cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.26008/1912/bco-dmo.883227.1
title: Pooled sequencing data of field-collected Eurytemora affinis copepods from nine locations in North America collected October 2012 to March 2014

description: This dataset consists of pooled whole-genome sequencing data (Pool-seq) of Eurytemora affinis complex copepods collected from nine locations across North America.  Each sample consists of 100 pooled individuals with an approximate 1:1 sex ratio, sequenced using the Nextera DNA library preparation kit and Illumina HiSeq platform. Population sampling targeted nine wild populations of the E. affinis complex from two genetically distinct lineages (the Gulf and Atlantic clades) including both native saline and invaded freshwater locations. The data were generated to investigate evolutionary genomic factors underlying successful invasion of freshwater habitats and were collected by Drs. Martin Bontrager, David B. Stern, and Carol E. Lee of the University of Wisconsin-Madison.
DOI: 10.26008/1912/bco-dmo.883412.1
title: O2 microsensor profiling conducted alongside the destructive sampling of Chesapeake Bay sediments during incubation experiments at Horn Point Lab

description: These data were collected as part of a sediment incubation experiment, to investigate potential interactions between estuarine cable bacteria and their associated microbial community. Sediments were collected from the main channel of Chesapeake Bay at a mesohaline station that experiences seasonal oxygen depletion. The upper 10 centimeters (cm) of sediment was homogenized under anaerobic conditions, packed into polycarbonate core liners, and incubated in a dark climate-controlled room in aerated aquaria with artificial seawater (S=15.5; T=16 degrees Celsius). In a sub-set of core tubes, a 0.2 micron polycarbonate filter was held embedded at 0.5 cm depth, to block the downward growth of cable bacteria while allowing for porewater diffusion. The sediments (with and without embedded filters) were destructively sampled on 6 dates over 46 days, at which time nucleic acids, samples for microscopy, and samples for porewater geochemistry were collected. Microsensor profiling (oxygen (O2), pH, hydrogen sulfide (H2S)) was conducted alongside the destructive sampling. Associated nucleic acid data are available through NCBI Sequence Read Archive, under Bioproject PRJNA833464. Sediment porewaters were handled anaerobically, and were extracted by centrifugation followed by filtration (0.2 micron in-line filters). Geochemical data include porewater anions (sulfate and chloride) measured by ion chromatography, and ammonium and ferrous iron concentrations measured by standard colorimetric methods. Microscopy data include both counts of cable bacteria measured with FISH oligoprobe DSB706, and total single cell bacteria. The dataset was generated by Pinky Liau under the supervision of Dr. Sairah Malkin, Horn Point Laboratory, U. Maryland Center for Environmental Sciences.
DOI: 10.26008/1912/bco-dmo.883488.1
title: pH microsensor profiling conducted alongside the destructive sampling of Chesapeake Bay sediments during incubation experiments at Horn Point Lab

description: These data were collected as part of a sediment incubation experiment, to investigate potential interactions between estuarine cable bacteria and their associated microbial community. Sediments were collected from the main channel of Chesapeake Bay at a mesohaline station that experiences seasonal oxygen depletion. The upper 10 centimeters (cm) of sediment was homogenized under anaerobic conditions, packed into polycarbonate core liners, and incubated in a dark climate-controlled room in aerated aquaria with artificial seawater (S=15.5; T=16 degrees Celsius). In a sub-set of core tubes, a 0.2 micron polycarbonate filter was held embedded at 0.5 cm depth, to block the downward growth of cable bacteria while allowing for porewater diffusion. The sediments (with and without embedded filters) were destructively sampled on 6 dates over 46 days, at which time nucleic acids, samples for microscopy, and samples for porewater geochemistry were collected. Microsensor profiling (oxygen (O2), pH, hydrogen sulfide (H2S)) was conducted alongside the destructive sampling. Associated nucleic acid data are available through NCBI Sequence Read Archive, under Bioproject PRJNA833464. Sediment porewaters were handled anaerobically, and were extracted by centrifugation followed by filtration (0.2 micron in-line filters). Geochemical data include porewater anions (sulfate and chloride) measured by ion chromatography, and ammonium and ferrous iron concentrations measured by standard colorimetric methods. Microscopy data include both counts of cable bacteria measured with FISH oligoprobe DSB706, and total single cell bacteria. The dataset was generated by Pinky Liau under the supervision of Dr. Sairah Malkin, Horn Point Laboratory, U. Maryland Center for Environmental Sciences.
DOI: 10.26008/1912/bco-dmo.883506.1
title: H2S microsensor profiling conducted alongside the destructive sampling of Chesapeake Bay sediments during incubation experiments at Horn Point Lab

