The basis for rainforest diversity and biosphere 2

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The basis for rainforest diversity and biosphere 2
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xviii, 342 leaves : ill. ; 29 cm.
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Thesis:
Thesis (Ph.D.)--University of Florida, 1999.
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Includes bibliographical references (leaves 332-341).
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by Linda Susan Leigh.
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Typescript.
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Vita.

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THE BASIS FOR RAINFOREST DIVERSITY AND BIOSPHERE 2


By


LINDA SUSAN LEIGH













A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL
OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT
OF THE REQUIREMENTS FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY



UNIVERSITY OF FLORIDA


1999













ACKNOWLEDGMENTS


Dr. H. T. Odum has been the quintessential mentor, finding no idea too
trivial to explore and no emergy analysis or comparison too radical to
consider. I thank him for his encouragement of both creative imagination
and scholarship. I would like to thank my committee members for the
inspiration they provided throughout my doctoral program: Dr. M. T. Brown,
Dr. C. L. Montague, Dr. C. S. Holling, and Dr. F. N. Scatena.

I am indebted to the original Biosphere 2 rainforest design team with
whom I worked in my role as Biome Design Coordinator from 1985 to 1993:
Ghillean Prance (rainforest biome design 'captain'), Tony Burgess (desert
biome design 'captain'), Peter Warshall (food web design), Scott Miller
(entomology), Harry Scott biomee design and species selections), John Druitt
biomee design and species selections), Walter Adey (aquatic systems), Julia
Bennett (plant propagation and management), Bob Scarborough (soils),
Stephen Storm (soils) Phil Hawes (architectural design), Michael Balick (plant
selections), Andrew Henderson (plant selection, collections), and others.
I completed the third plant survey with the assistance of Jessica Bolson, and
measurements in 1998 with assistance of the students of the Spring 1998
Columbia University Earth Semester at Biosphere 2.
Some of the data for this dissertation were assembled from the
following reports, which are on file at Columbia University's Biosphere 2
Center in Oracle, Arizona: biomass estimates for 1990 and 1991 (Alan
Haberstock, Dec. 1991); biomass estimates for 1993 (Mark Bierner, Oct. 1993);








soil chemical and physical properties in 1993 (Harry J. Scott, Dec. 1994); maps
and survey data (Jeremiah Teague and Co., Sept. 1991); soils design, assembly,
and placement (Robert Scarborough, Mar. 1993). Access to the Biosphere and
logistic support was facilitated by Adrian Southern and John Adams. Eda
Melendez provided data from El Verde.

An educational grant was received from Edward Bass, a scholarship
fund from the Drylands Institute, and a Graduate Assistantship in the
contract between the Institute of Tropical Forestry, U.S. Department of
Agriculture and the University of Florida, H. T. Odum, Principal Investigator.

Unconditional thanks are extended to Richard Felger, Silke Schneider,
Roy Walford, Kathleen Dyhr, Bernd Zabel, Dan Levinson, Randall Gibson,
and Bonnie Knickerbocker; Carlos Nagel, the late Alfredo Rivera, Sherry and
Casey Brandt-Williams, Joanie Breeze, Tony Burgess, Jerry Leigh; and a long
list of loyal friends.

"Never say die" and "Keep the voyage going, going, but never gone"
reflect the attitudes of me and my fellow crew members inside Biosphere 2 --
Gaie Ailing, Taber MacCallum, Jane Poynter, Roy Walford, Mark Nelson,
Sally Silverstone, and Mark Van Thillo -- and they continue to inspire.

I extend a special acknowledgment and heartfelt thanks to Ren Hinks
who encouraged me on a daily basis.













TABLE OF CONTENTS



ACKNOWLEDGMENTS......................................................................................... ii

LIST O F TA BLES............................................................................................ ...........viii

LIST O F FIG U RES........................................................................................... ......... xii

A BSTR A C T ........................................................................................................... xvii

1 INTRODUCTION................................................................................................. 1

Review of Diversity-Influencing Processes in Other Studies ......................2
Species and A rea ............................................................................................ 2
Species and Individuals..............................................................................6
Succession........................................................................................................ 7
Theories of Diversity..................................................................................... 9
D diversity D ecline.......................................................................................... 14
A Conceptual Model of Ecosystem and Diversity...................... ...........20
Carrying Capacity of Systems for Diversity ..................................................30
Spatial Organization....................................................................................30
Hierarchical Organization.......................... ...........................................30
Rainforest in Biosphere 2............................................................................... 31
Design Elements and Description .............................................................34
A Conceptual Model of Diversity in Rainforest of
Biosphere 2..............................................................................................38
Rainforest in Puerto Rico....................................................................................41

2 M ETH O D S.................................................................................................. .......... 43

Construction and Operation of the Rainforest in Biosphere 2....................43
Procedures Used in Starting the Ecosystem...............................................45
Soil Components and Placement..................................................................45
Collection and Initial Placement of Plants...........................................47
Habitat Assembly ..........................................................................................49
Climate Maintenance Systems.....................................................................53
Human Intervention ...................................................................................56
Plant Mapping and Identifications..................................................................57
Initial Mapping and Identifications: 1990-1991...................................57
Species Additions and Removals ............................................................57









Field Measurements..........................................................................................58
Second Survey: Transition period, 1993-1994............................................58
Third Survey: June-August 1996...............................................................59
Surveys of Species Found per 1000 Individuals Counte...........................61
Leaf A rea Index............................................................................................. 62
Number of Seedlings per m2........................................................................62
Percent of Holes in Leaves ..........................................................................63
Number of Green or Yellow Fallen Leaves per m2..............................63
C alculations.........................................................................................................63
D diversity Index .............................................................................................63
Biomass Estimates ........................................................................................64
Growth Form Spectra..................................................................................65
Poisson D istribution........................................................................... ..........65
Sim ulation M ethod........................................................................ ......................66
Emergy Evaluation............................................................................................67

3 RESU LTS .................................................... ......................................................... 72

Characterization of and Changes in Biosphere 2 Rainforest........................72
Soil ....................................................................................................... ................72
Plants............................................ ................................................................ 77
Spatial Distribution of Plants ................................................................. 90
Cumulative Species per Cumulative Individuals Counted....................90
Leaf A rea Index.............................................................................................. 94
Number of Seedlings and Green and Yellow
Fallen Leaves per m2 ...............................................................................94
Percent of Holes in Leaves............................................................................97
Litterfall and Decomposition Rates .......................................................97
Carbon Uptake and Respiration .................................................................99
Cutting and Consumers............................................................................101
D diversity Index ............................................................................................ 101
Biomass Estimates ......................................................................................101
Comparisons Between Biosphere 2 and Tabonuco Forest in
Puerto R ico............................................................................................... 101
Physical Environment............................................. ....................................103
Soil ................................................................................................. ....................105
P plants ........................................... .............................................................. 105
Overview Simulation Models .......................................................................122
Production and Biomass Minimodel Description......................... ...126
Results of Simulating the Production and Biomass Minimodel..........130
Production and Diversity Minimodel Description ................................138
Results of Simulating the Production and Diversity Minimodel ........143
Emergy Evaluation of Rainforest in Biosphere 2.........................................148




v










4 D ISCU SSIO N ................................................................. ..................................... 154

Succession with Declining Diversity............................................................154
Effect of First Arrivals.............................................................................155
Limited Access to Genes.............................................................................156
Declining Diversity and a Species Plateau............................................156
Extrapolation of Species Composition According to
R eproduction........................................................................................ 158
Simulation of Species Decline ...................................................................160
Mechanisms Affecting Diversity in Biosphere 2..........................................163
Excess Resources and Diversity....................................................................163
Effect of Trimming Weedy Growth.........................................................164
Pulsing Disruption ....................................................................................165
C onsum ers ........................................................................................................166
Graphical Representation of Cumulative Species-Individual
C ounts .................................................................................................... 166
Effect of Spatial Characteristics of Plants in Biosphere 2.........................169
Comparisons with El Verde .............................................................................169
Comparisons Between Rainforest Structure in Biosphere 2 and
El V erde..................................................................................................170
Soil Structure..................................................................................... ..........170
Absence of Most animals and Simplification of Food Webs...............171
Plant Reproduction ................................................................................. 171
Species and Individuals...............................................................................172
General Implications.......................................................................................174
Comparison of Biosphere 2 with Role and Trends of
G lobal Biodiversity.................................................................................... 174
Declining Diversity and Downsizing.....................................................175
Comparing Succession of Diversity in Biosphere 2 with
Global Cultural Change..........................................................................175
Carrying Capacity of Systems for Diversity ..............................................176

APPENDICES

A BIOSPHERE 2 RAINFOREST PLANT MAPS ........................................177

B BIOSPHERE 2 RAINFOREST PLANT LISTS........................................199

C PRODUCTION AND BIOMASS MINIMODEL................................. 306

D PRODUCTION AND DIVERSITY MINIMODEL.............................. 323

REFERENCES .........................................................................................................332

BIOGRAPHICAL SKETCH.....................................................................................342












LIST OF TABLES


Table page

1-1. Definitions and concepts used in this dissertation
(after Odum 1996) .................................................... ............................ 3

1-2. Symbols for the energy systems language used in this
dissertation ............................................................................................ 22

1-3. Parts and processes of ecosystem model that affect species
numbers and account for observed declines ......................................... 24

2-1. Chronology of Biosphere 2 rainforest construction
and operation................................................... ................................... 44

2-2. Rainforest soil components and their origins. From
Scarborough (1994)............................................... .............................. 46

2-3. Percent of components in topsoil mixture specifications and their
corresponding habitats. From Scarborough (1994). Totals
are approxim ate............................................... ................................... 48

2-4. Spreadsheet used to calculate coefficients for single tank
biodiversity model in Figure 2-3, calibrated at steady
state............................................................... ....................................... 69

3-1. Characteristics of Biosphere 2 rainforest soils from
samples taken on different dates ....................................... ............. .. 73

3-2. Soil bulk density and percentage coarse fragments in Biosphere 2
rainforest from samples made in November 1993.
From Scott (1999)................................................. ............................... 76

3-3. Total number of species and individual plants seeded in the
Biosphere 2 rainforest............................................... ......................... 78

3-4. Number of individual plants and species recorded in 1991, 1993,
and 1996 surveys of Biosphere 2 rainforest. The first number
in each entry includes plants from the 1991 planting, the second
number from the 1993 planting, and third is plants that have
self-propagated. Species reported are for species new to
the rainforest....................................... ................................................ 81








3-5. Leaf and branch interceptions per observation through vertical
points in Biosphere 2 rainforest. Data for 1993 from
O dum et al. (1993) ................................................................................. 96

3-6. Distribution of seedlings found in 30, 0.54 m2 circular plots
in Biosphere 2 rainforest understory in 1998........................................... 96

3-7. Distribution of green and yellow leaves in 0.54 m2 circular plots
on lowland rainforest ground, April 1998 ............................................ 98

