BCO-DMO ERDDAP
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Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute NC_GLOBAL acquisition_description String Sample collection:  \n Five Porites astreoides colonies and a sand patch were selected and marked\nwith flagging tape by divers on Ram Head reef (18\\u00ba18\\u201907.3\\u201d N,\n64\\u00ba42\\u201914.5\\u201d W; 8 m depth in sand) in St. John, U. S. Virgin\nIslands. Colonies of various sizes (3 \\u2013 16 inches in diameter) from a\nrange of heights above the seafloor (1 \\u2013 27 cm) were selected and these\ncolonies were labeled A through E. Additionally, colonies were evenly\ndistributed across the reef in order to minimize location effects (range of\n3.6 to 14 meters between each colony). All colonies were located directly next\nto sand patches based on colony size constraints and the space needed for\ndeployment of the custom made Coral Ecosphere Sampling Devices (CESD). Six\nCESD made out of aluminum strut material were deployed adjacent to each\nsampling location with sand screws. The last CESD was placed in a wide sand\npatch with no corals or benthic organisms located in its vicinity and this\nsampling location was used as a \\u2018no-coral\\u2019 control. Divers\npositioned the CESD so that a 60 ml syringe with an attached filter holder\ncould be placed 5 cm away from the middle of the colony. Light and temperature\nloggers (8K HOBO/PAR loggers; Onset, Wareham, MA) were zip-tied to the end of\neach CESD and programmed to collect temperature and relative light intensity\nmeasurements every 5 minutes over the course of the three-day study. An hour\nafter CESD deployment, scuba divers collected the first set of samples (Day 1,\n3:00 pm). Filter holders were pre-loaded with 0.22 \\u00b5m pore size\nSupor\\u00ae filters (Pall Corporation, Ann Arbor, MI, USA) and were contained\nwithin sterile Whirl-pack\\u00ae bags prior to sampling.\\u00a0 Divers also\ndescended with acid-washed polyethylene nutrient bottles (30 ml volume) to\ncollect seawater samples for unfiltered inorganic nutrient analysis and flow\ncytometry. At depth, seawater samples (60 ml) collected for amplicon-based\nmicrobial community analysis were conducted at 2 different stationary\nlocations relative to the CESD device (with the exception of collections\ncompleted at the sand-patch location). Reef-depth samples were collected first\nat the top of the CESD (2 m from the colony) in order to minimize stirring\nclose to the coral ecosphere sampling area. To collect the sample, a diver\nattached a piece of acid-cleaned Masterflex silicone tubing to connect the end\nof the filter holder to the mouth of the syringe and then used reverse\nfiltration to pull seawater through the filter. The filter-holder was then\nplaced in an individual Whirl-pack\\u00ae bag and sealed. After collection of\nmicrobial biomass with the syringe, a nutrient sample was collected. After\ncollection of the reef-depth sample, a diver attached the filter holder to the\nsyringe, slowly descended closer to the coral colony, but behind the CESD to\nmaintain sufficient distance from the sampling area and then placed the\nsyringe into the syringe holder located on the horizontal arm of the CESD. As\nbefore, the diver first collected the coral ecosphere sample (5 cm from the\ncolony) onto the filter followed by a nutrient sample in the same location.\nReplicate samples collected for DNA analysis were collected from both seawater\nenvironments surrounding each colony on the first dive, but were not collected\non the following dives due to time constraints. Surface seawater samples (< 1\nm) were collected using 60 mL syringes at each time point from the dive boat.\n \nThis sampling scheme was repeated at approximately 3 am and 3 pm for the next\nthree days, totaling up to 6 sampling time points. Divers sampled each colony\nand collected samples in the same order (reef-depth followed by coral\necosphere) during all time points. After collection, samples were placed in a\ncooler equipped with blue-ice packs for the transit from the reef to the lab\nand then samples were processed immediately. Over the course of sampling, 85\nseawater samples were collected.