Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Remple, K. L., Silbiger, N. J., Quinlan, Z. A., Fox, M. D., Kelly, L. W., Donahue, M. J., & Nelson, C. E. Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment. Npj Biofilms and Microbiomes, 7(1), (2021): 84, https://doi.org/10.1038/s41522-021-00252-1.Work on marine biofilms has primarily focused on host-associated habitats for their roles in larval recruitment and disease dynamics; little is known about the factors regulating the composition of reef environmental biofilms. To contrast the roles of succession, benthic communities and nutrients in structuring marine biofilms, we surveyed bacteria communities in biofilms through a six-week succession in aquaria containing macroalgae, coral, or reef sand factorially crossed with three levels of continuous nutrient enrichment. Our findings demonstrate how biofilm successional trajectories diverge from temporal dynamics of the bacterioplankton and how biofilms are structured by the surrounding benthic organisms and nutrient enrichment. We identify a suite of biofilm-associated bacteria linked with the orthogonal influences of corals, algae and nutrients and distinct from the overlying water. Our results provide a comprehensive characterization of marine biofilm successional dynamics and contextualize the impact of widespread changes in reef community composition and nutrient pollution on biofilm community structure.This work was supported through grants from the National Science Foundation for Biological Oceanography (1923877 to C.E.N. and M.J.D., 1949033 to C.E.N. and 2118687 to L.W.K., and 1924281 to N.J.S.) and the National Fish and Wildlife Foundation (grant no. 44447 to C.E.N.). This paper is funded in part by the National Oceanic and Atmospheric Administration, Project A/AS-1, which is sponsored by the University of Hawaii Sea Grant College Program, SOEST, under Institutional Grant No. NA18OAR4170076 from NOAA Office of Sea Grant, Department of Commerce. This is CSUN marine biology contribution #365, UH Sea Grant contribution UNIHI-SEAGRANT-JC-21-06, and UH SOEST contribution 11435

Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine

Abstract Background Migraine is a common heritable neurovascular disorder typically characterised by episodic attacks of severe pulsating headache and nausea, often accompanied by visual, auditory or other sensory symptoms. Although genome-wide association studies have identified over 40 single nucleotide polymorphisms associated with migraine, there remains uncertainty about the casual genes involved in disease pathogenesis and how their function is regulated. Results We performed an epigenome-wide association study, quantifying genome-wide patterns of DNA methylation in 67 migraine cases and 67 controls with a matching age and sex distribution. Association analyses between migraine and methylation probe expression, after adjustment for cell type proportions, indicated an excess of small P values, but there was no significant single-probe association after correction for multiple testing (P < 1.09 × 10− 7). However, utilising a 1 kb sliding window approach to combine adjacent migraine-methylation association P values, we identified 62 independent differentially methylated regions (DMRs) underlying migraine (false discovery rate < 0.05). Migraine association signals were subtle but consistent in effect direction across the length of each DMR. Subsequent analyses showed that the migraine-associated DMRs were enriched in regulatory elements of the genome and were in close proximity to genes involved in solute transportation and haemostasis. Conclusions This study represents the first genome-wide analysis of DNA methylation in migraine. We have identified DNA methylation in the whole blood of subjects associated with migraine, highlighting novel loci that provide insight into the biological pathways and mechanisms underlying migraine pathogenesis

Impact of opioid-free analgesia on pain severity and patient satisfaction after discharge from surgery: multispecialty, prospective cohort study in 25 countries

Background: Balancing opioid stewardship and the need for adequate analgesia following discharge after surgery is challenging. This study aimed to compare the outcomes for patients discharged with opioid versus opioid-free analgesia after common surgical procedures.Methods: This international, multicentre, prospective cohort study collected data from patients undergoing common acute and elective general surgical, urological, gynaecological, and orthopaedic procedures. The primary outcomes were patient-reported time in severe pain measured on a numerical analogue scale from 0 to 100% and patient-reported satisfaction with pain relief during the first week following discharge. Data were collected by in-hospital chart review and patient telephone interview 1 week after discharge.Results: The study recruited 4273 patients from 144 centres in 25 countries; 1311 patients (30.7%) were prescribed opioid analgesia at discharge. Patients reported being in severe pain for 10 (i.q.r. 1-30)% of the first week after discharge and rated satisfaction with analgesia as 90 (i.q.r. 80-100) of 100. After adjustment for confounders, opioid analgesia on discharge was independently associated with increased pain severity (risk ratio 1.52, 95% c.i. 1.31 to 1.76; P &lt; 0.001) and re-presentation to healthcare providers owing to side-effects of medication (OR 2.38, 95% c.i. 1.36 to 4.17; P = 0.004), but not with satisfaction with analgesia (beta coefficient 0.92, 95% c.i. -1.52 to 3.36; P = 0.468) compared with opioid-free analgesia. Although opioid prescribing varied greatly between high-income and low- and middle-income countries, patient-reported outcomes did not.Conclusion: Opioid analgesia prescription on surgical discharge is associated with a higher risk of re-presentation owing to side-effects of medication and increased patient-reported pain, but not with changes in patient-reported satisfaction. Opioid-free discharge analgesia should be adopted routinely

ConCISE: Consensus Annotation Propagation of Ion Features in Untargeted Tandem Mass Spectrometry Combining Molecular Networking and In Silico Metabolite Structure Prediction

