Long-term measurements of microbial biomass and activity at the Hubbard Brook Experimental Forest, 1994 - present
TITLE
Long-term measurements of microbial biomass and activity at the Hubbard Brook Experimental Forest, 1994 - present
PRINCIPAL INVESTIGATOR(s)
Peter M. Groffman
Cary Institute of Ecosystem Studies
Box AB
Millbrook, NY 12545
USA
Email: GroffmanP@caryinstitute.org
OTHERS INVOLVED
Patrick J. Bohlen
Linda Pardo
Jennifer Pett-Ridge
Adam Welman
Jason Demers
Abraham Parker
Amanda Thimmayya
Lisa Martel
Evan Grant
Jackie Wilson
Lynn Christenson
Robin Schmidt
Neil Bettez
Stephanie Juice
ABSTRACT:
Long-term monitoring of soil nitrate (NO3-) and ammonium (NH4+) concentrations, microbial biomass carbon (C) and nitrogen (N) content, microbial respiration, potential nitrification and N mineralization rates, and denitrification potential has been ongoing at the Hubbard Brook Experimental Forest since 1994. Samples have been collected in the Bear Brook Watershed (west of Watershed 6) beginning in 1994. In 1998, our sampling regime was extended to Watershed 1 in an effort to monitor and quantify microbial response to a whole-watershed calcium addition.
KEYWORD SET: Hubbard Brook Ecosystem Study LTER
ammonium, carbon, denitrification, HBEF Watershed 1, HBEF Bear Brook Watershed, HBR, Hubbard Brook LTER, microbe, microbial biomass, mineralization, nitrate, nitrification, nitrogen, respiration, soil.
KEYWORD SET: LTER Core Research Areas
inorganic nutrients, primary production.
BEGIN DATE
1994-05-19
END DATE
2014-07-08
LOCATION
Bear Brook Watershed, located west of Watershed 6.
West bounding coordinate: -71.743462
East bounding coordinate: -71.735649
North bounding coordinate: 43.957001
South bounding coordinate: 43.949928
Watershed 1
West bounding coordinate: -71.731339
East bounding coordinate: -71.726311
North bounding coordinate: 43.959286
South bounding coordinate: 43.952053
LOCATION DESCRIPTION
We have initiated a long-term effort to monitor soil nitrate (NO3-) and ammonium (NH4+) concentrations, microbial biomass carbon (C) and nitrogen (N) content, microbial respiration, potential nitrification and N mineralization rates, and denitrification potential in the experimental watersheds at Hubbard Brook. In 1994 we began sampling in the Bear Brook Watershed (west of Watershed 6). In 1998, we added Watershed 1 to our sampling regime in an effort to monitor and quantify microbial response to a whole-watershed calcium addition (http://www.hbrook.sr.unh.edu/current/new_current.htm).
In the Bear Brook Watershed we used the “west of watershed 6 litter trap transects” described by Hughes and Fahey (1994). These are four 100 m transects, 50 m apart with five traps per transect located at low, mid, upper and high elevations - 20 traps per elevation. We sampled within 1.5 m of five traps at each elevation. Litter quality, quantity and composition have been monitored on these transects since 1984. In 1997 we sampled at the upper and high elevations and also at four locations just above and to the west of Rain Gauge 9 in a mixed stand dominated by red spruce and balsam fir. In 1998 we began regularly sampling more extensively in the spruce/fir zone, and discontinued our sampling at the "upper" site. We sampled within 1.5 m of the center of each of 5 randomly chosen sites in this spruce/fir area. Vegetation in the Bear Brook Watershed is roughly equivalent to that in Watershed 6, which is an approximately 80 year old “reference” watershed dominated by northern hardwoods (American beech, sugar maple, yellow birch) at the lower elevations with moderate amounts of red spruce, balsam fir and white birch at the “high” elevation sites.
In Watershed 1 we sampled near a subset of the lysimeter sites established for the calcium addition study. Our sites included the "spruce/fir" Lysimeter Site 2 at the top of Watershed 1, the "high" Lysimeter Site 3, the "mid" Lysimeter Site 4, and the "low" Lysimeter Site 6. These site types and elevations correspond to those in the Bear Brook Watershed. At each lysimeter site we chose 5 replicate plots that were all within ~30 m of the center lysimeter stake. We revisited the same approximate plot during each sampling date. In 1999 we marked out 2 X 3 m plots in these areas, covered them during the helicopter wollastonite addition, then uncovered them and hand-applied wollastonite. We have sampled entirely within these marked plots since the application.
SAMPLING DESIGN
Samples were collected three times each year (note the above exceptions) to correspond with key plant phenological stages: pre-green, peak green, and senescence. Sampling dates were generally in May, July, and October. We also sampled once in December 1999, two months after the wollastonite addition, to determine if there were immediate responses to the calcium. In 1994, May and July 1995, May and July 1996, and from July 1998 to July 1999 we sampled soils using a bulb corer method. In October 1995 and 1996, all of 1997, and in May 1998 we used a pin block method. From May 2000 to 2010 we sampled using a split-PVC corer method.ay 2000 on we have sampled using a split-PVC corer method.
