Metadata and Data Sets

| Bouldin Alfalfa || Bouldin Corn || DWR Corn || East End || East Pond || Gilbert Tract || Hill Slough || Mayberry || Sherman Barn || Sherman Island || Sherman Wetland || Tonzi || Twitchell Alfalfa || Twitchell Rice || Vaira || West Pond |

Summary

| Soils || Water Level || Lidar || Dist & Mgmt || Leaf Level || Spectra || Report || Isotope || Harvest || LAI || Ground Penetrating Radar || Soil Moisture || Tree Survey || Water Potential |

IdTypeSiteDates FrequencyTitle Description
5 Dist & Mgmt BA 2016-08-15 - Present Various as needed Farm operations and observed phnomena Dates and information on farm operations, grazing and observed phenomena gleaned from field visits, camera images and conversations.
17 Ground Penetrating Radar TZ 2011-05-03 - 2011-05-05 Once Ground Penetrating Radar by Naama Ground Penetrating Radar by Naama. Six tree location were sampled using 8mx8m grids with 20cm line spacing. Two 100cm x 60cm pits were dug to bed rock at 0.5 and 1.5m from each main bole for calibration. For more details see:
Raz-Yaseef, N., Koteen, L., Verfaillie, J., Baldocchi, D. (2013) Root system structure of a water limited oak savanna estimated with a ground penetrating radar. Journal of Geophysical Research, Biogeosciences.
14 Harvest BC, BA 2016-01-01 - 2019-01-01 Annual harvest estimates Bouldin Island annual farmer yield estimates, 2016, 2017, 2018 Corn silage and alfalfa yield estimates from farmers on Bouldin Island, 2016, 2017, 2018
12 Isotope SW 2017-06-01 - Present 30 min Patty's LGR CO2 and H2O Isotope Laser Installed June 2017.
16 LAI BC, BA, TA 2017-07-26 - 2020-07-30 Approx. monthly during growing season with field visits Optical LAI measured in-situ ~10 measurements taken each time with a LAI-2200C. Most of the measurements were taken with the 2-wand method, where an "above" wand was set up on a tripod and took measurements every 5 sec, and a "below" wand was used to collect data below the crop canopy. The data were processed in the Licor software FV2200, where each "below" measurement was paired with the "above" measurement closest in time; LAI was calculated and corrected for scattering (based on 4A scattering data).
Twitchell Alfalfa: 2017 (2), 2018 (2)
Bouldin Alfalfa: 2017 (3), 2018 (9)
Bouldin Corn: 2017 (5), 2018 (7)
37 LAI TZ 2022-07-19 - 2023-07-25 Once or twice a year during summer Optical LAI measured in-situ 50+ measurements taken each time with a LAI-2200C. Most of the measurements were taken with the 2-wand method, where an "above" wand was set up on a tripod in the open area east of the Tonzi tower and took measurements every 5 sec, and a "below" wand was used to collect data below the tree canopy. The data were processed in the Licor software FV2200, where each "below" measurement was paired with the "above" measurement closest in time; LAI was calculated. Some files were corrected for scattering (based on 4A scattering data); scattering correction usually affected the LAI by <0.05.
7 Leaf Level TZ 2001-01-01 - 2008-12-31 Mostly bi-weekly during the summer Various leaf level measurements Leaf level measurements from 2001 to 2008 compiled by Jessica Osuna. Measurements include A-Ci, A-RH, A-PAR, water potential, stable isotopes, sap flow, etc. This is mostly Tonzi data but also data from Russel Ranch, Oak Ridge and UMBS. Also includes DBH, grass height, LAI.

This entry needs to be updated as this pile of data gets better organized.
10 Leaf Level EE, WP, SW 2017-07-12 - 2018-06-26 Handful of dates LI-6400 measurements of Tule and Cattail Leaf level measurements of tule and cattails including at least one 24 hour measurement period.

