Harvard Forest

Data Archive

HF293

Soil Carbon in a Hemlock Stand Infected by Hemlock Woolly Adelgid at Harvard Forest since 2015

Related Publications

Data

• hf293-01: soil respiration, 2015-2019 (preview)
• hf293-02: soil respiration, 2020-2021 (preview)
• hf293-03: soil temperature and water content (preview)
• hf293-04: dry root biomass (preview)
• hf293-05: root percent C N (preview)
• hf293-06: soil C N (preview)
• hf293-07: soil respiration, 2022-2023 (preview)

Overview

• Lead: Adrien Finzi, Ashley Keiser, Marc-Andre Giasson, Matthew Nieland
• Investigators: Mark VanScoy
• Contact: Information Manager
• Start date: 2015
• End date: 2023
• Status: ongoing
• Location: Prospect Hill Tract (Harvard Forest)
• Latitude: +42.539 degrees
• Longitude: -72.180 degrees
• Elevation: 355 meter
• Datum: WGS84
• Taxa: Tsuga canadensis (eastern hemlock)
• Release date: 2026
• Language: English
• EML file: knb-lter-hfr.293.10
• DOI: digital object identifier
• EDI: data package
• DataONE: data package
• Related links:
• Long-Term Impacts of the Hemlock Woolly Adelgid on Forest Carbon at Harvard Forest 2008-2011
• Study type: long-term measurement
• Research topic: forest-atmosphere exchange; invasive plants, pests and pathogens; soil carbon and nitrogen dynamics
• LTER core area: organic matter movement, disturbance patterns
• Keywords: biomass, carbon, hemlock, hemlock woolly adelgid, nitrogen, roots, soil organic matter, soil respiration, soil water content
• Abstract:

  The main objective of this research is to study changes in soil carbon stocks (soil C, root biomass) and fluxes (soil respiration) in a hemlock stand that is currently infested by the hemlock woolly adelgid, and where trees are declining in vigor and dying off.

  Soil respiration is measured throughout the growing season using an automated system, which produces a long-term, high-temporal-resolution series of soil respiration over multiple locations.

  Soil carbon stocks and root biomass are estimated by sampling soil in multiple locations throughout the hemlock stand following the sampling design used by Serita Frey at Harvard Farm (“Conant plots”). The large number of samples will be used to determine how many should be resampled in the future to be able to determine if any difference in soil C content or root biomass is statistically significant. Soil and roots will be sampled every 5 to 10 years to evaluate the trends in soil carbon stocks during and after the decline of hemlock caused by the hemlock woolly adelgid infestation.

• Methods:

  Soil Respiration

  Starting in the fall of 2015, soil respiration (Rs) has been measured using an automated soil respiration chamber system based on the original design by Jim Tang. There are two sets of automated chambers. The first automated Rs system including 6 chambers (#1-6) was deployed near the Hemlock tower from October 6 to December 16, 2015 to field-test the system and collect preliminary data. In November, we determined that the sampling rate could be doubled, from hourly to half-hourly. The second system, located downstream from the Bigelow Brook weir, (chambers #7-12) was deployed in May 2016. Rs has been measured on each of 6 collars (#1 to 6) in 2015 and 12 collars (#1 to 12) in subsequent years. Chambers 1-6 are in an area visibly affected by the hemlock woolly adelgid while chambers 7-12 are in a relatively healthy hemlock stand. The collars are 7-cm lengths of schedule 80 PVC pipe inserted a few centimeters into the ground. The systems are deployed during the snow-free season.

  Each system comprises 6 chamber collars and lids which are opened and closed pneumatically. The control box includes an infrared gas analyzer (IRGA; LI-840A for box #1-Hemlock tower, LI-800 for box #2-Bigelow Brook), a pump (Brailsford TD-3LS 12VDC), a CR1000 datalogger, a SDM-CD16AC relay controller, a 12VDC power supply, and arrays of solenoid valves to direct compressed air to and from the pistons and to direct sampled air from the chambers to the IRGA.

  Chambers are activated sequentially, one every 5 minutes. At the beginning of each 5-minute measurement period, air is drawn from the selected chamber at 1LPM for 45 seconds while the chamber lid remains open, to flush the tubing. The lid is then closed for 4:15 and CO2 concentration is recorded at a rate of 1 hertz. Chamber lids remain open when the chambers are not activated.

