macroalgae dominated treatments and compared to a seawater only control treatment.ResultsIn both sponge holobionts differential transcript expression between the coral and macroalgae treatments was very low (DiscussionAfter 12 days of exposure sponges appear to opportunistically feed on different food sources without having to adjust their metabolic pathways or associated prokaryotic communities. This suggests that sponges could be well-adapted to predicted changes in food source availability due to coral-to-algal phase shifts on many coral reefs.</p

DataSheet_1_Sponges on shifting reefs: holobionts show similar molecular and physiological responses to coral versus macroalgal food.xlsx

IntroductionMany coral reefs witness an ongoing coral-to-algae phase shift. Corals and algae release large quantities of (in)organic nutrients daily, of which a large part is utilized by sponges. In turn, sponges are important cyclers of precious resources to other inhabitants on reefs residing in oligotrophic waters. Here, we investigated whether sponge holobionts (i.e., host and prokaryotic symbionts) adapt their physiology to food released by coral- versus macroalgae.MethodsThereto, two sponge species, Plakortis angulospiculatus and Halisarca caerulea (high and low microbial abundance, respectively), were continuously exposed for 12 days to coral and macroalgal exudates in running seawater aquaria. Transcript expression of host and prokaryotic symbionts, changes in prokaryotic community composition, and holobiont physiological responses (i.e., respiratory demand, fluxes of carbon and nitrogen) were investigated after coral- versus macroalgae dominated treatments and compared to a seawater only control treatment.ResultsIn both sponge holobionts differential transcript expression between the coral and macroalgae treatments was very low (DiscussionAfter 12 days of exposure sponges appear to opportunistically feed on different food sources without having to adjust their metabolic pathways or associated prokaryotic communities. This suggests that sponges could be well-adapted to predicted changes in food source availability due to coral-to-algal phase shifts on many coral reefs.</p

A multiomic analysis of in situ coral-turf algal interactions

Viruses, microbes, and host macroorganisms form ecological units called holobionts. Here, a combination of metagenomic sequenc- ing, metabolomic profiling, and epifluorescence microscopy was used to investigate how the different components of the hol- obiont including bacteria, viruses, and their associated metabolites mediate ecological interactions between corals and turf algae. The data demonstrate that there was a microbial assemblage unique to the coral -turf algae interface displaying higher microbial abun- dances and larger microbial cells. This was consistent with previ- ous studies showing that turf algae exudates feed interface and coral -associated microbial communities, often at the detriment of the coral. Further supporting this hypothesis, when the metabo- lites were assigned a nominal oxidation state of carbon (NOSC), we found that the turf algal metabolites were significantly more reduced (i.e., have higher potential energy) compared to the corals and interfaces. The algae feeding hypothesis was further sup- ported when the ecological outcomes of interactions (e.g., whether coral was winning or losing) were considered. For example, coral holobionts losing the competition with turf algae had higher Bacteroidetes-to-Firmicutes ratios and an elevated abundance of genes involved in bacterial growth and division. These changes were similar to trends observed in the obese human gut micro - biome, where overfeeding of the microbiome creates a dysbiosis detrimental to the long-term health of the metazoan host. Together these results show that there are specific biogeochemical changes at coral -turf algal interfaces that predict the competitive outcomes between holobionts and are consistent with algal exudates feeding coral -associated microbes

Three-Dimensional Molecular Cartography of the Caribbean Reef-Building Coral Orbicella faveolata

All organisms host a diversity of associated viruses, bacteria, and protists, collectively defined as the holobiont. While scientific advancements have enhanced the understanding of the functional roles played by various components of the holobiont, there is a growing need to integrate multiple types of molecular data into spatially and temporally resolved frameworks. To that end, we mapped 16S and 18S rDNA metabarcoding, metatranscriptomics, and metabolomic data onto three-dimensional reconstructions of coral colonies to examine microbial diversity, microbial gene expression, and biochemistry on two colonies of the ecologically important, reef-building coral, Orbicella faveolata and their competitors (i.e., adjacent organisms interacting with the corals: fleshy algae, turf algae, hydrozoans, and other corals). Overall, no statistically significant spatial patterns were observed among the samples for any of the data types; instead, strong signatures of the macroorganismal hosts (e.g., coral, algae, hydrozoa) were detected, in the microbiome, the transcriptome, and the metabolome. The 16S rDNA analysis demonstrated higher abundance of Firmicutes in the coral microbiome than in its competitors. A single bacterial amplicon sequence variant from the genus Clostridium was found exclusively in all O. faveolata samples. In contrast to microbial taxa, a portion of the functionally annotated bacterial RNA transcripts (6.86%) and metabolites (1.95%) were ubiquitous in all coral and competitor samples. Machine learning analysis of microbial transcripts revealed elevated T7-like cyanophage-encoded photosystem II transcripts in O. faveolata samples, while sequences involved in bacterial cell division were elevated in turf algal and interface samples. Similar analysis of metabolites revealed that bacterial-produced antimicrobial and antifungal compounds were highly enriched in coral samples. This study provides insight into the spatial and biological patterning of the coral microbiome, transcriptome, and metabolome