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  • 1
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    A new molecular isotopic toolkit to examine estuarine food webs and biogeochemistry: Compound specific isotope analyses of amino acids from aquatic and terrestrial plants of the Sacramento-San Joaquin Delta, California (2021)
    PANGAEA
    Details
    Publication Date: 2023-01-30
    Description: Aquatic and terrestrial plant materials were collected from the Sacramento-San Joaquin Delta region. Carbon and nitrogen isotope values of individual amino acids and bulk materials were measured. Fifty-six specimens were collected from three locations within the Delta, two flooded islands, Mildred and Liberty Islands, as well as an adjacent terrestrial riparian habitat (Big Break Regional Shoreline). Specimens included terrestrial trees, shrubs, forbs, and grasses as well as floating, submerged, and emergent aquatic plants. Bulk leaf tissues were processed and the carbon and nitrogen isotope values of bulk tissues were measured following Tipple and Ehleringer, 2018 (Oecologia, 187, 1053-1075). Amino acids were hydrolyzed, derivatized, and isolated following Vokhshoori et al., 2013 (Marine Ecology Progress Series, 504, 59-72). Carbon and nitrogen isotope values of individual amino acids were measured following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (PLoS ONE, 9, 6, e98087), respectively. The purpose of this research was to create a novel molecular isotope toolset to increase the understanding of biogeochemistry and food web structure of the Sacramento-San Joaquin Delta's tidal wetlands and estuarine marshes.
    Keywords: California; CSIA; ecology; estuaries; Food web; San Francisco Bay; trophic discrimination factor; trophic level; trophic position
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 2
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    Amino acid nitrogen isotopic analysis of aquatic and terrestrial plants from an estuarine delta (2021)
    PANGAEA
    Details
    Publication Date: 2023-01-30
    Description: Aquatic and terrestrial plants were collected from the Sacramento-San Joaquin River Delta. Nitrogen isotope values of bulk plant tissue and individual amino acids were measured. Fifty-six specimens from thirty-nine native, introduced and invasive species were collected. Growth forms and habits include trees, shrubs, forbs, and grasses as well as floating, submerged, and emergent aquatic plants. Bulk tissues were processed and the nitrogen isotope values were measured following Tipple and Ehleringer, 2018 (Oecologia, 187, 1053-1075). Amino acids were hydrolyzed, derivatized, and the carbon isotope values of individual amino acids were measured following Vokhshoori and McCarthy, 2013 (PLoS ONE, 9, 6, e98087). The purpose of this study was to assess trophic discriminate factors at the base of estuarine systems with multiple primary producers. This study provides an authentic dataset of primary producers for trophic position assessments in estuarine and mixed terrestrial-marine source environments.
    Keywords: 2,4,6-Tribromophenol; Alanine, δ15N; Alanine, δ15N, standard deviation; Aspartic acid, δ15N; Aspartic acid, δ15N, standard deviation; Big_Break_Regional_Shoreline; California; CSIA; DATE/TIME; ecology; estuaries; Event label; Food web; Glutamic acid, δ15N; Glutamic acid, δ15N, standard deviation; Glycine, δ15N; Glycine, δ15N, standard deviation; HAND; Isoleucine, δ15N; Isoleucine, δ15N, standard deviation; LATITUDE; Leucine, δ15N; Leucine, δ15N, standard deviation; Liberty_Island; LONGITUDE; Lysine, δ15N; Lysine, δ15N, standard deviation; Mildred_Island; Phenylalanine, δ15N; Phenylalanine, δ15N, standard deviation; Plant functional type; Proline, δ15N; Sacramento-San Joaquin River Delta, California, U.S.A.; Sample ID; Sampling by hand; San Francisco Bay; Serine, δ15N; Serine, δ15N, standard deviation; Site; Species; Species, common name; Threonine, δ15N; Threonine, δ15N, standard deviation; trophic discrimination factor; trophic level; trophic position; Valine, δ15N; Valine, δ15N, standard deviation; δ15N, bulk sediment
    Type: Dataset
    Format: text/tab-separated-values, 1677 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 3
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    Stable carbon isotope amino acids fingerprints of estuarine and freshwater macrophyte and terrestrial primary producers (2021)
    PANGAEA
    Details
    Publication Date: 2023-02-12
    Description: Plant material was collected from aquatic and terrestrial environments from the Sacramento-San Joaquin River Delta. Carbon isotope values of bulk plant tissue and individual amino acids were measured. Fifty-five specimens were collected, including trees, shrubs, forbs, and grasses as well as floating, submerged, and emergent aquatic plants. Bulk tissues were processed and the carbon isotope values were measured following Tipple and Ehleringer, 2018 (Oecologia, 187, 1053-1075). Amino acids were hydrolyzed, derivatized, and isolated following Vokhshoori et al., 2013 (Marine Ecology Progress Series, 504, 59-72). Carbon isotope values of individual amino acids were measured following Vokhshoori et al., 2013. The purpose of this study was to assess if amino acid fingerprints of macrophyte primary producers were distinct from those of marine primary producers and terrestrial vascular plant species. The goal of this study was to provide a benchmark dataset for the next generation of food web monitoring programs within estuarine and mixed source environments.
