Dataset: Low-pH springs: water samples

Name: Measured and calculated geochemistry values and uncertainty for water samples taken from the water column of Celestun Lagoon, Yucatan, Mexico in May of 2015
Published: 2024-10-25
Keywords: boron isotopes, groundwater, benthic foraminifera, coastal pH, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:20.95318 E:-90.32955 S:20.77012 W:-90.41782

Celestún Biosphere Reserve, Yucatan, Mexico. 20.88 N 90.36 E depth 0.5 m.

Temporal Extent: 2015-05-25 - 2015-05-26

Project:

Calcification in low saturation seawater: What can we learn from organisms in the proximity of low pH; undersaturated submarine springs (CalcificationLowSatSeawater)

Program:

Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES): Ocean Acidification (formerly CRI-OA) (SEES-OA)

Principal Investigator:

Adina Paytan (University of California-Santa Cruz, UCSC)

Co-Principal Investigator:

Jorge A. Herrera-Silveira (Unidad Mérida del Centro de Investigación y de Estudios Avanzados, CINVESTAV)

Chen-Feng You (National Cheng Kung University)

Scientist:

Hou-Chun Arrien Liu (National Cheng Kung University)

Joseph H. Street (University of California-Santa Cruz, UCSC)

Tzu-Hao David Wang (National Cheng Kung University)

Student:

Kyle H. Hardage (University of California-Santa Cruz, UCSC)

Contact:

Adina Paytan (University of California-Santa Cruz, UCSC)

Data Manager:

Kyle H. Hardage (University of California-Santa Cruz, UCSC)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-10-25

Restricted:

Validated:

Current State:

Data not available

Measured and calculated geochemistry values and uncertainty for water samples taken from the water column of Celestun Lagoon, Yucatan, Mexico in May of 2015

Abstract:

Measured and calculated geochemistry values and uncertainty for water samples taken from the water column of Celestun Lagoon, Yucatan, Mexico in May of 2015. This dataset was collected in coordination with the following study (See also "Related Datsets" section): Isotopes (δ11B, 87Sr/86Sr, δ18O, δ13C), elemental concentrations (B, Mg, Ca), and carbon content were collected from the foraminifera Ammonia parkinsoniana and sediments in Celestun Lagoon, Yucatan, Mexico in June 2009 and May 2015. Sediment cores were taken with push corers and piston corers. Sampling site were distributed unevenly along a transect along the lagoon. These data were collected to investigate the influence of low-pH groundwater-seawater mixing on the boron isotope pH proxy.

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Methods & Sampling

Location: Celestún Biosphere Reserve, Yucatan, Mexico. 20.88 N 90.36 E depth 0.5 m.
Collection: Data collected from dinghy. No vessel name. June 2009 and May 2015.

Water samples from 2015 were filtered (0.45 um) and analyzed for salinity, pH, and elemental concentrations. Analytical methods involved MC-ICPMS for boron and strontium isotopes, with careful sample preparation, including microsublimation for δ11B, Sr-spec resin for 87Sr/86Sr, and isotope ratio mass spectrometry for δ18O and δ13C. Elemental concentrations (B, Mg, Ca) and sediment organic matter were analyzed using ICPMS and elemental analyzer IRMS. Reproducibility was verified using established standards.

Additional methods citations:

Boron isotope method: Wang et al. (2020).
Strontium isotope method: Liu et al. (2012).
pH and borate equations: Foster et al. (2016).
Organic carbon in sediments. Modified to use chilled sulfuric acid with sonication to ensure complete decarbonation: Verardo et al. (1990).

Related dataset descriptions (See section "Related Datasets" for data citations):

The water sample data in this dataset were collected concurrently with the May 2015 sampling event in BCO-DMO dataset https://www.bco-dmo.org/dataset/941327 which contains isotope data, elemental concentrations, and carbon content collected from the foraminifera Ammonia parkinsoniana and sediments in Celestun Lagoon, Yucatan, Mexico in June 2009 and May 2015.

This study and Paytan (2021, BCO-DMO dataset https://www.bco-dmo.org/dataset/564766) both derive groundwater from the same regional aquifer in Yucatan, Mexico, and both studies review the effects of low-pH springs on saturation and calcification of organisms. They are different sample material.

