AndreaBozzo/ceres-open-data-index huggingface dataset:
Riparian vegetation data used for comparing sampling methods along the Colorado River, Grand Canyon, Arizona

These data were collected as part of a methodological comparison for collecting riparian vegetation data. Two common methods for collecting vegetation data were used: line-point intercept and 1m2 ocular quadrats (visual cover estimates). At each site and transect, both methods were used to collect cover and composition data by four different observers. The same transects and quadrats were utilized for both methods and all observers. Field data collected included percent cover for total living foliar cover, each plant species encountered, litter, dead plant material that is still standing, and ground cover features (biological soil crust, rock, sand, and fine soil particles). Line-point intercept data were collected at 25 cm intervals along each transect and at four points along the edge of each 1m2 quadrat. Since transects varied in length, the number of data points collected along each transect also varied. A pin flag was dropped vertically to the ground at 25 cm intervals and every plant species and ground cover element that touched the pin flag was recorded in the order it touched the pin flag from top to bottom, including any species that would touch the pin flag if it continued upward indefinitely. Each species was only recorded once at each point. Ocular quadrat data were collected at each of the 1 m2 quadrats. Cover estimates were recorded to the nearest 5% other than those estimates under 5% which were recorded as either 1% or “trace”. Observers calibrated their ocular estimates at the beginning of sampling and when a new observer started sampling. Observers were given reference cards illustrating multiple levels of percent cover (1 – 95%), which were used during calibration and throughout data collection. Five observers with three levels of experience participated in this study. Two observers had extensive experience with identification of plant species in the study area, as well as with the methods used. One observer was familiar with the methods as well as riparian plant identification, but had not previously worked in this study area. Two observers had not worked in this system or with these methods before, but had experience conducting vegetation surveys. All observers received on-site training. At each site, four observers sampled the entire site using both field methods.

Tags: arizona, biological-sampling, biota, colorado-river, field-sampling, glen-canyon-dam, glen-canyon-national-recreation-area, grand-canyon, lees-ferry, line-point-intercept, northern-arizona, ocular-quadrat, riparian-ecosystems, riparian-environments, riparian-vegetation, usgs-5beef04ae4b08f163c2dcb8e, vegetation, vegetation-sampling-methods
Organization: Department of the Interior
Circa 1975 Land Area in Coastal Louisiana - Spatial Data - Landsat MSS

The dataset presented here represents a circa 1975 land/water delineation of coastal Louisiana used in part of a larger study to quantify landscape changes from 1932 to 2016.  
The dataset contains two categories, land and water.  For the purposes of this effort, land includes  areas characterized by emergent vegetation, upland, wetland forest, or scrub-shrub were classified as land, while open water, aquatic beds, and mudflats were classified as water.  For additional information regarding this dataset, refer to USGS SIM 3381.

Tags: central-louisiana-coastal, east-central-louisiana-coastal, eastern-louisiana-coastal, louisiana, louisiana-coastal, usgs-5bfc392de4b045bfcae302d2, west-central-louisiana-coastal, wetland-change, wetland-gain, wetland-loss, wetlands
Organization: Department of the Interior
Metagenomics analysis of groundwater, surface water, and sand samples at Jeorse Park in East Chicago, Indiana, 2017

This dataset provides results of a targeted bacterial community metagenomic analysis of surface water, groundwater, and sand samples at Jeorse Park on Lake Michigan in East Chicago, Indiana. Seventy-two samples were collected from 6 sites in 2017. Samples were analyzed for the 16S ribosomal RNA (16S rRNA) gene (the S in 16S refers to the rate of sedimentation, in Svedberg units, of the RNA molecule in a centrifugal field), and one sample was excluded because it produced too few reads. The 16S rRNA gene is the most conserved of three rRNA genes (16S, 23S, and 5S) and is considered the most reliable for identification and taxonomic classification of bacterial species (Bouchet and others, 2008). Taxonomic analysis was performed using Illumina paired-end sequencing by MiSeq to sequence V3-V4 of the gene. Determination of the relative abundance of bacterial species found in water can be used to track sources of fecal contamination by detecting host-specific markers in the sample.  
The U.S. Geological Survey (USGS), in cooperation with the Great Lakes Restoration Initiative, collected data to study the sources and occurrences of continual high E. coli detections at urban beaches along the Lake Michigan shoreline in Northwest Indiana and northeastern Illinois. High E. coli detections cause the beaches to be closed for recreational use until results from additional samples verify that E. coli levels have fallen below the threshold of 235 cells per 100 ml. The project used microbial source tracking (MST) and metagenomics analyses to identify the sources of E. coli. Additionally, continuous water quality parameters and surface-water samples were collected to look at biological and environmental indicators. Synoptic surveys of water quality, circulation/transport, and bathymetry were done to help study surface-water flow patterns. Groundwater samples were taken to compare with surface-water E. coli results. Groundwater wells were installed at Jeorse Park Beach in 2017 and additional wells were installed at Whihala West beach in late 2017 and early 2018.  
This data release contains three files. One file, entitled "metagenomics_sample_identification.txt,” contains a list of each sample, along with the site identifier (site ID), station name, replicate number, date of sampling, and substrate from which the sample was taken.  The next file, entitled “metagenomics_taxonomy.txt,” contains a taxonomic classification of the 16S rRNA sequences obtained from every sample.  The third file, contains metadata regarding the collection and analysis of the samples. 
Reference: 
Bouchet, Valerie, Huot, Heather, and Goldstein, Richard, 2008, Molecular genetic basis of ribotyping: Clinical Microbiology Reviews, 21(2), 262-273, https://doi.org/10.1128/cmr.00026-07.