  We convert chamber gas concentrations in ppm to μmol CO2 using the chamber volume, ambient air temperature, and the ideal gas law. Rs is then calculated as the rate of increase in CO2 concentration over the 1-minute period showing the best linear increase during the 4:15 measurement period. The flux is then converted to μmol CO2 m-2 s-1 using the collar surface area (0.0646328 m2). Each flux measurement is visually inspected to make sure the best linear relationship of increasing CO2 concentration with time is used. Data are deleted when no good linear relationship is found. Due to prolonged data gaps due to hardware replacements, there is no gap-filling in the 2022-2023 dataset.

  When measuring CO2 concentration in air, water vapor must be accounted for to prevent potentially significant errors in the CO2 flux calculation introduced by dilution and band broadening. The LI-840A (box #1) measures both CO2 and H2O and applies the correction automatically. On the other hand, the LI-800 (box #2) measures only CO2, which prevents us from directly calculating the correction to apply.

  In the lab, we tested the impact of the H2O correction by back-calculating the corrections applied to the LI-840A data. 18 flux recalculations showed that not applying the H2O correction led to an underestimation of the fluxes of 0.016% ± 2%. Thus we decided not to apply a correction factor to the LI-800 data (box #2).

  Finally, in soil respiration data through 2021, we fill gaps in the data series. Gaps 1-hour long or less are filled by linear interpolation. Longer gaps are filled using a modified version of the Fluxnet-Canada gap-filling algorithm which is usually used to gap-fill and partition eddy covariance fluxes. Briefly, an empirical logistic relationship between Rs and soil temperature is fit to the data for the whole year for a given chamber. The relationship is allowed to vary over time using a 100-point moving window and introducing an empirical parameter. This relationship is then used to estimate missing Rs values (i.e., to fill gaps in the data series). Gap filling was not continued for 2022-2023 due to long periods when the instrument was under repair.

  Soil Temperature and Water Content

  Soil temperature is measured, using a Campbell Scientific 107 probe, at the interface of the organic and mineral soil horizons besides each soil respiration collar.

  At each of the two sampling sites, soil water content (SWC) is measured at two locations in the area where the collars are located. At each location, SWC is measured at the top of the mineral soil using a Campbell Scientific CS616 probe. At one of the locations, SWC is also measured using homemade half-bridge sensors developed by Borken et al. (Borken, W., Davidson, E.A., Savage, K., Gaudinski, J., Trumbore, S.E., 2003. Drying and Wetting Effects on Carbon Dioxide Release from Organic Horizons. Soil Sci. Soc. Am. J. 67:1888–1896). Half-bridge sensors are used to measure two repetitions of SWC at 2-cm and 6-cm depth in the organic horizon.

  At the moment, field calibration of the half-bridge sensors has not been done. Consequently, measured voltages have not been converted to soil water content but the data can be used as an index of soil water content in the organic horizon.

  Soil temperature and water content sensors are left in place over the winter to continue acquiring data.

  Soil Carbon and Root Biomass

  To estimate soil carbon stocks and root biomass, soil samples were collected in 17 plots located in different areas in the hemlock stand. In July and August 2015, 3 plots were established in the flux footprint of the Hemlock tower and 3 others in the Bigelow Brook Weir area. In June 2016, 10 plots were added in the flux footprint of the Hemlock tower and 1 in the Bigelow Brook Weir area.

  Samples have been collected in 6 subplots in each plot following the sampling design used by Serita Frey at Harvard Farm (“Conant plots”). In each subplot, we collected a 10 cm × 20 cm (plots 1-6) or 10 cm × 10 cm (plots 7-17) organic horizon monolith and sampled the underlying mineral soil to a depth of 30 cm in 10 cm increments using a 4.7cm-diameter corer. The large number of samples will be used to determine how many should be resampled in the future to be able to determine if any difference in soil C content or root biomass is statistically significant.

  Samples were brought to Boston University and kept refrigerated at 4°C until being processed. Samples were homogenized by sieving through 2-mm mesh and removing rocks and woody debris. At the same time, roots were picked and set aside. Unfortunately, rocks were not weighed separately for plots #1-6. The mass listed in file Soil_CN.csv for these plots is the average rock mass of plots #7-16.

  Subsamples of the sieved soils were dried at 60°C for at least 48 hours to determine soil gravimetric water content. The dry soil was later ground to a fine powder and burned in an elemental analyzer (model NC2500, CE Elantech) to determine carbon and nitrogen content.