description: These data were collected as part of a sediment incubation experiment, to investigate potential interactions between estuarine cable bacteria and their associated microbial community. Sediments were collected from the main channel of Chesapeake Bay at a mesohaline station that experiences seasonal oxygen depletion. The upper 10 centimeters (cm) of sediment was homogenized under anaerobic conditions, packed into polycarbonate core liners, and incubated in a dark climate-controlled room in aerated aquaria with artificial seawater (S=15.5; T=16 degrees Celsius). In a sub-set of core tubes, a 0.2 micron polycarbonate filter was held embedded at 0.5 cm depth, to block the downward growth of cable bacteria while allowing for porewater diffusion. The sediments (with and without embedded filters) were destructively sampled on 6 dates over 46 days, at which time nucleic acids, samples for microscopy, and samples for porewater geochemistry were collected. Microsensor profiling (oxygen (O2), pH, hydrogen sulfide (H2S)) was conducted alongside the destructive sampling. Associated nucleic acid data are available through NCBI Sequence Read Archive, under Bioproject PRJNA833464. Sediment porewaters were handled anaerobically, and were extracted by centrifugation followed by filtration (0.2 micron in-line filters). Geochemical data include porewater anions (sulfate and chloride) measured by ion chromatography, and ammonium and ferrous iron concentrations measured by standard colorimetric methods. Microscopy data include both counts of cable bacteria measured with FISH oligoprobe DSB706, and total single cell bacteria. The dataset was generated by Pinky Liau under the supervision of Dr. Sairah Malkin, Horn Point Laboratory, U. Maryland Center for Environmental Sciences.
DOI: 10.26008/1912/bco-dmo.865193.1
title: Incubation experiments were conducted in St. John, US Virgin Islands to investigate the macronutrient drawdown response of reef seawater microbial communities to exudates released from the coral species Porites astreoides and Gorgonia ventalina.

description: Incubation experiments were conducted in St. John, US Virgin Islands to investigate the composition of exudates released from different species of benthic organisms, and the response of reef seawater microbial communities to mixed exudates released from different species and to specific metabolites. Exudates were collected from the stony coral Porites astreoides, and the octocoral Gorgonia ventalina after an 8 hour incubation. Reef seawater microbial communities were incubated separately in the presence of exudates from P. astreoides and G. ventalina for 48 hours and samples were collected to monitor changes in macronutrient concentrations.
DOI: 10.26008/1912/bco-dmo.865739.1
title: Incubation experiments were conducted in St. John, US Virgin Islands to investigate the response of reef seawater microbial communities to the mixed exudates released from the coral species Porites astreoides and Gorgonia ventalina.

description: Incubation experiments were conducted in St. John, US Virgin Islands to investigate the composition of exudates released from different species of benthic organisms, and the response of reef seawater microbial communities to mixed exudates released from different species and to specific metabolites. Exudates were collected from the stony coral Porites astreoides, and the octocoral Gorgonia ventalina after an 8 hour incubation. Reef seawater microbial communities were incubated separately in the presence of exudates from P. astreoides and G. ventalina for 48 hours and samples were collected to monitor changes in microbial abundance via flow cytometry and microbial community composition via 16S rRNA gene sequencing. Complementary Targeted and Untargeted metabolomic data from these incubation experiments is available on the MetaboLights database under accession number MTBLS2855.
DOI: 10.26008/1912/bco-dmo.883426.1
title: Evolutionary and acclimatory shifts in gene expression of Eurytemora affinis copepods reared in saline and freshwater conditions during laboratory experiments from 2011-2014

description: To explore mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome‐wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common‐garden conditions (0 vs. 15 PSU). These data include the RNA-seq Illumina short paired end reads (101 base pairs) of 10 freshwater and 12 saline copepods Eurytemora affinis samples. The freshwater copepod samples were collected in Lake Michigan (Racine Harbor), while the saline copepods were collected in Baie de L'Isle Verte, St. Lawrence marsh, Quebec, Canada. These data have important implications for our understanding of the evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.
DOI: 10.26008/1912/bco-dmo.865159.1
title: Incubation experiments were conducted in St. John, US Virgin Islands to investigate the response of reef seawater microbial communities to the specific metabolites riboflavin, pantothenic acid, and caffeine.

