Selective Uptake of Pelagic Microbial Community Members by Caribbean Reef Corals

Coral reefs are possible sinks for microbes; however, the removal mechanisms at play are not well understood. Here, we characterize pelagic microbial groups at the CARMABI reef (Curaçao) and examine microbial consumption by three coral species: Madracis mirabilis, Porites astreoides, and Stephanocoenia intersepta. Flow cytometry analyses of water samples collected from a depth of 10 m identified 6 microbial groups: Prochlorococcus, three groups of Synechococcus, photosynthetic eukaryotes, and heterotrophic bacteria. Minimum growth rates (µ) for Prochlorococcus, all Synechococcus groups, and photosynthetic eukaryotes were 0.55, 0.29, and 0.45µ day-1, respectively, and suggest relatively high rates of productivity despite low nutrient conditions on the reef. During a series of 5-h incubations with reef corals performed just after sunset or prior to sunrise, reductions in the abundance of photosynthetic picoeukaryotes, Prochlorococcus and Synechococcus cells, were observed. Of the three Synechococcus groups, one decreased significantly during incubations with each coral and the other two only with M. mirabilis. Removal of carbon from the water column is based on coral consumption rates of phytoplankton and averaged between 138 ng h-1and 387 ng h-1, depending on the coral species. A lack of coral-dependent reduction in heterotrophic bacteria, differences in Synechococcus reductions, and diurnal variation in reductions of Synechococcus and Prochlorococcus, coinciding with peak cell division, point to selective feeding by corals. Our study indicates that bentho-pelagic coupling via selective grazing of microbial groups influences carbon flow and supports heterogeneity of microbial communities overlying coral reefs. Importance We identify interactions between coral grazing behavior and the growth rates and cell abundances of pelagic microbial groups found surrounding a Caribbean reef. During incubation experiments with three reef corals, reductions in microbial cell abundance differed according to coral species and suggest specific coral or microbial mechanisms are at play. Peaks in removal rates of Prochlorococcus and Synechococcus cyanobacteria appear highest during postsunset incubations and coincide with microbial cell division. Grazing rates and effort vary across coral species and picoplankton groups, possibly influencing overall microbial composition and abundance over coral reefs. For reef corals, use of such a numerically abundant source of nutrition may be advantageous, especially under environmentally stressful conditions when symbioses with dinoflagellate algae break down

Cellular traits regulate fluorescence-based light-response phenotypes of coral photosymbionts living in-hospite

Diversity across algal family Symbiodiniaceae contributes to the environmental resilience of certain coral species. Chlorophyll-a fluorescence measurements are frequently used to determine symbiont health and resilience, but more work is needed to refine these tools and establish how they relate to underlying cellular traits. We examined trait diversity in symbionts from the generas Cladocopium and Durusdinium, collected from 12 aquacultured coral species. Photophysiological metrics (ΦPSII, σPSII, ρ, τ1, τ2, antenna bed quenching, non-photochemical quenching, and qP) were assessed using a prototype multi-spectral fluorometer over a variable light protocol which yielded a total of 1,360 individual metrics. Photophysiological metrics were then used to establish four unique light-response phenotypic variants. Corals harboring C15 were predominantly found within a single light-response phenotype which clustered separately from all other coral fragments. The majority of Durusdinium dominated colonies also formed a separate light-response phenotype which it shared with a few C1 dominated corals. C15 and D1 symbionts appear to differ in which mechanisms they use to dissipate excess light energy. Spectrally dependent variability is also observed across light-response phenotypes that may relate to differences in photopigment utilization. Symbiont cell biochemical and structural traits (atomic C:N:P, cell size, chlorophyll-a, neutral lipid content) was also assessed within each sample and differ across light-response phenotypes, linking photophysiological metrics with underlying primary cellular traits. Strong correlations between first- and second-order traits, such as Quantum Yield and cellular N:P content, or light dissipation pathways (qP and NPQ) and C:P underline differences across symbiont types and may also provide a means for using fluorescence-based metrics as biomarkers for certain primary-cellular traits

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

High-temperature acclimation strategies within the thermally tolerant endosymbiont Symbiodiniumtrenchii and its coral host, Turbinariareniformis, differ with changing pCO2 and nutrients