In the pin block method, long (13.2 cm) nails are driven through holes along the edge of a 15 X 15 cm square of ~1 cm plywood that has been placed on the forest floor. There are 4 holes on each side of the pin block. These nails firmly attach the block to the soil, and enclose a "box" of soil for sampling. We use a small saw to cut away roots and soil from the edge of the nails and from underneath the block. We then remove the soil contained by the block and the nails (15 X 15 X 13.2 cm). In 1997 Oe and Oa were collected as a single horizon, and mineral soil was discarded. In other years we separated the organic soil into two layers (Oi/Oe and Oa/A horizons), discarded the mineral soil from the pin block, and used a bulb corer to take a 10 cm mineral core directly under the (removed) soil block.
In the bulb corer method, a typical flower planting and gardening bulb corer is used. These corers are metal, have a handle on top, and have a diameter that gets slightly narrower from top to bottom. The diameter at the bottom of the corer we used is 6.5 cm. Typically, anywhere from 2-8 cores are taken at a given site, depending on horizon depth and density of soils. The corer is inserted 10 cm into the soil and removed with an intact core. The core is pushed out through the top of the corer onto a plastic sheet, where horizon depths are noted and horizons are separated. The mineral soil is discarded and the remaining soil is split into two layers (Oi/Oe and Oa/A horizons). Each layer is measured and placed into a sample bag, with all cores composited by horizon. To obtain a mineral sample we dig down to the first sign of mineral soil (E or B, depending on the site) and attempt to take a full 10 cm core. If it is not possible to obtain a full 10 cm mineral core we take 2-3 partial mineral cores and combine them.
In the split-PVC corer method, a 5 cm diameter split PVC corer is used to take all samples. A split PVC corer consists of a piece of 2 inch (5 cm) PVC pipe, about 15-20 cm long, split lengthwise on both sides. The corer is actually in two pieces. We put the corer together along the cuts, and duct-tape one side -- the "hinge" side. Holding the corer firmly together, we hammer it 10-15cm into the ground. The corer is removed and then opened with the intact soil core inside. The soil is split into three layers (Oi/Oe, Oa/A, and mineral horizons). Each horizon is measured and placed into a sample bag. We typically collect 2-8 cores per site, compositing all cores by horizon.
DATA DESCRIPTION
In most cases, Oi and Oe horizons were composited into one sample, as were Oa and A horizons. Mineral samples generally consist of the top 10 cm of mineral soil beginning below the A horizon. In 1994 and May and July 1995, only Oi/Oe and Oa/A horizons were sampled. In 1997 only Oe and Oa horizons were collected, and they were composited into one sample. Samples are either collected once (July) or three times a year (May, July, and October). Samples were also collected in December 1999.
NOTE ON OUTLIERS IN THE DATA SET
All outliers were left in the data set unless it was evident that there was a contamination or laboratory procedure problem. In 2005, at the W1 high site, rep 3 of the Oi/Oe sample had biomass C, Respiration, Biomass N, Nitrification, Mineralization and DEA that were values that were, in some cases, 10 times higher than the next highest value. It was determined that since this pattern was evident in multiple lab analyses it was not due to laboratory errors, and must represent a "hot spot" of activity in the soil. These data were left in the dataset. In 2001, at the Bear Brook high elevation site, the mineral horizon had extremely high NH4 levels. This mean is the result of 5 data points, 2 of which were very high. These data were also left in the dataset.
LABORATORY PROCEDURES
Samples were stored at 4o C between sampling and analysis (from less than 1 week to up to three weeks). From 1994 to 1996 soils were sieved (>4 mm). From 1997 to 2010 soils were manually homogenized: all large rocks, roots, and other non-decomposed organic material were removed, and samples were thoroughly mixed. No more than three minutes were spent homogenizing any sample. All samples were held at field moisture before analysis. Soil water content was determined gravimetrically.