More details needed here.
18 Lidar TZ 2003-08-24 Once Lidar flight by Airborne1 On August 24, 2003, laser altimetry data were acquired with Optech ALTM 2025, which recorded both first and last returns for each laser pulse. The scanning pattern was z-shape. The claimed vertical accuracy from the data provider is 18 cm with 95% confidence and the horizontal accuracy is 1/3000 of the flying height. The swath is ca. 300m and the flying altitude is ca. 500m. The footprint size is about 18 cm. The average posting density is 9.5 points per square meter, resulting in an average spot spacing of about 32 cm. To obtain such a high pulse density, the site was flown twice.
UTM zone 10, NAD83 / NAVD88, meters, ascii
Bald Earth (t e n z i)
Extracted Features (t e n z i)
0.50m Grids (e n z)
Model Keypoints (e n z)
First Pulse all-shots (t e n z i)

citation
Chen, Q., D. Baldocchi, P. Gong, and M. Kelly (2006), Isolating individual trees in a savanna woodland using small footprint lidar data, Photogrammetric Engineering and Remote Sensing, 72(8), 923-932.
6 Lidar SI, MB, SB 2007-02-01 Once Sherman Island part of DWR Delta wide 2007 Lidar flight These data are from LIDAR flights of the Sacramento-San Joaquin Delta conducted during late January and February of 2007. The work was conducted under contract issued by California Department of Water Resources to URS Corporation. All data are registered to UTM Zone 10, NAD83, vertical datum NAVD88. The elevation units in the point files are in meters. The elevations for the ESRI grids are in decimeters (done to allow integer type grids to save file size).

The bare earth grid is of one meter resolution.

The accuracy specifications are as follows:

Vertical accuracy: 95% at 0.6’ (<18.5cm) and 90% at 0.5’ (15cm)
Horizontal accuracy: 1.0’ (30cm), 1 sigma.
19 Lidar TZ 2009-04-20 Once Lidar flight by Airborne 1 Corporation The LiDAR data were collected for the study area on April 20, 2009. The sensor recorded the first and last return pulses. The scanning pattern was z-shaped. The scanning angle was 15°, and the flying altitude was about 900 m, corresponding to a swath of about 500 m. The average horizontal GPS solution difference from two base stations was 10–15 cm. The vertical accuracy was −0.01 ± 0.05 m, based on the comparison of 819 test points and interpolated digital elevation model elevations. The footprint size was about 18 cm. The average posting density was 4.1 points per square meter, resulting in an average spot spacing of about 0.5 m.
NAD83/NAVD88, UTM Zone 10, meters
Last Pulse and First Pulse in LAS and XYZ formats

Kobayashi, H.,Baldocchi, D.D., Ryu, Y., Chen, Q., Ma, S, Osuna, J., Ustin, S. 2011. Modeling Energy and Carbon Fluxes in a Heterogeneous Oak Woodland: A Three-Dimensional Approach. Agricultural and Forest Meteorology. 152:83-100
20 Lidar TZ 2012-03-21 Once Terrestial Lidar by Martin Beland - no leaves Approximately six locations were scanned resulting in a total of 36 individual scans. Control points are included to tie scans together. The VZ-400 terrestrial LiDAR instrument used at Tonzi emits laser pulses at a wavelength of 1550 nm and can cover 360◦azimuthally and from −40◦ to +60◦ in elevation angle. The instrument has three important features which are not common among other terrestrial LiDAR scanners: (1) it can perform scans rapidly at a speed of 122,000 measurements per second, (2) it offers the possibility of using specially designed targets to make multiple scan co-registration significantly more efficient when combined with the RiScan Pro software (Riegl inc., Austria), and (3) the instrument can record full-waveform data (i.e., all pulse echoes are recorded at a small temporal interval) but this comes at a cost in acquisition time. The diameter of the laser pulse when leaving the instrument is7 mm, and the pulse divergence is 0.3 mrad. The trees were scanned from a distance of about 10–12 m. At this distance, the pulse cross section diameter for the Riegl VZ-400 is about 1 cm. The overall plot area was scanned from six different locations. All leaf-off and leaf-on scans were carried out from the same positions using the same angular resolution of about 280 urad. Depending on the coverage area settings used, each scan took between 2 and 6 min to complete.

As of 2019-06-05 the data is on the Synology file server in room 107
21 Lidar TZ 2012-05-15 Once Terrestial Lidar by Martin Beland - leaves on Approximately six locations were scanned resulting in a total of 36 individual scans. Control points are included to tie scans together. The VZ-400 terrestrial LiDAR instrument used at Tonzi emits laser pulses at a wavelength of 1550 nm and can cover 360◦azimuthally and from −40◦ to +60◦ in elevation angle. The instrument has three important features which are not common among other terrestrial LiDAR scanners: (1) it can perform scans rapidly at a speed of 122,000 measurements per second, (2) it offers the possibility of using specially designed targets to make multiple scan co-registration significantly more efficient when combined with the RiScan Pro software (Riegl inc., Austria), and (3) the instrument can record full-waveform data (i.e., all pulse echoes are recorded at a small temporal interval) but this comes at a cost in acquisition time. The diameter of the laser pulse when leaving the instrument is7 mm, and the pulse divergence is 0.3 mrad. The trees were scanned from a distance of about 10–12 m. At this distance, the pulse cross section diameter for the Riegl VZ-400 is about 1 cm. The overall plot area was scanned from six different locations. All leaf-off and leaf-on scans were carried out from the same positions using the same angular resolution of about 280 urad. Depending on the coverage area settings used, each scan took between 2 and 6 min to complete.