The dinoflagellate Symbiodiniumtrenchii associates with a wide array of host corals throughout the world, and its thermal tolerance has made it of particular interest within the context of reef coral resilience to a warming climate. However, future reefs are increasingly likely to face combined environmental stressors, further complicating our understanding of how S. trenchii will possibly acclimatize to future climate scenarios. Over a 33-day period, we characterized the individual and combined affects of high temperature (26.5 vs. 31.5 °C), pCO2 (400 vs. 760 µatm), and elevated nutrients (0.4 and 0.2 vs. 3.5 and 0.3 µmol of NO3/NO2 and PO43-$${\text{PO}}_{4}^{3 - }$$, respectively) on S. trenchii within the host coral species Turbinariareniformis. Global analysis across all treatments found temperature to be the largest driver of physiological change. However, exposure to elevated temperature led to changes in symbiont physiology that differed across pCO2 concentrations. Net photosynthesis and cellular chlorophyll a increased with temperature under ambient pCO2, whereas temperature-related differences in cellular volume and its affect on pigment packaging were more pronounced under elevated pCO2. Furthermore, increased nutrients mitigated the physiological response to high temperature under both ambient and elevated pCO2 conditions and represented a significant interaction between all three physical parameters. Individual responses to temperature and pCO2 were also observed as cellular density declined with elevated temperature and calcification along with respiration rates declined with increased pCO2. Symbiodiniumtrenchii remained the dominant symbiont population within the host across all treatment combinations. Our results reveal distinct physiological changes in response to high temperature within the S. trenchii/T. reniformis symbioses that are dependent on pCO2 and nutrient concentration, and represent important interactive effects to consider as we consider how corals will respond under future climate change scenarios

Correction to: High-temperature acclimation strategies within the thermally tolerant endosymbiont Symbiodiniumtrenchii and its coral host, Turbinariareniformis, differ with changing pCO2 and nutrients

Correction to: "High-temperature acclimation strategies within the thermally tolerant endosymbiont Symbiodiniumtrenchii and its coral host, Turbinariareniformis, differ with changing pCO2 and nutrients

Coral calcification under environmental change: a direct comparison of the alkalinity anomaly and buoyant weight techniques

Two primary methods—the buoyant weight (BW) and alkalinity anomaly (AA) techniques—are currently used to quantify net calcification rates (G) in scleractinian corals. However, it remains unclear whether they are directly comparable since the few method comparisons conducted to date have produced inconsistent results. Further, such a comparison has not been made for tropical corals. We directly compared GBW and GAA in four tropical and one temperate coral species cultured under various pCO2, temperature, and nutrient conditions. A range of protocols for conducting alkalinity depletion incubations was assessed. For the tropical corals, open-top incubations with manual stirring produced GAA that were highly correlated with and not significantly different from GBW. Similarly, GAA of the temperate coral was not significantly different from GBW when incubations provided water motion using a pump, but were significantly lower than GBW by 16% when water motion was primarily created by aeration. This shows that the two techniques can produce comparable calcification rates in corals but only when alkalinity depletion incubations are conducted under specific conditions. General recommendations for incubation protocols are made, especially regarding adequate water motion and incubation times. Further, the re-analysis of published data highlights the importance of using appropriate regression statistics when both variables are random and measured with error. Overall, we recommend the AA technique for investigations of community and short-term day versus night calcification, and the BW technique to measure organism calcification rates integrated over longer timescales due to practical limitations of both methods. Our findings will facilitate the direct comparison of studies measuring coral calcification using either method and thus have important implications for the fields of ocean acidification research and coral biology in general

Host–symbiont combinations dictate the photo-physiological response of reef-building corals to thermal stress

High sea surface temperatures often lead to coral bleaching wherein reef-building corals lose significant numbers of their endosymbiotic dinoflagellates (Symbiodiniaceae). These increasingly frequent bleaching events often result in large scale coral mortality, thereby devasting reef systems throughout the world. The reef habitats surrounding Palau are ideal for investigating coral responses to climate perturbation, where many inshore bays are subject to higher water temperature as compared with offshore barrier reefs. We examined fourteen physiological traits in response to high temperature across various symbiotic dinoflagellates in four common Pacific coral species, Acropora muricata, Coelastrea aspera, Cyphastrea chalcidicum and Pachyseris rugosa found in both offshore and inshore habitats. Inshore corals were dominated by a single homogenous population of the stress tolerant symbiont Durusdinium trenchii, yet symbiont thermal response and physiology differed significantly across coral species. In contrast, offshore corals harbored specific species of Cladocopium spp. (ITS2 rDNA type-C) yet all experienced similar patterns of photoinactivation and symbiont loss when heated. Additionally, cell volume and light absorption properties increased in heated Cladocopium spp., leading to a greater loss in photo-regulation. While inshore coral temperature response was consistently muted relative to their offshore counterparts, high physiological variability in D. trenchii across inshore corals suggests that bleaching resilience among even the most stress tolerant symbionts is still heavily influenced by their host environment