    Keywords: Alanine, δ13C; Alanine, δ13C, standard deviation; Aspartic acid, δ13C; Aspartic acid, δ13C, standard deviation; Big_Break_Regional_Shoreline; California; CSIA; DATE/TIME; ecology; estuaries; Event label; Food web; Glutamic acid, δ13C; Glutamic acid δ13C, standard deviation; HAND; Homalophiura inornata; Isoleucine, δ13C; Isoleucine, δ13C, standard deviation; LATITUDE; Leucine, δ13C; Leucine, δ13C, standard deviation; Liberty_Island; LONGITUDE; Lysine, δ13C; Lysine, δ13C, standard deviation; Mildred_Island; Ophiactis asperula; Phenylalanine, δ13C; Phenylalanine, δ13C, standard deviation; Plant functional type; Proline, δ13C; Proline, δ13C, standard deviation; Sacramento-San Joaquin River Delta, California, U.S.A.; Sample ID; Sampling by hand; San Francisco Bay; Serine, δ13C; Serine, δ13C, standard deviation; Site; Species; Species, common name; Threonine, δ13C; Threonine, δ13C, standard deviation; trophic discrimination factor; trophic level; trophic position; Valine, δ13C; Valine, δ13C, standard deviation; δ13C, bulk carbonate
    Type: Dataset
    Format: text/tab-separated-values, 1650 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 4
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    Seasonal variations in the compound specific isotope analyses of amino acids from co-occurring clams in the San Francisco Bay-Sacramento/San Joaquin Delta (2023)
    PANGAEA
    Details
    Publication Date: 2023-05-24
    Description: Amino acids were isolated from the muscle tissue of Corbicula fluminea and Potamocorbula amurensis; two co-occurring invasive clams within the San Francisco Bay-Delta system. Clam specimens were collected near Montezuma Slough (Contra Costa County, California) at the confluence of the Sacramento and San Joaquin Rivers twice during the hydrological extremes of 2010 water year (November, 2009 and May, 2010). Carbon and nitrogen isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 2.1 and processed following Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from clam muscle tissue, derivatized, and isolated following Vokhshoori et al. (2013; doi:10.3354/meps10746). The measurement of the carbon and nitrogen isotope values of individual amino acids were conducted following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (doi:10.1371/journal.pone.0098087), respectively. The purpose of this study was to monitor biogeochemistry during 2010 water year and assess dietary difference between two co-occurring invasive species. This study focused on two species, C. fluminea and P. amurensis, benthic sessile primary consumers that can inhabit the same environment. USGS Site 2.1 was specifically selected as it exhibited the environmental conditions where both clam species co-existed during 2010 water year. This design allowed for interspecies variation to be explored. Nitrogen isotopes of amino acids were used to isolate variations in nutrient baseline from dietary changes across the season between the two species. Carbon isotopes of amino acid were utilized to understand the diet of the two species at two points in the season.
    Keywords: amino acids; biogeochemistry; Bivalve; carbon isotope; diet; Estuary; invasive species; nitrogen isotope; stable isotope analysis
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 5
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    A twenty-year record of biogeochemical changes in the San Francisco Bay Estuary: Timeseries of compound specific isotope analyses of amino acids from a benthic filter-feeder, Potamocorbula amurensis (2023)
    PANGAEA
    Details
    Publication Date: 2023-05-24
    Description: Amino acids were isolated from the muscle tissue of Potamocorbula amurensis, an invasive clam species, collected from two locations in the northern portion of the San Francisco Bay. Clam specimens were collected biannually in 1997, 2002, and from 2009-2017 at both locations. The carbon and nitrogen isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 4.1 (Suisun Bay) and 8.1 (Carquinez Strait) in the San Francisco Bay and processed as described in Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from P. amurensis, derivatized, and isolated following Vokhshoori et al. (2013; doi:10.3354/meps10746). Carbon and nitrogen isotope values of individual amino acids were measured following Vokhshoori et al., 2013 and Vokhshoori and McCarthy, 2013 (doi:10.1371/journal.pone.0098087), respectively. The purpose of this study was to assess long-term changes in the biogeochemistry of the San Francisco Bay estuary following the arrival of invasive P. amurensis. Sites were selected both due to species occurrence as well as significantly different salinity ranges. This design allowed for intraspecies and site-specific variations to be explored. Nitrogen isotopes of amino acids were used to isolate variations in nutrient baseline over the twenty-year period. Carbon isotopes of amino acid were utilized to understand long-term changes in dietary sources and/or changes in the baseline carbon isotope value of the estuary's food-web.
