cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26008/1912/bco-dmo.897359.1
title: Dissolved organic phosphorus (DOP) hydrolysis rates from Ruegeria pomeroyi laboratory cultures

description: Dissolved organic phosphorus (DOP) hydrolysis rates from marine bacterium Ruegeria pomeroyi laboratory cultures.

These data were collected as part of a study of &quot;Dissolved organic phosphorus utilization by the marine bacterium Ruegeria pomeroyi DSS-3 reveals chain length-dependent polyphosphate degradation&quot; (Adams et al., 2022).

Study abstract:
Dissolved organic phosphorus (DOP) is a critical nutritional resource for marine microbial communities. However, the relative bioavailability of different types of DOP, such as phosphomonoesters (P-O-C) and phosphoanhydrides (P-O-P), is poorly understood. Here we assess the utilization of these P sources by a representative bacterial copiotroph, Ruegeria pomeroyi DSS-3. All DOP sources supported equivalent growth by R. pomeroyi, and all DOP hydrolysis rates were upregulated under phosphorus depletion (-P). A long-chain polyphosphate (45polyP) showed the lowest hydrolysis rate of all DOP substrates tested, including tripolyphosphate (3polyP). Yet the upregulation of 45polyP hydrolysis under -P was greater than any other substrate analyzed. Proteomics revealed three common P acquisition enzymes potentially involved in polyphosphate utilization, including two alkaline phosphatases, PhoD and PhoX, and one 5'-nucleotidase (5’-NT). Results from DOP substrate competition experiments show that these enzymes likely have broad substrate specificities, including chain length-dependent reactivity toward polyphosphate. These results confirm that DOP, including polyP, are bioavailable nutritional P sources for R. pomeroyi, and possibly other marine heterotrophic bacteria. Furthermore, the chain-length dependent mechanisms, rates and regulation of polyP hydrolysis suggest that these processes may influence the composition of DOP and the overall recycling of nutrients within marine dissolved organic matter.
DOI: 10.26008/1912/bco-dmo.897371.1
title: Optical density and cell counts from flow cytometry of Ruegeria pomeroyi laboratory cultures

description: Optical density (OD) and cell counts from flow cytometry (FCM) of marine bacterium Ruegeria pomeroyi laboratory cultures.

These data were collected as part of a study of &quot;Dissolved organic phosphorus utilization by the marine bacterium Ruegeria pomeroyi DSS-3 reveals chain length-dependent polyphosphate degradation&quot; (Adams et al., 2022).

Study abstract:
Dissolved organic phosphorus (DOP) is a critical nutritional resource for marine microbial communities. However, the relative bioavailability of different types of DOP, such as phosphomonoesters (P-O-C) and phosphoanhydrides (P-O-P), is poorly understood. Here we assess the utilization of these P sources by a representative bacterial copiotroph, Ruegeria pomeroyi DSS-3. All DOP sources supported equivalent growth by R. pomeroyi, and all DOP hydrolysis rates were upregulated under phosphorus depletion (-P). A long-chain polyphosphate (45polyP) showed the lowest hydrolysis rate of all DOP substrates tested, including tripolyphosphate (3polyP). Yet the upregulation of 45polyP hydrolysis under -P was greater than any other substrate analyzed. Proteomics revealed three common P acquisition enzymes potentially involved in polyphosphate utilization, including two alkaline phosphatases, PhoD and PhoX, and one 5'-nucleotidase (5’-NT). Results from DOP substrate competition experiments show that these enzymes likely have broad substrate specificities, including chain length-dependent reactivity toward polyphosphate. These results confirm that DOP, including polyP, are bioavailable nutritional P sources for R. pomeroyi, and possibly other marine heterotrophic bacteria. Furthermore, the chain-length dependent mechanisms, rates and regulation of polyP hydrolysis suggest that these processes may influence the composition of DOP and the overall recycling of nutrients within marine dissolved organic matter.
DOI: 10.26008/1912/bco-dmo.896706.1
title: Benthic fluxes of solutes measured by in-situ benthic flux chambers along two depth transects in the Santa Barbara Basin during November 219