Microbial biomass C and N content was measured using the chloroform fumigation-incubation method (Jenkinson and Powlson 1976). Soils were fumigated to kill and lyse microbial cells in the sample. The fumigated sample was inoculated with fresh soil and sealed in a jar, and microorganisms from the fresh soil grew vigorously using the killed cells as substrate. The flushes of carbon dioxide (CO2) and 2 M KCl extractable inorganic N (NH4+ and NO3-) released by the actively growing cells during a 10-day incubation at field moisture content were assumed to be directly proportional to the amount of C and N in the microbial biomass of the original sample. A proportionality constant (0.41) was used to calculate biomass C from the CO2 flush in the fumigated samples. Biomass N is the total inorganic N flush in the fumigated samples.
Inorganic N and CO2 production were also measured in "control" samples. Control samples were prepared in the same fashion as those listed above, but were not fumigated. These incubations provided estimates of microbial respiration and potential net N mineralization and nitrification. Microbial respiration was quantified from the amount of CO2 evolved over the 10-day incubation. Potential net N mineralization and nitrification were quantified from the accumulation of NH4+ plus NO3- and NO3- alone during the 10-day incubation. We measured 2 M KCl extractable inorganic N in the fresh soil samples to determine the initial soil NO3- and NH4+ concentrations. Carbon dioxide was measured by thermal conductivity gas chromatography. Inorganic N was measured colorometerically using an autoanalyzer.
Denitrification enzyme activity was measured using the short-term anaerobic assay described by Smith and Tiedje (1979). Sieved soils were amended with NO3- (100 mg N kg-1), dextrose or glucose (40 mg kg-1), chloramphenicol (10 mg kg-1) and acetylene (10 kPa) and were incubated under anaerobic conditions for 90 minutes. Gas samples were taken at 30 and 90 minutes, stored in evacuated glass tubes and analyzed for N2O by electron capture gas chromatography. For more information on any of the methods described above, refer to Standard Soil Methods for Long-Term Ecological Research (1999).
CALCULATIONS
All results are expressed on a per gram of dry soil basis. Values can be converted to a “per area” basis using data on the mass of different soil horizons found elsewhere on the data page of this website.
REFERENCES
  • Bohlen, P.J., Groffman, P.M., Driscoll, C.T., Fahey, T.J., and Siccama, T.G. 2001. Plant-soil-microbial interactions in a northern hardwood forest. Ecology 82:965-978.
  • Fiorentino, I., Fahey, T., Groffman, P., Driscoll, C., Eagar, C., and Siccama, T. 2003. Initial responses of phosphorus biogeochemistry to calcium addition in a northern hardwood forest ecosystem. Can. J. For. Res. 33:1864-1873.
  • Groffman, P.M., Driscoll, C.T., Fahey, T.J., Hardy, J.P., Fitzhugh, R.D., and Tierney, G .L. 2001. Effects of mild winter freezing on soil nitrogen and carbon dynamics in a northern hardwood forest. Biogeochemistry 56:191-213.
  • Groffman, P.M., Hardy, J.P., Fisk, M.C., Fahey, T.J., and Fahey, C.T. 2009. Climate variation and nitrogen and carbon cycle processes in a northern hardwood forest. Ecosystems 12:927-943.
  • Groffman, P., Fisk, M., Driscoll, C., Likens, G., Fahey, T., Eagar, C., and Pardo, L. 2006. Calcium additions reduce nitrogen cycling in a northern hardwood forest. Ecosystems 9:1289-1305.
  • Hughes, J.W., and Fahey, T.J. 1994. Litterfall dynamics and ecosystem recovery during forest development. Forest Ecology and Management 63:181-198.
  • Jenkinson, D.S., and Powlson, D.S. 1976. The effects of biocidal treatments on metabolism in soil V. A method for measuring soil biomass. Soil Biology and Biochemistry 8:209-213.
  • Paul, E.A., and Clark, F.E. 1996. Soil Microbiology and Biochemistry. Academic Press
  • Robertson, G.P., Coleman, D.C., Bledsoe, C.S., and Sollins, P. 1999. Standard Soil Methods for Long-Term Ecological Research.
  • Smith, M.S., and Tiedje, J.M. 1979. Phases of denitrification following oxygen depletion in soil. Soil Biology and Biochemistry 11:262-267.
  • Voroney, R.P., and Paul, E.A. 1984. Determination of kc and kn in situ for calibration of the chloroform fumigation-incubation method. Soil Biology and Biochemistry 16:9-14.
DATA ACCESS GUIDELINES
Data from 1994-1996 have been published (Bohlen et al. 2001), data from 2001 are published in Fiorentino et al. (2003), data from 1998 – 2003 comparing the Ca treated watershed (watershed 1) and the long-term sites “west of watershed 6” are published in Groffman et al. (2006). Other data will be published in manuscripts that are currently in preparation by the investigators. Other Hubbard Brook microbial biomass and activity data can be found in Groffman et al. (2001, 2010). People are free to use these data for informational purposes but they cannot be used in any publication without permission of the author. Contact Linda Pardo (USDA Forest Service, PO Box 968, Burlington, VT 05402; 802-951-6771 x1330; lpardo@fs.fed.us) for questions about, and before using, all 1997 data.