  Roots were washed with deionized water and sorted into dead and live root pools according to their diameter (fine: less than 2mm, medium: 2-10mm, coarse: greater than 10mm). In some cases, roots were mistakenly not separated between alive and dead. In such a case, it has been noted in the data file. It should be kept in mind that separating roots between alive and dead is a pretty subjective process and we can’t guarantee that all roots labelled as alive or dead have been sorted into the correct category.

  Roots were then dried at 60°C until weight was stable (at least 48 hours). Dry root biomass was recorded. Several root samples were ground to a fine powder and burned in an elemental analyzer to determine carbon and nitrogen content of the live/dead and different diameter pools of each plot.

  In theory, all mineral soil samples should be 10cm thick (0-10cm, 10-20cm, 20-30cm). In practice, some samples are smaller than that, generally because we hit a large rock during sampling. The actual thickness of each sample is listed in the column labelled “Thickness”.

• Organization: Harvard Forest. 324 North Main Street, Petersham, MA 01366, USA. Phone (978) 724-3302. Fax (978) 724-3595.

• Project: The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. (ROR).

• Funding: National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210.

• Use: This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

• License: Creative Commons Zero v1.0 Universal (CC0-1.0)

• Citation: Finzi A, Keiser A, Giasson M, Nieland M. 2026. Soil Carbon in a Hemlock Stand Infected by Hemlock Woolly Adelgid at Harvard Forest since 2015. Harvard Forest Data Archive: HF293 (v.10). Environmental Data Initiative: https://doi.org/10.6073/pasta/a4ebf6b3eb19d832fcf09c81ec6dfa73.

Detailed Metadata

hf293-01: soil respiration, 2015-2019

1. datetime: date and time (EST)
2. year: year (EST)
3. month: month (EST)
4. day: day (EST)
5. hour: hour (EST) (unit: number / missing value: NA)
6. minute: minute (EST) (unit: number / missing value: NA)
7. chamber: chamber identification number
8. rs: soil respiration (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
9. tsoil: soil temperature at the organic horizon and mineral soil interface (unit: celsius / missing value: NA)
10. rsgf: gap-filled soil respiration (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
11. tsoilgf: gap-filled soil temperature at the organic horizon and mineral soil interface (unit: celsius / missing value: NA)

hf293-02: soil respiration, 2020-2021

1. datetime: date and time (EST)
2. year: year (EST)
3. month: month (EST)
4. day: day (EST)
5. hour: hour (EST) (unit: number / missing value: NA)
6. minute: minute (EST) (unit: number / missing value: NA)
7. chamber: chamber identification number
8. rs: soil respiration (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
9. tsoil: soil temperature at the organic horizon and mineral soil interface (unit: celsius / missing value: NA)
10. rsgf: gap-filled soil respiration (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
11. tsoilgf: gap-filled soil temperature at the organic horizon and mineral soil interface (unit: celsius / missing value: NA)