3-8. Percent of holes in leaves in Biosphere 2 rainforest trees.
Data for 1993 from Odum et al. (1993) ................................................... 98

3-9. System metabolism of Biosphere 2 rainforest for summer, 1996.
NEE=Net ecosystem exchange, R,=Soil respiration, Ac=Canopy
assimilation, RUE=Radiation use efficiency, Rp=Plant
respiration. From Lin et al. (1999).......................................................... 100

3-10. Shannon-Wiener index of diversity in Biosphere 2 rainforest for
1991, 1993, and 1996 ................................................................................. 102

3-11. Aboveground plant biomass estimates in Biosphere 2 rainforest
for 1990, 1991, and 1993. From Haberstock (1991) and
Bierner (1993)............................................................................................ 102

3-12. Environmental variables at El Verde and Biosphere 2 forests.
From Odum (1970), Romer (1985), Ahrain et al. (1998), and
Cuevas et al. (1991) .................................................................................. 104

3-13. Comparison of soil properties of Puerto Rico and Biosphere 2
forests. From Edmisten (1970), Silver et al. (1994),
Scott (1999), and Lin et al. (1998 and 1999). ......................................... 106

3-14. Soil bulk density in Biosphere 2 rainforest and Puerto Rico
tabonuco forest. From Scott (1999), Edmisten (1970), and
Silver et al. (1994) .............. ........................................................................ 108

3-15. Plant species occurring in El Verde that were originally
planted in Biosphere 2 forest, with an inventory of
individuals counted per species in 1991 and 1996 .............................. 109

3-16. Sampling sites for species/individual counts, and number
of species/ 1000 individuals................................................................ 113

3-17. Leaf-area indices of Puerto Rico tabonuco forest and
Biosphere 2 rainforest. From Odum(1970), Jordan (1969),
Odum and Pigeon (1970), and Odum et al. (1993) ............................. 120








3-18. Seedling density in Biosphere 2 and tabonuco rainforest.
Tabonuco forest data from Odum (1970b)............................................. 121

3-19. Percent of holes in leaves in Biosphere 2 and tabonuco
forest trees. Tabonuco forest data from Odum (1970b). ..................... 121

3-20. Litterfall rates in Biosphere 2 rainforest habitats and tabonuco
forests. From Nelson (1999), Wiegert (1970),
Cuevas et al. (1991), Lugo (1992), and Lodge (1991).......................... 123

3-21. Decomposition rates of litter in Biosphere 2 rainforest and
tabonuco forest in Puerto Rico. From Nelson (1999) and
W iegert (1970)........................................................................................... 123

3-22. Nutrient content of leaves in percent of dry weight in
Biosphere 2 and El Verde forests. From Odum (1970a),
Ovington (1970), Medina et al. (1981), and Lin et al. (1999) ............... 124

3-23. Carbon exchange in Biosphere 2 (summer) and tabonuco
rainforests. Rs=Soil respiration, A,=Canopy assimilation
From Lin et al. (1999) ............................................................................... 125

3-24. Estimates of aboveground biomass density in Biosphere 2 and
tabonuco forests. From Haberstock (1991), Bierner (1993),
Ovington and Odum (1970), Scatena et al. (1993), and
Lugo (1992) ............................................................................................... 125

3-25. Accumulated emergy inputs to Biosphere 2 rainforest for
start-up of the system prior to material closure in 1991 ..................... 150

3-26. Comparison of energy in developing rainforest in Biosphere 2
in 1991 and 25-year-old natural tabonuco forest................................. 153

4-1. Extrapolation of species composition of Biosphere 2 rainforest
to 100 years with 30 species. H=Herb, T=Tree, P=Palm,
G=Giant herb, A=Bamboo, C=Climber, S=Shrub ................................. 161

4-2. Species/1000 individuals and slope of log-log graphs for all
study sites. K=slope of log-log graph.................................................... 173

B-1. Individual plants in the Biosphere 2 rainforest.......................................... 199

B-2. Species from the first planting of the Biosphere 2 rainforest,
with inventories from 1991, 1993 and 1996. T=Tree,
S=Shrub, P=Arboreal palm, R=Graminoid, C=Climber,
A=Woody graminoid, such as bamboo, H=Herb,
G-Giant herb, E=Epiphyte................................................................. 283








B-3. Species from the second planting of the Biosphere 2
rainforest, with inventories from 1993 and 1996, or
self-propagated. T=Tree, S=Shrub, P=Arboreal palm,
R=Graminoid, C=Climber, A=Woody graminoid, such as
bamboo, H=Herb, G-Giant herb, E=Epiphyte...................................... 299

C-1. EXCEL spreadsheet used to calculate coefficients for
Biosphere 2 rainforest production and biomass minimodel
under predicted steady state conditions ................................................ 308

C-2. Program in BASIC for the simulation of metabolism of the
rainforest in Biosphere 2, Model B2METAB in Figure 3-19................ 313

D-1. EXCEL spreadsheet used to calculate coefficients for
Biosphere 2 rainforest diversity and production minimodel,
SP D IV ........................................................................................................ 324

D-2. Program in BASIC for the simulation of production and
diversity in the Biosphere 2 rainforest, Model SPDIV
in Figure 3-28............................................................................................ 327













LIST OF FIGURES


Figure page

1-1. Systems diagram representing theories of ecosystem diversity ..............21

1-2. Areas w within Biosphere 2............................................................................ 32

1-3. Continuous photosynthetically active radiation, CO2,
and temperature in terrestrial wilderness biomes of
Biosphere 2 during the first material closure.......................................33

1-4. Side view of rainforest biome....................................................................35

1-5. Habitats delineated within the Biosphere 2 rainforest..................................37

1-6. Systems diagram representing ecosystem diversity within
Biosphere 2 rainforest. .................................... .........................................39

2-1. Hydrologic connection of Biosphere 2 rainforest to the rest of
the Biosphere 2 system ............................................................................54

2-2. Diagram and equations for species diversity on an island as
described by MacArthur and Wilson (1967) and drawn by
Beyers and Odum (1993) ................................... .......................................68

2-3. Single tank model of biodiversity as a balance of steady inflow
pathw ay coefficients...............................................................................68

2-4. Single tank model of biodiversity with calibration values for
flow s and storage. ......................................................................................69

2-5. Simulation of number of species Q for different starting values
using the single storage model in Figure 2-3..........................................70

3-1. Map section #3 showing location, growth form, and canopy
size of individual plants in the Biosphere 2 rainforest in
September 1991. The twenty map sections are given in
Figure A-1. Approximate scale: 1 cm=0.6 m..........................................79

3-2. Change in plant species abundance and distribution in
Biosphere 2 rainforest, 1991-1996, for plants from the
first planting...................................................................................... .. 83








3-3. Number of individual plants in Biosphere 2 rainforest
time including 2 planting periods, 1991 and 1993.................................84

3-4. Number of species in Biosphere 2 rainforest through time and
with two planting periods, 1991 and 1993................................................84

3-5. Relationship of number of species to number of individuals
over time in Biosphere 2 rainforest on linear (upper figure)
and semilog (lower figure) scale. Open triangles are plants
from 1991 planting, squares from 1993 planting, and circles
combine plants from both. Survey data are from
1991, 1993 and 1996................................................................................... 86

3-6. Number of individuals within growth forms in Biosphere 2
rainforest in 1991, 1993 and 1996. Data include only plants
from first planting. H=Herb, T=Tree, S=Shrub, C=CIimber,
G=Giant herb, P=Arborescent palm, E=Epiphyte,
R=Graminoid, A=Bamboo .....................................................................87

3-7. Number of species within growth forms in Biosphere 2 rainforest
in 1991, 1993 and 1996. Data include only plants from first
planting. H=Herb, T=Tree, S=Shrub, C=Climber, G-Giant
herb, P=Arborescent palm, E=Epiphyte, R=Graminoid,
A =B am boo ...................................................................................................... 88

3-8. Change in number of species within growth forms from 1991
planting in Biosphere 2 rainforest through time.................................89

3-9. Change in distribution of species within growth forms from 1991
planting in Biosphere 2 rainforest through time.................................90

3-10. Spatial distribution of plants in Biosphere 2 rainforest in
1991 (solid squares) compared to Poisson distribution (open
trian g les)..................................................................................... ..................91

3-11. Cumulative plant species as a function of cumulative
individuals in Biosphere 2 rainforest, 1991. Data for all
habitats except cliff faces and surface aquatic systems are
plotted on linear (a), semi-log (b) and log-log (c) scales......................92

3-12. Cumulative plant species as a function of individuals in
Biosphere 2 rainforest, April 1998. Open squares have
Scindapsus and Syngonium subtracted...............................................93








3-13. Cumulative species as a function of cumulative individuals
in Biosphere 2 rainforest in 1991 (solid circles), 1998a
(all plants, open squares) and 1998b (Syngonium and
Scindapsus deleted, crosses)...................................................................95

3-14. Growth form spectra of Biosphere 2 rainforest and El Verde
tabonuco forest. B2=Biosphere 2. Data for El Verde from
Sm ith (1970)......................................................... .................................. 112

3-15. Cumulative plant species as a function of cumulative
individuals >0.5 m tall counted on an 11-year-old
landslide at El Verde site ...................................................................... 114

3-16. Cumulative plant species as a function of cumulative
individuals counted in Biosphere 2 rainforest (solid circles)
and on an 11-year-old landslide at El Verde site
(open squares) ...................................................................................... 115

3-17. Cumulative plant species as a function of cumulative
individuals counted on El Verde landslide (open circles),
Radiation Center (open triangles), and Bisley grid (crosses)............ 116

3-18. Cumulative plant species as a function of cumulative
individuals counted on El Verde landslide, Radiation
Center, Bisley grid and Biosphere 2 rainforest for
1991 and 1998...................................................... ................................ 118

3-19. Systems diagram for simulating production and biomass in
Biosphere 2 rainforest showing storage, pathway
coefficients, and equations.................................. .................................127

3-20. Systems diagram for simulating production and biomass in
Biosphere 2 rainforest showing calibration values projected
for steady state after 20 years of operation....................................131

3-21. Ten-year simulation of production and biomass minimodel,
B2METAB in Figure 3-19. Final values for plant biomass
are on the right side of their graphs. g/m2 = grams per
square meter, dry weight for biomass.....................................................132

3-22. One-hundred-year baseline simulation of production and
biomass in the minimodel, B2METAB in Figure 3-19.
Final values for plant biomass are on the right side of
their graphs. g/m2 = grams per square meter, dry weight
for biom ass..... ......................................................................................133








3-23. Comparison of simulations of biomass by the model in
Figure 3-19 showing effects of light, elimination of weedy
biomass, limited pruning, and altered airflow on mature
and weedy plant biomass. Values for biomass at 100 years
are given on the right side of the graphs in grams of dry
biomass per square meter. Scales are the same for each
box. M=Mature plants, W=Weedy plants.............................................135

3-24. Comparison of effects of light, elimination of weedy biomass,
limited pruning, and altered airflow on system production
ratio, Pg/Rp. Scales are the same for each box, with the
center line = 1...............................................................................................136

