Introduction to BiomeBGC Ryan Anderson September 23 2009

Introduction to Biome-BGC Ryan Anderson* September 23, 2009 *With thanks to Jordan Golinkoff, Faith Ann Heinsch, Matt Jolly, and anybody else whose slides or work made it into this document

“All models are wrong, but some are useful” -G. E. Box • Models are an abstraction of reality • Goal is to represent the relevant processes in sufficient detail to answer research or management questions • Simplifying assumptions need to be made • Making a model more detailed or complicated does not necessarily make it better

Biome-BGC • Biome = A major regional or global community, characterized chiefly by the dominant forms of vegetation and the prevailing climate • BGC = Bio. Geo. Chemical – Bio = living organisms (plant responses) – Geo = Earth (soils) – Chemical = chemical reactions, specifically carbon, nitrogen, and water Biome-BGC is a process-based model that tracks Carbon, Water, Nitrogen, and Energy Fluxes through terrestrial ecosystems.

Process based vs. Empirical Models

The BIOME-BGC Terrestrial Ecosystem Process Model BIOME-BGC estimates fluxes and storage of energy, water, carbon, and nitrogen for the vegetation and soil components of terrestrial ecosystems. Model algorithms represent physical and biological processes that control fluxes of energy and mass: • • • • New leaf growth and old leaf litterfall Sunlight interception by leaves, and penetration to the ground Precipitation routing to leaves and soil Snow (SWE) accumulation and melting Drainage and runoff of soil water Evaporation of water from soil and wet leaves Transpiration of soil water through leaf stomata Photosynthetic fixation of carbon from CO 2 in the air N uptake from the soil Distribution of C and N to growing plant parts Decomposition of fresh plant litter and old soil organic matter Plant mortality Plant phenology Fire/disturbance The model uses a daily time-step with daily updating of vegetation, litter, and soil components.

The BIOME-BGC Terrestrial Ecosystem Process Model • Not an individual Species Model • Most Biological Process represented at the Canopy Level (i. e. a ‘Big Leaf’ or ‘Green Sponge’ Model) • Daily Time Step • No Defined Spatial Scale (pools and fluxes are represented on a per unit area basis) • Not a Spatial Model (no linkages between gridcells) • Prognostic Model

BIOME-BGC General Concepts • Growth (Uptake CO 2 for photosynthesis) • F(temp, humidity, radiation, soil water deficits) • Farquhar photosynthesis equation • Differentiated by sunlit and shaded leaves • Reduced by environmental constraints • Allocation • Once photosynthesis takes place, the model must allocate fixed carbon to different places (I. e. roots, leaves, stems, etc…, ) • Respiration • Both for maintaining current biomass and growing new biomass. Net loss of CO 2 to the atmosphere.

Digging Deeper: How does Biome BGC represent important biological and physical processes? • Pools and Fluxes • Photosynthesis • Stomatal Conductance • Radiation interception and transmission • Transpiration and Evaporation • Links to Photosynthesis – Stomatal Conductance, energy balance • Routing of Precipitation • Growth and Maintenance Respiration • Decomposition – Heterotrophic Resipration • Carbon Allocation • Nutrient Availability

Biome-BGC’s Carbon and Nitrogen Pools

Biome-BGC’s Carbon and Nitrogen Fluxes

Photosynthesis 6 CO 2 + 6 H 20 C 6 H 12 O 6 + 6 O 2 Rubisco catalyzes both the carboxylation and oxygenation of Ru. BP!