As of 2019-06-05 the data is on the Synology file server in room 107
26 Lidar BA, BC, EE, MB, SB, SW, TA, WP 2016-12-01 - 2017-03-07 Once Delta-wide USGS Lidar flight Winter time Lidar flight commissioned by the USGS and flown by Woolpert. Horizontal datum: NAD83 (NSRS2007) Epoch 2017.95, UTM Zone 10N, meters. Vertical datum: NAVD88, GEOID12B, US Survey Feet, Orthometric. Includes classified point cloud, features shape files, bare earth DEM, orthometric imagery (0.3-meter16-bit 4-band RGB-IR tiles in TIFF format with World Files). The entire Delta is covered by 8 points per m2, 0.5m DEM.
3 Lidar BA, BC, WP, EP, EE, TA, TW, MB, SB, SW 2018-09-20 Once NCALM Lidar Flight Lidar flight data collection from Kyle Hemes NCAL project: Ecosystem Structure as a Driver of Climatic, Habitat, and Hydrological Services in Heterogeneous Restored Wetlands. Point clouds (*.las files), 1m resolution DEM and DSM (arcgis GridFloat files), visible imagery (*.tif files) of Sherman, Twitchel and Bouldin Islands. UTM Zone 10N, meters, NAD83(2011) epoch 2010.00 / NAVD88 (GEOID12B)
15 Report EE 2015-07-19 - 2016-02-25 Once Bad sonic U description and resolution A broken wire in the sonic cable caused U to be record as noise rather than signal. It did not significantly affect the flux calculation but u-star, wind speed and wind direction were not recoverable. These variables were filled with regressions of TA data.
11 Report SW 2017-01-01 every time processing fixing nighttime uptake at SW Sherman wetland (once pasture) was flooded winter 2016, and we sawuptake spikesat night -there wasno vegetation yet.
13 Report SW 2017-06-23 - 2017-08-02 Once 7550 configuration file correction –June to August 2017 From 2017-06-23(DOY 174)to 2017-08-02 (DOY 214) an incorrect 7500 configuration file was running on the tower. We tried to back out the coefficients but could not determine what coefficients the data had been recorded with. We ended up generating a regression with the 30min data from MB and correction the 20Hz data with that regression.
22 Soil Moisture TZ 2011-05-10 - Present houly approximately COSMOS areal soil moisture Soil moisture from the COSMOS project. The method involves measuring low-energy cosmic-ray neutrons above the ground, whose intensity is inversely correlated with soil water content and with water in any form above ground level (Note: the contributions from subsurface and surface waters are distinguishable). This non-contact technique is capable of measuring average soil water content over a footprint of 34 hectares (a circle with a radius of 330 m) and depths up to 50 cm (10-20cm for Tonzi). Neutron counts in two energy bands (fast, >1 keV; and thermal, <0.5 eV) are measured.
1 Soils SI 2007-11-08 Once Sherman Island Soil Profiles Soil profiles six location from 0-60cm, Carbon, Nitrogen, Bulk Density, pH, Cation Exchange Capacity, Volumetric Water Content
Method: Used trencher to dig ~6m trench on north side of enclosure, Dug 2 parallel 3" trenches about one foot apart and dug out space between them with a shovel. The profiles are about 1 m from each other, and there are five in total. Yit took 0-10 cm surface samples with his sampling apparatus (un-even volume precision).
From field notes, samples were taken on several dates by Ben Runkle from 2007-10-11 to 2007-12-18.
29 Soils SI 2010-04-29 Once Sherman Island Levee Soil Sampling Jacyln took soil samples from tidal area at the levee location. Not sure where the data is.
23 Soils TZ 2011-05-03 - 2012-05-04 Once Soil cores for C:N and root samples Soils and roots were sampled near five trees and two clusters. 16 locations per site were sampled for roots with a 3.2cm corer in 10cm increment profiles to 60cm. 14 locations per site were sampled for C:N with a 3.2cm corer in 10cm increment profiles to 50cm. For more details see:
Koteen, L. E., N. Raz-Yaseef, and D. D. Baldocchi (2014), Spatial heterogeneity of fine root biomass and soil carbon in a California oak savanna illuminates plant functional strategy across periods of high and low resource supply, Ecohydrology, doi: 10.1002/eco.1508
35 Soils WP, MB 2013-08-30 - 2013-10-14 Once Delta-wide soil survey by JGI Susannah Tringe Soil samples collected by Wyatt Hartman and Susie Theroux from Susannah Tringe's group at LBL. Sites were sampled for bulk density, C/N/anions/elements in the soil and porewater, and microbial communities. Soil samples were incubated in the lab to measure greenhouse gas fluxes.