Recent developments in molecular networking have expanded our ability to characterize the metabolome of diverse samples that contain a significant proportion of ion features with no mass spectral match to known compounds. Manual and tool-assisted natural annotation propagation is readily used to classify molecular networks; however, currently no annotation propagation tools leverage consensus confidence strategies enabled by hierarchical chemical ontologies or enable the use of new in silico tools without significant modification. Herein we present ConCISE (Consensus Classifications of In Silico Elucidations) which is the first tool to fuse molecular networking, spectral library matching and in silico class predictions to establish accurate putative classifications for entire subnetworks. By limiting annotation propagation to only structural classes which are identical for the majority of ion features within a subnetwork, ConCISE maintains a true positive rate greater than 95% across all levels of the ChemOnt hierarchical ontology used by the ClassyFire annotation software (superclass, class, subclass). The ConCISE framework expanded the proportion of reliable and consistent ion feature annotation up to 76%, allowing for improved assessment of the chemo-diversity of dissolved organic matter pools from three complex marine metabolomics datasets comprising dominant reef primary producers, five species of the diatom genus Pseudo-nitzchia, and stromatolite sediment samples

Nutrient pollution disrupts key ecosystem functions on coral reefs

There is a long history of examining the impacts of nutrient pollution and pH on coral reefs. However, little is known about how these two stressors interact and influence coral reef ecosystem functioning. Using a six-week nutrient addition experiment, we measured the impact of elevated nitrate (NO−3) and phosphate (PO3−4) on net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities. Our study had four major outcomes: (i) NCC rates declined in response to nutrient addition in all substrate types, (ii) the mixed community switched from net calcification to net dissolution under medium and high nutrient conditions, (iii) nutrients augmented pH variability through modified photosynthesis and respiration rates, and (iv) nutrients disrupted the relationship between NCC and aragonite saturation state documented in ambient conditions. These results indicate that the negative effect of NO−3 and PO3−4 addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion

Seawater carbonate chemistry and net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities

There is a long history of examining the impacts of nutrient pollution and pH on coral reefs. However, little is known about how these two stressors interact and influence coral reef ecosystem functioning. Using a six-week nutrient addition experiment, we measured the impact of elevated nitrate (NO−3) and phosphate (PO3−4) on net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities. Our study had four major outcomes: (i) NCC rates declined in response to nutrient addition in all substrate types, (ii) the mixed community switched from net calcification to net dissolution under medium and high nutrient conditions, (iii) nutrients augmented pH variability through modified photosynthesis and respiration rates, and (iv) nutrients disrupted the relationship between NCC and aragonite saturation state documented in ambient conditions. These results indicate that the negative effect of NO−3 and PO3−4 addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion

Engineered Substrates Reveal Species-Specific Inorganic Cues for Coral Larval Settlement

The widespread loss of stony reef-building coral populations has been compounded by pervasive recruitment failure, i.e., the low or absent settlement and survival of coral juveniles. To combat global coral reef stressors and rebuild coral communities, restoration practitioners have developed workflows to rear and settle vulnerable coral larvae in the laboratory and subsequently outplant settled juveniles back to natural and artificial reefs. These workflows often make use of the natural biochemical settlement cues present in crustose coralline algae (CCA), which can be presented to swimming larvae as extracts, fragments, or live algal sheets to induce settlement. In this work, we investigated the potential for inorganic chemical cues to complement these known biochemical effects. We designed settlement substrates made from lime mortar (CaCO3) and varied their composition with the use of synthetic and mineral additives, including sands, glasses, and alkaline earth carbonates. In experiments with larvae of two Caribbean coral species, Acropora palmata (elkhorn coral) and Diploria labyrinthiformis (grooved brain coral), we saw additive-specific settlement preferences (>10-fold settlement increase) in the absence of any external biochemical cues. Interestingly, these settlement trends were independent of bulk surface properties such as surface roughness and wettability. Instead, our results suggest that not only can settling coral larvae sense and positively respond to soluble inorganic materials, but that they can also detect localized topographical features more than an order of magnitude smaller than their body width. Our findings open a new area of research in coral reef restoration, in which engineered substrates can be designed with a combination of organic and inorganic additives to increase larval settlement, and perhaps also improve post-settlement growth, mineralization, and defense

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

Illuminating the Dark Metabolome of Pseudo-nitzschia-microbiome Associations

The exchange of metabolites mediates algal and bacterial interactions that maintain ecosystem function. Yet, while 1000s of metabolites are produced, only a few molecules have been identifiedin these associations. Using the ubiquitous microalgae Pseudo-nitzschia sp., as a model, we employed an untargeted metabolomics strategy to assign structural characteristics to themetabolites that distinguished specific diatom-microbiome associations. We cultured five species of Pseudo-nitzschia, including two species that produced the toxin domoic acid, and examinedtheir microbiomes and metabolomes. A total of 4826 molecular features were detected by tandem mass spectrometry. Only 229 of these could be annotated using available mass spectral libraries,but by applying new in-silico annotation tools, characterization was expanded to 2710 features. The metabolomes of the Pseudo-nitzschia-microbiome associations were distinct and distinguished by structurally diverse nitrogen compounds, ranging from simple amines andamides to cyclic compounds such as imidazoles, pyrrolidines, and lactams. By illuminating the dark metabolomes, this study expands our capacity to discover new chemical targets that facilitatemicrobial partnerships and uncovers the chemical diversity that underpins algae-bacteria interactions