Michaelis-Menten Enzyme Kinetics Reaction rate depends on the maximum reaction rate , the concentration of the substrate (CO 2), and the MM constant (Km). Rubisco reacts with both CO 2 and oxygen, so it has an MM constant for each. MM constant, adjusted for effect of competition with oxygen CO 2 concentration

Factors controlling Vc. Max (lnc) x (flnr) x (fnr) x (act) = (Vcmax) Rubisco activity = f(Tleaf) Determined from protein structure (constant 7. 16 g. R/g. N – Rubisco is approximately 14% nitrogen by mass) Fraction of leaf N in Rubisco Area-based leaf N concentration = 1/ (SLA C: Nleaf)

Regeneration of RUBP can also limit photosynthesis • Light is required to produce ATP required to regenerate RUBP • Plants have evolved such that light harvesting capacity is closely linked to maximum carboxylation rates (Jmax = 2. 1 * Vmax, Wullschleger 1993) • Realized Rate(J) of RUBP regeneration is related to light intensity(ppfd) according to a quadratic function: 0. 7 J 2 – (Jmax + (ppfd/2))J + Jmax(ppfd/2) = 0

Regeneration of RUBP can also limit photosynthesis Apply some stoichiometry and we get the radiation (RUBP) limited rate of photosynthesis: This equation is based on the energy requirements of the Calvin Cycle and the relationship between rubisco carboxylation and oxygenation as expressed through the CO 2 compensation point. Don’t worry about the details.

Biome-BGC’s Energy Balance

CO 2 must diffuse through stomates in order for photosynthesis to take place Tradeoff-CO 2 gain leads to water loss feedback between carbon and water cycles

Stomatal aperture is controlled by many variables • Cold temperatures • Hot temperatures • Low soil water availability – Supply • High atmospheric demand for water – –Demand • Changes in the gradient of CO 2 • Any of these will reduce photosynthesis – –Weather drives ecological processes Modeling plant ecosystem processes requires that we treat the most important components

Gs = gsmax * mppfd * mt * msoil * m. VPD

Photosynthesis in Biome-BGC A= g * (Ca – Ci) Stomatal Conductance limit Carboxylation Limit Substrate Regeneration limit Variables impacting photosynthetic rate: -CO 2 concentration (and an assumed oxygen concentration) -Temperature -Stomatal Conductance -Solar Radiation -Leaf Nitrogen -Leaf Respiration rate (which, as we will see, is a function of leaf nitrogen and temperature)

Differing light environments of leaves are important for modeling canopy scale photosynthesis Vertical Gradient of Leaf Traits with Canopy Depth High light = high leaf N, thick, short lived leaves with large maintenance respiration costs Low Light = Lower leaf N, thinner, longer lived leaves with lower respiration costs

Two Layer Canopy in Biome-BGC • User specifies a ratio of sunlit to shaded leaves • User specifies a ratio of sunlit SLA to shaded SLA • Biome-BGC calculates leaf area for each based on total leaf C • Stomatal Conductance, Transpiration, and Vc. Max are calculated Seperately for each layer • Photosynthesis Routine is run separately for each layer

Biome-BGC’s Water Balance

Penman-Monteith Equation provides Basis for ET estimates s. A+ρCp(esat – e)/ra λE= s+γ(1+rs/ra) esat (Pa) λ = latent heat of evaporation (J/kg – a function of temperature) ρ = air density (kg/m 3 _ function of temperature) s = slope of the saturated VP vs. Temp curve (at right) 8000 7000 γ = A constant (Pa/K) 6000 A = Net Radiation (W/m 2) 5000 Cp = Specific Heat of Air (J/Kg/K) 4000 3000 e = Vapor Pressure 2000 Esat = Saturated Vapor Pressure 1000 0 Ra = aerodynamic resistance (s/m) 0 Rs = surface resistance (s/m) Evaporation is driven by: 1) available Energy 2) Vapor Pressure Deficit 3) Resistance terms 10 20 30 Temp (C) 40 50

(MPa) BIOME-BGC 1 Soil Water – Soil Water Potential Curves (%) Soil Class β-value VWC_sat PSI_sat Silt loam -4. 625 0. 48 -0. 0073 Silt -3. 84 0. 48 -0. 0078 Loam -5. 275 0. 41 -0. 0013 1 after Cosby et al. , 1984

Autotrophic Respiration • Maintenance Respiration: • Empirical relationship with tissue nitrogen • Computed separately for each live tissue pool • Scaled to temperature using a Q 10 formula Q 10 represents the change in respiration rate that occurs with a 10 degree change in temperature MR = 0. 218 kg C / kg N day * N * 2. 0(T – 20)/10

Autotrophic Respiration • Growth Respiration: – 30% of all carbon allocated to new tissue is respired.