hf293-03: soil temperature and water content

1. datetime: date and time (EST)
2. year: year (EST)
3. month: month (EST)
4. day: day (EST)
5. hour: hour (EST) (unit: number )
6. minute: minute (EST) (unit: number / missing value: NA)
7. paneltemp1: datalogger panel temperature in control box 1 (chambers #1-6) (unit: celsius / missing value: NA)
8. battvolt1: datalogger voltage in control box 1 (chambers #1-6) (unit: volt / missing value: NA)
9. paneltemp2: datalogger panel temperature in control box 2 (chambers #7-12) (unit: celsius / missing value: NA)
10. battvolt2: datalogger voltage in control box 2 (chambers #7-12) (unit: volt / missing value: NA)
11. tsoil1: soil temperature at chamber 1 (unit: celsius / missing value: NA)
12. tsoil2: soil temperature at chamber 2 (unit: celsius / missing value: NA)
13. tsoil3: soil temperature at chamber 3 (unit: celsius / missing value: NA)
14. tsoil4: soil temperature at chamber 4 (unit: celsius / missing value: NA)
15. tsoil5: soil temperature at chamber 5 (unit: celsius / missing value: NA)
16. tsoil6: soil temperature at chamber 6 (unit: celsius / missing value: NA)
17. tsoil7: soil temperature at chamber 7 (unit: celsius / missing value: NA)
18. tsoil8: soil temperature at chamber 8 (unit: celsius / missing value: NA)
19. tsoil9: soil temperature at chamber 9 (unit: celsius / missing value: NA)
20. tsoil10: soil temperature at chamber 10 (unit: celsius / missing value: NA)
21. tsoil11: soil temperature at chamber 11 (unit: celsius / missing value: NA)
22. tsoil12: soil temperature at chamber 12 (unit: celsius / missing value: NA)
23. swc1: Soil water content at the top of the mineral horizon for control box 1 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
24. swc2: soil water content at the top of the mineral horizon for control box 1 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
25. swc3: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
26. swc4: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
27. swc5: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
28. swc6: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
29. swc7: Soil water content at the top of the mineral horizon for control box 2 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
30. swc8: soil water content at the top of the mineral horizon for control box 2 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
31. swc9: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
32. swc10: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
33. swc11: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
34. swc12: soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
35. tsoil1gf: gap-filled soil temperature at chamber 1 (unit: celsius / missing value: NA)
36. tsoil2gf: gap-filled soil temperature at chamber 2 (unit: celsius / missing value: NA)
37. tsoil3gf: gap-filled soil temperature at chamber 3 (unit: celsius / missing value: NA)
38. tsoil4gf: gap-filled soil temperature at chamber 4 (unit: celsius / missing value: NA)
39. tsoil5gf: gap-filled soil temperature at chamber 5 (unit: volt / missing value: NA)
40. tsoil6gf: gap-filled soil temperature at chamber 6 (unit: volt / missing value: NA)
41. tsoil7gf: gap-filled soil temperature at chamber 7 (unit: celsius / missing value: NA)
42. tsoil8gf: gap-filled soil temperature at chamber 8 (unit: celsius / missing value: NA)
43. tsoil9gf: gap-filled soil temperature at chamber 9 (unit: celsius / missing value: NA)
44. tsoil10gf: gap-filled soil temperature at chamber 10 (unit: celsius / missing value: NA)
45. tsoil11gf: gap-filled soil temperature at chamber 11 (unit: celsius / missing value: NA)
46. tsoil12gf: gap-filled soil temperature at chamber 12 (unit: celsius / missing value: NA)
47. swc1gf: gap-filled soil water content at the top of the mineral horizon for control box 1 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
48. swc2gf: gap-filled soil water content at the top of the mineral horizon for control box 1 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
49. swc3gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
50. swc4gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
51. swc5gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
52. swc6gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 1 measured using homemade sensor (unit: volt / missing value: NA)
53. swc7gf: gap-filled soil water content at the top of the mineral horizon for control box 2 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
54. swc8gf: gap-filled soil water content at the top of the mineral horizon for control box 2 measured with CS616 probe (m3 m-3) (unit: dimensionless / missing value: NA)
55. swc9gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
56. swc10gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
57. swc11gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
58. swc12gf: gap-filled soil water electric signal (NOT converted to water content) at 2-cm depth in the organic horizon for control box 2 measured using homemade sensor (unit: volt / missing value: NA)
59. swc1gf.corr: gap-filled soil water content at the top of the mineral horizon for control box 1 measured with CS616 probe, corrected (see methods for details)(m3 m-3) (unit: dimensionless / missing value: NA)
60. swc2gf.corr: gap-filled soil water content at the top of the mineral horizon for control box 1 measured with CS616 probe, corrected (see methods for details)(m3 m-3) (unit: dimensionless / missing value: NA)
61. swc7gf.corr: gap-filled soil water content at the top of the mineral horizon for control box 2 measured with CS616 probe, corrected (see methods for details)(m3 m-3) (unit: dimensionless / missing value: NA)
62. swc8gf.corr: gap-filled soil water content at the top of the mineral horizon for control box 1 measured with CS616 probe, corrected (see methods for details)(m3 m-3) (unit: dimensionless / missing value: NA)

