Geochemical data to characterize chemical water column properties of flooded caves (Ox Bel Ha and Cenote Crustacea) within the coastal aquifer of the Yucatan Peninsula, Quintana Roo, from December 2013 to January 2015

Frequently anticipated questions:

• What does this data set describe?
  1. How might this data set be cited?
  2. What geographic area does the data set cover?
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
  5. What is the general form of this data set?
  6. How does the data set represent geographic features?
  7. How does the data set describe geographic features?
• Who produced the data set?
  1. Who are the originators of the data set?
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
• Why was the data set created?
• How was the data set created?
  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
  3. What similar or related data should the user be aware of?
• How reliable are the data; what problems remain in the data set?
  1. How well have the observations been checked?
  2. How accurate are the geographic locations?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
  5. How consistent are the relationships among the data, including topology?
• How can someone get a copy of the data set?
  1. Are there legal restrictions on access or use of the data?
  2. Who distributes the data?
  3. What's the catalog number I need to order this data set?
  4. What legal disclaimers am I supposed to read?
  5. How can I download or order the data?
• Who wrote the metadata?

What does this data set describe?

1. How might this data set be cited?
   Brankovits, David, and Pohlman, John W., 20220915, Geochemical data to characterize chemical water column properties of flooded caves (Ox Bel Ha and Cenote Crustacea) within the coastal aquifer of the Yucatan Peninsula, Quintana Roo, from December 2013 to January 2015: data release DOI:10.5066/P91D2OUN, U.S. Geological Survey, Coastal and Marine Geology Program, Woods Hole Coastal and Marine Science Center, Woods Hole, MA.

   Online Links:

   • https://doi.org/10.5066/P91D2OUN
   • https://www.sciencebase.gov/catalog/item/63069f18d34e3b967a8bd9cc

   Other_Citation_Details:

   Collected in support of PhD thesis research of David Brankovits, Texas AM University

   This is part of the following larger work.
   Brankovits, David, Pohlman, John W., Lapham, Laura L., Casso, Michael, Mann, Adrian G., and Jennifer A. O'Keefe Suttles, 2022, Water column properties and temporal hydrologic and chemical records from flooded caves (Ox Bel Ha and Cenote Crustacea) within the coastal aquifer of the Yucatan Peninsula, Quintana Roo, from December 2013 to January 2015: data release DOI:10.5066/P91D2OUN, U.S. Geological Survey, Reston, VA.

   Online Links:

   • https://doi.org/10.5066/P91D2OUN
   • https://www.sciencebase.gov/catalog/item/625579ffd34e21f8276f4872

   Other_Citation_Details:

   Suggested citation: Brankovits, D., Pohlman, J.W., Lapham, L.L., Casso, M., Mann, A.G., and O'Keefe Suttles, J.A., 2022, Water column properties and temporal hydrologic and chemical records from flooded caves (Ox Bel Ha and Cenote Crustacea) within the coastal aquifer of the Yucatan Peninsula, Quintana Roo, from December 2013 to January 2015: U.S. Geological Survey data release, https://doi.org/10.5066/P91D2OUN.

2. What geographic area does the data set cover?

   West_Bounding_Coordinate: -87.5693
   East_Bounding_Coordinate: -87.4166
   North_Bounding_Coordinate: 20.2829
   South_Bounding_Coordinate: 20.1084
   

3. What does it look like?

   https://www.sciencebase.gov/catalog/file/get/63069f18d34e3b967a8bd9cc?name=geochem.jpg&allowOpen=true (JPEG)

   Salinity-property plots: methane concentration (CH4) and methane carbon isotopic composition (d13C-CH4) in Cenote Odyssey (Tulum, Mexico) in 2014 and 2015. Symbols of individual data points contain the uncertainty of the measured values.

4. Does the data set describe conditions during a particular time period?

   Calendar_Date: 04-Dec-2013

   Currentness_Reference:

   ground condition

5. What is the general form of this data set?

   Geospatial_Data_Presentation_Form: tabular digital data
   

6. How does the data set represent geographic features?
   1. How are geographic features stored in the data set?
      This is a Point data set. It contains the following vector data types (SDTS terminology):
      • Point (99)
   2. What coordinate system is used to represent geographic features?
      Horizontal positions are specified in geographic coordinates, that is, latitude and longitude. Latitudes are given to the nearest 0.00001. Longitudes are given to the nearest 0.00001. Latitude and longitude values are specified in Decimal degrees. The horizontal datum used is World Geodetic System 1984.
      The ellipsoid used is WGS 84.
      The semi-major axis of the ellipsoid used is 6378137.
      The flattening of the ellipsoid used is 1/298.257.
      