\n \nAfter the last time point, coral tissue was collected from each colony (close\nto the area where the coral ecosphere seawater was sampled) using a hammer and\nchisel and the CESD were removed. Sand was also collected in the location\nwhere the sand control CESD device was deployed.\n \nSample processing:  \n In the laboratory, sterile syringes were used to remove residual seawater\ntrapped within filter holders and then filters were placed into cryovials,\nflash-frozen in a dry shipper charged with liquid nitrogen, and then\ntransferred into a\\u00a0 -20 C freezer.\n \nSeawater collected for flow cytometric analysis was subsampled from unfiltered\nnutrient samples and preserved with paraformaldehyde (Electron Microscopy\nSciences, Allentown, PA) to a final concentration of 1% (by volume). Nutrient,\nDNA, and flow cytometry samples were shipped frozen back to Woods Hole\nOceanographic Institution and ultimately stored at -80 C prior to analysis.\nThe coral tissue and sand samples were stored in a second dry shipper and\nultimately at -80 C until they were processed.\\u00a0\n \nMacronutrient analysis and flow cytometry:  \n Frozen and unfiltered nutrient samples were analyzed with a continuous\nsegmented flow-system using previously described methods (as in Apprill and\nRappe 2011). The concentrations of NO2- + NO3-, NO2-, PO43-, NH4+, and\nsilicate were measured in all of the samples. Nitrate concentrations were\nobtained by subtracting the nitrite concentration from the nitrite + nitrate\nmeasurements for each sample.\n \nSamples collected for flow cytometry were analyzed using colinear analysis\n(laser excitation wavelength of 488 nm, UV) on an Altra flow cytometer\n(Beckman Coulter, Pasadena, CA.). Unstained subsamples were used to enumerate\nthe abundances of picocyanobacteria (Prochlorococcus, Synechococcus) and\npicoeukaryotes. Stained (Hoechst stain, 1 \\u00b5g ml-1 final concentration)\nsubsamples were analyzed to estimate the abundance of unpigmented cells (an\nestimate of heterotrophic bacterial abundance) (Marie et al. 1997). FlowJo (v.\n6.4.7) software was used to estimate the abundance of each cell type. The\nabundance of total cells was calculated by adding the cell counts obtained for\neach of the respective picoplankton classes together for each sample.\n \nDNA extraction, amplification, pooling, and sequencing:  \n DNA was extracted from filters using a sucrose-lysis extraction method and\nQiagen spin-columns (Santoro et al. 2010) Control extractions were also\ncompleted with unused filters (control filters without biomass) in order to\naccount for contamination from the filters or extraction reagents. Lastly,\ndiluted DNA from a synthetic staggered mock community (BEI Resources,\nManassas, VA, USA) was used to account for amplification and sequencing errors\nin downstream microbial community analysis. Coral tissue was removed from the\nskeleton using air-brushing with autoclaved 1% phosphate-buffered-saline (PBS)\nsolution (Apprill et al. 2016; Weber et al. 2017). The coral tissue slurry was\npelleted using a centrifuge and the PBS supernatant was discarded. DNA was\nextracted from each pellet (300 mg of tissue) using a modified version of the\nDNeasy DNA extraction kit protocol (Qiagen, Germantown, MD). The lysis buffer\nin the kit was added to each tube followed by approximately 300 mg of garnet\nbeads (from a MOBIO DNA extraction kit) and 300 mg of Lysing B matrix beads\n(MP Biomedicals, Solon, OH). The tubes were subjected to a bead-beating step\nfor 15 minutes so that the beads could break up the coral tissue (Weber et al.\n2017). After bead-beating, 20 \\u00b5l of proteinase-k was added to each tube\nand the samples were incubated with gentle agitation for 10 minutes at 56\n\\u00b0C. After these modifications, the DNeasy protocol (Qiagen) was followed\nto complete extractions.\n \nExtracts were amplified with barcoded primers targeting the V4 hypervariable\nregion of the bacterial and archaeal small subunit ribosomal RNA gene (Kozich\net al. 2013). The forward primer: 5\\u2019 TATGGTAATTGTGTGYCAGCMGCCGCGGTAA\n3\\u2019 (Parada et al. 2016) and reverse primer: 3\\u2019\nAGTCAGTCAGCCGGACTACNVGGGTWTCTAAT 5\\u2019 (Apprill et al. 2015) were used,\nalong with the barcodes, to amplify and tag each sample prior to pooling. We\nused forward and reverse primers with degeneracies in order to eliminate\namplification biases against Crenarchaeota/ Thaumarchaeota (Parada et al.