3-25. Systems diagram for simulating diversity and production in
Biosphere 2 rainforest showing storage, pathway
coefficients and equations....................................................................140

3-26. Systems diagram for simulating production and diversity in
Biosphere 2 rainforest showing calibration values for
storage and flow s ............................................................................... 144

3-27. Baseline simulation of diversity and production minimodel
SPDIV, in Figure 3-25 for Biosphere 2 rainforest for
10 years. Final values for plant biomass and species are on
the right side of their graphs, g/m2 = grams of dry biomass
per square m eter.................................................................................... 145

3-28. Baseline simulation of diversity and production minimodel,
SPDIV, in Figure 3-25 for Biosphere 2 rainforest for 100
years. Final values for plant biomass and number of species
are on the right side of their graphs. g/m2 = grams of dry
biom ass per square m eter ........................................................................147

3-29. Emergy analysis summary diagram of Biosphere 2 rainforest............149

4-1. Extrapolation of number of plants in El Verde rainforest to a
possible diversity plateau (solid triangle) for the
Biosphere 2 rainforest. Measured data from Biosphere 2
are shown with solid circles (1991) and open squares (1998).............159

A-1. Map cells showing the location of individual plants in the
Biosphere 2 rainforest ............................................................................177


xiv








C-1. One-hundred-year simulation of Biosphere 2 rainforest
production and biomass minimodel, B2METAB, with
light increased 20% over baseline. Final values for plant
biomass are on the right side of their graphs. g/m2=grams
per square meter, dry weight for biomass.............................. ............316

C-2. One-hundred-year simulation of Biosphere 2 rainforest
production and biomass minimodel, B2METAB, with
no weedy biomass. Final values for plant biomass are
on the right side of their graphs. g/m2=grams per square
m eter, dry w eight for biom ass ................................................................317

C-3. One-hundred-year simulation of Biosphere 2 rainforest
production and biomass minimodel, B2METAB, where
all pruned biomass is put onto the soil. Final values for
plant biomass are on the right side of their graphs.
g/m2=grams per square meter, dry weight for biomass.....................318
C4. One-hundred-year simulation of Biosphere 2 rainforest
production and biomass minimodel, B2METAB, with
no pruning by humans. Final values for plant biomass
are on the right side of their graphs. g/m2=grams per
square meter, dry weight for biomass.....................................................319

C-5. One-hundred-year simulation of Biosphere 2 rainforest
production and biomass minimodel, B2METAB, human
effort is reduced to .75 of the baseline. Final values for
plant biomass are on the right side of their graphs.
g/m2=grams per square meter, dry weight for biomass......................320
C-6. One-hundred-year simulation of Biosphere 2 rainforest
production and biomass minimodel, B2METAB, human
effort is reduced to .85 of the baseline. Final values for
plant biomass are on the right side of their graphs.
g/m2=grams per square meter, dry weight for biomass....................321
C-7. One-hundred-year simulation of Biosphere 2 rainforest
production and biomass minimodel, B2METAB, with
airflow cut off from the rest of the Biosphere. g/m2=grams
per square meter, dry weight for biomass..............................................322

D-1. Simulation of Biosphere 2 rainforest with continuous
additions of 5 and 20 species per year over 10 years. Final
values for plant biomass and species are on the right side
of their graphs, g/m2=grams of dry biomass per square meter........329








D-2. Simulation of Biosphere 2 rainforest with continuous
additions of 5 and 20 species per year over 100 years. Final
values for plant biomass and species are on the right side
of their graphs. g/ m2=grams of dry biomass per square meter.......330

D-3. Simulation of Biosphere 2 rainforest when 50 species are
added after the second year. Final values for plant biomass
and species are on the right side of their graphs. g/ m2=grams
of dry biomass per square meter ....................................................331













Abstract of Dissertation Presented to the Graduate School
of the University of Florida in Partial Fulfillment of the
Requirements for the Degree of Doctor of Philosophy


THE BASIS FOR RAINFOREST DIVERSITY AND BIOSPHERE 2

By

Linda Susan Leigh

August 1999



Chairman: H. T. Odum
Major Department: Environmental Engineering Sciences

A miniature rainforest created in the glass-enclosed Biosphere 2

mesocosm in Arizona was compared with montane rainforest in Puerto Rico to

study the basis for biodiversity and succession. Initial seeding of high plant

diversity was a technique for determining by extrapolation the carrying capacity

in Biosphere 2 and in disturbed areas in Puerto Rico. In Biosphere 2 the

rainforest area was started in 1991 with 1890 plants of 316 species in 0.19

hectares. Three hundred and thirty-nine plants in 92 species were added in 1993.

A diversity index, species per 1000 individuals counted, decreased from 250 in

1991 to 96 in 1998 compared to 60 in the comparison forest while the Shannon-

Wiener index decreased from an initial 5.39 to 4.64 in 1996 compared to 4.62 in

the comparison forest. Although normal populations of insects and pollinators

were absent, vegetative reproduction established productivity, diversity,








hierarchy and developed soil profiles approaching those in the comparison

forest.

Graphs of cumulative species versus individuals counted were analyzed

to identify mechanisms affecting diversity including seeding, competition for

excess nutrients and carbon dioxide, extinction rate, seasonal change in

insolation, and pruning and management by humans.

The productive basis for diversity was simulated with a model of

production, consumption, and recycle that included management alternatives.

Simulation runs showed total biomass production highest when the weedy vine

biomass was regularly trimmed and removed.

Another model of main factors affecting diversity was simulated with a

minimum species limit to help explain the observed patterns and anticipate

species carrying capacity. With an addition of 50 new species after 2 years, the

simulation showed an increase in diversity and decrease in biomass after 10

years when compared to the simulation without further additions. Emergy and

emdollar evaluation showed resources required for developing the rainforest in

Biosphere 2 were 2300 times larger than those for the natural succession.


xviii














CHAPTER 1
INTRODUCTION


The basis for biodiversity is a principal question in ecology and other
fields. Whereas most studies of succession and development of ecosystems

have concerned periods of increase and diversification, less studied are the
limits to diversity. Are there general systems principles controlling the self-
organization of diversity in all systems? What happens when there is initial
seeding of high diversity and limited area? In this dissertation the self-
organization of the rainforest in Biosphere 2, the glass-enclosed mesocosm in

Arizona, is compared with the tabonuco rainforest in Puerto Rico. Floristic
studies, measurements, and models are used to account for patterns of growth
and diversity.

Suppose a system is defined to include a newly added set of individual
organisms and species. Immediately, relationships develop between these
and the flows of energy and matter and some between each other. Parts and
relationships can be represented with systems diagrams that give an
overview of the whole and the parts. Diversity and structure are the
information of the system that, like other storage, requires energy for its
maintenance. The amount and quality of energy available to a system in part
determines which of the energy requirements for diversity, structure, and
their connections can be supported, thus shaping its biodiversity. Science of
the parts of ecosystems, such as physiology, and science of the whole, such as
systems ecology, are converging with respect to understanding biodiversity.








To improve the synthesis when science of the parts is applied, ecosystems and

energy are included in systems models.

This dissertation considers the self-organization of the diversity of
systems with limited resources. Do systems have a carrying capacity for
diversity? How do resources and mechanisms of system interaction account

for observed patterns? The next section is a literature review of the theories
and processes that have been offered to account for decreases in diversity and

structure. In order to clearly relate diversity to its resource basis, Table 1-1
provides definitions of the measures used.


Review of Diversity-Influencing Processes in Other Studies

Observations of diversity patterns over scales of time, space, or energy
inputs suggest causal mechanisms affecting the processes that contribute to
diversity. A comparative approach is often used in studying diversity in
ecological systems.

Species and Area

Diversity is the number of kinds of units in an area. In an ecosystem it
may be the number of species found. Patterns of diversity have been
observed and compared for decades over spatial scales ranging from the entire

biosphere (latitudinally) to continents, regions and localities
(Rosensweig 1995).

A general pattern in the relationship of species and area show that
within a taxonomic group, large areas support more species than small areas.
A clear description of the pattern was first published by Jaccard (1912), and in
1921 Arrhenius published a mathematical description of the curve, which










Table 1-1. Definitions and concepts used in this dissertation (after Odum
1996).


DEFINITION


Emergy


Power


Empower

Transformity



Species richness




Diversity






Diversity indices:
Shannon index


Margalef index


Species/1000
individuals


The amount of available energy of one particular type
that was used up, directly and indirectly, to make
something (product or service). The unit with the
prefix "em" is used with the units summed to indicate
that it is an emergy rather than an energy scale. This
study uses solar joules as energy units and solar
emjoules as emergy units.

Flow of useful energy per unit time.

Flow of emergy per unit time.

A measure of energy quality defined as the emergy per
unit available energy of a product or service. Units are
emjoules per joule.

The number of species found in an area. This is often
used interchangeably with diversity, though richness
only accounts for the number of species and not their
distribution in an area.

The accounting of different types within a system
using taxonomic, functional, size, trophic levels,
information content, etc., as the categories. The
number of species and their relative abundances
within an area are often used to calculate an index of
diversity using various formulas.

H' = -Y pi In pi
p, is the proportion of individuals found in the ith
species.

(S-1)/ln N
S = number of species, N = number of individuals


A form of the Margalef index


TERM












Table 1-1 -- continued.
TERM
Logarithmic
index

Information




Maximum
empower
theory

System


Energy hierarchy


DEFINITION
log S/log N


The units, connections, and configurations of a system
requiring some form of energy as their carrier.
Information is useful if it can make its system operate.
Genetic codes are an example of useful information.

Self-organizing systems prevail by developing designs
that maximize emergy inputs and effective use (Odum
1996).

A part of nature with components defined by artificial
or real boundaries, where 'windows' of time and space
delimit the system of study. Single organisms or
single populations are systems since they have
relationships to their external factors and among their
parts. A set of organisms is a system even if the units
are new and not interacting much with each other.
They are interacting with the light, material and heat
flows. A system can be any size.

The natural arrangement of energy transformation
processes in a chain in which each process uses energy
of one kind to generate less energy of a different kind.
Available energy decreases along the chain, but
transformity increases.


.





5


was quickly refuted by Gleason (1922). Extensive dialogue regarding the
significance of the mathematical relationship has followed.

A plot of the increase of species as the sample size increases within an
ecosystem is called the species/area curve. The first species/area curve is
attributed to H. C. Watson in 1835 (Connor and McCoy 1979). The curve is

used to indicate the number of species within an area of study larger than the
sampled area; to determine the rate at which species accumulate within an
area for comparison with other areas; and to determine the minimum
sampling size needed to adequately characterize diversity of an area. Vestal
(1949) attempted to calculate equivalent reference areas for vegetation types in
about 240 areas worldwide. The reference areas were used to compare plant
diversity within the area as well as to calculate sampling size required to
characterize the vegetation type. The following site differences were cited as
reasons for the necessity of varying the area sampled to determine diversity:
size of plants or clumps of plants; degree of species dominance; low density of
plants overall; productivity of the site; size and shape of the site; degree of
heterogeneity of the environment; complexity of the community; floristic
richness; abundance among species; successional stage; stand condition.
Studies of diversity have to be carefully related to area. Though these reasons
are plausible explanations for the need of varying sample sizes, his results
have been considered "dubious", "purely hypothetical and probably wrong"
due to methods he used in data conversions (Goodall 1952).