    Keywords: amino acids; biogeochemistry; Biological sample; BIOS; Bivalve; carbon isotope; compound-specific isotope analysis; ecology; invasive species; nitrogen isotope; San Francisco Bay, California; Site 4.1; Site 8.1; stable isotope analysis; USGS_4-1; USGS_8-1
    Type: Dataset
    Format: application/zip, 2 datasets
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 6
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    A twenty-year record of carbon isotope values of amino acids from Potamocorbula amurensis (2023)
    PANGAEA
    Details
    Publication Date: 2023-05-24
    Description: Amino acids were isolated from the muscle tissue of Potamocorbula amurensis, an invasive clam species, collected from two locations in the northern portion of the San Francisco Bay. Clam specimens were collected biannually in 1997, 2002, and from 2009-2017 at both locations. The carbon isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 4.1 (Suisun Bay) and 8.1 (Carquinez Strait) in the San Francisco Bay and processed as described in Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from P. amurensis, derivatized, isolated and the carbon isotope values were measured following Vokhshoori et al. (2013; doi:10.3354/meps10746). The purpose of this study was to assess long-term changes in dietary sources and/or changes in the baseline carbon isotope value of the estuary's food-web following the invasion of P. amurensis.
    Keywords: Alanine, δ13C; Alanine, δ13C, standard deviation; amino acids; Aspartic acid, δ13C; Aspartic acid, δ13C, standard deviation; biogeochemistry; Biological sample; BIOS; Bivalve; carbon isotope; compound-specific isotope analysis; DATE/TIME; ecology; Glutamic acid, δ13C; Glutamic acid δ13C, standard deviation; Glycine, δ13C; Glycine, δ15N, standard deviation; invasive species; Isoleucine, δ13C; Isoleucine, δ13C, standard deviation; LATITUDE; Leucine, δ13C; Leucine, δ13C, standard deviation; LONGITUDE; Lysine, δ13C; Lysine, δ13C, standard deviation; nitrogen isotope; Phenylalanine, δ13C; Phenylalanine, δ13C, standard deviation; Proline, δ13C; Proline, δ13C, standard deviation; Sample ID; San Francisco Bay, California; see description in data abstract; Serine, δ13C; Serine, δ13C, standard deviation; Site; Site 4.1; Site 8.1; Species; stable isotope analysis; Threonine, δ13C; Threonine, δ13C, standard deviation; USGS_4-1; USGS_8-1; Valine, δ13C; Valine, δ13C, standard deviation; δ13C, bulk muscle tissue
    Type: Dataset
    Format: text/tab-separated-values, 1176 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 7
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    A two-decade timeseries of baseline nutrient variations in the San Francisco Bay as recorded in nitrogen isotope values of amino acids from benthic filter-feeders (2023)
    PANGAEA
    Details
    Publication Date: 2024-02-20
    Description: Amino acids were isolated from the muscle tissue of Potamocorbula amurensis, an invasive clam species, collected from two locations in the northern portion of the San Francisco Bay. Clam specimens were collected biannually in 1997, 2002, and from 2009-2017 at both locations. The nitrogen isotope values of individual amino acids were measured. Clam specimens were collected at USGS Sites 4.1 (Suisun Bay) and 8.1 (Carquinez Strait) in the San Francisco Bay and processed as described in Stewart et al. (2013; doi:10.3354/meps10503). Amino acids were hydrolyzed from P. amurensis, derivatized, and isolated following Vokhshoori et al. (2013; doi:10.3354/meps10746). Nitrogen isotope values of individual amino acids were measured following Vokhshoori and McCarthy, 2013 (doi:10.1371/journal.pone.0098087). The purpose of this study was to isolate variations in nutrient baseline over the twenty-year period following the arrival of invasive P. amurensis.