description: Pre-filtered reef seawater microbial communities collected from Lameshur Bay, U.S. Virgin Islands were incubated separately in the presence of the individual metabolites riboflavin, pantothenic acid, and caffeine for 24 hours and samples were collected to monitor changes in microbial community composition using 16S rRNA gene sequencing and microbial abundances using flow cytometry.  Targeted metabolomic data from these incubations is available on the MetaboLights database under accession number MTBLS3286.
DOI: 10.26008/1912/bco-dmo.873083.1
title: Seagrass community composition surveys around artificial reefs in shallow coastal waters off of Abaco Island, The Bahamas

description: These data represent seagrass community composition surveys conducted from May to December 2021 around artificial reefs in shallow (less than 4 meters) coastal waters in The Bight of Old Robinson, off of Abaco Island, The Bahamas.
DOI: 10.26008/1912/bco-dmo.873092.1
title: Seagrass surveys of blade height around artificial reefs in shallow coastal waters off of Abaco, The Bahamas

description: These data are from seagrass surveys of blade height around artificial reefs in shallow (less than 4 meters) coastal waters in The Bight of Old Robinson, off of Abaco Island, The Bahamas from May to December 2021.
DOI: 10.26008/1912/bco-dmo.872990.1
title: Fish surveys following the construction of clusters of artificial reefs in shallow coastal waters off of Abaco, The Bahamas from May to December 2021

description: These data are fish surveys from May to December 2021 following the construction of the clusters of artificial reefs. There are three clusters, each with 9 artificial reefs all of which are spaced the same distance and each differs per cluster (1 meter, 3 meters, and 5 meters). Reefs were constructed in less than 4 meters of water in the Bight of Old Robinson, on Abaco, The Bahamas.
DOI: 10.26008/1912/bco-dmo.826798.2
title: Seawater data (2018-2021) recorded from the Friday Harbor Laboratories Ocean Observatory (FHLOO)

description: To our knowledge, the FHL Ocean Observatory serves as the only multi-sensor array (~2 m from the surface) in the San Juan Islands archipelago that monitors for temperature, salinity, pH(total), carbon dioxide, dissolved oxygen, chlorophyll concentration, turbidity, and current velocity. In addition to the suite of ocean properties listed above, we also monitor the microplanktonic community using a camera system called the Imaging FlowCytoBot (IFCB). The IFCB is an automated imaging flow cytometer that is designed for the continuous monitoring of phytoplankton and microzooplankton. Using a laser-triggered, high-resolution camera, the IFCB generates images and optical data of individual plankton and other particles in the size range of &gt;10-150 mm. Data produced by this project may be of interest to chemical and biological oceanographers, and climate scientists interested in the role of biogeochemistry in the global/regional climate system. This dataset includes pH, pCO2, temperature, salinity, and dissolved oxygen data recorded from 2018-2021.
DOI: 10.26008/1912/bco-dmo.875283.1
title: Viral consortia in Stony Coral Tissue Loss Disease- affected, disease-exposed, and disease-unexposed coral colonies from a transmission experiment conducted on samples collected from Rupert’s Rock in St. Thomas, U.S. Virgin Islands in 2019

description: To understand the extent to which (if any) viruses are associated with stony coral tissue loss disease (SCTLD) in stony corals of the U.S. Virgin Islands, we leveraged viral metatranscriptomes generated from SCTLD-affected, SCTLD-exposed, and control (unexposed) coral holobionts sampled during a SCTLD transmission experiment. Sequence data is available in NCBI Genbank under BioProject accession PRJNA788911.
DOI: 10.26008/1912/bco-dmo.882390.1
title: Synechococcus (WH8102 and CC9311) growth and genetic sequence accessions from experiments with variable pCO2 treatments from 2016 to 2018

description: Synechococcus (WH8102 and CC9311) growth and genetic sequence accessions from experiments with variable pCO2 treatments. These data were produced as part of a study of the &quot;Community context and pCO2 impact the transcriptome of the &quot;helper&quot; bacterium Alteromonas in co-culture with picocyanobacteria&quot; (Barreto Filho et al., 2022).  Sequences files are accessible from the National Center for Biotechnology Information (BioProject PRJNA377729).

The following results abstract describes these data along with related datasets which can be accessed from the &quot;Related Datasets&quot; section of this page.

Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene expression in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the ‘helper’ bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different expression of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene expression patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing expression patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes inMIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of “help” provided by EZ55 to MIT9312 under elevated pCO2. The data and code stored in this archive will allow the reconstruction of our analysis pipelines.  Additionally, we provide annotation mapping files and other resources for conducting transcriptomic analyses with Alteromonas sp. EZ55.
DOI: 10.26008/1912/bco-dmo.881942.1
title: Pipelines for transcriptome analyses conducted as part of  &quot;Community context and pCO2 impact the transcriptome of the &quot;helper&quot; bacterium Alteromonas in co-culture with picocyanobacteria&quot;

description: Pipelines for transcriptome analyses conducted as part of  &quot;Community context and pCO2 impact the transcriptome of the &quot;helper&quot; bacterium Alteromonas in co-culture with picocyanobacteria&quot; (Barreto Filho et al., 2022). The provided code, documentation, input and output files include all the information needed to replicate our findings.