Though the pattern of diversity increasing with area may seem
obvious or trivial, Huston (1994, p. 35) claims that, "...the underlying
mechanisms include most of those that are potentially important in
regulating diversity." Three hypotheses were suggested by Connor and
McCoy (1979) in examining the causal mechanisms behind the pattern. The








first is considered the null hypothesis, and states that the pattern is a statistical
sampling phenomenon (Gotelli and Graves 1996). The alternate hypotheses

are the result of biological processes. The first suggests that diversification of

species is greater in heterogeneous habitats, which occur with greater
frequency as total area increases. The second suggests that the extinction rate
is higher in smaller areas where populations are smaller, and that
immigration rates don't change between areas.

As the area over which species occur increases, the available resources
for species support increase proportionally. Species-area curves comparing
local and regional scales show the species increasing as the total energy
available to support diversity increases. In a study of 82 different variably
sized terrestrial ecosystems, Orrell (1997) found correlation between species
richness and the energy flow of each ecosystem.

Due to difficulties in comparing species/area curves where different
areas have been sampled, other researchers have recommended using a plot
of the number of species that accumulate for the number of individuals
counted. Research by Condit et al. (1996b) in tropical forests demonstrate that
diversity estimates can be compared over sites where an identical number of
stems have been counted.

Species and Individuals

A common pattern measured in nature is the relationship between the
cumulative number of species found and the individuals counted within a
system. The typical pattern is a curve of decreasing slope (example Figure 3-
11), and is the same type of pattern as the species/area curve (Huston 1994).
The pattern holds for total enumeration of individuals within a site as well as








for subsets, such as trees within a particular stem diameter range (Condit et al.

1996b). Documentation of this pattern has been repeated with various taxa
such as aufwuchs in natural springs and a laboratory microcosm (Odum and
Hoskin 1957; Yount 1956), fishes (Angermeier and Schlosser 1989), and insects
(Fisher et al. 1943).


Succession

Succession is the process of self-organization of an ecosystem after a
disturbance. It is linked to diversity in that species composition and
dominance change in an area over time due to processes within the system or
processes at a larger scale. Clements (1936) initially suggested succession as a
phenomenon whereby early successional species facilitate later successional
species. According to his conceptual model, each stage of succession paves the
way for the next stage by altering soils, humidity, nutrients and water
availability. Connell and Slatyer (1977) suggest 3 categories of causal
mechanisms for successional changes, adding to Clements' facilitation
category: facilitation, inhibition, and tolerance. With their model, the net
effect of an earlier successional species on the establishment of a later species
can be either positive (facilitation), negative (inhibition), or neutral
(tolerance). A neutral effect allows equal probability of all organisms to
become established in an area, and "leads to a community composed of those
species most efficient in exploiting resources, presumably each specialized on
different kinds or proportions of resources." (Connell and Slatyer 1977). All
three of these mechanisms along with life history characteristics of organisms
are important in any given ecosystem (Ricklefs 1990).








Gutierrez and Fey (975) developed a model simulating the general
dynamic patterns of succession, relating ecosystem structure to successional
patterns. Simulations of their model suggest that the internal feedback

structure of an ecosystem drive secondary succession. Ulanowicz (1980) uses

community flow networks through ecosystems to describe the development

and information content of the systems, suggesting that flows by themselves

adequately describe ecosystem succession.

Four stages of succession are suggested by Holling (1986): exploitation,
conservation, creative destruction, and renewal (recycle). During the
exploitation and conservation phases, an ecosystem develops structure,

functions, and diversity from available energy and matter. Disturbances the
creative destruction phase occur as pulses on widely varying spatial and
time scales which are generally characteristic of a given ecosystem.
Disturbances may be caused by abiotic elements or by biotic factors. The pulse
of nutrients made available allows their recycle into a newly developing

ecosystem, which may have very different configurations than the previous
ecosystem (Holling 1986).

When a disturbance is widespread, the successional process may be in
the same phase over the entire area of disturbance. In the case of treefalls, the
successional process starts over in small local areas, creating a discontinuous,

mosaic landscape. Remmert (1991) calls this a 'mosaic-cycle', where various-

aged patches of different sizes occur throughout an ecosystem. The
importance of spatial and temporal landscape patterns to vertebrate species
diversity has been documented for avian species in Panama by Karr and
Freemark (1983).

Diversity of an ecosystem is generally reduced after the creative
destruction phase. During the establishment and conservation phases,








diversity generally increases, though there are cases where diversity declines

during these 2 phases. Diversity decline has been observed just after the

point where all species (both opportunist and mature life-histories) occur at

the same time. Eventually, the opportunist species are out-competed for

resources, and a species decline is seen (Remmert 1991) where later

successional species dominate.


Theories of Diversity

Since species diversity reflects the sum of additions and removals of
species from an area, local and regional processes that add or subtract species

are important to its understanding. Species are added to an area by evolution
or by immigration. They are subtracted from an area by total extinction or by

one of following processes: change in physical conditions that no longer meet
the needs of the species, such as catastrophes or climate change; random
events that affect rates of propagation and mortality; or exclusion by local

processes due to interactions between individuals, such as competition,
predation, and pollination (Hawksworth and Kalin-Arroyo 1990).

Many theories have been offered to explain differences in diversity.
They include both equilibrium and non-equilibrium processes. Theories
invoking equilibrium dynamics suggest that the rate of addition and removal

of species from a region is equivalent, and that areas have their own
equilibrium value of species diversity. If species are lost, the processes of
adding or subtracting species will adjust the value so that it remains constant.
On the local scale, equilibrium theory suggests that species interactions
account for the level of diversity saturation, and that local diversity is fed by
the regional species pool (Ricklefs 1990). Non-equilibrium or dynamic








equilibrium theory suggests that communities have fluctuating species
diversity resulting from an approximate balance between local and regional
processes (Ricklefs 1990). Competitive exclusion and its prevention are the
basis of this theory, according to Huston (1994).

The following broad theories suggest underlying processes of observed
patterns of diversity: 1) Diversity through fluctuations; 2) Time theory; 3)
Diversity proportional to resources; 4) Energy or empower diverted for
physiological adaptation; 5) Population mechanisms affecting diversity; and
6) Habitat heterogeneity theory.

Diversity through fluctuations
More diversity is predicted when fluctuations of conditions affecting
species is large enough so that no one species can gain competitive
dominance, but not so large as to cause extinctions. This is the basis of the
"intermediate disturbance hypothesis" proposed by Connell (1978), who
applied it to rainforests. Rainforests have numerous gaps, evidence that
there is almost perpetual disturbance of small areas. Gaps are thought to

occur before competitive exclusion within the forest can reduce its diversity.
Hence, a high diversity is maintained in rainforests.
Previously, Hutchinson (1961) questioned the mechanism of co-
existence of many species of phytoplankton in relatively large lakes as well as
the co-existence of large numbers of species in other ecosystems. He framed
his argument using the competitive exclusion theory, and maintained that if
disturbance in the ecosystem recurred more frequently than the time over
which species would have been excluded due to interspecific competition,
species richness should remain high.








Fluctuations may cause extinction of rare species, leaving a lower
diversity at least temporarily. Pimm (1991) discusses 2 ways in which species
extinction rates increase for small populations: one due to random
demographic causes, such as all individuals growing in one year are the same
sex, and the second due to fluctuations that add to the risk of random
extinction. Supporting this, Tilman and El Haddi (1992) reported a 40%
extinction rate of species in grassland ecosystems due to drought. Most of the
species lost were rare before the drought. Hall et al. (1992) suggest that the
geographic distribution of individuals of a species reflects the net energy
balance of the species, occurring in a gradient that can be divided over 3 parts
of the distribution: the range over which the stored energy is sufficient for
reproduction and long term existence of the species; the range over which
stored energy is adequate for survival but not reproduction; and the range
wherein energy reserves must be consumed for survival. The extremes of
the gradient may be the areas over which a species becomes rare, and has a
higher probability of extinction with fluctuations that will take energy for
adaptation.

Seasonal fluctuations can increase diversity of an ecosystem. For
example, in arid lands a large annual flora may flourish during seasonal
rainfall events. Since the perennial plants of arid lands are widely spaced,
probably due to competition for water, seasonal invasion by annual plants is
possible when water is available (Colinvaux 1986).

Time theory

The amount of time over which a region has been undisturbed by
major climatic changes, such as glaciations, may influence the number of
species that are in the area. Tropical areas may have had more time for








evolution to occur than temperate regions. Periods of drying may also have

created refugia for tropical moist species, providing the isolation believed
important to speciation. Temperate and arctic regions also have ancient floral

elements, however, so the time that floras have had to evolve may not be as
different as originally proposed (Ricklefs 1990), though temperate and arctic

regions have been periodically nearly eliminated by expansion of glaciers.

Sanders (1968) proposed the stability-time hypothesis, which addressed
the high diversity of the deep sea benthos compared to continental shelf
benthos. He suggested that the difference was due to stability of the

environment of the deep sea, allowing evolutionary specialization and low
extinction rates due to environmental fluctuations. In addition, respiratory
costs of living in the environment would be very low.

Diversity proportional to resources

More diversity is predicted when there is more energy to support the
greater complexity of the system of more species. Odum (1960, 1970 and 1971)
related diversity to the energy requirements using permutations and square
functions to relate number of species to energy requirement. Where the
levels of energy supporting an ecosystem decrease, species diversity has been

observed to decrease. For example: Energy theory was suggested by Connell
and Orias (1964) but they later retracted their view. Odum (1970a, 1970b)
offered energy theory of diversity for a rainforest in Puerto Rico.

Wright (1983) proposes a species-energy theory, predicting diversity of
species from either actual evapotranspiration (for plants) or total net primary
production (for breeding land or freshwater bird species) of island biota.
Wright showed that on islands of varying sizes and locations, as the basic
energy resources decrease, as with increased latitude or seasonal changes,








species diversity decreases. Since lower populations of species are supported
with less energy, there is a higher probability of species extinctions. More

recently Rosenzweig and Abramsky (1993) suggested a decrease of diversity
with a decrease of primary productivity, as well as a diversity decrease with an

increase of primary productivity above a certain level. In other words, the
proposed pattern on a regional scale is hump-shaped.

The relationship between energy and species richness is scale-
dependent. Wright et al. (1993) show the relationship on regional and local
scales. He emphasizes the importance of using extensive measures of
incoming energy to a system (total amount per area) for the correlation rather
than intensive (amount per m2).