27 Soils EE 2013-12-16 - 2013-12-16 Once East End preflood soil sampling 107 samples for C/N, 20 samples for Fe, 88 samples for bulk density. Single depth, 107 spatial locations with high precision GPS. Higher density in EE tower footprint and two other possible portable tower locations.
28 Soils SW 2016-01-01 - 2016-05-30 Once Sherman Wetland preflood soil sampling Dennis remembers Tyler Anthony take a whole bunch of samples (including bulk density measurements) right before we set up the tower in May 2016. Not sure where if we have the data or if Tyler has it.
30 Soils SB, BC, Bouldin 1, Staten 2016-08-01 - 2018-03-15 Once %C, %N sampled by Tyler Anthony Tyler Anthony (Whendee Silver's lab) analyzed %C and %N from shallow soils:
-Sherman Barn (Tyler refers to it as "Sherman Pasture"), 0-10cm, probably sampled in Spring 2018
-Bouldin Corn, 0-15cm, sampled 2017-05-16
-Bouldin 1 (Tyler's alfalfa auto-chamber site by the barn), 0-15cm?, sampled 2016-08-01
-Staten ("taken from a corn field west of the road), 0-10cm, sampled 2018-03-15
25 Soils SB, BC, EP, EE, BA, SW, MB 2018-08-27 - 2018-08-28 Once Soil cores for C:N and microbial community Soil samples were collected to be analyzed for soil moisture, bulk density, C:N, and microbial community. Generally at each site, two transects were sampled (T1 to the north, T2 south), starting near the tower and going to the west. Each transect had 5 sampling locations each (P1-P5), each location about 5m apart. At wetland locations (SW, MB, EE, EP, WP), soils were collected at 0-15cm depth. At agricultural locations (BA, BC, SB), soils were collected at 3 depths: 0-15cm, 15-30cm, and 30-60cm. For more information, see the field notes from each day.
2018-08-27
-Sherman Barn: The water table was around 50-60cm.
-Bouldin Corn: Transects starting from the first corn rows running parallel away from the tower. Dry peat layer around 60 cm.
-Bouldin Alfalfa: Transects starting roughly 5m from the tower. A smaller subsample was taken for microbial analysis.
-East End: Transects starting 5-10m from the tower, going west/southwest through dense veg with the T2P4 and T2P5 taken from veg near the open water section. A smaller subsample was taken for microbial analysis.
-East Pond: Transects starting about 7m from tower to the west (T1) and southwest (T2). (i.e. after the big open pond section by the solar panels). A smaller subsample was taken for microbial analysis. T2P5 was taken from the more uniformly vegetated area to the west. Other samples were mostly from fairly open water areas near clusters of veg.
2018-08-28
-Mayberry: Two transects (T1 in veg, T2 near the open water) each going northwest of the tower and took microbial subsamples from each core.
-Sherman Wetland: We took two transects (T1 to the north, T2 south) going west from the tower starting where the water was about 20 cm deep and following the low vegetation.
24 Soils TZ, VR 2019-04-30 - 2019-04-30 Once Soil cores for C:N and microbial community Soil samples were collected to be analyzed for soil moisture, bulk density, C:N, and microbial community. At each sampling location, soil samples were taken with a narrow corer at four depths: 0-10, 10-20, 20-30, 30-40 cm. At Vaira, samples were taken in six locations surrounding the tower site. At Tonzi, samples were taken in twelve locations in open locations and near trees.
38 Soils HS 2021-07-07 - 2021-07-08 Once Preflood base line sampling 2021-07-07 to 2021-07-08. Soil cores were collected from nine locations at Hill Slough. At each location, three short cores (up to 30 cm) and one long core (up to 60-99 cm) were collected. Two of the short cores were cut into approximately 2.5 cm sections, and one at 1 cm thick intervals in the lab. Long cores were sliced at 5 cm intervals in the field. Soil samples were analyzed for delta13C, delta15N, C, N, and organic matter content. Additionally, at locations 1, 2, and 4, soils were analyzed for Pb-210. Scott Jones from USGS conducted vegetation and RTK-GPS (Real Time Kinematics with centimeter resolution) measurements for the sample locations and additional points in between sample locations on 2021-07-20.