    Keywords: Alanine, δ15N; Alanine, δ15N, standard deviation; amino acids; Aspartic acid, δ15N; Aspartic acid, δ15N, standard deviation; biogeochemistry; Biological sample; BIOS; Bivalve; carbon isotope; compound-specific isotope analysis; DATE/TIME; ecology; Glutamic acid, δ15N; Glutamic acid, δ15N, standard deviation; Glycine, δ15N; Glycine, δ15N, standard deviation; invasive species; Isoleucine, δ15N; Isoleucine, δ15N, standard deviation; LATITUDE; Leucine, δ15N; Leucine, δ15N, standard deviation; LONGITUDE; Lysine, δ15N; Lysine, δ15N, standard deviation; nitrogen isotope; Phenylalanine, δ15N; Phenylalanine, δ15N, standard deviation; Proline, δ15N; Proline, δ15N, standard deviation; Sample ID; San Francisco Bay, California; See description in dataset comment; Serine, δ15N; Serine, δ15N, standard deviation; Site; Site 4.1; Site 8.1; Species; stable isotope analysis; Threonine, δ15N; Threonine, δ15N, standard deviation; USGS_4-1; USGS_8-1; Valine, δ15N; Valine, δ15N, standard deviation; δ15N, bulk muscle tissue
    Type: Dataset
    Format: text/tab-separated-values, 1175 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 8
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    Carbon and nitrogen isotope fractionation of amino acids in an avian marine predator, the gentoo penguin (Pygoscelis papua) (2015)
    John Wiley & Sons
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 5 (2015): 1278–1290, doi:10.1002/ece3.1437.
    Description: Compound-specific stable isotope analysis (CSIA) of amino acids (AA) has rapidly become a powerful tool in studies of food web architecture, resource use, and biogeochemical cycling. However, applications to avian ecology have been limited because no controlled studies have examined the patterns in AA isotope fractionation in birds. We conducted a controlled CSIA feeding experiment on an avian species, the gentoo penguin (Pygoscelis papua), to examine patterns in individual AA carbon and nitrogen stable isotope fractionation between diet (D) and consumer (C) (Δ13CC-D and Δ15NC-D, respectively). We found that essential AA δ13C values and source AA δ15N values in feathers showed minimal trophic fractionation between diet and consumer, providing independent but complimentary archival proxies for primary producers and nitrogen sources respectively, at the base of food webs supporting penguins. Variations in nonessential AA Δ13CC-D values reflected differences in macromolecule sources used for biosynthesis (e.g., protein vs. lipids) and provided a metric to assess resource utilization. The avian-specific nitrogen trophic discrimination factor (TDFGlu-Phe = 3.5 ± 0.4‰) that we calculated from the difference in trophic fractionation (Δ15NC-D) of glutamic acid and phenylalanine was significantly lower than the conventional literature value of 7.6‰. Trophic positions of five species of wild penguins calculated using a multi-TDFGlu-Phe equation with the avian-specific TDFGlu-Phe value from our experiment provided estimates that were more ecologically realistic than estimates using a single TDFGlu-Phe of 7.6‰ from the previous literature. Our results provide a quantitative, mechanistic framework for the use of CSIA in nonlethal, archival feathers to study the movement and foraging ecology of avian consumers.
    Description: This research was funded by National Science Foundation Office of Polar Programs [grants ANT-0125098, ANT-0739575] and the 2013 Antarctic Science Bursaries.
    Keywords: Amino acid ; Avian ; Compound-specific stable isotope analysis ; Diet ; Fractionation ; Penguin ; Trophic position
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Format: application/msword
    Location Call Number Limitation Availability
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    PAPER (OA)
  • 9
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    Treatment description and growth parameters for Thalassiosira weissflogii generating d13C-AA, collected on R/V Meteor M77 in the Peruvian ocean margin from November to December 2008. (2019)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Algal treatments
    Description: Treatment description and growth parameters for Thalassiosira weissflogii generating d13C-AA, collected on R/V Meteor M77 in the Peruvian ocean margin from November to December 2008. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/715856
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1131816
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
    Location Call Number Limitation Availability
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  • 10
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    Mean d15N of individual amino acids and bulk organic matter for five plankton size fractions (2019)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Atlantic ZooPlankton AA 15N values
    Description: Mean d15N of individual amino acids and bulk organic matter for five plankton size fractions from R/V Sarmiento de Gamboa Malaspina_2011 in the Subtropical North Atlantic Ocean from January to March 2011 For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/715977
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1131816
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
    Location Call Number Limitation Availability
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