\n2016)\\u00a0 and SAR 11 (Apprill et al. 2015). Triplicate Polymerase Chain\nReactions (25 l volume) were run with 2 l of DNA template from each sample\nusing the same barcodes in order to minimize the formation of chimeras during\namplification. The reaction conditions included: a 2-minute hot start at 95\n\\u00b0C followed by 36 cycles of 95 \\u00b0C for 20 seconds, 55 \\u00b0C for 15\nseconds, and 72 \\u00b0C for 5 minutes. The final extension step was 72 \\u00b0C\nfor 10 minutes. Triplicate barcoded amplicons were pooled and screened using\ngel electrophoresis to assess the quality and the relative concentration of\namplicons. Amplicons were purified using the MinElute Gel Extraction Kit\n(Qiagen) and pooled to form the sequencing library. The library was sequenced\n(paired-end 2x250 bp) at the Georgia Genomics and Bioinformatics Core with a\nMiseq (Illumina, San Diego, CA) sequencer and raw sequence reads are available\nat the NCBI Sequence Read Archive under BioProject # PRJNA550343.\n \nMicrobial community analyses:  \n Raw sequences were quality-filtered and grouped into amplicon sequence\nvariants (ASVs) using DADA2 (Callahan et al. 2016). Reads were filtered,\ntrimmed, dereplicated and error rates were calculated using the program\\u2019s\nparametric error model. The DADA2 algorithm was used to infer the number of\ndifferent ASVs (8357 distinct ASVs), paired reads were merged, an ASV table\nwas constructed, and chimeras were removed (1% of all ASVs). Taxonomy was\nassigned to each ASV using the Silva v.132 reference database (Quast et al.\n2013). Mock communities were used to assess the performance of the program as\nwell as sequencing error rates. DADA2 inferred 15, 17, and 17 strains within\nthe mock community (compared to the 20 expected stains present at different\nconcentrations within the staggered community) and 13, 14, and 14 of the\nstrains were exact matches to the expected sequences from the mock community\nreference file. Sequence recovery is slightly lower than expected, but is\ncomparable to normal performance of DADA2 on this staggered mock community\n(Callahan et al. 2016).\n \nThe R packages Phyloseq (McMurdie and Holmes 2013), Vegan (Oksanen et al.\n2017), DESeq2 (Love et al. 2014), and ggplot2 (Wickham 2016) were used for\ndownstream analysis of the microbial community. Sequences were not subsampled,\nbut samples with less than 1000 reads (2 samples) were removed. In addition,\nASVs identifying as chloroplasts were removed.\\u00a0 Sequences representing\nASVs that identified as \\u201cNA\\u201d at the Phylum level were checked using\nthe SINA aligner and classifier (v.1.2.11) (Pruesse et al. 2012) and then\nremoved if not identified as bacteria or archaea at 70% similarity. The\naverage number of reads across all seawater samples used in microbial\ncommunity analyses was 58,398 (\\u00b1 32,184 standard deviation) with a range\nof 11,502 \\u2013 206,689 reads. The average number of reads in coral tissue\nsamples was 38,096 (\\u00b123,854) with a range of 11,538 \\u2013 59,437 reads.\nDNA extraction control communities were initially inspected and then removed\nbecause they fell out as outliers compared to the highly similar seawater\nmicrobial communities. Taxonomic bar plots, metrics of alpha diversity\n(observed richness of ASVs), and boxplots of alpha diversity were made and\ncalculated using Phyloseq. Alpha diversity was also calculated for samples\nafter Prochlorococcus and Synechococcus ASVs were removed in order to\nunderstand how much their dynamics influenced observed richness. Constrained\nanalysis of principal coordinates (CAP) based on Bray \\u2013 Curtis\ndissimilarity was completed (using \\u2018capscale\\u2019 in Vegan) and variance\npartitioning was used to identify which of the measured environmental\nparameters significantly (p<0.01) contributed to shifts in the microbial\ncommunity composition over time. Permutational Multivariate Analysis of\nVariance using distance matrices (PERMANOVA/Adonis) tests identified\ncategorical factors that significantly (p<0.05) contributed to a similarity\nbetween the microbial communities. DESeq2 was used to identify differentially\nabundant ASVs between day and night as well as reef-associated (reef-depth and\ncoral ecosphere) compared to surface microbial communities (using the\n\\u201clocal\\u201d fitType parameter to estimate gene dispersion). Lastly, the\nRhythmicity Analysis Incorporating Non-parametric methods (RAIN)\\u00a0 R\npackage was used to identify ASVs that experienced rhythmic change in relative\nabundance over a period of 24 hours (Thaben and Westermark 2014). This\nanalysis was completed separately for reef-depth and coral ecosphere seawater\nand the input ASV matrix was center log-ratio transformed and detrended\nfollowing previous methods (Hu et al. 2018). Only ASVs with significant\np-values (p<0.05) after adaptive Benjamini-Hochberg correction were reported\nto control for false recovery rates (Benjamini and Hochberg 2000).