Data Use Policy



The re-use of scientific data has the potential to greatly increase communication, collaboration and synthesis within and among disciplines, and thus is fostered, supported and encouraged. Permission to use this dataset is granted to the Data User free of charge subject to the following terms:

1) Acceptable use. Use of the dataset will be restricted to academic, research, government or other not-for-profit professional purposes.

2) Redistribution. The data and metadata are provided for use by the Data User. The Data User will not redistribute the original Data Set or metadata to others without the explicit permission of the Principal Investigator.

3) Citation. It is considered a matter of professional ethics to acknowledge the work of other scientists. Thus, the Data User will properly attribute the Data Set in any publications or in the metadata of any derived data products that were produced using the Data Set. Citation should take the following general form: Creator, Year of Data Publication, Title of Dataset, Publisher, Dataset identifier.

Citation example: Holmes, R.T. 2012. Bird Abundances at Hubbard Brook (1969-2010) and on three replicate plots (1986-2000) in the White Mountain National Forest. Durham, NH. Hubbard Brook Data Archive [Database]. http://hubbardbrook.org/data/dataset.php?id=81 (23 July 2012)

4) Acknowledgment: The Data User should acknowledge any institutional support or specific funding awards referenced in the metadata accompanying this dataset in any publications where the Data Set contributed to its content. Acknowledgments should identify the supporting party, the party that received the support, and any identifying information such as grant numbers.

Acknowledgment example: Data on [topic] were provided by [name of PI] on [date]. These data were gathered as part of the Hubbard Brook Ecosystem Study (HBES). The HBES is a collaborative effort at the Hubbard Brook Experimental Forest, which is operated and maintained by the USDA Forest Service, Northern Research Station, Newtown Square, PA. Significant funding for collection of these data was provided by [agency]-[grant number], [agency]-[grant number], etc.

5) Consultation and questions. Data users are strongly encouraged to consult with the Principal Investigator(s) who collected these data for further information. Also, when appropriate, Data Users should consider including the Principal Investigator as a collaborator and/or co-author in the use of these data.