description: This dataset includes benthic fluxes of solutes (ammonium, nitrate, phosphate, and iron) measured by in-situ benthic flux chambers along two depth transects in the Santa Barbara Basin during the November 2019 R/V Atlantis cruise AT42-19.
DOI: 10.26008/1912/bco-dmo.896754.1
title: DOM analysis by liquid chromatography 21T fourier transform ion cyclotron resonance mass spectrometry with filtered seawater collected during a Bermuda Atlantic Time Series cruise AE1912 aboard R/V Atlantic Explorer in June of 2019

description: This data set includes raw files obtained from the analysis of solid phase extracted marine dissolved organic matter (DOM) from the North Atlantic Subtropical Gyre by liquid chromatography coupled with ultra-high resolution mass spectrometry. Filtered seawater samples were collected in June 2019 during a Bermuda Atlantic Time Series cruise. DOM was isolated by solid phase extraction and analyzed by high pressure liquid chromatography with 21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. The results provide insight into the molecular composition of DOM throughout the upper 1000m.
DOI: 10.26008/1912/bco-dmo.870956.1
title: Model output of the hydrographic properties, velocity, and diagnostic terms from a West Antarctic Peninsula model with a simulation covering 2006-2012

description: Model output of the hydrographic properties, velocity, and diagnostic terms from a West Antarctic Peninsula model.  These data were published in Wang et al. (2022).
DOI: 10.26008/1912/bco-dmo.892348.1
title: Activities of 210Po and 210Pb on particles in two size classes obtained by in situ pumping on Leg 1 (Seattle, WA to Hilo, HI) of the US GEOTRACES Pacific Meridional Transect (PMT) cruise (GP15, RR1814) on R/V Roger Revelle from September to October 2018

description: This project is part of the international GEOTRACES program, which was created to allow a comprehensive, coordinated study of trace elements and isotopes (TEIs) in the oceans. This project uses the radionuclide pair Lead-210 (210Pb) and its grand-daughter Polonium-210 (210Po) to provide important biogeochemical rate information pertinent to the TEIs that were measured during the US GEOTRACES Meridional Transect in the Pacific from Alaska to Tahiti in late 2018. 

Many processes in the ocean cannot be directly observed and, as such, tracers such as 210Po and 210Pb can be used to provide important constraints on their rates and pathways. 210Po (half-life = 138 days) and 210Pb (half-life = 22.3 years) decay on timescales that are useful to study 1) atmospheric deposition of trace elements, 2) scavenging of particle-reactive trace elements, 3) export of particulate organic carbon (POC) from the photic zone, and 4) the fate of hydrothermal plumes dispersed from the mid-ocean ridge system. 

Data reported here are activities of 210Po and 210Pb on particles in two size classes obtained by in situ pumping. Sampling was conducted in 2018 at various depths through the water column at eleven stations along the GEOTRACES Pacific Meridional Transect (GP15). Particulate samples were collected by Phoebe Lam's group using McLane in-situ pumps (Lam et al., 2015). Two particle sizes were collected by pumping: a large particle fraction collected on a 142-millimeter (mm) 51-micrometer (μm) polyester mesh prefilters (Sefar 07-51/33) and a small particle fraction collected on paired 0.8-μm polyethersulfone Pall Supor 800 membrane filters. The filters were dried on board in a laminar flow hood, split, and placed in a polyethylene bag. Aliquots sent to Stony brook comprised 28-280 liters (L) (average ~100L) filtered for the small particle fraction and 60-330L (average ~250L) for the large particle fraction.
DOI: 10.26008/1912/bco-dmo.896181.1
title: Field physiochemical parameters including nutrient concentrations and nitrogen specific uptake rates from samples collected between 2017 and 2019 from the Arctic Ocean, California Coastal Current, and a Chesapeake Bay estuary

description: Nitrogen is an important macronutrient for biological growth and while research has been traditionally focused on the dissolved inorganic nitrogen pool, dissolved organic nitrogen (DON) is an important, but historically less understood source of nitrogen. This work focused on creatine, a DON metabolite recognized in human nutrition that has not been heavily studied in aquatic systems. Our research investigates the extent and rate at which aquatic organisms may uptake (use) creatine and compares those rates to other nitrogen compounds including ammonium, nitrate, urea, and amino acids. Samples were collected between 2017 and 2019 and cover three North American regions. These include the polar Arctic Ocean, the California Coastal Current (Baja), and a Chesapeake Bay estuary (York River). Included in this dataset are ambient physiochemical parameters for these systems, along with measured specific uptake rates.
DOI: 10.26008/1912/bco-dmo.889551.1
title: Carbon content and radioisotope data from sampling conducted at the Compass Station in Bedford Basin, Nova Scotia, Canada from February to August 2019

