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Completed (or nearly so) Projects

Cross-site Comparison of Nutrient Cycling and Root Dynamics Along a Calcium Supply Gradient

Jamie Shanley, U.S. Geological Survey; Ruth Yanai, SUNY-ESF; Scott Bailey, USDA-Forest Service; Don Ross, University of Vermont; Tim Fahey, Cornell University; and Tom Siccama, Yale University

We combined existing data and new measurements to compute annual nutrient (nitrogen, phosphorus, sulfur, calcium, magnesium, and potassium) flux in net throughfall, litterfall, and aboveground biomass increment, as well as to account for the belowground biomass component in hardwood and coniferous forest types under contrasting conditions of soil calcium status in Sleepers River, VT; Hubbard Brook, NH; and Cone Pond, NH. The major new effort in this project was directed at measurements of root turnover.

Neither aboveground biomass and production nor belowground biomass were related to soil calcium or calcium: aluminum ratios across the calcium gradient. Hardwood stands had 37% higher aboveground biomass and 44% higher leaf litter production than the conifer stands, on average. Fine root biomass (<2 mm in diameter) in the upper 35 cm of the soil, including the forest floor, was very similar in hardwoods and conifers (5.92 and 5.93 Mg ha−1). The turnover of fine roots increased significantly with soil exchangeable calcium. As a result, calculated fine root production was clearly higher in sites with higher soil calcium in both hardwood and conifer stands. The relationship we observed between soil Ca availability and root production suggests that cation depletion might lead to reduced carbon allocation to roots in these ecosystems.  This project was funded by the Northeastern States Research Cooperative.

Read More: 

Park, B.B., R.D. Yanai, T.J. Fahey, T.G. Siccama, S.W. Bailey, J.B. Shanley, and N.L. Cleavitt. 2008. Fine root dynamics and forest production across a calcium gradient in northern hardwood and conifer ecosystems.  Ecosystems 11(2):325-341 PDF

Non-Destructive Soil Inventory using Inelastic Neutron Scattering:  An Application to Nitrogen Controls on Soil Carbon Storage

Ruth Yanai, State University of New York College of Environmental Science and Forestry, Lucian Wielopolski, Brookhaven National Laboratory, Christy Goodale, Cornell University, Ivan Fernandez, University of Maine, Steven McNulty, USDA Forest Service, and Steven Hamburg, Environmental Defense Fund

Until now, there has not been a method for accurate and rapid evaluation of belowground carbon and nutrient stores, in spite of their ecological, environmental, and economic importance.  The variability of forest soils has made it difficult to test factors hypothesized to influence C storage in roots and soil organic matter in realistic field experiments.  In particular, anthropogenic N deposition is expected to have a positive effect on belowground C storage, but this effect has not been detectable even in accelerated N deposition experiments.

We propose to demonstrate and develop a transformative new technology for analysis of soil carbon and nutrients. This new technology uses inelastic neutron scattering (INS) to non-destructively quantify belowground stores of carbon and other elements, including coarse roots, which were previously difficult to sample, and around rocks, which were previously obstacles.  Our objectives include the development and transfer of this technology for C and N in forest soils and also the advancement of ecosystem science pertaining to soil C and N storage.

In the first year of the proposed project, we will validate the INS measurements with cores taken in the footprint of the INS in stands previously described with quantitative soil pits in the Bartlett Experimental Forest, NH.  The capability of the INS to measure N and not just C will be tested for the first time.

In the second year of the project, we will apply INS measurements to permanent plots in two long-term N addition studies.  At Mount Ascutney, VT, N has been added to high-elevation spruce-fir forests at rates of 15 and 31 kg/ha/yr since 1988.  At Bear Brook Watershed in Maine, 25 kg N/ha/yr has been added to one of a pair of watershed since 1989.  The INS measurements will test the hypothesis of increased C storage and also provide a baseline for future sampling.  Previous measurements using traditional destructive methods could not be made at the same point on the ground and were thus limited in their statistical power to detect change over time.

Before the INS technology can be widely adopted, it requires demonstration and development.  Applying the test of the INS approach in forested sites in stony soils will provide confidence that the system can be used in almost any environment. If successful, the INS technology will allow carbon sequestration projects to come closer to full carbon accounting, making it feasible to include belowground carbon in offset activities in cap and trade programs.

This project is support by the Northeastern States Research Cooperative, SUNY-ESF Seed Grant, and a Edna Sussman Baily Internship.