The maximum empower theory predicts this. Empower (definition
Table 1-1) is a measure of the rate of resource use by an ecosystem which

combines different resources in one energy-evaluated unit. Emergy is used to
combine inputs and processes on a common basis insolationn, precipitation,
transpiration, evaporation, and primary production). Energy concentration

has been proposed as a third measure of scale (with time and space) for
relation to diversity.

Population mechanisms affect diversity

Population approaches to diversity describe processes occurring at the
scale of individual organisms and their interactions with and effects on each
other. These include predation, competition, and mutualism. The
implication is that population densities change by each individual
responding to its local conditions rather than in response to average
conditions across an area (Tilman et al. 1997).








Three approaches to understanding population dynamics are discussed
by Tilman et al. (1997): metapopulation-like models, cellular-automaton-like
models, and reaction-diffusion models. Huston (1994) concludes that

competition has a direct effect on species diversity only under a very restricted
set of condition.

Spatial heterogeneity theory

Large-scale equilibrium dynamics are implied with the spatial
heterogeneity theory (Huston 1994). Higher diversity is maintained by
having enough different, local patches within a region so that there is a
balance of losses and additions. Patches that are caused by disturbance will
support species of different successional stages. Patches that are caused by
environmental heterogeneity will support different species than the
surrounding environment due to availability of different resources or the
rate at which the resources can be exploited.

Diversity Decline

Insight into the way diversity may be limited comes from the study of
situations with declining diversity. In studies of contained microcosms
started with high diversity, an initial decline in diversity is generally
observed (Beyers and Odum 1993). For any system, diversity decline may
result from processes within the system or from those outside of the system.

A survey of common knowledge and published examples suggested
the following circumstances where species diversity has been observed to
decrease in natural and experimental systems.








Catastrophic destruction

Whether by human hands or by large scale planetary events,
destruction of part of an ecosystem reduces the number of species.

Externally driven diurnal and seasonal changes

Declines in species are observed as part of the ups and downs of abiotic
influences such as climatic cycles. For example: The Sonoran Desert in
Arizona has a rich winter ephemeral flora appearing only in the years when

the rainfall regime meets certain criteria. When the dry season begins,
ephemeral species die and the local diversity decreases. Animal migrations

also follow seasonal patterns of resource abundance, with a decline in local
diversity occurring on a yearly cycle.

Oscillations

Declines in species are observed during parts of the oscillatory cycles
due to internal rhythms. Diversity has been observed to rise and fall. For
example: Ecosystems pulse with recurring cycles of production and
consumption (Odum 1994), often due to recurring natural perturbations such
as forest fires or floods. In general, systems grow and exhibit successional

stages towards a climax stage which is followed by a descent; this oscillation is
repeated through time.

Concentrated seeding

Wherever species are assembled in higher concentrations than can be
supported, declines follow. For example: Experiments using microcosms
showed that an initial high seeding of species in a microcosm were followed

by a decrease of species to a lower level (Dickerson and Robinson 1986). This
may be the result of competitive exclusion due to limited resources in a small
volume, as well as due to the increased maintenance costs of species as they
aged (Beyers and Odum 1993).








Competitive overgrowth by enriched populations

Where conditions for growth become enriched, rapid growth by some

species can displace others. The result is generally an increase in the density

or biomass of one or a few species, reducing the available resources (such as

light) to remaining species which may then become locally extinct.

Cultural eutrophy is an example of available resources increasing
abruptly. In a five month field plot experiment, Kent (1996) documented

species declines due to the surge of competition with the abundant growth of

cattails, water hyacinths, and other species that could most effectively use the

excess resource.

In a study of old field succession in Michigan, Tilman (1993) recorded a

decline of species in plots that were fertilized with nitrogen compared to

those that were not fertilized. An increase in productivity of the plots was

correlated both with an increased loss of species and a decreased rate of

establishment of species, both contributing to a reduction in the number of

species. Increased loss of species was attributed to competitive interactions,

and decreased establishment of new species.

Changed conditions

Where environmental conditions change so that existing species are

not adapted, species decreases are observed at least temporarily. For example:

In a Barro Colorado Island study, a long term drying trend showed a decline

and predicted extinction of 16 species, while colonizer species were increasing
(Condit et al. 1996a). A similar decline in species was documented in a prairie
ecosystem, where it was attributed to drought (Tilman and El Haddi 1992).

Decreased resources

Also, diversity decreases with decreasing production. Production is
strongly correlated with precipitation. Though diversity in general decreases








with less rain, correlations made of diversity and precipitation is not as

compelling as diversity and evaporation. Increased competition due to a

change in resources may cause the diversity decline.

Decreasing diversity along gradients

The number of woody plant species in 0.1 ha plots within 69
neotropical forests was compared, and richness was correlated with soils and

climatic data (Clinebell et al. 1995). The most important variables correlated
with number of species were annual rainfall and rainfall seasonality.

Gentry and Dodson (1987) showed richness of epiphytes in western
Ecuador and southern Central America to decrease with decreasing absolute
precipitation, using data from local floras.

Wright (1992) reports a consistent decrease in number of species with
decreased rainfall in tropical forests, emphasizing the inverse relationship of
rainfall and seasonality throughout the wet tropics. The standard forest plots

that he examined showed a fivefold decrease in plant species densities in the
Neotropics in rainfall gradient from 4000 to 1000 mm; and sixfold decrease
over a Ghanan rainfall gradient of 1750 to 750 mm.

The number of species declines polewards from the equator and
coincides with decreasing rainfall, temperature, evapotranspiration,
insolation, and primary production. Whether these relationships are merely
correlative or causal has been addressed widely, but the patterns have been
observed for many life forms. For example: Based on 74 samples of 0.1 ha
lowland sites, Gentry (1988) reports an order of magnitude downsizing in

number vascular plant species between rich tropical forests and temperate
forest.








Gentry (1982) used total plant species numbers in 0.1 ha samples across
the upland Neotropics, and showed a strong correlation between diversity
and precipitation in the Neotropics. He later discussed that this relationship
may be a special case relevant to the Neotropics where there is a strong
correlation of total annual rainfall and strength of dry season (Gentry 1988).

Such a relationship was not apparent in the samples from tropics of Africa.
In addition, he found that the relationship at the high end of actual
precipitation was nonlinear, becoming asymptotic above 4,000 mm. This may
show saturation level for species diversity. He also warns that the asymptote
may be an artifact of sampling methods species-area curves do not level off
for the highest diversity sites; thus the area sampled at the lower sites may
not reflect diversity at the highest-diversity sites. He further strengthens the
relationship between rain and number of species with data from 1 ha plots
measuring trees and lianas > 10 cm diameter. In upper Amazonia, adjacent
forest types were shown to have different species and were growing on
different substrates, with little change in species diversity.

Overlaying the latitudinal pattern of diversity are regional or local
declines in diversity with reduced rainfall. This often is associated with
effects of local or regional topography influencing temperature and rainfall
patterns. In arid northern Chilean Andes above the Atacama Desert, Arroyo
et al. (1988) report a steep gradient of plant species diversity corresponding
with the rainfall gradient. Surveys in 1620 minimum area quadrats were
made on 6 transects 1/4 degree latitude wide and between 18-28 S, running
from the edge of the Atacama Desert (1500-3000m) to the elevational limit for
vascular plants (4500-5000 m depending on latitude). Data showed species
diversity decline with increasing aridity on a latitudinal gradient along the








western side of the Andes as well as from east to west across the Andes along

the rainfall gradient.

Based on surveys in 48 sites in the Neotropics (lowland tropics of
Middle and South America, montane cloud forests, and supra-treeline of

Andes), Duellman (1988) found a decline in diversity from wet to dry regions

and from low to high elevations for the entire anuran fauna.

Both a decrease in structure and diversity occurs with the decreased
input of rainfall and temperature. Evapotranspiration is a function of both
rainfall and temperature directly related to plant production.

Decreased information exchange due to fragmentation

Diversity has been observed to decrease where ecosystem areas are
fragmented by insertion of other uses of space, and are isolated from

exchanges of species and seeding with adjacent areas. Bierregard et al. (1992)

documented loss of species in lowland tropical rainforest where habitat
islands were created by the removal of forest around various size fragments.

Diversity decline due to fragmentation of habitat is also reported on the
islands that were created by the formation of Gatun Lake for the opening of
the Panama Canal (Leigh et al. 1993).

Onset of stable conditions

Some researchers have related species decline to the onset of stable
conditions after times of greater fluctuation. Whereas competitive exclusion

may be pre-empted due to disturbance, the lack of disturbance will allow
interspecies competition to cause a higher rate of extinction.

Growth in size

Where space is limited during a time of growth, increasing size of
dominant species by occupying more space, may exclude species. This is









demonstrated in a successional sequence of a very limited area of forest where

a dominance hierarchy develops, shading out species in the understory.

Loss of controllers

Where species are dependent on control actions by other species, loss of
the control species may cause loss of species. For example, plants dependent

on insects for pollination were lost when insects were not available.

Physiological demand

Where special conditions require energy to be diverted to sustain life,
diversity has been observed to decrease. For example: Increased levels of

toxic stress may result in reduced diversity accompanied by an increase in

biomass. Pratt et al. (1987) report a decrease of microorganism species present
in microcosms with increasing zinc concentration.


A Conceptual Model of Ecosystem and Diversity

In order to overview the principal parts and processes of an ecosystem
and the role of diversity, a conceptual model was developed in Figure 1 -1. By

using the energy systems language, Table 1-2, the main components and
processes that appear to be involved in determining the diversity are shown
not separately but as part of a connected whole. Enough parts and pathways
of interaction are included to consider the observations and alternative
theories discussed in the previous sections. The model diagram is a way to
combine and synthesize the factors affecting diversity such as energy,
competitors, nutrient materials, outside pulses, and internal oscillations. The
conceptual model may be used for all scales over which diversity is studied.

A systems model is a complex hypothesis. To account for diversity
declines, a systems model must have the main parts and processes that affect


























future Biomass

Species
Structure







CONCEPTUAL MODEL OF
ECOSYSTEM DIVERSITY




Figure 1-1. Systems diagram representing theories of ecosystem diversity.









Table 1-2. Symbols for the energy systems language used in this dissertation.
From Odum (1983).


Symbol


Explanation


0*

-0Q







-9


Energy circuit: A pathway whose flow is proportional to the
quantity in the storage or source upstream.
Source: Outside source of energy delivering forces according to
a program controlled from outside; a forcing function.
Tank: A compartment of energy storage within the system
storing a quantity as the balance of inflows and outflows; a state
variable.
Heat sink: Dispersion of potential energy into heat that
accompanies all real transformation processes and storage; loss
of potential energy from further use by the system.
Interaction: Interactive intersection of two pathways coupled to
produce an outflow in proportion to a function of both;control
action of one flow on another; limiting factor action;work gate.
Consumer: Unit that transforms energy quality, stores it, and
feeds it back autocatalytically to improve inflow.

Switching action: A symbol that indicates one or more switching
actions.

Producer: Unit that collects and transforms low-quality energy
under control interactions of high-quality flows.