description: These data include carbon content and radioisotope (234Th-excess) data collected at the Compass Station in Bedford Basin, Nova Scotia, Canada at four time periods from February to August 2019. A four-core multicorer was used to obtain the cores and samples were analyzed via beta counting (234Th) and CHN analysis (carbon content). These data were collected in conjunction with water column samples that were measured for total 234Th, particulate 234Th, and particulate carbon to assess carbon export and the carbon budget of Bedford Basin.
DOI: 10.26008/1912/bco-dmo.892360.1
title: Activities of 210Po and 210Pb on particles in two size classes obtained by in situ pumping on Leg 2 (Hilo, HI to Papeete, French Polynesia) of the US GEOTRACES Pacific Meridional Transect (PMT) cruise (GP15, RR1815) on R/V Roger Revelle from Oct-Nov 2018

description: This project is part of the international GEOTRACES program, which was created to allow a comprehensive, coordinated study of trace elements and isotopes (TEIs) in the oceans. This project uses the radionuclide pair Lead-210 (210Pb) and its grand-daughter Polonium-210 (210Po) to provide important biogeochemical rate information pertinent to the TEIs that were measured during the US GEOTRACES Meridional Transect in the Pacific from Alaska to Tahiti in late 2018. 

Many processes in the ocean cannot be directly observed and, as such, tracers such as 210Po and 210Pb can be used to provide important constraints on their rates and pathways. 210Po (half-life = 138 days) and 210Pb (half-life = 22.3 years) decay on timescales that are useful to study 1) atmospheric deposition of trace elements, 2) scavenging of particle-reactive trace elements, 3) export of particulate organic carbon (POC) from the photic zone, and 4) the fate of hydrothermal plumes dispersed from the mid-ocean ridge system. 

Data reported here are activities of 210Po and 210Pb on particles in two size classes obtained by in situ pumping. Sampling was conducted in 2018 at various depths through the water column at eleven stations along the GEOTRACES Pacific Meridional Transect (GP15). Particulate samples were collected by Phoebe Lam's group using McLane in-situ pumps (Lam et al., 2015). Two particle sizes were collected by pumping: a large particle fraction collected on a 142-millimeter (mm) 51-micrometer (μm) polyester mesh prefilters (Sefar 07-51/33) and a small particle fraction collected on paired 0.8-μm polyethersulfone Pall Supor 800 membrane filters. The filters were dried on board in a laminar flow hood, split, and placed in a polyethylene bag. Aliquots sent to Stony brook comprised 28-280 liters (L) (average ~100L) filtered for the small particle fraction and 60-330L (average ~250L) for the large particle fraction.
DOI: 10.26008/1912/bco-dmo.882086.1
title: Microsatellite and chloroplast 23S genotypes of Breviolum sp. symbionts within Orbicella faveolata adults from reefs in the Florida Keys from 2009-2011 (SymBioSys project)

description: Microsatellite genotypes and chloroplast 23S genotypes (based on length heteroplasmy in domain V of chloroplast large subunit (cp23S) ribosomal DNA sequences) of Breviolum sp. symbionts within Orbicella faveolata adults in the Florida Keys.
DOI: 10.26008/1912/bco-dmo.889642.1
title: Seawater radioisotope (234Th) and carbon from sampling conducted at the Compass Station in Bedford Basin, Nova Scotia, Canada from April to August 2019

description: These data include seawater radioisotope (234Th) and carbon data collected at the Compass Station in Bedford Basin, Nova Scotia, Canada at three time periods from April to August 2019. Niskins (2L to 10L) were used to obtain the water samples. Four liters of water were used for total 234Th and ~42 L were used to filter size-fractionated particulate 234Th and carbon. Two in-line filters were used: &gt;51 µm and ~ 1 µm. Filters were analyzed via non-destructive beta counting (234Th) and then for carbon content. These data were collected in conjunction with sediment coring samples that were measured for 234Th and carbon content to assess carbon export and the carbon budget of Bedford Basin.
DOI: 10.26008/1912/bco-dmo.882097.1
title: Breviolum symbiont CP23S genotypes in Orbicella faveolata recruits from 2009-2011 (SymBioSys project)