Read More: 

Levine, C.R. 2010.  Development of an inelastic neutron scattering approach to assess carbon and nitrogen contents of forest soils:  an internship with the Brookhaven National Laboratory, Upton, NY.  Edna Sussman Foundation Research Report.  PDF

Wielopolski, L.,  R.D. Yanai, C.R. Levine, S. Mitra, and M.A Vadeboncoeur.  2010.  Rapid, non-destructive carbon analysis of forest soils using neutron-induced gamma-ray spectroscopy. For. Ecol. Manag.  260(7): 1132-1137 PDF

WERC: Size of discolored hearts of sugar maple

Ruth Yanai and Ren Germain, SUNY College of Environmental Science and Forestry

Because the most valuable sugar maple trees are those with small hearts, foresters, loggers and landowners would benefit from a heart-size prediction model. Few studies have examined the relationship between dark discoloration size and site or individual tree factors.  The initial phase of this study, based on data (bark type, diameter, slope, aspect, etc.) collected from 52 timber sales in 6 states, is nearly complete. The next phase will involve the intensive field study of sites to develop and validate a heart-size prediction model.  Future analysis will include stand history and exposure to injury, which is commonly thought to influence dark discoloration in sugar maple. This project is was funded in whole or in part through a grant awarded by the Wood Education and Resource Center, Northeastern Area State and Private Forestry, Forest Service, U.S. Department of Agriculture. In accordance with Federal law and U.S. Department of Agriculture policy, this institution is prohibited from discriminating on the basis of race, color, national origin, sex, age, or disability. To file a complaint of discrimination, write USDA Director, Office of Civil Rights, Room 326-W, Whitten Building, 1400 Independence Avenue, SW, Washington, DC 20250-9410 or call (202) 720-5964 (voice and TDD). USDA is an equal opportunity employer.

Read More: 

Yanai, R.D., R.H. Germain, N.M. Anderson, T.A. Coates, and A.K. Mishler.  2009. Heart size of sugar maple sawlogs across the northeastern United States.  Journal of Forestry 107(2):  95-100  PDF

Yanai, R.D., Germain, R.H., R.D. Yanai, A.K. Mishler, Y. Yang, and B.B. Park. 2015.. Predicting dark heart size in sugar maple.  Journal of Forestry.  In press.

Modeling forest susceptibility to decline following defoliation by forest tent caterpillar

R.D. Yanai, D. Parry, L.K. Lautz, and D.C. Allen, SUNY College of Environmental Science and Forestry

In the northeastern US, we are in the fourth year of an outbreak of forest tent caterpillar.  We are seeking funding to examine the factors that cause some stands to suffer dieback and mortality following defoliation, while other stands recover.  This project involves monitoring forest health, analyzing geographic information, including aerial coverage of defoliation history, and working with state agencies and other stakeholders.   This project is funded by the Northeastern States Research Cooperative

Read More: 

Wood, D.M, R.D. Yanai, D.C. Allen, and S. Wilmot.  2009.  Sugar maple decline following defoliation by  forest tent caterpillar. Journal of Forestry 107(1): 29-37  PDF

Biotic control of calcium cycling

Mary Arthur, University of Kentucky; Joel Blum, University of Michigan; Melany Fisk, Appalachian State University; Steven Hamburg, Brown University; Elizabeth Hane, Rochester Institute of Technology; and Ruth Yanai, SUNY-ESF

We are looking at differences in Ca cycling with stand age, and determing the source of Ca mobilized from mineral soil in young stands. Hypothesis testing uses both an extensive approach, involving 13 previously studied stands, and intensive one using replicate stands of three ages at a single site.  The Northern Hardwood Calcium Project is now part of the Multiple Element Limitation in Northern Hardwood Ecosystems (MELNHE) project

Read More: 

Blum, J., A.A. Dasch, S.P. Hamburg, R.D.Yanai, and M.A. Arthur. 2008. Use of foliar Ca/Sr discrimination and 87Sr/86Sr ratios to determine soil Ca sources to sugar maple foliage in a northern hardwood forest.  Biogeochemistry 87(3):287-296  PDF  From SU/ESF:  HTML

Yanai, R.D., J.D. Blum, S.P. Hamburg, M.A. Arthur, C.A. Nezat, T.G. Siccama.  2005.  New insights into calcium depletion in northeastern forests.  Journal of Forestry. 103: 14-20.  PDF