\n \nStatistical analyses:  \n A Principal Coordinates Analysis (PCA) was completed to summarize changes in\npicoplankton abundances, inorganic nutrient concentrations, and relative light\nand temperature information collected from the HOBO loggers and reduce the\ndimensionality of this data. Separate PCAs were also generated using samples\ncollected during either day or night to observe trends specific to these\ntimes. Kruskal-Wallis rank sums tests were used to test for significant\ndifferences (p<0.05) in alpha diversity between the different sample\ngroupings. Pairwise post-hoc Dunn\\u2019s tests with Bonferonni corrections\nwere used to identify which groups were significantly different from each\nother. These tests were also used to test for significant differences in\npicoplankton cell abundance overtime, between day and night samples, and\nbetween coral ecosphere and reef-depth samples.
attribute NC_GLOBAL awards_0_award_nid String 746195
attribute NC_GLOBAL awards_0_award_number String OCE-1736288
attribute NC_GLOBAL awards_0_data_url String http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1736288 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Daniel Thornhill
attribute NC_GLOBAL awards_0_program_manager_nid String 722161
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String Diel, daily, and spatial variation of coral reef seawater microbial communities, US Virgin Islands, 2017 \n   PI: A. Apprill (WHOI) \n   version date: 2019-08-12
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3  19 Dec 2019
attribute NC_GLOBAL date_created String 2019-08-14T13:23:09Z
attribute NC_GLOBAL date_modified String 2019-08-19T12:17:28Z
attribute NC_GLOBAL defaultDataQuery String &amp;time&lt;now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.775229.1
attribute NC_GLOBAL Easternmost_Easting double -64.70403
attribute NC_GLOBAL geospatial_lat_max double 41.5265
attribute NC_GLOBAL geospatial_lat_min double 18.30204
attribute NC_GLOBAL geospatial_lat_units String degrees_north
attribute NC_GLOBAL geospatial_lon_max double -64.70403
attribute NC_GLOBAL geospatial_lon_min double -70.6731
attribute NC_GLOBAL geospatial_lon_units String degrees_east
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/775229 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String Nutrient Autoanalyzer
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Used to analyze nutrient samples.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 775252
attribute NC_GLOBAL instruments_0_description String Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified.  In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB04/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String Nutrient Autoanalyzer
attribute NC_GLOBAL instruments_0_instrument_nid String 558
attribute NC_GLOBAL instruments_0_supplied_name String A continuous segmented flow-system
attribute NC_GLOBAL instruments_1_acronym String Automated Sequencer
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Used to obtain genetic data.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 775254
attribute NC_GLOBAL instruments_1_description String General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute NC_GLOBAL instruments_1_instrument_name String Automated DNA Sequencer
attribute NC_GLOBAL instruments_1_instrument_nid String 649
attribute NC_GLOBAL instruments_1_supplied_name String Miseq (Illumina, San Diego, CA) sequencer
attribute NC_GLOBAL instruments_2_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Used for measuring cell concentrations. Samples collected for flow cytometry were analyzed using colinear analysis (laser excitation wavelength of 488 nm, UV) on an Altra flow cytometer (Beckman Coulter, Pasadena, CA.).