Box: Miscellaneous symbol to use for whatever unit or function
is labeled.

Constant-gain amplifier: A unit that delivers an output in
proportion to the input I but is changed by a constant factor as
long as the energy source S is sufficient.

Transaction: A unit that indicates a sale of goods or services
(solid line) in exchange for payment of money (dashed line).
Price (P) is shown as an external source.


4r

-*E
IFs








the species numbers and are capable of accounting for observed declines.

Figure 1-1 is used here to suggest what parts and processes are important and
how they may account for diversity decline in an ecosystem. Of course,

whether the model and its inherent hypotheses are appropriate can only be
verified by study of the behavior of the real systems. In Table 1-3,
explanations for ways that diversity may decrease are suggested as
consequences of the way the model was formulated.

External sources entering the system

The box drawn in Figure 1-1 defines the boundary of a system.
Everything outside of the box is not considered part of the system. Inflows
from sources outside the system are represented by circles outside of the box,
with pathways crossing the boundary into the system. The external sources
operate on larger spatial scales than the system.

The circle on the left labeled "energy" represents the energy sources
sun, wind and rain that enter the system. The inflow may vary over time
scales, such as diurnal, seasonal, and geological depending upon the scale of
the system being studied. The total amount of energy entering is in
proportion to the area of the system being studied, as represented by the
interaction between the storage tank labeled "area" and the energy source.
Thus, the total energy entering a larger area will be greater than that entering
a smaller area in the same region. Some of the energy entering the system is
used by the producers, represented with bullet-shaped characters. Some of the
energy entering the system flows through the system without being used, and
is shown as a pathway with an arrow exiting the system. An example is sun
that is reflected from surfaces in the system.










Table 1-3. Parts and processes of ecosystem model that affect species numbers and account for observed declines.

Symbol Explanation

External Energy Sources
Area
The main energy inputs from the left (sun, rain, wind) support all the
processes in the system. The inflow may vary diurnally, seasonally,
and over geologic time depending upon the scale of the system being
Energy studied.

Reduction of the inflow of energy sources causes a decrease in all
the storage and flows in the system, including the number of
species. If the area over which energy is flowing into the system
is reduced, primary production decreases proportionally, resulting
in a similar decrease in number of species.

Biomass
eEnergy Ses n~ sA' As the energy from outside sources increases primary productivity will
strur B ^iomassX increase.
Other
Species
Structure

Nutrients
utrients
An increase of nutrient inflow, whether from rainfall, run-in,
wandering wildlife, or additions such as fertilizer or sewage, can
increase productivity of plants resulting in increased biomass of the
utrient species that can respond most quickly to those additions.

In such cases where only several species can make use of the
additional nutrient loads, the number of species in the system may
decrease due to competition with the species that could not respond.










Table 1-3--continued.

Symbol Explanation


Consumers

The consumer tank includes decomposers as well as herbivores and
carnivores. An increase in plant biomass will result in more
consumers consumer biomass. The waste products from the consumers feeds
back into the nutrient tank.



-umber Number of Species
of
Species The number of species in a system is a result of, extinctions,
emigration, immigration, and evolution.
Species
Structure A decrease in the number of species occurs with increased extinction
species or emigration or decreased immigration or evolution.
Structure


seeding Seeding (immigration)

New species are shown inflowing from the upper right of the diagram,
/d balancing the extinction pathways. The rate of immigration can be
number affected by a change in the distance to seed source, change in pollen
of carriers, and loss of an organism that disperses another.


Reducing the seeding rate decreases the number of species.










Table l-3--ontinued.
Symbol


Explanation


Stress from outside system

Additional stresses from outside the system, as shown in the top
center of the diagram, can necessitate physiological adjustment of
species that are present in the system. Such changes increase the
maintenance costs of the biomass supported in the system, resulting
in an increase in the extinction rate.


Catastrophe

Pulse on a scale much larger scale than the system being studied,
considered a 'reset' of systems.








Over a latitudinal gradient from the equator to the poles, the energy
from outside sources decreases. The reduction of energy to the system causes

a decrease in all the storage and flows in the system, including the number of

species per unit or area. If the area over which energy is flowing into the
system is reduced, such as the fragmentation of a forest surrounded by clear-
cutting for agriculture, primary production and number of species decrease
proportionally.

External nutrient sources can enter the system with rainfall, run-in,
wandering wildlife, air pollution or additions such as fertilizer or sewage. A
sudden increase of nutrients may result in a rapid rise in productivity of the
system, in which case one or several plant species may respond with rapid
growth. Some species may become locally extinct from competitive
interactions such as shading, resulting in a system with fewer species.
Examples of stress from external sources are changes in water relations
such as drought, temperature extremes, or input of substances resulting in
toxic buildup in the soil. Plant response to adapt to stress may require use of
energy, taking energy away from other uses. This may result in the diversion
of energy from biomass production and diversity support in order to support
adaptations for survival of the stressful condition.

Seeding from sources external to the system depends on dispersal
methods and distance from the seed source. As distance (d) from the source
increases, dispersal of propagules into the system decreases (1/d2). Where
ecosystems are separated in space from similar ecosystems that supply

propagules, species with seeds that do not have a vector for farther dispersal
may be eliminated from seeding an area.
Catastrophes cause a pulse of nutrients to a system and a resetting of
successional pathways to an earlier stage. Systems are often adapted to








certain frequencies, amplitudes and sizes of catastrophes such as hurricanes or

fires. If one of these 3 changes, the results may be systems with lower
diversity than the initial system.

Internal processes
Competition for light is shown between the opportunistic plant species
and other species. Opportunistic species are those that establish as early
successional species, or species that are 'weedy'. The opportunistic species

draw light from the energy pathway first, before those species that are later
successional species indicative of a more mature system (labeled "other
species structure"). As the later successional species grow, they are able to pull
more light for production and overshade the early successional species. Local
diversity may show an increase when species from both early and later

successional stages are present, and a decrease when the earlier species
become locally extinct from overshading. As external energy sources increase,
primary production increases. The symbol showing the mature species also
shows physiology, which reflects the respiratory costs of physiological
adjustment to changing conditions within the system. As stress from the
outside increases, the energetic cost of plant adaptation increases. This is
shown on the diagram as an increase in the constant-gain amplifier (triangle),
which in turn increases the extinction rate from the species diversity tank.

Plant biomass is shown with 4 outflowing pathways. The first pathway
flows into the nutrient storage. This occurs through decomposition of plant
material from litterfall, plant mortalities including those due to catastrophe,
and exudates. Another pathway shows biomass feeding consumers, where
all consumers in the system are aggregated into one consumer storage. The
other 2 pathways from biomass lead to the species diversity tank. Biomass








(representing suitable habitat) interacts with seeding on one pathway,
allowing colonization of new species when the energy base can support it. As
the rate of seeding decreases, the rate of colonization also decreases. The
second flow to diversity represents the habitat base supporting extant species.
Pathways from the diversity tank are either extinction pathways or
pathways that feed back to the primary production of the system. The
quadratic extinction pathway represents extinction due to competition with
other species. The rate of extinction increases when opportunist species
increase, such as with increase due to a pulse of nutrients. It also increases
when the stress from outside the system increases, requiring more energy for
plant adaptation to new conditions. The second extinction pathway is a linear

pathway, representing extinction due to causes other than competition.
Feedback pathways show an increased efficiency of the system due to new
species or additional species added to the system.
Nutrients are added to the system either from outside sources or from
cycling of biomass or through consumers. Available nutrients decrease when
they are immobilized by plant uptake, or when they flow out of the system in
processes such as runoff or soil erosion.

In any real ecosystem more than one of these mechanisms affecting
diversity may be operating. Simulation is used to relate the complex
hypothesis to the observations.

Because of its feedback amplifier loops (autocatalytic input designs and
material cycles), the diversity model is consistent with the maximum
empower concept. This principle may be stated as follows: Self-organizing
systems prevail by developing designs that maximize emergy inputs and
effective use.








The model in Figure 1-1 includes the general premise that some species
variety is necessary to maximize a system's processes. To fit the principle,
increasing or decreasing diversity needs to be consistent with increasing
and/or sustaining resource inputs or increasing functional efficiencies.


Carrying Capacity of Systems for Diversity

A general question asked by those responsible for maintaining
diversity in public lands and parks is whether there is a carrying capacity of an
ecosystem for diversity. If the maximum empower principle applies,

ecosystems sustain that diversity that promotes total system function.
Priority in self-organization may go for physiological adaptation of fewer
species where this is necessary to maximize system productivity and
efficiency.

Spatial Organization

There are extensive published observations on the spatial patterns
developed by ecosystems, including the patterns of horizontal plant
organization on the forest floor and patterns of vertical structure.
Explanations for observed distributions have to include the role of light
energy and the apparently general tendency for self-organization to form
hierarchies. Obviously changes of diversity are affected by the seeding, which
determines the locations and survival of plants. In situations where humans
do the planting, how does self-organization develop afterwards?








Hierarchical Organization

Like other ecosystems, the rainforest develops components and

processes in an energy hierarchy, which is represented in model diagrams by

position from left to right. Items on the left have more energy (low quality

energy), turnover faster, and have smaller territory. Position of a

component or pathway flow in an energy hierarchy is measured by its
transformity. Transformity is the emergy per unit energy (Table 1-1). Emergy
is the energy of one kind previously used directly and indirectly to make a

product or service. Calculating emergy and transformities of ecosystem

components and flows is a way of determining the pattern of energy
hierarchy. Maps of transformity and changes of transformity over time may

be estimated.


Rainforest in Biosphere 2

Biosphere 2 is a 1.25 hectare mesocosm in Arizona designed to be
closed to material exchanges with the environment outside of its glass

boundary, but open to exchanges of energy and some types of information.

Areas within Biosphere 2 were established to represent different biomes of
earth, and included aquatic (ocean and estuary) and terrestrial (savannah,
desert, and rainforest) wilderness areas and a habitat for human residents and

their agricultural systems (Figure 1-2). Whereas the atmospheric chemistry
and water systems were global phenomena among all of the areas of
Biosphere 2, temperatures, rainfall regimes, and humidities were maintained
locally within each area. Figure 1-3 shows the photosynthetically active
radiation, CO2 concentration and temperature for terrestrial wilderness areas
in the Biosphere.


















Desert biome

, \ .i


biome


U






[I
II


Rainforest biome


Figure 1-2. Areas within Biosphere 2.


-Or













2000
1800 -- ------ Rainforest
---- Desert
1600- External
's 1400-
E 1200
051000-
E
= 800 -
S600 -
400- -
200-
0
0 ------,--.--------------..... ------ ,

4500
S4000 i-------Rainforest
. ----- Savanna .- \ 1
a. 3500-- ----Desert
3000
T 2500-- .
1 2000- \
o 1500
0
S1000--
500



29
28 -------Rainforest
i -- Savanna
27 ----Desert
0 26 ,
2 25 ,- .. -
24 24
1 23






3 C on o s a ,o, a n
20 -% -



N 0 C N C 4 M cu M M
z l 0 C -
Z 0 M M 7 3 Ci)
(I) 0a) 0 0



Figure 1-3. Continuous photosynthetically active radiation, C02, and
temperature in terrestrial wilderness biomes of Biosphere 2 during the
first material closure.