Regarding the post-fixes on the sample names: N denotes North, E = East, S = South, and L = Long. The long core at each plot was collected at the center of the triangle formed by N, E, and S (with approximately 2 meters distance between cores). Due to a shortage of acrylic short tubes, from site 5 to 9, we collected N, E, and L cores.
8 Spectra BA 2017-08-23 - Present Approx. monthly during summer with field visits Handheld Spectral Reflectance Spectral typically collected with and Ocean Optics JAZ spectrometer (sn JAZA2903) 400nm-900nm useful spectrum. An incoming reference, dark and reflected sample spectra are collected to generate reflectance spectra. A cosine corrected diffuse head is held by hand at about shoulder height facing up or down.
31 Tree Survey TZ 2018-06-06 - 2018-06-08 Once Tree Survey By Miriam The survey was a census of 14 circular plots, pseudo-randomly placed in the approximate eddy covariance tower flux footprint (within 500 m from the tower). Plot placement aimed to sample tree species (Quercus douglasii QUDO, Pinus sabiniana PISA) and sizes that were roughly representative of the entire footprint, according to a 2003 lidar survey (itself deemed insufficiently accurate for initialization). Eleven plots had a radius of 13 m and three had a radius of 20 m, for a total area censused of 9,610 m2. In each plot, we measured trees which were > 1.5 m tall. We recorded: geographical location (Trimble GeoXT 6000 with external antenna and ArcPad software, differentially corrected using base station data to an accuracy of <50 cm [75.07% of data], 0.5 - 1 m [17.71% of data], 1 - 2 m, [6.47 % of data], or 2 - 5 m [0.75% of data]), diameter at breast height (DBH), and height (Nikon Forestry Pro laser rangefinder; 3 point method; reported distance accuracy is ± 1 m at distances shorter than 300 m).
32 Tree Survey TZ 2018-06-08 Once Pines for tree rings cores by Miriam 20 pines (Pinus sabiniana PISA) were measured and cored as part of Jackie Ho's undergrad thesis. We aimed for large trees but not so large that the borer couldn't get to the center. For relatively straight-standing trees and for trees on slopes (which have growth more likely to reflect water deficit). Locations are from a phone GPS, diameter at breast height (DBH), and height (Nikon Forestry Pro laser rangefinder; 3 point method; reported distance accuracy is ± 1 m at distances shorter than 300 m).
33 Tree Survey TZ 2019-12-16 Once DBH and crown size by Miriam and Ana Measurements of 20 QUDO & 20 PISA crown diameters (in 2 directions, not necessarily perpendicular) and DBHs. The purpose of data collection was to get a general idea of DBH~crown diameter allometry, but note that these trees were chosen in an ad-hoc manner and were not a random sample. DBH measured with a tape; crown width measured by two people with a tape, looking up to position the ends of the tape appropriately. GPS points from a phone, IDOL alcatel, with the 'GPS coordinates' app. Measurements done 12/16/19.
34 Tree Survey TZ 2023-04-26 Multi year Partial survey of banded trees by Sophie and Megan Sophie Ruehr and Megan Hur, 93 of the banded tress were measured and photographed, band increment and circumference.
2 Water Level EP 2018-04-17 - Present Approx. bi-weekly with field visit Water Level from Staff Gauge Manual reading of water level from the staff gauge. The staff gauge is bolted to the tower scaffolding and should not move. It was inserted into the water column until resistance was encountered. There are about 40cm of muck and vegetation in the water column above the bottom on the staff gauge.
36 Water Potential TZ 2001-03-01 - Present Bi-weekly during green leaf season Oak tree leaf water potential Leaf water potential using a pressure bomb to force water out of sprigs of oak leaves (some pine too) have been measured by many different people over the years. Generally three trees have been used (102, 255 and 92 aka Liu Kang's tree) although some times the tree ids were not recorded (2010, 2011, 2012). Also young and old pine trees but again not always recorded. Usually small sprigs of multiple oak leave were cut from the tree in multiple (sunlit, shade, different height) locations and immediately measured. Midday is the most prevalent measurement time, but many predawn measurements were done, and occasionally multiple times throughout the day. Sometimes only qualitative times of "predawn" and "midday" were recorded these were assumed to be 30min before sunrise and solar noon.