7. How does the data set describe geographic features?

   geochem_2013-2015

   Aquatic geochemical data from samples collected from the Ox Bel Ha cave (Cenote Jailhouse, Cenote Naach Wennen Ha, and Cenote Odyssey) and another cave (Cenote Crustacea) in the Yucatan Peninsula, Quintana Roo, Mexico, between December 2013 and January 2015. There are a total of 99 data records in the dataset. (Source: U.S. Geological Survey)

   Location

   General description of location where samples were obtained (Source: U.S. Geological Survey) Character set (text).

   Latitude

   Latitude of location as determined by Garmin GPSmap 60CSx GPS in decimal degrees. (Source: U.S. Geological Survey)

   Range of values
   Minimum:	20.17
   Maximum:	20.781
   Units:	decimal degrees

   Longitude

   Longitude of location as determined by Garmin GPSmap 60CSx GPS in decimal degrees. (Source: U.S. Geological Survey)

   Range of values
   Minimum:	-87.49
   Maximum:	-86.947
   Units:	decimal degrees

   Station

   Text description of sampling location within cave passage. (Source: U.S. Geological Survey)

   Value	Definition
   JAH-S1	JAH-S1 is found in the main corridor approximately 50 meters upstream from the entrance pool in the freshwater layer.
   JAH-S2	JAH-S2 is found in the main corridor where the passage connects to a deeper passage network approximately 70 meters upstream from the entrance pool. Halocline between fresh/brackish and saline waters are accessible at this station.
   JAH-S3	JAH-S3 is found in the deeper corridor more than 100 meters upstream from the entrance pool in the saline groundwater layer.
   CRU-S1	CRU-S1 is found in the main corridor 10 to 50 meters downstream from the entrance pool.
   CRU-S2	CRU-S2 is found in the main corridor more than 50 meters downstream from the entrance pool and near the second opening.
   CRU-S3	CRU-S3 is found in the main corridor more than 70 meters downstream from the entrance pool where passage drops deeper into the saline groundwater section.
   CRU-S4	CRU-S4 is found in the main corridor further downstream from CRU-S3 in the deeper passage (mostly in saline groundwater).
   ODY-S0	ODY-S0 is found in the main corridor located near the entrance pool (flooded sinkhole) in the freshwater.
   ODY-S1	ODY-S1 is found in the main corridor located approximately 20 meters upstream from the entrance in the freshwater.
   ODY-S2	ODY-S2 is found in the main corridor located approximately 50 meters upstream from the entrance in the saline groundwater.
   NWH-S0	NWH-S0 is the passage descending from the entrance pool to the main corridor.
   NWH-S1	NWH-S1 is found in the main corridor located approximately 50 meters downstream from the entrance in the fresh/brackish water.
   NWH-S2	NWH-S2 is found in the main corridor located approximately 70 meters downstream from the entrance in the brackish water.
   NWH-S3	NWH-S3 is found in the main corridor located more than 100 meters downstream from the entrance in the brackish water.

   Sample_ID

   Format for sample id for the study. YUC represents "Yucatan Peninsula," and the numeric code is the unique identifier. Apparent gaps in numbers are a result of different mode of sample collection (thus, those samples are not included in this data release) OR lost samples. (Source: U.S. Geological Survey) Character set (text).

   Depth(m)

   Water depth where sample was collected by diver, obtained with a Piezo-resistive depth sensor in Shearwater Petrel dive computer. (Source: U.S. Geological Survey)

   Range of values
   Minimum:	1.5
   Maximum:	23.0
   Units:	meter

   Date

   Calendar date water sample was collected in the format MM/DD/YYYY (Source: U.S. Geological Survey) Character set (text).