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 775253
attribute NC_GLOBAL instruments_2_description String Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.\n(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_2_instrument_nid String 660
attribute NC_GLOBAL instruments_3_dataset_instrument_description String Measured temperature and relative light level.
attribute NC_GLOBAL instruments_3_dataset_instrument_nid String 775251
attribute NC_GLOBAL instruments_3_description String Records temperature data over a period of time.
attribute NC_GLOBAL instruments_3_instrument_name String Temperature Logger
attribute NC_GLOBAL instruments_3_instrument_nid String 639396
attribute NC_GLOBAL instruments_3_supplied_name String Light temperature loggers (8K HOBO/PAR loggers; Onset, Wareham, MA)
attribute NC_GLOBAL keywords String accession, ammonia, ammonium, Ammonium_uM, bco, bco-dmo, bio, biological, cells, chemical, chemistry, collection, Collection_Date, Collection_location, Collection_time, colony, concentration, coral, Coral_Colony_or_sand, data, dataset, date, depth, Depth_Feet, dmo, earth, Earth Science > Oceans > Ocean Chemistry > Ammonia, Earth Science > Oceans > Ocean Chemistry > Nitrate, Earth Science > Oceans > Ocean Chemistry > Phosphate, Earth Science > Oceans > Ocean Chemistry > Silicate, erddap, latitude, levels, light, longitude, management, mass, mass_concentration_of_phosphate_in_sea_water, mass_concentration_of_silicate_in_sea_water, mole, mole_concentration_of_ammonium_in_sea_water, mole_concentration_of_nitrate_in_sea_water, mole_concentration_of_nitrite_in_sea_water, n02, ncbi, NCBI_BioProject_accession_number, NCBI_BioSample_accession_number, nh4, nitrate, Nitrate_uM, nitrite, Nitrite_uM, no3, number, ocean, oceanography, oceans, office, phosphate, Phosphate_uM, picoeukaryotes, Picoeukaryotes_cells_mL, po4, preliminary, prochlorococcus, Prochlorococcus_cells_mL, project, relative, Relative_light_levels, sample, Sample_ID, Sample_type, sand, science, sea, seawater, silicate, Silicate_uM, synechococcus, Synechococcus_cells_mL, temperature, Temperature_F, time, type, unpigmented, Unpigmented_cells_cells_mL, water
attribute NC_GLOBAL keywords_vocabulary String GCMD Science Keywords
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/775229/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/775229 (external link)
attribute NC_GLOBAL Northernmost_Northing double 41.5265
attribute NC_GLOBAL param_mapping String {'775229': {'Depth_Feet': 'master - depth', 'lat': 'master - latitude', 'lon': 'master - longitude'}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/775229/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_0_affiliation_acronym String WHOI
attribute NC_GLOBAL people_0_person_name String Amy Apprill
attribute NC_GLOBAL people_0_person_nid String 553489
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI
attribute NC_GLOBAL people_1_person_name String Laura Weber
attribute NC_GLOBAL people_1_person_nid String 662109
attribute NC_GLOBAL people_1_role String Contact
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL people_2_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_2_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_2_person_name String Nancy Copley
attribute NC_GLOBAL people_2_person_nid String 50396
attribute NC_GLOBAL people_2_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_2_role_type String related
attribute NC_GLOBAL project String Coral Exometabolomes
attribute NC_GLOBAL projects_0_acronym String Coral Exometabolomes
attribute NC_GLOBAL projects_0_description String NSF abstract:\nCoral reefs are some of the most diverse and productive ecosystems in the ocean. Globally, reefs have declined in stony (reef-building) coral abundance due to environmental variations, and in the Caribbean this decline has coincided with an increase in octocoral (soft coral) abundance. This phase shift occurring on Caribbean reefs may be impacting the interactions between the sea floor and water column and particularly between corals and picoplankton. Picoplankton are the microorganisms in the water column that utilize organic matter released from corals to support their growth. These coral-picoplankton interactions are relatively unstudied, but could have major implications for reef ecology and coral health. This project will take place in the U.S. territory of the Virgin Islands (USVI) and will produce the first detailed