description: Chloroplast 23S genotypes (based on length heteroplasmy in domain V of chloroplast large subunit (cp23S) ribosomal DNA sequences) of Breviolum sp. symbionts within Orbicella faveolata recruits that were outplanted to reefs in the Florida Keys.
DOI: 10.26008/1912/bco-dmo.887265.1
title: Microsatellite genotypes of Breviolum sp. symbionts within Orbicella faveolata recruits outplanted to reefs in the Florida Keys from 2009-2011 (SymBioSys project)

description: Microsatellite genotypes of Breviolum sp. symbionts within Orbicella faveolata recruits reared in a field-based lab and then outplanted to reefs in the Florida Keys.
DOI: 10.26008/1912/bco-dmo.893256.1
title: Ruegeria pomeroyi RB-TnSeq Transponson Mutant Library Screen Experimental Data February 2021 (C-CoMP Marine Bacterial Transporters project)

description: A barcoded transposon mutant library (RB-TnSeq) of Ruegeria pomeroyi DSS-3 was screened on 23 substrates, each as a sole carbon source. In February of 2021 the RB-TnSeq library was grown in the laboratory in minimal medium with a substrate of interest, cultures were sequentially transfered four times to increase selection. Mutants with phenotypes that decreased fitness on the substrate of interest grow at a lower rate than mutants with no loss of fitness. Sequencing the barcodes of mutants after the screen shows which mutants are enriched or depleted on each substrate, indicating the fitness advantage provided by each gene when grown on each substrate. This can indicate genes that are involved in the uptake and metabolism of each substrate.
DOI: 10.26008/1912/bco-dmo.892279.1
title: Pulse Amplitude Modulation (PAM) fluorometer measurements from Porites astreoides colonies in St. John, US Virgin Islands from July to August of 2019

description: These data represent the raw Diving Pulse Amplitude Modulation (PAM) fluorometer measurements from Porites astreoides colonies classified as inside or outside of octocoral canopies. These data were used to test for the potential effect of light regimes created by octocoral canopies on the photophysiology of autotrophic taxa within the understories of octocoral forests. Additionally, these datasets contain information on the octocoral community surrounding each P. astreoides colony. Data was collected between July and August of 2019 at ~ 7.0 ± 0.5-m depth at three sites (White Point, Tektite, Cabritte Horn) in Lameshur Bay St. John, U.S. Virgin Islands.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).
DOI: 10.26008/1912/bco-dmo.894179.1
title: High Resolution Growth Screen of Ruegeria pomeroyi Transporter Mutants Data September 2021 - June 2022 (C-CoMP Marine Bacterial Transporters project)

description: High resolution growth screens were used to confirm the phenotype of Ruegeria pomeroyi DSS-3 transporter knockout mutants. Mutants which had demonstrated growth defects on a given substrate as sole carbon source during an initial growth screen were selected and used here. Each mutant was grown on the substrate(s) of interest along side a wildtype analog (pooled-TnSeq library). Growth curves were generated by reading the optical density at 600 nm hourly. The annotations of a transporter's cognate substrate was confirmed when the mutant of said transporter demonstrated significant defect relative to the wildtype analog on the substrate of interest.
DOI: 10.26008/1912/bco-dmo.892265.1
title: Octocoral height, density, and genera from in situ observations within octocoral forests in Lameshur Bay St. John, U.S. Virgin Islands from July 2019 to Jan 2020

description: These data represent the individual octocoral genera, height, and density that compose octocoral forests in in Lameshur Bay St. John U.S. Virgin Islands.  These data were used in conjunction with invertebrate abundance data to test for an association between octocoral forest parameters and benthic invertebrate community composition. Surveys of octocoral forests were conducted on SCUBA during July – August of 2019 and in January of 2020 quadrats (1 m2) placed at ≤ 13-m depth.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).
DOI: 10.26008/1912/bco-dmo.892286.1
title: Steady state photosynthesis (photosynthetic induction time) from Porites astreoides colonies in St. John, US Virgin Islands from July to August of 2019