   Salinity(psu)

   Salinity value of water sample calculated by multiplying the ion chromatograph determined chloride concentration by 0.0018066. (Source: U.S. Geological Survey)

   Range of values
   Minimum:	0.15
   Maximum:	36.57
   Units:	unitless

   Chloride(milliM)

   Chloride concentration of water sample measured by ion chromatography. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Range of values
   Minimum:	2.34
   Maximum:	570.9
   Units:	millimolar (mM)

   Sulfate(milliM)

   Sulfate concentration of water sample measured by ion chromatography. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Range of values
   Minimum:	0.15
   Maximum:	29.96
   Units:	millimolar (mM)

   SO4/Cl

   Calculated ratio of sulfate to chloride concentration of the water sample. Blank values indicate data from inputs not available. (Source: U.S. Geological Survey)

   Range of values
   Minimum:	0.049
   Maximum:	0.168
   Units:	unitless

   DIC(milliM)

   Dissolved inorganic carbon concentration of the water samples as measured by coulometry. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Value	Definition
   << empty cell >>	No Data

   Range of values
   Minimum:	1.02
   Maximum:	8.07
   Units:	millimolar (mM)

   delta13C-DIC(permil)

   Carbon isotopic ratio (13C/12C) of dissolved inorganic carbon (DIC) of the water samples relative to the Vienna Pee Dee Belemnite (VPDB) standard expressed in the standard permil notation. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Value	Definition
   << empty cell >>	No Data

   Range of values
   Minimum:	-27.32
   Maximum:	6.78
   Units:	per mil relative to VPDB

   CH4(nanoM)

   Dissolved methane concentration of the water sample determined by analysis by gas chromatography flame-ionization detection. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Value	Definition
   << empty cell >>	No Data

   Range of values
   Minimum:	37.8
   Maximum:	19227.12
   Units:	nanomolar (nM)

   delta13C-CH4(permil)

   Carbon isotopic ratio (13C/12C) of dissolved methane (CH4) in the water sample relative to the Vienna Pee Dee Belemnite (VPDB) standard expressed in the standard permil notation. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Value	Definition
   << empty cell >>	No Data

   Range of values
   Minimum:	-66.743
   Maximum:	-37.065
   Units:	per mil relative to VPDB

   DOC(microM)

   Dissolved organic carbon (DOC) of the water sample determined by high temperature combustion (HTC) oxidation. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Value	Definition
   << empty cell >>	No Data

   Range of values
   Minimum:	18.70
   Maximum:	1175.61
   Units:	micromolar (microM)

   delta13C-DOC(permil)

   Carbon isotopic ratio (13C/12C) of dissolved organic carbon (DOC) of the water sample relative to the Vienna Pee Dee Belemnite (VPDB) standard expressed in the standard permil notation. Blank values indicate sample was either not collected or has not been analyzed. (Source: U.S. Geological Survey)

   Value	Definition
   << empty cell >>	No Data

   Range of values
   Minimum:	-28.52
   Maximum:	-23.02
   Units:	per mil relative to VPDB

   Entity_and_Attribute_Overview:

   The dataset contains one Excel file (geochem_2013-2015.xlsx) with one tab (geochem_2013-2015), and one CSV file (geochem_2013-2015.csv) that corresponds to the tab with the same name in the spreadsheet. The first row (header line) of the CSV file contains the column labels (and is the same information as these attributes). The first row of the Excel spreadsheet contains a header line that includes a short description of the project and the years the data were obtained, the second row indicates the mode of sampling, the third row is the column label with special characters, and the fourth row is the column label without special characters (and it corresponds with the first row of the CSV file). Additionally, a browse graphic (geochem.jpg) and the CSDGM metadata in XML format are provided.

   Entity_and_Attribute_Detail_Citation: U.S. Geological Survey
   

Who produced the data set?

1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
   • David Brankovits
   • John W. Pohlman
2. Who also contributed to the data set?
3. To whom should users address questions about the data?
   U.S. Geological Survey

   Attn: John W. Pohlman

   Research Geochemist

   384 Woods Hole Rd

   Woods Hole, MA
   

   USA

   508-548-8700 x2213 (voice)

   jpohlman@usgs.gov

Why was the data set created?

How was the data set created?