hf293-04: dry root biomass

1. date: sampling date
2. plot: plot number
3. subplot: subplot number
4. depth: depth
   • OH: organic horizon
   • 0-10cm: 0-10 cm in the mineral soil
   • 10-20cm: 10-20 cm in the mineral soil
   • 20-30cm: 20-30 cm in the mineral soil
5. thickness: sample thickness (unit: centimeter / missing value: NA)
6. live.fine.mass: dry mass of live roots, diameter less than 2 mm (unit: gram / missing value: NA)
7. live.medium.mass: dry mass of live roots, diameter 2-10 mm (unit: gram / missing value: NA)
8. live.coarse.mass: dry mass of live roots, diameter greater than 10 mm (unit: gram / missing value: NA)
9. dead.fine.mass: dry mass of dead roots, diameter less than 2 mm (unit: gram / missing value: NA)
10. dead.medium.mass: dry mass of dead roots, diameter 2-10 mm (unit: gram / missing value: NA)
11. dead.coarse.mass: dry mass of dead roots, diameter greater than 10 mm (unit: gram / missing value: NA)
12. notes: notes

hf293-05: root percent C N

1. plot: plot number
2. subplot: subplot number
3. depth: depth
   • OH: organic horizon
   • 0-10cm: 0-10 cm in the mineral soil
   • 10-20cm: 10-20 cm in the mineral soil
   • 20-30cm: 20-30 cm in the mineral soil
4. live.fine.per.c: percent carbon content of live roots, diameter less than 2 mm (unit: dimensionless / missing value: NA)
5. live.medium.per.c: percent carbon content of live roots, diameter 2-10 mm (unit: dimensionless / missing value: NA)
6. live.coarse.per.c: percent carbon content of live roots, diameter greater than 10 mm (unit: dimensionless / missing value: NA)
7. dead.fine.per.c: percent carbon content of dead roots, diameter less than 2 mm (unit: dimensionless / missing value: NA)
8. dead.medium.per.c: Percent carbon content of dead roots, diameter 2-10 mm (unit: dimensionless / missing value: NA)
9. dead.coarse.per.c: percent carbon content of dead roots, diameter greater than 10 mm (unit: dimensionless / missing value: NA)
10. live.fine.per.n: percent nitrogen content of live roots, diameter less than 2 mm (unit: dimensionless / missing value: NA)
11. live.medium.per.n: percent nitrogen content of live roots, diameter 2-10 mm (unit: dimensionless / missing value: NA)
12. live.coarse.per.n: percent nitrogen content of live roots, diameter greater than 10 mm (unit: dimensionless / missing value: NA)
13. dead.fine.per.n: percent nitrogen content of dead roots, diameter less than 2 mm (unit: dimensionless / missing value: NA)
14. dead.medium.per.n: percent nitrogen content of dead roots, diameter 2-10 mm (unit: dimensionless / missing value: NA)
15. dead.coarse.per.n: percent nitrogen content of dead roots, diameter greater than 10 mm (unit: dimensionless / missing value: NA)

hf293-06: soil C N

1. date: sampling date
2. plot: plot number
3. subplot: subplot number
4. depth: depth
   • OH: organic horizon
   • 0-10cm: 0-10 cm in the mineral soil
   • 10-20cm: 10-20 cm in the mineral soil
   • 20-30cm: 20-30 cm in the mineral soil
5. thickness: sample thickness (unit: centimeter / missing value: NA)
6. soil.mass: mass of wet soil, not including rocks greater than 2 mm (unit: gram / missing value: NA)
7. rocks.mass: mass of rocks in sample. For plots #1-6, rocks mass is the average of plots 7-16. (unit: gram / missing value: NA)
8. dry.wet: dry soil mass to wet soil mass ratio (unit: dimensionless / missing value: NA)
9. bulk.density: bulk density (unit: gramsPerCubicCentimeter / missing value: NA)
10. soil.c.per: percent carbon content of soil (unit: dimensionless / missing value: NA)
11. soil.n.per: percent nitrogen content of soil (unit: dimensionless / missing value: NA)
12. soil.c.mass: mass of carbon in soil (unit: gram / missing value: NA)
13. soil.n.mass: mass of nitrogen in soil (unit: gram / missing value: NA)
14. notes: notes

hf293-07: soil respiration, 2022-2023

1. datetime: date and time (EST)
2. year: year (EST)
3. month: month (EST)
4. day: day (EST)
5. hour: hour (EST) (unit: number / missing value: NA)
6. minute: minute (EST) (unit: number / missing value: NA)
7. chamber: chamber identification number
8. rs: soil respiration (unit: micromolePerMeterSquaredPerSecond / missing value: NA)
9. tsoil: soil temperature at the organic horizon and mineral soil interface (unit: celsius / missing value: NA)