description: These datasets represent the time to steady state photosynthesis (photosynthetic induction time) of Porites astreoides colonies classified as inside or outside of octocoral canopies. These data were used to test for the potential effect of light regimes created by octocoral canopies on the photophysiology of autotrophic taxa within the understories of octocoral forests. Additionally, these datasets contain information on the octocoral community surrounding each P. astreoides colony. Data was collected between July and August of 2019 at ~ 7.0 ± 0.5-m depth at three sites (White Point, Tektite, Cabritte Horn) in Lameshur Bay St. John, U.S. Virgin Islands.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).
DOI: 10.26008/1912/bco-dmo.892293.1
title: Octocoral canopy metrics (mean height, density, and closure) in St. John, US Virgin Islands in March of 2019

description: These data represent the octocoral canopy metrics (mean height, density, and closure) in quadrats (1 m2) where light regimes were quantified. Surveys took place at the Yawzi Point (~8-m depth) and East Cabritte (~9-m depth) sites in St. John, U.S. Virgin Islands during March of 2019.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).
DOI: 10.26008/1912/bco-dmo.892272.1
title: Light intensity (lux) of downwelling light upon the benthos along differing conditions of octocoral canopy formation in Lameshur Bay St. John, U.S. Virgin Islands in March of 2019

description: These data represent the light intensity (lux) of downwelling light upon the benthos along differing conditions of octocoral canopy formation. Measurements were recorded every second from 05:00:00 to 23:05:21 (Local Time, Atlantic Standard Time, GMT-04:00) on March 12th, 2019 using HOBO light loggers (model UA-0002-64). Loggers were placed at ~8-m depth at Yawzi point, in Lameshur Bay, St. John U.S. Virgin Islands. These data were used to evaluate the potential creation of differential light regimes between sparse and dense octocoral canopies consistent with sunflecking.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).
DOI: 10.26008/1912/bco-dmo.892300.1
title: Light intensity (lux) of downwelling light upon the benthos along differing conditions of octocoral canopy formation in East Cabritte, in Grootpan Bay, St. John U.S. Virgin Islands in March of 2019

description: These data represent the light intensity (lux) of downwelling light upon the benthos along differing conditions of octocoral canopy formation. Measurements were recorded every second from 05:00:00 to 15:38:00 (Local Time, Atlantic Standard Time, GMT-04:00) on March 10th, 2019 using HOBO light loggers (model UA-0002-64). Loggers were placed at ~9-m depth at East Cabritte, in Grootpan Bay, St. John U.S. Virgin Islands. These data were used to evaluate the potential creation of differential light regimes between sparse and dense octocoral canopies consistent with sunflecking.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).
DOI: 10.26008/1912/bco-dmo.892248.1
title: Benthic invertebrate abundances associated with octocoral forests in St. John, US Virgin Islands from July 2019 to Jan 2020

description: These data represent the benthic invertebrates counted in association with various octocoral canopies as well as the composition of individual octocorals and the physical parameters (mean height, mean closure, and density) of octocoral canopies. 

These data were used to test for the association of benthic invertebrate communities across a gradient of octocoral forest formation. Arborescent octocorals were excluded from invertebrate counts used to test for community association. Benthic surveys of invertebrates and octocoral forests were conducted on SCUBA during July – August of 2019 and in January of 2020 using the same quadrats (1 m2) placed at ≤ 13-m depth.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).
DOI: 10.26008/1912/bco-dmo.892308.1
title: Simultaneous light intensity measurements from a HOBO light intensity logger and a cosine-corrected PAR sensor in Lameshur Bay, St. John, U.S. Virgin Islands in January of 2021

description: These data represent simultaneous measurements taken by a HOBO light intensity logger (model UA-0002-64) measuring in lux and a cosine-corrected PAR sensor (LI-192, Li-Cor Biosciences) fitted by the manufacturer into a logger (miniPAR, Precision Measurement Engineering) measuring PAR in µmol photon m-2 s-1. This was done at the Tektite site at 9 m depth in Lameshur Bay, St. John, U.S. Virgin Islands during January of 2021. This was done to cross-calibrate illuminance data (lux) from the HOBO logger to PAR (µmol photon m-2 s-1) (after Long et al. 2012) for assistance in the ecological interpretation of illuminance data.

These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).