1. From what previous works were the data drawn?
2. How were the data generated, processed, and modified?

   Date: 2015 (process 1 of 2)

   Discrete water samples were collected from Ox bel Ha cave (Cenote Jailhouse, Cenote Odyssey, and Cenote Naach Wennen Ha) and another cave (Cenote Crustacea) during three sampling events: December 2013, August 2014, and January 2015. Cenote and cave samples were collected by scuba divers following protocols established by the American Academy of Underwater Sciences and the National Speleological Society Cave Diving Section. Water samples for geochemical analysis of dissolved materials were collected near sonde profile locations in plastic 60 ml syringes fitted with 3-way stopcocks. The syringes were rinsed with distilled water and dried prior to the dive, and flushed with sample water prior to closing the stopcock. Samples were kept cool during transport to the field lab and preserved within eight hours of collection. More details related to the processing of the samples after collection are provided in the Methods section of Brankovits and others, 2017. Person who carried out this activity:
   

   US Geological Survey

   Attn: John Pohlman

   Research Geochemist

   384 Woods Hole Rd

   Woods Hole, MA
   

   508-548-8700 x2213 (voice)

   jpohlman@usgs.gov

   Date: 2015 (process 2 of 2)

   Analysis of the samples was performed at the Woods Hole Oceanographic Institution (WHOI) and U.S. Geological Survey (USGS) in Woods Hole MA, USA. Sulfate and chloride concentrations were determined using a Metrohm 881 Compact Plus ion chromatograph (IC) equipped with a Metrosep A Supp 5-250 anion column. Chloride concentrations milliMolar (mM) were converted to milligrams per liter (mg l-1) and multiplied by 0.0018066 to determine salinity (psu). The analytical error for chloride and sulfate was +/-3.5 percent (%) of the IAPSO standard sulfate and chloride values.
   Dissolved inorganic carbon (DIC) concentrations were determined with a Model 5011 UIC coulometer and quantified relative to a seawater certified reference material (CRM) with a relative standard deviation (RSD) of 4 percent (%) relative to the CRM value (2.2 millimolar, mM). The stable carbon isotopic content of the DIC was measured with a Thermo-Finnigan DELTAplus XP IRMS with an analytical error (1-sigma) of 1.1 per mil.
   Headspace methane concentrations were determined using a Shimadzu 14-B gas chromatograph (GC) equipped with a flame ionization detector (FID). Headspace concentrations were converted to dissolved concentrations using the method of Magen and others, 2014 and are reported with a relative standard deviation of 2 percent (%).
   The stable carbon isotope composition of methane from the headspace of the serum vials was determined using a Thermo-Finnigan DELTAPlus XL isotope ratio mass spectrometer (IRMS) coupled to an Agilent 6890 Gas Chromatograph (GC) via a Finnigan GCCIII combustion interface with 1-sigma deviation of 1.6 per mil.
   DOC concentration and d13C were analyzed by high-temperature combustion-isotope ratio mass spectrometry (HTC-IRMS) at the USGS-WHOI Dissolved Carbon Isotope Lab (DCIL). The DCIL HTC-IRMS system consists of an OI 1030C total carbon analyzer and a Graden molecular sieve trap interfaced to a Thermo-Finnigan DELTA-PLUS XL IRMS. DOC concentrations are reported with an RSD of less than 5 percent (%) of the measured value. Stable carbon isotope ratios for DIC, methane and DOC are reported in the standard delta-notation relative to VPDB (Vienna Pee Dee Belemnite) with a 1-sigma deviation of less than 0.5 per mil.
   All sample analyses were performed by David Brankovits under the supervision of John Pohlman. More details about the laboratory analyses are described in the Geochemical Analysis portion of the Methods section of Brankovits and others, 2017). Sample processing occurred between 2014 and 2015. Person who carried out this activity:
   

   US Geological Survey

   Attn: John Pohlman

   Research Geochemist

   384 Woods Hole Rd

   Woods Hole, MA
   

   508-548-8700 x2213 (voice)

   jpohlman@usgs.gov

3. What similar or related data should the user be aware of?
   Brankovits, David, Pohlman, John W, Niemann, Helge, Leigh, Mary Beth, Leewis, Mary Catherine, Becker, Kevin W, Iliffe, Thomas M, Alvarez, Fernando, Lehmann, Moritz F., and Phillips, Bil, 2017, Methane- and dissolved organic carbon-fueled microbial loop supports a tropical subterranean estuary ecosystem: Nature Communications 8, Macmillan Publishers Limited, London, United Kingdom.

   Online Links:

   • https://doi.org/10.1038/s41467-017-01776-x

   Magen, C., Lapham, L., Pohlman, J.W., Marshall, K., Bosman, S., Casso, M., and Chanton, J., 20140908, A simple headspace equilibration method for measuring dissolved methane: Limnology and Oceanography: Methods vol. 12, issue 9, Wiley, Hoboken, NJ.