The following results abstract describes these data along with related datasets which can be accessed from the &quot;Related Datasets&quot; section of this page.

Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene expression in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the ‘helper’ bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different expression of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene expression patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing expression patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes in MIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of “help” provided by EZ55 to MIT9312 under elevated pCO2. The data and code stored in this archive will allow the reconstruction of our analysis pipelines.  Additionally, we provide annotation mapping files and other resources for conducting transcriptomic analyses with Alteromonas sp. EZ55.
DOI: 10.26008/1912/bco-dmo.882970.1
title: Pipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes conducted as part of  &quot;Community context and pCO2 impact the transcriptome of the &quot;helper&quot; bacterium Alteromonas in co-culture with picocyanobacteria&quot;

description: Pipeline for phylogenetic analysis of the GlcDEF, GOX/LOX, and tsar genes conducted as part of  &quot;Community context and pCO2 impact the transcriptome of the &quot;helper&quot; bacterium Alteromonas in co-culture with picocyanobacteria&quot; (Barreto Filho et al., 2022). The provided code, documentation, input and output files include all the information needed to replicate our findings.

The following results abstract describes these data along with related datasets which can be accessed from the &quot;Related Datasets&quot; section of this page.

Many microbial photoautotrophs depend on heterotrophic bacteria for accomplishing essential functions. Environmental changes, however, could alter or eliminate such interactions. We investigated the effects of changing pCO2 on gene expression in co-cultures of 3 strains of picocyanobacteria (Synechococcus strains CC9311 and WH8102 and Prochlorococcus strain MIT9312) paired with the ‘helper’ bacterium Alteromonas macleodii EZ55. Co-culture with cyanobacteria resulted in a much higher number of up- and down-regulated genes in EZ55 than pCO2 by itself. Pathway analysis revealed significantly different expression of genes involved in carbohydrate metabolism, stress response, and chemotaxis, with different patterns of up- or down-regulation in co-culture with different cyanobacterial strains. Gene expression patterns of organic and inorganic nutrient transporter and catabolism genes in EZ55 suggested resources available in the culture media were altered under elevated (800 ppm) pCO2 conditions. Altogether, changing expression patterns were consistent with the possibility that the composition of cyanobacterial excretions changed under the two pCO2 regimes, causing extensive ecophysiological changes in both members of the co-cultures. Additionally, significant downregulation of oxidative stress genes in MIT9312/EZ55 cocultures at 800 ppm pCO2 were consistent with a link between the predicted reduced availability of photorespiratory byproducts (i.e., glycolate/2PG) under this condition and observed reductions in internal oxidative stress loads for EZ55, providing a possible explanation for the previously observed lack of “help” provided by EZ55 to MIT9312 under elevated pCO2. The data and code stored in this archive will allow the reconstruction of our analysis pipelines.  Additionally, we provide annotation mapping files and other resources for conducting transcriptomic analyses with Alteromonas sp. EZ55.
DOI: 10.26008/1912/bco-dmo.881536.1
title: Oyster density of restored reef edge/interior in Quonochontaug Pond, RI in May 2019

description: This dataset represents oyster density measurements of restored reef edge/interior in Quonochontaug Pond, Rhode Island, USA determined by scuba divers in May of 2019. Reef relief and quadrat relief were calculated by subtracting water depth at each quadrat (quadrat relief) or the highest point on the reef (reef relief) from water depth on the adjacent unstructured bottom.
DOI: 10.26008/1912/bco-dmo.882140.1
title: Radium isotope measurements from bottom waters in the South Atlantic Bight from 2015-2020 (SAB BMA project)

description: These are measurements of radium isotopes collected from bottom waters in the South Atlantic Bight during 2015-2020. These data were used to verify an episode of submarine groundwater discharge that occurred in August 2019.
DOI: 10.26008/1912/bco-dmo.882177.1
title: Vertical profiles of water quality parameters at sampling stations in the South Atlantic Bight from 2015-2020 (SAB BMA project)

description: Vertical profiles of depth, conductivity, salinity, temperature, pH, and dissolved O2 were measured on selected dates from 7 June 2018 to 10 August 2021 in nearshore shelf waters off Charleston, SC. The survey area was located in the region of 32° 42’ N, 79° 50’ W and 32° 51’ N, 79° 09’W. Profiles were obtained using a YSI 6820 sonde deployed by hand. These data were used to map the physical structure of the water column and assess inputs of groundwater effects on phytoplankton and benthic microalgae. Results may be of interest to others conducting research projects off Charleston, SC. Data were collected and interpreted by Jay Pinckney at the University of South Carolina, Columbia, SC.