The sediment cores and assemblages in Hardage et al.Hardage et al. (2021, doi:10.1016/j.talanta.2011.10.050) at NOAA provide the sample material for the geochemistry reported in this study (foraminifera, bulk sediment, physical observations). The Hardage et al. (2021) dataset also contains additional lithology and geochemistry that can be paired with these new data for interested parties.

Instrument and equipment list:

LDPE bottles: water samples were collected in acid-washed LDPE bottles for trace metals.
rubber septum glass vials: water samples were collected in ashed glass bottles for nutrients.
Piston, Bolivia, Livingstone corers: coring devices used to collect sediments.
0.5 mL micro-centrifuge tubes: used to store crushed foraminifera for cleaning.
Yellow Springs Instrument Model 63 handheld sonde and pH probe.
Neptune multi-collector inductively coupled plasma mass spectrometer (MC-ICPMS).
Lachat QuikChem 8000.
UIC Carbon Coulometer Analyzer.
Orion 950 Titrator.
Thermo Scientific Element XR ICPMS.
ThermoFinnigan Delta Plus XP isotope ratio mass spectrometer.
Kiel IV Carbonate Device.
ThermoScientific MAT-253 dual-inlet isotope ratio mass spectrometer.
Carlo Erba elemental analyzer IRMS.

Data Processing Description

Element data were corrected for blank, drift, mass bias, and calcium matrix effects.

Boron isotopes were corrected using the standard-sample-standard bracket technique to correct drift and bias across each individual sample.

pKB* was calculated according to Hain et al. (2015).

Global Biogeochemical Cycles using the MATLAB code implemented by Rae (2018).

Boron Isotopes.

δ11B borate was calculated using Table A2.2 of

Hönisch et al. (2019). Boron Proxies in Paleoceanography and Paleoclimatology.

Note about aggregated data (means, standard deviations):
The averages are from the instruments themselves, not from true replicates. They typically take 4 to 10 readings and average the result, depending on the instrument. Since these are mass spectrometers counting individual ions, this averaging is necessary to reduce noise.

BCO-DMO Processing

* Data table from submitted file "Hardage_boron_water_parameter_values.csv" was imported into the BCO-DMO data system for this dataset. Values "-999" imported as missing data values.
** In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.

* Datetime with timezone (UTC) added as column from local dates and times provided in GMT-6 (Central Standard Time in Yucatan, Mexico)

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1040952

Deployments

None available yet

Instruments

Automatic titrator

Supplied Name: Orion 950 Titrator

Supplied Description:

Instrument Type

Generic Name: Automatic titrator

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB12/

Generic Description:

Instruments that incrementally add quantified aliquots of a reagent to a sample until the end-point of a chemical reaction is reached.

Bottle

Supplied Name:

Supplied Description:

LDPE bottles: water samples were collected in acid-washed LDPE bottles for trace metals.
Rubber septum glass vials: water samples were collected in ashed glass bottles for nutrients.

Instrument Type

Generic Name: Bottle

Generic Description:

A container, typically made of glass or plastic and with a narrow neck, used for storing drinks or other liquids.

Elemental Analyzer

Supplied Name: Carlo Erba elemental analyzer IRMS

Supplied Description:

Instrument Type

Generic Name: Elemental Analyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/

Generic Description:

Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.

Inductively Coupled Plasma Mass Spectrometer

Supplied Name: Thermo Scientific Element XR ICPMS

Supplied Description:

Instrument Type

Generic Name: Inductively Coupled Plasma Mass Spectrometer

Acronym: ICP Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB15/

Generic Description:

An ICP Mass Spec is an instrument that passes nebulized samples into an inductively-coupled gas plasma (8-10000 K) where they are atomized and ionized. Ions of specific mass-to-charge ratios are quantified in a quadrupole mass spectrometer.

Isotope-ratio Mass Spectrometer

Supplied Name: ThermoFinnigan Delta Plus XP isotope ratio mass spectrometer.

Supplied Description:

Instrument Type

Generic Name: Isotope-ratio Mass Spectrometer

Acronym: IR Mass Spec; IRMS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).

Isotope-ratio Mass Spectrometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Isotope-ratio Mass Spectrometer

Acronym: IR Mass Spec; IRMS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).

Isotope-ratio Mass Spectrometer

Supplied Name: ThermoScientific MAT-253 dual-inlet isotope ratio mass spectrometer

Supplied Description:

Instrument Type

Generic Name: Isotope-ratio Mass Spectrometer

Acronym: IR Mass Spec; IRMS

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer).