Decomposition

Decomposition Labile Cellulose Lignin

Decomposition

Biome-BGC’s Carbon and Nitrogen Fluxes

Carbon Allocation • User specified, constant allometric ratios: – Percent of storage – New fine root : new leaf – New stem : new leaf – New live wood : new total wood – New coarse root : new stem • Each compartment has a C: N ratio • Used to calculate Nitrogen demand of potential new growth • If soil mineral nitrogen is insufficient, the day’s production is reduced • Allocation ratios are difficult to parameterize from the literature, but have important impacts on production, respiration rates, and pool sizes

Disturbance in Biome-BGC

The problem of initial conditions

Summary - Carbon • Photosynthesis • Rates are determined by leaf nitrogen • Needs water from the soil • Reduced by water supply/demand, carbon supply/demand • Respiration • Loss of carbon from the system • Maintenance and growth • Autotrophic • Heterotrophic

Summary - Water • Transpiration • Water lost by stomata which also control CO 2 uptake • Canopy interception of precipitation • Determined by the amount of carbon fixed by photosynthesis that is allocated to leaf • Soil water evaporation • Driven by the weather • Outflow Determined by excess water not taken up by the plant

Summary - Nitrogen • Nitrogen in the leaves • Determine maximum photosynthetic rate • Atmospheric N deposition (pollution) • Additional inputs to the system • Soil N limitations • Plants compete with soil microbes for nitrogen to incorporate into plant tissue

Running Biome-BGC – what is required? • Site Physical Description (part of ini file) • Vegetation Ecophysiological Parameters (epc file) • Meteorology (met file) • Model run instructions (part of ini file)

Meteorological Parameters Required by Biome-BGC • • • Daily maximum temperature (°C) Daily minimum temperature (°C) Daylight average temperature (°C) Daily total precipitation (cm) Daylight average partial pressure of water vapor (Pa) • Daylight average shortwave radiant flux density (W/m 2) • Daylength (s)

Example Met. Data Input (Generated from MT-CLIM) Missoula, 1950 -1993 : Sample input for MTCLIM v 4. 1 OUTPUT FILE : Tue Aug 25 10: 15: 00 1998 year yday Tmax Tmin Tday prcp VPD (deg C) (cm) (Pa) 1950 1 -3. 90 -13. 90 -6. 65 0. 10 158. 19 1950 2 -7. 80 -21. 70 -11. 62 0. 00 136. 27 1950 3 -16. 10 -23. 30 -18. 08 0. 00 53. 36 1950 4 -11. 70 -20. 60 -14. 15 0. 10 83. 07 1950 5 -13. 90 -25. 00 -16. 95 0. 00 78. 17 1950 6 0. 60 -14. 40 -3. 53 0. 10 264. 00 1950 7 4. 40 -4. 40 1. 98 0. 00 297. 13 1950 8 -2. 20 -11. 70 -4. 81 0. 10 182. 84 1950 9 -2. 20 -12. 20 -4. 95 0. 00 193. 26 srad (W m-2) 123. 31 183. 78 140. 67 119. 72 177. 64 142. 03 158. 19 126. 15 173. 66 daylen (s) 30229 30284 30344 30408 30476 30549 30626 30707 30793