knowledge about the chemical diversity and composition of organic matter released from diverse stony coral and octocoral species. This project will advance our understanding of coral reef microbial ecology by allowing us to understand how different coral metabolites impact picoplankton growth and dynamics over time. The results from this project will be made publically accessible in a freely available online magazine, and USVI minority middle and high school students will be exposed to a lesson about chemical-biological interactions on coral reefs through established summer camps. This project will also contribute to the training of USVI minority undergraduates as well as a graduate student.\nCoral exometabolomes, which are the sum of metabolic products of the coral together with its microbiome, are thought to structure picoplankton communities in a species-specific manner. However, a detailed understanding of coral exometabolomes, and their influences on reef picoplankton, has not yet been obtained. This project will utilize controlled aquaria-based experiments with stony corals and octocorals, foundational species of Caribbean reef ecosystems, to examine how the exometabolomes of diverse coral species differentially influence the reef picoplankton community. Specifically, this project will capitalize on recent developments in mass spectrometry-based metabolomics to define the signature exometabolomes of ecologically important and diverse stony corals and octocorals. Secondly, this project will determine how the exometabolomes of these corals vary with factors linked to coral taxonomy as well as the coral-associated microbiome (Symbiodinium algae, bacteria and archaea). With this new understanding of coral exometabolomes, the project will then apply a stable isotope probe labeling approach to the coral exometabolome and will examine if and how (through changes in growth and activity) the seawater picoplankton community incorporates coral exometabolomes from different coral species over time. This project will advance our ability to evaluate the role that coral exometabolomes play in contributing to benthic-picoplankton interactions on changing Caribbean reefs.
attribute NC_GLOBAL projects_0_end_date String 2020-09
attribute NC_GLOBAL projects_0_geolocation String U.S. Virgin Islands
attribute NC_GLOBAL projects_0_name String Signature exometabolomes of Caribbean corals and influences on reef picoplankton
attribute NC_GLOBAL projects_0_project_nid String 746196
attribute NC_GLOBAL projects_0_start_date String 2017-10
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL Southernmost_Northing double 18.30204
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL subsetVariables String NCBI_BioProject_accession_number
attribute NC_GLOBAL summary String Bacterial and archaeal diversity and composition, microbial cell abundances, inorganic nutrient concentrations, and physicochemical conditions were determined and measured in coral reef seawater over a three-day, diel time series on one reef in St. John, U.S. Virgin Islands.
attribute NC_GLOBAL title String Diel, daily, and spatial variation of coral reef seawater microbial communities from US Virgin Islands, 2017
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL Westernmost_Easting double -70.6731
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable Sample_ID String
attribute Sample_ID bcodmo_name String sample
attribute Sample_ID description String sample identifier
attribute Sample_ID long_name String Sample ID
attribute Sample_ID nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Sample_ID units String unitless
variable NCBI_BioProject_accession_number String
attribute NCBI_BioProject_accession_number bcodmo_name String accession number
attribute NCBI_BioProject_accession_number description String NCBI BioProject accession number
attribute NCBI_BioProject_accession_number long_name String NCBI Bio Project Accession Number
attribute NCBI_BioProject_accession_number units String unitless
variable NCBI_BioSample_accession_number String
attribute NCBI_BioSample_accession_number bcodmo_name String accession number
attribute NCBI_BioSample_accession_number description String NCBI BioSample accession number
attribute NCBI_BioSample_accession_number long_name String NCBI Bio Sample Accession Number
attribute NCBI_BioSample_accession_number units String unitless
variable Sample_type String
attribute Sample_type bcodmo_name String sample_type