The footprint of the tropical rainforest biome within Biosphere 2 is
1900 m2. The highest point of the pyramidal glass structure enclosing it is 22
m, measured from the soil surface in the lowland rainforest (Figure 1-4). The

total volume of the rainforest is about 35,000 m3 (Dempster 1993), nearly 17%
of the total Biosphere 2 volume. The contribution of the rainforest to the

atmospheric chemistry of the larger scale mesocosm has been modeled by
Engel and Odum (1999). Their simulations suggest that the rainforest may be
responsible for up to 50% of the whole Biosphere 2 metabolic rate.
The rainforest biome was designed to be functionally analogous to the
planetary rainforest biome. It was built and its climate managed to emulate
the general structure and function of a New World tropical rainforest. It is a
geographical island, disjunct from the larger system from which its
components were obtained.

Design Elements and Description

The climate of the Biosphere 2 rainforest was created by control of rain,
temperature, humidity and air flow so as to support plant species from
various humid tropical regions. The annual changes in day length were
greater in Biosphere 2 than in a planetary rainforest, and temperature and
atmospheric CO2 ranges were greater on both a daily and annual basis.

The rainforest soils were created from a local desert grassland soil
combined with other organic materials. The design objectives were to
produce a functional equivalent of tropical rainforest soils, to allow soils to
develop in place, and to provide a horticulturally adequate substrate. Over
time, the formation of humic and fulvic acids was expected to reduce the soil
pH, similar to a planetary rainforest (Scarborough 1994). The soils were
designed to be deep enough to allow expansion of roots needed to stabilize






































Figure 1-4. Side view of rainforest biome.








aboveground canopy expansion and to contain a storage of elements

necessary plant growth.

The design challenge of the Biosphere 2 rainforest was to consider
diversity over a hundred year time scale, as well as across the scales of

population, community, and ecosystem, including functional diversity. The
rainforest was excessively species-packed for self-organization over time

under minimal influence of human management. Since no biotic
introductions were to be made during the study period after the initial closure

in 1991, initial planting had to include all of the species for succession and

mature development. In contrast, an unconfined rainforest experiences
continuing immigration during successional changes. Therefore, a much

larger number of species was planted than could survive, letting extinction
occur as a natural process in the system. Though effort was made through
pruning to reduce competition for light during the first years of operation to

ensure the survival of certain key species, decline in the number of plant
species was expected. It was hypothesized that the rainforest structure would
change over time from that of a recently cleared ecosystem to a complex

primary forest (Prance 1991). The final mix of plant species was eclectic with a
bias toward Neotropical taxa.

Eight separate habitats were initially delineated in the rainforest
(Prance 1991). The habitats were named lowland rainforest, ginger belt,
virzea, cloud bowl, surface aquatic systems, bamboo belt, mountain terraces,
and cliff faces (Figure 1-5).

The conceptual design for the rainforest began in 1985; plant collections
were made from 1986 to 1991; planting began in 1990; animal introductions
began in 1991; and a total survey and mapping of every plant was completed
prior to the first material closure, which lasted from September 1991 through













(40 meters>


5



Figure 1-5. Habitats delineated within the Biosphere 2 rainforest.


~_______~_____1_11_1__-_








September 1993. A total re-survey of plants in the rainforest was made after

the 2-year closure and again in 1996.
Measurements of energy flows and storage made during and after the
period of closure included temperature, relative humidity, rainfall duration,
plant sizes, light level, atmospheric CO2 and 02, and trace gas concentrations.

An artificial ecosystem such as the Biosphere 2 rainforest or a botanic
garden might be expected to behave according to models of a natural
ecosystem with equivalent energy inputs and available information. What
are the different options for ecosystems to maximize power, and what aspects
of human management of 'artificial' systems will alter this?


A Conceptual Model of Diversity in Rainforest of Biosphere 2

Whereas Figure 1-1 has the main features of any system believed to
affect the diversity of stored information, Figure 1-6 represents these concepts
for the rainforest biome area of Biosphere 2. The diagram is a complex
hypothesis for understanding diversity changes in Biosphere 2. The
differences between parts and processes of the earlier conceptual model of
diversity in ecosystems (Figure 1-1) and the model of the Biosphere 2
rainforest are as follows.

External sources entering the system

The striped border in Figure 1-6 defines the glass boundary of the
Biosphere 2 structure that physically separates it from the outside. The inner,
solid box in the diagram represents the rainforest biome, one of 7 biomes
inside. There was no physical barrier separating the rainforest biome from
the other biomes. Though many of the parts and processes within the




































Figure 1-6. Systems diagram representing ecosystem diversity within Biosphere 2 rainforest.








rainforest model are the same as the earlier, general model, the external

sources are quite different.

The primary energy source entering the rainforest was sunlight; rain

and wind do not enter from an external source. Since the Biosphere 2

rainforest was contained, its area was constant and the tank for land area

interacting with energy has been deleted. During periods of material closure,
no nutrients entered the Biosphere from outside. Certain stress-causing
external conditions could have affected the producers, such as a long period of

reduced sunlight. Electricity and information were external sources used to
operate and design the mechanical systems providing the subsidies normally

produced by nature, such as waves in the ocean, airflow throughout the
Biosphere, and rainfall operated by a sprinkler system.

The species that were planted in the rainforest were selected from the
earth's species pool, with human decisions rather than habitat and dispersal
characteristics determining which plant species would colonize the area.

Catastrophes from outside sources would be those that would have affected
the operating systems or caused massive collapse of the external structure. A

total shutdown of the power systems, for example, may have caused

overheating during the day, resulting in plant mortalities. This would have
resulted in a pulse of dead biomass that would have been placed in the dry
biomass storage, shown with the interaction of catastrophe and biomass
pathways, flowing into the dry biomass storage tank.

Internal processes

The cycling of nutrients between the rainforest and other areas inside
the Biosphere included flows driven by the operating equipment. Airborne
nutrients such as CO2 were exchanged by airflow through the air handlers.








Soil borne nutrients exited the rainforest in water that percolated through the

soil profile and was pumped to a central storage reservoir, where it was mixed

with water from the other areas. Some of these nutrients were then pumped

back to the rainforest in rain water.

Biospherians lived in their habitat area outside of the rainforest, but
visited the rainforest regularly. The model shows an interaction of the

Biospherian pathway with biomass, representing pruning of the weedy

biomass. Much of the weedy biomass was dried and stored, shown with the
pathway to the dry biomass tank.
Some of the rainforest consumers traveled between areas in the

Biosphere. This is shown with a flow pathway crossing over and then
returning to the rainforest system. Examples were the galagos that

concentrated their activities in the rainforest but traveled throughout the
wilderness biomes.

Though the process of colonization of the rainforest by plant species
differed from wild systems, the extinction process occurred similarly. This is
shown in both conceptual models with a quadratic function representing
competition with other plant species and a linear function representing other
reasons for extinction.


Rainforest in Puerto Rico

The rainforest compared with that in Biosphere 2 is in the Luquillo
Experimental Forest (USDA) of northeastern Puerto Rico. The area has 4
different vegetation zones tabonuco forest, colorado forest, sierra palm
brake, and elfin forest. The tabonuco rainforest, named after its dominant








tree species, has been the most extensively studied (Reagan and Waide 1996)

and is the type used for comparison in this study.
Long-term data are available for the El Verde study site and the Bisley
watersheds and MAB biodiversity plots. An extensive study of the tabonuco
forest type funded by the Atomic Energy Commission was undertaken from
1963-1968, before and after irradiation (Odum and Pigeon 1970). Subsequently,
a volume was published (Reagan and Waide 1996) describing the food web of
El Verde.

Among the many papers that deal with plant diversity and
successional patterns in the tabonuco forest are the following: Lugo (1992)
compared the plant species in pairs of tree plantations and secondary forests;
Taylor et al. (1996) analyzed numbers and densities of species by life form in
an irradiated area of the tabonuco forest over 23 years after irradiation with
data from 8 surveys; landslide succession has been documented by Myster and
Walker (1997), Walker et al. (1996), and Guariguata (1990); Crow (1980) studied

species changes in a 0.72 ha plot over 30 years, and Johnston (1990) followed
Crow's work with a dissertation documenting successional change in the
same plots.

Recent papers describing the effects of Hurricane Hugo on the tabonuco
forest system and the re-development of the system to pre-hurricane
conditions are published in a special issue of the journal Biotropica, Volume
28(4a), 1996.













CHAPTER 2
METHODS


In this study, measurements of diversity were related to measures of
the resources and productivity in Biosphere 2, in the rainforest in Puerto Rico
and other situations where limited resources may have restricted diversity.


Construction and Operation of the Rainforest in Biosphere 2

A chronology of the construction and operation of the mechanical,
structural and life systems of the Biosphere 2 rainforest from 1987 through
1999 is shown in Table 2-1. Three different modes of operation of Biosphere 2
are distinguished by degree of material closure from the outside or the
separation between biomes on the inside of the structure, and degree of
control over composition of the atmosphere, as follows: (1) Complete
material closure, with the entire atmosphere inside Biosphere 2 interacting as
a unit separate from the outside atmosphere. (2) Forced airflow through the
entire Biosphere from the outside. (3) Physical separation of the wilderness
systems from the habitat and agriculture systems; separation of the
wilderness biomes from each other with curtains; and forced airflow from
outside. Construction and engineering details of Biosphere 2 are given in
Zabel et al. (1999).















Table 2-1. Chronology of Biosphere 2 rainforest construction and operation.


EVENT
Groundbreaking
Interior structure
Placement of soils
Exterior structure
Mechanical systems
Planting
Plant mapping
Plant survey
Animals introduced
Mission 1 closure
Weedy biomass pruned
Transition
Mission 2 closure
Change to continuous
flow
Removal of biomass
from Biosphere 2
Exchange of water in
south lung
Separation of rainforest
from other areas


87 88 89 90 91 92 93 94 95 96 97 98 99


~also=alliam
BIB
ME
a


-----------------------------------











Procedures Used in Starting the Ecosystem


Soil Components and Placement

The soil profile was assembled with subsoil and topsoil layers. The
subsoil was a mix of a coarse sandy loam (highly weathered granitic grus)
extracted from a local quarry and 5-15 cm granite rocks. It had uniform
composition throughout the rainforest, and its thickness varied from 0 to
about 5 m depending upon specifications made for root growth and the
architectural structure over which it was placed. Criteria for subsoil selection
were good downward percolation of water after repeated wettings; radon
emissions not greater than background crustal emissions; low heavy metal

content; price-competitiveness; and proximity to the Biosphere 2 site
(Scarborough 1994). The subsoil volume was estimated to be 3340 cubic
meters, based on measured volumes of the structure into which it was placed.
Table 2-2 lists the quarry locations of the materials extracted for the rainforest
soils. The subsoil was placed over a shallow gravel layer which covered and
surrounded drainage pipes that carried water percolated through the soils to a
collection trough, from which it was pumped to a global storage system inside
the Biosphere.