Biome-BGC Initialization file Biome-BGC v 4. 1. 2 example : (normal simulation, Missoula, evergreen needleleaf) MET_INPUT (keyword) start of meteorology file control block metdata/miss 5093. mtc 41 meteorology input filename 4 (int) header lines in met file RESTART (keyword) start of restart control block 0 (flag) 1 = read restart file 0 = don't read restart file 0 (flag) 1 = write restart file 0 = don't write restart file 1 (flag) 1 = use restart metyear 0 = reset metyear restart/enf_test 1. endpoint input restart filename restart/enf_test 1. endpoint output restart filename TIME_DEFINE 44 44 1950 0 6000 (keyword - do not remove) (int) number of meteorological data years (int) number of simulation years (int) first simulation year (flag) 1 = spinup simulation 0 = normal simulation (int) maximum number of spinup years (if spinup simulation) CLIM_CHANGE 0. 0 1. 0 (keyword - do not remove) (deg C) offset for Tmax (deg C) offset for Tmin (DIM) multiplier for Prcp (DIM) multiplier for VPD (DIM) multiplier for shortwave radiation

Biome-BGC Initialization file, continued CO 2_CONTROL 0 294. 842 xxxxxx (keyword - do not remove) (flag) 0=constant 1=vary with file 2=constant, file for Ndep (ppm) constant atmospheric CO 2 concentration (file) annual variable CO 2 filename SITE 1. 0 30. 0 50. 0 20. 0 977. 0 46. 8 0. 2 0. 0001 0. 0004 (keyword) start of site physical constants block (m) effective soil depth (corrected for rock fraction) (%) sand percentage by volume in rock-free soil (%) silt percentage by volume in rock-free soil (%) clay percentage by volume in rock-free soil (m) site elevation (degrees) site latitude (- for S. Hem. ) (DIM) site shortwave albedo (kg. N/m 2/yr) wet+dry atmospheric deposition of N (kg. N/m 2/yr) symbiotic+asymbiotic fixation of N RAMP_NDEP 0 2099 0. 0001 (keyword - do not remove) (flag) do a ramped N-deposition run? 0 o, 1=yes (int) reference year for industrial N deposition (kg. N/m 2/yr) industrial N deposition value EPC_FILE epc/enf. epc (keyword - do not remove) (file) evergreen needleleaf forest ecophysiological constants

Biome-BGC Initialization file, continued W_STATE 0. 0 0. 5 (keyword) start of water state variable initialization block (kg/m 2) water stored in snowpack (DIM) initial soil water as a proportion of saturation C_STATE 0. 001 0. 0 0. 0 (keyword) (kg. C/m 2) (kg. C/m 2) N_STATE 0. 0 (keyword) start of nitrogen state variable initialization block (kg. N/m 2) litter nitrogen, labile pool (kg. N/m 2) soil nitrogen, mineral pool start of carbon state variable initialization block first-year maximum leaf carbon first-year maximum stem carbon coarse woody debris carbon litter carbon, labile pool litter carbon, unshielded cellulose pool litter carbon, lignin pool soil carbon, fast microbial recycling pool soil carbon, medium microbial recycling pool soil carbon, slow microbial recycling pool soil carbon, recalcitrant SOM (slowest)

Biome-BGC Initialization file, continued OUTPUT_CONTROL outputs/oth 1 (flag) 1 = 1 (flag) for (keyword - do not remove) (text) prefix for output files write daily output 0 = no daily output monthly avg of daily variables 0 = no monthly avg annual avg of daily variables 0 = no annual avg write annual output 0 = no annual output on-screen progress indicator DAILY_OUTPUT (keyword) 9 (int) number of daily variables to output 623 13 summary. daily_gpp 624 14 summary. daily_mr 625 15 summary. daily_gr 626 16 summary. daily_hr 627 17 summary. daily_fire 636 18 summary. vegc 637 19 summary. litrc 638 20 summary. soilc 639 21 summary. totalc ANNUAL_OUTPUT (keyword) 2 (int) number of annual output variables 545 0 annual maximum projected LAI 636 1 vegetation C END_INIT (keyword) indicates the end of the initialization file

Verification of BIOME-BGC Daily and Seasonal Dynamics: Comparisons with Tower Eddy-flux Measurements Mature Aspen Stand (SSA-OA BERMS site) Mature Black Spruce Stand (NSA-OBS Ameriflux site) ET NEP Kimball et al. , 1997 a, b