Yanai, R.D., R.P. Phillips, M.A. Arthur, T.G. Siccama, and E. Hane.  2005.  Spatial and temporal variation in calcium and aluminum in northern hardwood forest floors.  Water, Air, and Soil Pollution. 160: 109-118. PDF

Hamburg, S,P., R.D. Yanai, M.A. Arthur, J.D. Blum and T.G. Siccama.  2003.  Biotic control of calcium cycling in northern hardwood forests: acid rain and aging forests.  Ecosystems 6: 399-404.  PDF

Sources of Calcium in Northern Hardwood Forests: Implications for Repeated Harvests and Calcium Depletion

Ruth Yanai, SUNY-ESF; Joel Blum, University of Michigan;  Steven Hamburg, Brown University; Mary Arthur, University of Kentucky

We collected and analyzed soil samples from a total of 24 sites in Maine, New Hampshire (all 14 located in the White Mountain National Forest), New York and Pennsylvania: The results of this work  have been surprising. 

First, we found that apatite is indeed an important source of Ca in soils in rocks derived from granitoid parent materials, but it is less important in sedimentary rocks.  One paper, published in the Journal of Forestry in 2005, describes this finding, and another is in preparation by Carmen Nezat, which treats the subject in more detail.

The method for identifying apatite in soils is an important product of this research.  Another manuscript has recently been submitted soon to Chemical Geology describing the sequential extraction procedure we developed, also led by Carmen Nezat.

We had intended to describe the relative importance of apatite as a calcium source in stands of different ages and species composition by comparing the composition of tree foliage to that of the major Ca sources, using trace metals and isotopes.  This analysis is not as simple as we had hoped, because trees fractionate strontium and calcium, and tree species differ in the degree to which they do so.  Amanda Dasch is preparing a manuscript describing this problem, and when it is completed, Joel Blum will be in a position to apply a modified approach to addressing our original question. 

This project has been supported by grants from the USDA Forest Service Agenda 2020 Sustainable Forest Research program, National Science Foundation and the New York State Energy Research and Development Authority.

Read More:

Nezat, C.A., J.D. Blum, R.D. Yanai, S.P. Hamburg, and B.B. Park. 2008. Mineral sources of calcium and phosphorus in soils of the northeastern USA.  Soil Science Society of America Journal 72(6): 17861794 PDF

Nezat, C.A., J.D. Blum, R.D. Yanai and S.P. Hamburg. 2007.  A sequential extraction to selectively dissolve apatite for determination of soil nutrient pools with an application to Hubbard Brook Experimental Forest, New Hampshire, USA. Applied Geochemistry  22:  24062421 PDF

Yanai, R.D., J.D. Blum, S.P. Hamburg, M.A. Arthur, C.A. Nezat, T.G. Siccama.  2005.  New insights into calcium depletion in northeastern forests.  Journal of Forestry. 103: 14-20.  PDF

NYSERDA:  Assessing the sensitivity of New York Forests to cation depletion

Ruth Yanai, SUNY College of Environmental Science and Forestry and Joel Blum, University of Michigan

Information concerning the distribution of sources of calcium (Ca) and the ability of tree species to access calcium is essential for predicting the sensitivity of forests across New York State to Ca depletion resulting from acidic deposition. The data accumulated through this project will provide a more accurate assessment of the likelihood that New York State forests will be adversely affected by the depletion of calcium and other exchangeable cations. In particular, this project sought to:

Read More:

Park, B.B., R.D. Yanai, M.A. Vadeboncoeur, and S.P. Hamburg.  2007. Estimating root biomass in rocky soils using pits, cores and allometric equations. Soil Sci. Soc. Am. J. 71:206-213. PDF

Yanai, R.D., B.B. Park, and S.P. Hamburg.  2006. The vertical and horizontal distribution of roots in northern hardwoods of varying age.  Can. J. For. Res. 36(2): 450-459.     PDF

A project update and draft summary report are available.  As per agreement with NYSERDA, data from this study are available for subsequent study.  Please request access to virtual study archives by email to

Nutrient Uptake and Content

F.R. Fatemi and R.D. Yanai

M.S. Lucash, R.D. Yanai and J.D. Joslin 

Plant nutrient uptake is difficult to estimate at the ecosystem scale.  Several indirect methods are used to quantify stand-level nutrient uptake such as nutrient budgets and simulation models.  In nutrient budgets, nutrient uptake is generally estimated by using fluxes such as litter fall, biomass accumulation, and root turnover. Simulation models, on the other hand, predict uptake utilizing measurements such as root length, soil solution concentrations, and uptake capacity.