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CONTACT PERSON

Information Manager, Hubbard Brook LTER
234 Mirror Lake Road
North Woodstock, NH 03262
USA

Phone: (603) 726-8902
Email: hbr-im@lternet.edu

Data file: micbio.txt
Description: Microbial biomass and activity at the Hubbard Brook LTER site.
Notes on Data: DATA DESCRIPTION Data from 1994-1996 have been published (Bohlen et al. 2001), data from 2001 are published in Fiorentino et al. (2003), data from 1998 – 2003 comparing the Ca treated watershed (watershed 1) and the long-term sites “west of watershed 6” are published in Groffman et al. (2006). Other data will be published in manuscripts that are currently in preparation by the investigators. Other Hubbard Brook microbial biomass and activity data can be found in Groffman et al. (2001, 2010). People are free to use these data for informational purposes but they cannot be used in any publication without permission of the author. Contact Linda Pardo (USDA Forest Service, PO Box 968, Burlington, VT 05402; 802-951-6771 x1330; lpardo@fs.fed.us) for questions about, and before using, all 1997 data. The data is physically located at the Cary Institute of Ecosystem Studies in Millbrook, NY
ColumnVariableDescriptionUnitsCoded?Missing value label
1DateSample dateYYMMDDnnone
2YearYearYYYYnnone
3SeasonSeason sample collectednoneynone
4SiteSampling Locationnoneynone
5ElevationElevationnoneynone
6SampleSample locationnoneynone
7HorizonSoil horizonnoneynone
8BIOCMicrobial biomass CmilligramPerKilogramn
-9999.99
9RESPCSoil respirationmilligramPerKilogramPerDayn
-9999.99
10BIONMicrobial biomass NmilligramPerKilogramn
-9999.99
11NO3Soil nitratemilligramPerKilogramn
-9999.99
12NH4Soil ammoniummilligramPerKilogramn
-9999.99
13NITPotential net nitrificationmilligramPerKilogramPerDayn
-9999.99
14MINPotential net N mineralizationmilligramPerKilogramPerDayn
-9999.99
15DEADenitrification enzyme activitymicrogramPerKilogramPerHourn
-9999.99
16H2ODenitrification enzyme activitymicrogramPerKilogramPerHourn
-9999.99

CODES

Variable: Season
Code
Description
F
Fall
W
Winter
SP
Spring
SU
Summer
Variable: Site
Code
Description
WS1
Watershed 1
BB
Bear Brook Watershed (West of WS6)
Variable: Elevation
Code
Description
SF
Spruce/Fir, ~790m, SF (Bear Brook); Lysimeter Site #2 (WS1)
H
High, ~750m, litter traps 101-120 (Bear Brook); Lysimeter #3 (WS1)
U
Upper, ~675m, litter traps 121-140 (Bear Brook)
M
Mid, ~600m, litter traps 141-160 (Bear Brook); Lysimeter #4 (WS1)
L
Low, ~525m, litter traps 161-180 (Bear Brook); Lysimeter #6 (WS1)
Variable: Sample
Code
Description
LT###
Litter Trap # (Bear Brook only)
LY#-#
Lysimeter Site # - Plot Replicate # (WS1 only)
LY#
Lysimeter Site # (WS1 only)
SF#
Spruce/Fir Site (Bear Brook Only)
Variable: Horizon
Code
Description
Oi/Oe
Oi and Oe horizons combined
Oa/A
Oa and A horizons combined
O
The entire O horizon: Oi, Oe, and Oa combined
Min
The first 10 cm of mineral soil below the A horizon (E and/or B)

MISSING VALUE CODES
Variable
Missing Value Code
Code Explanation
BIOC
-9999.99
Data missing or not taken at this time
RESPC
-9999.99
Data missing or not taken at this time
BION
-9999.99
Data missing or not taken at this time
NO3
-9999.99
Data missing or not taken at this time
NH4
-9999.99
Data missing or not taken at this time
NIT
-9999.99
Data missing or not taken at this time
MIN
-9999.99
Data missing or not taken at this time
DEA
-9999.99
Data missing or not taken at this time
H2O
-9999.99
Data missing or not taken at this time