attribute Sample_type description String Sample type
attribute Sample_type long_name String Sample Type
attribute Sample_type units String unitless
variable Coral_Colony_or_sand String
attribute Coral_Colony_or_sand bcodmo_name String sample
attribute Coral_Colony_or_sand description String Coral Colony or sand identifier
attribute Coral_Colony_or_sand long_name String Coral Colony Or Sand
attribute Coral_Colony_or_sand nerc_identifier String https://vocab.nerc.ac.uk/collection/P02/current/ACYC/ (external link)
attribute Coral_Colony_or_sand units String unitless
variable Collection_time String
attribute Collection_time bcodmo_name String time
attribute Collection_time description String Collection time (day or night) and day relative to the start of the study
attribute Collection_time long_name String Collection Time
attribute Collection_time nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AHMSAA01/ (external link)
attribute Collection_time units String unitless
variable Collection_Date String
attribute Collection_Date bcodmo_name String date
attribute Collection_Date description String Collection Date; fomatted as Mon-yyyy
attribute Collection_Date long_name String Collection Date
attribute Collection_Date nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/ADATAA01/ (external link)
attribute Collection_Date units String unitless
variable Collection_location String
attribute Collection_location bcodmo_name String site
attribute Collection_location description String Collection location
attribute Collection_location long_name String Collection Location
attribute Collection_location units String unitless
variable latitude double
attribute latitude _CoordinateAxisType String Lat
attribute latitude _FillValue double NaN
attribute latitude actual_range double 18.30204, 41.5265
attribute latitude axis String Y
attribute latitude bcodmo_name String latitude
attribute latitude colorBarMaximum double 90.0
attribute latitude colorBarMinimum double -90.0
attribute latitude description String latitude; north is positive
attribute latitude ioos_category String Location
attribute latitude long_name String Latitude
attribute latitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LATX/ (external link)
attribute latitude standard_name String latitude
attribute latitude units String degrees_north
variable longitude double
attribute longitude _CoordinateAxisType String Lon
attribute longitude _FillValue double NaN
attribute longitude actual_range double -70.6731, -64.70403
attribute longitude axis String X
attribute longitude bcodmo_name String longitude
attribute longitude colorBarMaximum double 180.0
attribute longitude colorBarMinimum double -180.0
attribute longitude description String longitude; east is postive
attribute longitude ioos_category String Location
attribute longitude long_name String Longitude
attribute longitude nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/LONX/ (external link)
attribute longitude standard_name String longitude
attribute longitude units String degrees_east
variable Prochlorococcus_cells_mL int
attribute Prochlorococcus_cells_mL _FillValue int 2147483647
attribute Prochlorococcus_cells_mL actual_range int 11250, 47419
attribute Prochlorococcus_cells_mL bcodmo_name String cell_concentration
attribute Prochlorococcus_cells_mL description String concentration of Prochlorococcus
attribute Prochlorococcus_cells_mL long_name String Prochlorococcus Cells M L
attribute Prochlorococcus_cells_mL units String cell/milliliter
variable Synechococcus_cells_mL int
attribute Synechococcus_cells_mL _FillValue int 2147483647
attribute Synechococcus_cells_mL actual_range int 27721, 79875
attribute Synechococcus_cells_mL bcodmo_name String cell_concentration
attribute Synechococcus_cells_mL description String concentration of Synechococcus
attribute Synechococcus_cells_mL long_name String Synechococcus Cells M L
attribute Synechococcus_cells_mL units String cell/milliliter
variable Picoeukaryotes_cells_mL short
attribute Picoeukaryotes_cells_mL _FillValue short 32767
attribute Picoeukaryotes_cells_mL actual_range short 440, 4331
attribute Picoeukaryotes_cells_mL bcodmo_name String cell_concentration
attribute Picoeukaryotes_cells_mL description String concentration of Picoeukaryotes
attribute Picoeukaryotes_cells_mL long_name String Picoeukaryotes Cells M L
attribute Picoeukaryotes_cells_mL units String cell/milliliter