Lachat QuikChem 8000 flow injection analyzer and Ion Chromatography (IC) system

Supplied Name: Lachat QuikChem 8000

Supplied Description:

Instrument Type

Generic Name: Lachat QuikChem 8000 flow injection analyzer and Ion Chromatography (IC) system

Generic Description:

The Lachat QuikChem 8000 can operate flow injection analysis and ion chromatography simultaneously and independently on the same instrument platform. Instrument includes sampler, dilutor, sampling pump, electronics unit, and data station. Analysis takes 20-60 seconds, with a sample throughput of 60-120 samples per hour. Measurements are in the range of parts per trillion to parts per hundred.

Multi Collector Inductively Coupled Plasma Mass Spectrometer

Supplied Name:

Supplied Description:

Neptune multi-collector inductively coupled plasma mass spectrometer (MC-ICPMS).

Instrument Type

Generic Name: Multi Collector Inductively Coupled Plasma Mass Spectrometer

Acronym: MC-ICPMS

Generic Description:

A Multi Collector Inductively Coupled Plasma Mass Spectrometry (MC-ICPMS) is a type of mass spectrometry where the sample is ionized in a plasma (a partially ionized gas, such as Argon, containing free electrons) that has been generated by electromagnetic induction. A series of collectors is used to detect several ion beams simultaneously.

A MC-ICPMS is a hybrid mass spectrometer that combines the advantages of an inductively coupled plasma source and the precise measurements of a magnetic sector multicollector mass spectrometer. The primary advantage of the MC-ICPMS is its ability to analyze a broader range of elements, including those with high ionization potential that are difficult to analyze by Thermal Ionization Mass Spectrometry (TIMS). The ICP source also allows flexibility in how samples are introduced to the mass spectrometer and allows the analysis of samples introduced either as an aspirated solution or as an aerosol produced by laser ablation.

Multi Parameter Portable Meter

Supplied Name: Yellow Springs Instrument Model 63 handheld sonde and pH probe

Supplied Description:

YSI Model 63 Handheld pH, Conductivity, Salinity and Temperature System.

Instrument Type

Generic Name: Multi Parameter Portable Meter

Generic Description:

An analytical instrument that can measure multiple parameters, such as pH, EC, TDS, DO and temperature with one device and is portable or hand-held.

Piston Corer

Supplied Name:

Supplied Description:

Piston, Bolivia, Livingstone corers: coring devices used to collect sediments.

Instrument Type

Generic Name: Piston Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length.

UIC Carbon Coulometer Analyzer.

Supplied Description:

Instrument Type

no generic instrument available

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
site	Site code for water sample.	unitless	site
lat	Site latitude in WGS84; north is positive.	decimal degrees	lat
long	Site longitude in WGS84; east is negative.	decimal degrees	lon
distance	Distance along the central lagoon axis from the northern fringe mangrove to the southern lagoon opening to the ocean.	kilometers (km)	length
region	Biogeographic region of the lagoon identified by Hardage et al. (2022). J. Paleolim. 10.8 km is the dividing point.	unitless	site_descrip
date	Date of sample collection in ISO 8601 yyyy-mm-dd format. GMT-6 (Central Standard Time in Yucatan, Mexico) Format: %Y-%m-%d	unitless	date_local
time	Time of sample collection in ISO 8601 format HH:MM. GMT-6 (Central Standard Time in Yucatan, Mexico) Format: %H:%M	unitless	time_local
ISO_DateTime_UTC	Datetime with timezone of sample collection in ISO 8601 format (UTC). Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC
tide	Tide position based on the nearest tide gauge in Progreso, Yucatan, Mexico.	unitless	site_descrip
sample	Water sample type. Valid values are Lagoon Water, Seawater, Spring Water, Well Water.	unitless	sample_descrip
temperature	Water column temperature measured in situ.	Celsius	temp
salinity	Water column salinity measured with a salinometer against KCl.	practical salinity units (PSU)	sal
pH	Water column pH, measured in situ using standards on the National Bureau of Standards scale and converted to total scale using pH = value - 0.14.	total scale	pH
DIC	Water column dissolved inorganic carbon.	micromoles per kilogram (µmol/kg)	DIC
DIC_sd	Water column dissolved inorganic carbon standard deviation of replicate measurements.	micromoles per kilogram (µmol/kg)	DIC
TA	Water column total alkalinity. Uncertainty determined as 45 based on the Dickson Standard Batch 121.	micromoles per kilogram (µmol/kg)	TALK
NO3	Water column dissolved nitrate as N.	micromoles per kilogram (µmol/kg)	NO3
NO3_sd	Water column dissolved nitrate as N standard deviation of replicate measurements.	micromoles per kilogram (µmol/kg)	NO3
PO4	Water column dissolved phosphate. Uncertainty determined as Â±0.02 based on lab standards.	micromoles per kilogram (µmol/kg)	PO4
SiO4	Water column dissolved silica.	micromoles per kilogram (µmol/kg)	SiO4
SiO4_sd	Water column dissolved silica standard deviation of replicate measurements.	micromoles per kilogram (µmol/kg)	SiO4
Ca_conc	Water column dissolved calcium concentration.	millimolar (mM)	Ca
Mg_conc	Water column dissolved magnesium concentration.	millimolar (mM)	Mg
B_conc	Water column dissolved boron concentration.	micromolar (uM)	B
Sr8786	Water column radiogenic strontium ratio 87Sr/86Sr.	unitless	no_bcodmo_term
Sr8786_2sd	Water column radiogenic strontium ratio 87Sr/86Sr 2 standard deviations of replicate measurements.	unitless	no_bcodmo_term
d18O	Water column oxygen-18.	per mil (0/00)	d18O
d18O_sd	Water column oxygen-18 standard deviation based on replicate standards.	per mil (0/00)	d18O
d11B	Water column bulk boron-11.	per mil (0/00)	d11B
d11B_2sd	Water column bulk boron-11 2 standard deviations of replicate standards.	per mil (0/00)	d11B
pCO2	Water column partial pressure of carbon dioxide calculated using CO2SYS of Pierrot et al. (2011). Carbon dioxide information analysis center.	microatmospheres (uatm)	pCO2
pCO2_uncert	Water column partial pressure of carbon dioxide uncertainty, calculated by propagating error of measured parameters.	microatmospheres (uatm)	pCO2
CO2_conc	Water column dissolved carbon dioxide concentration calculated using CO2SYS of Pierrot et al. (2011).	micromoles per kilogram (µmol/kg)	CO2
CO2_uncert	Water column dissolved carbon dioxide concentration uncertainty, calculated using CO2SYS by propagating uncertainty of measured parameters.	micromoles per kilogram (µmol/kg)	CO2
CO3_conc	Water column dissolved carbonate ion concentration calculated using CO2SYS of Pierrot et al. (2011).	micromoles per kilogram (µmol/kg)	carbonate
CO3_uncert	Water column dissolved carbonate ion concentration uncertainty, calculated using CO2SYS by propagating uncertainty of measured parameters.	micromoles per kilogram (µmol/kg)	carbonate
HCO3_conc	Water column dissolved bicarbonate ion concentration calculated using CO2SYS of Pierrot et al. (2011).	micromoles per kilogram (µmol/kg)	bicarbonate
HCO3_uncert	Water column dissolved bicarbonate ion concentration uncertainty, calculated using CO2SYS by propagating uncertainty of measured parameters.	micromoles per kilogram (µmol/kg)	bicarbonate
saturation	Water column calcite saturation state, calculated using CO2SYS of Pierrot et al. (2011).	unitless	OM_ca
saturation_uncert	Water column calcite saturation state uncertainty, calculated using CO2SYS by propagating uncertainty of measured parameters.	unitless	OM_ca
delta_CO3	Water column degree of calcite saturation, defined as CO3 - (CO3 / saturation).	micromoles per kilogram (µmol/kg)	no_bcodmo_term
pKB	Stoichiometric dissociation (equilibrium) constant for the borate-boric acid system.	unitless	rate_constant
BOH4	Water column dissolved borate, calculated using code tools provided by Rae (2018). Boron Isotopes.	micromoles per kilogram (µmol/kg)	no_bcodmo_term
BOH4_uncert	Water column dissolved borate uncertainty, calculated by propagating uncertainty of measured parameters.	micromoles per kilogram (µmol/kg)	no_bcodmo_term
d11B_BOH4	Water column boron-11 ratio of borate ion, calculated using code tools provided by Rae (2018). Boron Isotopes.	per mil (0/00)	no_bcodmo_term
d11B_BO4_uncert	Water column boron-11 ratio of borate ion uncertainty, calculated by propagating uncertainty of measured parameters.	per mil (0/00)	no_bcodmo_term

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Dataset: Low-pH springs: water samples