   Online Links:

   • https://doi.org/10.4319/lom.2014.12.637

   Other_Citation_Details: ppg. 637-650
   

How reliable are the data; what problems remain in the data set?

1. How well have the observations been checked?
   The accuracy of each attribute is determined by that analysis specific to that attribute, and is provided in the process step for each measurement
2. How accurate are the geographic locations?
   The horizonal position (coordinates) of the entrance pool of the caves (Cenote Crustacea, Cenote Jailhouse, Cenote Odyssey, and Cenote Naach Wennen Ha) was obtained with a Garmin GPSmap 60CSx GPS, which has a positional accuracy of less than 10 meters. Coordinates for the sampling stations within the caves where the samples were collected from are not available because the GPS does not operate in overhead or underwater settings. The bounding coordinates provided in this data release incorporate the horizontal extent of the passages investigated in this study. However, as stated previously, the precise locations of the passages are unknown.
3. How accurate are the heights or depths?
   The approximate depth associated with each sample was obtained from the collecting divers depth gauge, which is accurate to +/-0.3 m.
4. Where are the gaps in the data? What is missing?
   For missing values, the sample was either not collected, lost in shipping or has not been analyzed. The condition of the missing values (e.g., not collected, lost in shipping or not analyzed), is not specified. Apparent gaps in numbers are a result of different mode of sample collection (thus, those samples are not included in this data release) OR lost samples.
5. How consistent are the relationships among the observations, including topology?
   All data provided in this release were obtained by PhD student David Brankovits under the supervision of USGS Research Geochemist John Pohlman. Although samples were collected over several years during differet sampling campaigns, the collection, processing, and analyses of samples followed the same protocols in a consistent manner.

How can someone get a copy of the data set?

1. Who distributes the data set? (Distributor 1 of 1)
   
   U.S. Geological Survey - ScienceBase

   Attn: GS ScienceBase

   Denver Federal Center, Building 810, Mail Stop 302

   Denver, CO
   

   1-888-275-8747 (voice)

   sciencebase@usgs.gov
2. What's the catalog number I need to order this data set? The geochemical dataset contains the following files: geochem_2013-2015.xlsx (data in an Excel spreadsheet), geochem_2013-2015.csv (same data in a comma-separated text file), a browse graphic (geochem.jpg), and FGDC CSDGM metadata in XML format.
3. What legal disclaimers am I supposed to read?
   Neither the U.S. Government, the Department of the Interior, nor the USGS, nor any of their employees, contractors, or subcontractors, make any warranty, express or implied, nor assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, nor represent that its use would not infringe on privately owned rights. The act of distribution shall not constitute any such warranty, and no responsibility is assumed by the USGS in the use of these data or related materials. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
4. How can I download or order the data?
   • Availability in digital form:

     Data format:	The geochemical dataset contains the data in XLSX and CSV formats along with associated metadata. in format XLSX (version Microsoft Excel For Mac version 16.60) Size: 2
     Network links:	https://sciencebase.gov/catalog/file/get/63069f18d34e3b967a8bd9cc https://sciencebase.gov/catalog/item/63069f18d34e3b967a8bd9cc https://doi.org/10.5066/P91D2OUN

     Data format:	The geochemical dataset contains the data in XLSX and CSV formats along with associated metadata. in format CSV (version Exported from Microsoft Excel For Mac version 16.60) Size: 2
     Network links:	https://sciencebase.gov/catalog/file/get/63069f18d34e3b967a8bd9cc https://sciencebase.gov/catalog/item/63069f18d34e3b967a8bd9cc https://doi.org/10.5066/P91D2OUN

   • Cost to order the data: None.

5. What hardware or software do I need in order to use the data set?
   The data are available in XLSX and CSV formats. The user must have software capable of reading the data formats.

Who wrote the metadata?

Dates:

Last modified: 19-Mar-2024

Metadata author:

U.S. Geological Survey

Attn: John Pohlman

Research Geochemist

384 Woods Hole Rd.

Woods Hole, MA

508-548-8700 x2213 (voice)

508-457-2310 (FAX)

whsc_data_contact@usgs.gov

Contact_Instructions:

The metadata contact email address is a generic address in the event the person is no longer with USGS. (updated on 20240319)

Metadata standard:

FGDC Content Standards for Digital Geospatial Metadata (FGDC-STD-001-1998)