Many studies of uptake capacity in trees have been conducted using seedlings, despite the fact that seedling uptake may differ dramatically from that of mature trees. Other studies in forest ecosystems have used excised roots to estimate uptake, even though carbohydrate and water supply is halted at the time of excision.  In this study we plan to measure uptake capacity of intact roots at several sites across the US in order to improve model estimates of ecosystem uptake.  Results from the simulation models will also be compared with nutrient budgets.  

Nitrogen immobilization by woodchip application in a northern hardwood forest.

Ren Germain, SUNY College of Environmental Science and Forestry

Leaf litter immobilizes N, reducing stream export, briefly, in the fall. We have conducted a 1-year study of the potential for wood chips to immobilize N following forest harvest, to reduce the peak nitrate delivery to streams.  This work is in the context of the New York City Watersheds in the Catskill Mountains of New York.  To date, Forestry BMPs (Best Management Practices) have addressed sedimentation of streams, but not stream chemistry.  This work could result in the development of a new BMP.

Read More:  Homyak, P.M., R.D. Yanai, D.A. Burns, R.D. Briggs, and R.H. Germain. 2008. Nitrogen immobilization by wood chip application: protecting water quality in a northern hardwood forest.  Forest Ecology and Management 255: 2589-2601.  PDF

Nutrient Uptake Modeling

We use a steady-state model of nutrient uptake (Nye and Tinker 1977, Yanai 1994), because it allows parameters such as  root length, root diameter, root length density (root length per unit soil volume), average soil solution concentration, buffer capacity, and the effective diffusion coefficient to vary over time.  In natural ecosystems, root length increases and decreases seasonally, and nutrient concentrations in solution reflect processes such as mineralization, immobilization, and weathering in addition to nutrient uptake.  We supply the model with values of root length, rooting density, soil solution and solid phase concentrations, transpiration rates, and soil moisture content at whatever time resolution data and depth resolution are available for each of our 6 sites (link to map of sites).

A multi-dimensional sensitivity analysis shows that the most important parameters in simulating nutrient uptake are the root length, soil solution concentration, and uptake kinetics (Williams and Yanai 1996).  Uncertainty analysis will be conducted for each site by running the model repeatedly using the observed distribution of parameter values (Gardner et al. 1983).  We will also test the value of time-varying input by simulating uptake using annual average values and comparing them to simulations at finer resolution.

To download the model:

Modeling Soil Solution Chemistry: YASE

YASE is a model that simulates the chemical composition of soil solutions as determined by chemical equilibria, organic matter transformations, and mineral weathering.  Different properties can be assigned to different soil layers in the model.  Uptake of solutes from the soil by plants, addition of organic matter, movement of soil solution between soil layers, and influx of solution from above or below the soil can be provided as inputs to YASE, either by the TREGRO model or by the user.  YASE can be run alone at any time step; when called by TREGRO it is called on a daily time step.

Chemical equilibria in YASE are based on the Chemical Equilibria in Soils and Solutions model, CHESS (Santore 1991).  CHESS uses a matrix representation of solution chemistry (Morel, 1983).  Equilibrium problems of any composition and complexity (or simplicity) can be simulated using this model, because the chemical components and the rules for combining them into species are supplied by the user.

Decomposition in YASE follows the algorithm of GEM (Rastetter et al., 1991): transformations among extractives, cellulose, lignin, and humus are affected by temperature, soil moisture, N availability, and a ligno-cellulose index.  Weathering in YASE is defined by the user using mineral compositions, weathering rates, and reaction orders with respect to pH and the amount of mineral present.  Cation exchange is treated as an equilibrium between adsorbed and dissolved species interrelated by selectivity coefficients.

YASE was developed to be compatible with TREGRO.  To be used in combination with TREGRO, YASE must be parameterized to include the nutrients of possible importance to the plant.  A HyperCard interface aids in the parameterization and running of the model, whether alone or in combination with TREGRO.

Nutrient Uptake using SUM Columns

M.S. Lucash, R.D. Yanai, J.D. Joslin and J.M. Scholberg

Most estimates of nutrient uptake are obtained using excised roots or roots recently excavated from soil.  Using this sand-culture method, we are able to obtain estimates of nitrate and ammonium uptake of seedlings.  We installed these SUM (soil uptake monitoring) columns in the field and plan to test this method using mature sugar maple and eastern hemlock in spring, 2004.

Root Growth and Developement

Sorting roots






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