variable Unpigmented_cells_cells_mL int
attribute Unpigmented_cells_cells_mL _FillValue int 2147483647
attribute Unpigmented_cells_cells_mL actual_range int 397448, 802850
attribute Unpigmented_cells_cells_mL bcodmo_name String cell_concentration
attribute Unpigmented_cells_cells_mL description String concentration of unpigmented cells
attribute Unpigmented_cells_cells_mL long_name String Unpigmented Cells Cells M L
attribute Unpigmented_cells_cells_mL units String cell/milliliter
variable Phosphate_uM float
attribute Phosphate_uM _FillValue float NaN
attribute Phosphate_uM actual_range float 0.13, 1.465
attribute Phosphate_uM bcodmo_name String PO4
attribute Phosphate_uM description String concentration of Phosphate_uM
attribute Phosphate_uM long_name String Mass Concentration Of Phosphate In Sea Water
attribute Phosphate_uM units String micromoles
variable Silicate_uM float
attribute Silicate_uM _FillValue float NaN
attribute Silicate_uM actual_range float 0.3, 13.7
attribute Silicate_uM bcodmo_name String SiOH_4
attribute Silicate_uM description String concentration of Silicate_uM
attribute Silicate_uM long_name String Mass Concentration Of Silicate In Sea Water
attribute Silicate_uM units String micromoles
variable Nitrate_uM float
attribute Nitrate_uM _FillValue float NaN
attribute Nitrate_uM actual_range float -0.001, 0.4004
attribute Nitrate_uM bcodmo_name String NO3
attribute Nitrate_uM colorBarMaximum double 50.0
attribute Nitrate_uM colorBarMinimum double 0.0
attribute Nitrate_uM description String concentration of Nitrate_uM
attribute Nitrate_uM long_name String Mole Concentration Of Nitrate In Sea Water
attribute Nitrate_uM nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/NTRAIGGS/ (external link)
attribute Nitrate_uM units String micromoles
variable Nitrite_uM float
attribute Nitrite_uM _FillValue float NaN
attribute Nitrite_uM actual_range float -0.02, 0.08
attribute Nitrite_uM bcodmo_name String NO2
attribute Nitrite_uM colorBarMaximum double 1.0
attribute Nitrite_uM colorBarMinimum double 0.0
attribute Nitrite_uM description String concentration of Nitrite_uM
attribute Nitrite_uM long_name String Mole Concentration Of Nitrite In Sea Water
attribute Nitrite_uM nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/NTRIAAZX/ (external link)
attribute Nitrite_uM units String micromoles
variable Ammonium_uM float
attribute Ammonium_uM _FillValue float NaN
attribute Ammonium_uM actual_range float 0.13, 2.23
attribute Ammonium_uM bcodmo_name String Ammonium
attribute Ammonium_uM colorBarMaximum double 5.0
attribute Ammonium_uM colorBarMinimum double 0.0
attribute Ammonium_uM description String concentration of Ammonium_uM
attribute Ammonium_uM long_name String Mole Concentration Of Ammonium In Sea Water
attribute Ammonium_uM nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/AMONAAZX/ (external link)
attribute Ammonium_uM units String micromoles
variable Temperature_F float
attribute Temperature_F _FillValue float NaN
attribute Temperature_F actual_range float 85.014, 86.641
attribute Temperature_F bcodmo_name String temperature
attribute Temperature_F description String Temperature
attribute Temperature_F long_name String Temperature F
attribute Temperature_F nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/TEMPP901/ (external link)
attribute Temperature_F units String degrees Fahrenheit
variable Depth_Feet double
attribute Depth_Feet _FillValue double NaN
attribute Depth_Feet actual_range double 23.0, 28.0
attribute Depth_Feet bcodmo_name String depth
attribute Depth_Feet colorBarMaximum double 8000.0
attribute Depth_Feet colorBarMinimum double -8000.0
attribute Depth_Feet colorBarPalette String TopographyDepth
attribute Depth_Feet description String Depth
attribute Depth_Feet long_name String Depth
attribute Depth_Feet nerc_identifier String https://vocab.nerc.ac.uk/collection/P09/current/DEPH/ (external link)
attribute Depth_Feet standard_name String depth
attribute Depth_Feet units String feet
variable Relative_light_levels short
attribute Relative_light_levels _FillValue short 32767
attribute Relative_light_levels actual_range short 0, 864
attribute Relative_light_levels bcodmo_name String unknown
attribute Relative_light_levels description String Relative_light_levels
attribute Relative_light_levels long_name String Relative Light Levels
attribute Relative_light_levels units String lumens/foot^2

 
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