Tags: 16s-rrna, bacteria, beach-health, east-chicago-in, gene-sequence-analysis, great-lakes, jeorse-park, lake-michigan, nearshore, northwest-indiana, usgs-5beeb5d1e4b08f163c24a1e2
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 2015 vegetation structure dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the vegetation structure dataset from 2015.

Tags: biodiversity, biota, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, species-composition, state-of-hawaii, usgs-5bee5f1ae4b08f163c24a18a, vegetation-structure
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 1977 vegetation structure  dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the vegetation structure dataset from 1977.

Tags: biodiversity, biota, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, species-composition, state-of-hawaii, usgs-5bee5f02e4b08f163c24a188, vegetation-structure
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 2015 vegetation species dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the vegetation species dataset from 2015.

Tags: biodiversity, biota, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, species-composition, state-of-hawaii, usgs-5bee5eede4b08f163c24a186, vegetation-species
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 2015 vegetation description dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the vegetation description dataset from 2015.

Tags: biodiversity, biota, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, species-composition, state-of-hawaii, usgs-5bee5eb5e4b08f163c24a182, vegetation-description
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 1977 vegetation description dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the vegetation description dataset from 1977.

Tags: biodiversity, biota, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, species-composition, state-of-hawaii, usgs-5bee5d96e4b08f163c24a17f, vegetation-description
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 2015 pig dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the pig dataset from 2015.

Tags: biodiversity, biota, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, pig-sign, species-composition, state-of-hawaii, usgs-5bee5d81e4b08f163c24a17d
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 1977 pig dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the pig dataset from 1977.

Tags: biodiversity, biota, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, pig-sign, species-composition, state-of-hawaii, usgs-5bee5d5be4b08f163c24a17b
Organization: Department of the Interior
Vertical electrical sounding (VES) geophysical data collected in the Scott M. Matheson Wetlands Preserve Near Moab, Utah

Vertical electrical soundings (VES) are used to develop depth-resolved models of aquifer resistivity by making electrical potential measurements at increasingly larger electrode spacing, with the array centered around a common point. 
Variations in modeled electrical resistivity with depth can be used to infer groundwater salinity and preferential fresh groundwater flow zones. Each of the 4 VES measurement integrates approximately 11 individual electrical soundings with 4 electrodes 
driven into the soil in a linear Wenner array with electrode spacings ranging from 1 to 40 m. Data were collected manually with a SuperSting electrical resistivity meter (AGI - Advanced Geosciences, Inc) and recorded by hand in a field book.

Tags: electromagnetic-surveying, environment, geophysics, geoscientificinformation, groundwater, hydrogeology, hydrology, inlandwaters, moab, scott-m-matheson-wetlands-preserve, surface-water, usgs-5bf46b60e4b045bfcae1e9a4, utah
Organization: Department of the Interior
Monitoring Hawaiian Biodiversity: Pilot study to assess changes to Hawaii Island forest birds and their habitat - 2015 bird dataset

The Hawaii Forest Bird Survey (HFBS) systematically characterized plant and bird communities across transects spanning all major Hawaiian Islands except O‘ahu. This extensive dataset has now been organized into a database and associated geographic information system (GIS) layers. This baseline provides an opportunity to assess how forest ecosystems and their constituent bird and plant populations have changed over time. As part of the HaBiTATS (Hawaiian Biodiversity Trends Across Time and Space) project, a select area on Hawai‘i Island was surveyed in 2015 with the objective of demonstrating the potential of using the HFBS methodology to reassess the status of bird and plant communities across multiple geographic regions and islands. The results of the comparative study presented herein highlight examples of the apparent vulnerability and resiliency of native-dominated Hawaiian ecosystems. Specific study objectives were to: (1) collect information on plant and bird species community composition, abundance, and spatial distribution following the original HFBS methodology; (2) assess changes in several biodiversity metrics; (3) examine changes in the distribution of invasive non-native species as well as changes in land use as potential drivers of native biodiversity patterns, and (4) demonstrate field and data analysis methods that may be applied to a large-scale biodiversity monitoring program. This is the bird dataset from 2015.

Tags: biodiversity, biota, birds, climate-change, ecological-drivers, hamakua, hawaii-island, invasive-species, land-use, pacific-ocean, species-composition, state-of-hawaii, usgs-5bee561ce4b08f163c24a170
Organization: Department of the Interior