Topsoils were placed on top of the subsoil. Their thickness varied from
0.3 3.2 m, averaging 0.9 m. Four mixtures formed the major volume (1750
cubic meters) of topsoil in the rainforest, with small amounts of 3 additional
mixes (16 cubic meters) used for more specialized habitats (Scarborough 1994).
Each mixture consisted of a different combination of the following materials:
a local desert grassland soil ('Wilson Pond soil'), organic matter, gravelly












Table 2-2. Rainforest soil components and their origins. From
Scarborough (1994).


Material
Coarse sandy loam (subsoil)


Wilson Pond soil


Gravelly sand
Compost, Coarse organic
material
Fine peat
Coarse peat
Canadian sphagnum moss
Pumice chunks


Origin
Kalamazoo sand and gravel quarry, just
southwest of San Manuel Copper Mine,
Mammoth, AZ
Along boundary between Secs 2 & 3, T10S,
R14E, 1200 feet south of highway 82 and 1.3
miles west of the Biosphere Road
Quarried on location
AAA Fertilizer, Tucson, AZ; various other
local suppliers of organic materials
Purchased commercially
Purchased commercially
Purchased commercially
Purchased commercially










sand, sandy loam, and pumice chunks. Table 2-3 shows the different
combinations and volumes of materials that were used and their placement
within the ecosystem. The 'Wilson Pond soil' was an organic-rich (4-5% OM)
silt loam to clay loam which was quarried from a large earthen cattle tank.
The organic amendments were compost (made from forest mulch, cotton gin
trash, rotted cattle silage, alfalfa hay, and cattle manure); coarse peat; coarse
organic material; and Canadian sphagnum moss. The gravelly sand was
quarried on location. Additional materials used in much smaller amounts
were the coarse sandy loam subsoil, pumice chunks, and fine peat.

The soil materials were either mixed with heavy equipment outside or
directly on conveyor belts feeding from the outside to the inside of the
Biosphere. Various types of heavy equipment (both track and wheel
vehicles), conveyor belts and/or shovels were used for soil placement inside
the rainforest. Leaf litter and humus from local natural ecosystems were
added to the soil surface after placement, and thousands of purchased
earthworms and a much smaller number of earthworm species that were
field-collected in southeastern Texas (Scott 1994) were placed in the soil.


Collection and Initial Placement of Plants

Starting in 1986, plants, seeds, and other propagules assembled for the
rainforest were grown in greenhouses located near Biosphere 2. Plant
accessions were acquired from botanic gardens, plant nurseries, and private
collections, and from field collections in Puerto Rico, Belize, Venezuela, and
Brazil. Permits were acquired for exportation from countries of origin and for
importation to the United States and Arizona; state and federal quarantine











Table 2-3. Percent of components in topsoil mixture specifications and their corresponding habitats.
From Scarborough (1994). Totals are approximations.

Component Mix Mix 2b Mix 3c Mix 4d Mix 5' Mix 6' Mix 7g Total (m3)
la
Coarse sandy loam (subsoil) 60 15 1
'Wilson Pond' soil 50 60 80 10 35 50 996
Gravelly sand 25 239
Compost 20 35 84
Fine peat 50 2
Coarse peat 40 50 30 167
Coarse organic material 25 239
Canadian sphagnum moss 40 37
Pumice chunks 10 15 2


a Lowland rainforest 688 m3
Bamboo belt 57 m3
East terrace and west side of mountain 203 m3
TOTAL: 948 m3
b Vdrzea 298 m3
SGinger belt and papaya areas 413 m3
d Cloud forest 92 m3
e Behind cliff face 8 m3
f Tree ferns -4 m3
g Ledges and planting pockets -4 m3










and inspection protocols were followed. Following soils placement in the
rainforest biome, plant accessions were transplanted from greenhouses into
Biosphere 2. The largest plants were placed first due to the logistics of
lowering them into the Biosphere with cranes before the glass was installed.
Plants were fertilized and watered in place with drip irrigation, sprinklers, or

by hand with hoses.

Each plant was mapped by standard survey methods (Thompson 1992)
using different symbols to represent plant growth forms. Measurements such
as basal diameter, crown width, and stem length were made. Each plant was
assigned a unique number, and data on location, geographic origin, size, and
phenology were recorded. Thus a history of every plant in the rainforest
biome could be tracked through time.

Habitat Assembly

The initial design (Prance 1991) created 8 habitats within the rainforest
biome, each planted with a different assemblage of plants including canopy
trees, ground cover, shrubs and intermediate level life forms, and epiphytes
and vines. Initial plantings of fast colonizers and secondary forest species
(Clitoria racemosa, Carica spp., Leucaena spp., Cecropia schreberiana)
provided shade and structure to the emerging and more characteristic
primary rainforest species (Prance 1991).

Lowland rainforest

The concave topography of the lowland rainforest area centered in the
southeast quadrant of the rainforest allowed trees to reach a height sufficient
for a layered canopy. The topsoil mixed for the lowland rainforest was 50%










loam, 25% gravelly sand, and 25% coarse organic material. There were lianas,

epiphytes, and many broad-leaved trees and shrubs.

Ginger belt

The ginger belt surrounded the rainforest on all sides bounded by glass,
excluding only the south edge which abutted the top of the beach cliff and the
upper savanna. Its purpose was to shield the forest understory from excessive

light. Studies on isolated patches of planetary rainforests show that the
typical understory vegetation is altered for some distance beyond the forest

edge in part by light penetration (Bierregaard et al. 1992). Thus this peripheral
dense belt of vegetation was planted to filter the light and allow the interior

of the forest to develop the shaded conditions that would foster an understory
more typical of extensive rainforests.

Ginger belt topsoils were a mix of 80% loam and 20% compost. Soil
depth was about 60 90 cm on the northwest and west side where no subsoil
underlies the topsoil, and 1 m on the northeast, east and southeast sides,
where it was underlain by a subsoil of variable thickness. The ginger belt

ranged from about 1 m to about 4 m wide. Plants in the Order Zingiberales
dominated the ginger belt. Plants in these genera were most abundant:
Musa, Heliconia, Alpinia, Strelitzia, and Costus.

Varzea

The vdrzea habitat was designed to resemble a forest that is seasonally
flooded. It featured a tightly meandering stream that ran from the pond to
the edge of the savanna biome. The stream course was made by first filling
the regular topsoil layers to the specified level; then excavating the stream
courses; and then lining them with concrete and thick PVC. The varzea
topsoil was 60% loam and 40% coarse peat. The vArzea was not flooded










during the study period. It was planted with Phytolacca dioica, Pachira
aquatica, Pterocarpus indicus, and palms.

Cloud bowl

Suggested by the tepui sandstone formation from eastern Venezuela,
the central mountain 'cloud bowl' was planned as a cooler and more humid
microclimate. The soil was less than 1 m deep. It was a mix of 40% Canadian
sphagnum moss, 50% coarse peat moss, and 10% loam. Soil in the planter
pockets extended all the way to the bottom of the mountain. Bryophytes,
carnivorous plants, shrubs, gingers and aquatic plants were introduced to this
habitat.

Surface aquatic habitats

Surface aquatic habitats in the rainforest biome were hydrologically
connected. The moss seep and upper pond in the cloud bowl spilled over a
cut in the edge of the cloud bowl, creating a waterfall. The waterfall poured
into a splash pool, which overflowed into the larger, lower pond and then
into the varzea stream. At the bottom of the stream water flowed over a weir
into a sump, from which the water was pumped back to the lower pond.
Another pump moved water back to the cloud bowl. The water systems were
underlain with a thick vinyl liner beneath a concrete layer. Taxa inhabiting
the aquatic habitats at the beginning of the first material closure were Azolla,
Eichhornia, Nymphaea, and Typha.

Bamboo belt

A bamboo belt was constructed along the south edge of the rainforest to
baffle any airborne salt particles from the forest interior. Soils of the bamboo
belt were 50% loam, 25% gravelly sand, and 25% coarse organic material,










varying between 30 90 cm deep and laying over air delivery plenums. There

was no subsoil beneath the topsoil in the bamboo belt. Bambusa multiplex, B.

tuldoides and other species of bamboo initially formed the major structure of
this habitat.

Mountain terraces

The mountain terraces skirted the rainforest mountain on the east,
north, and west sides, extending to the west side of the lower pond. Flagstone

walls were in place around the periphery of the terraces, separating them
from the ginger belt habitat on the west and north sides and from the lowland

rainforest habitat on the east. The flagstone was placed during construction to
prevent soil from eroding down the somewhat steep grade from the

mountain to the ginger belt. The topsoil mix for the mountain terraces was
50% loam, 25% gravelly sand, and 25% coarse organic material. The soils to
the west and north of the mountain were about 0.3 3 m deep, and those east

of the mountain were about 0.3 6 m deep. The plants on the terraces
initially included Carica papaya, Clitoria racemosa, Coffea arabica,

Carludovica palmata, Inga sp., Hibiscus rosa-sinensis, and Manihot esculenta.

The cliff faces of the mountain had pockets of soil to support vines,
bromeliads, and other plants that were to cloak its surface. Vines from the
Araceae, Passifloraceae, and Vitaceae family and ferns planted in the cliff face

planter pockets. Rhyolite pumice chunks were blended at 10 to 15% of the
total soil volumes. The high porosity of the pumice provides water-holding
capacity and releases trace nutrients as it weathers.











Climate Maintenance Systems


Water system

In contrast to the desert and savanna biomes, the rainforest plants were

active continuously; dormancy was not part of the yearly cycle. In the

tropical rainforest biome, water applied as rainfall flowed through and exited

the soil profile throughout the year. Figure 2-1 shows the water flows and

reservoirs of the rainforest biome and their connection with the global

system.

Rain was distributed to much of the rainforest biome through

overhead sprinklers mounted in the space frame; other areas were irrigated

with ground sprinklers or a drip irrigation system. Water vapor evaporated

from soil, rain, or surface waters, transpired from plants, or delivered

through a misting system could subsequently have been condensed from the

air using the air handlers located in the rainforest basement. Water

condensate that collected on the inside surface of the windows during late

autumn, winter and early spring was an additional, seasonal source of

condensate. Water from both of these sources was re-used in the wilderness

biomes, and was one of the sources of rainwater.

The major water reservoirs in the rainforest were atmosphere
(humidity), soil, water storage tanks, the surface aquatic habitats, and plants
and other biota. The major water flows among reservoirs in the rainforest

were rainfall and irrigation, subsoil drainage, reverse osmosis system flow,

condensation, mist, evaporation, root uptake, transpiration, and diffusion as
water vapor to other areas.





















































Figure 2-1. Hydrologic connection of Biosphere 2 rainforest to the rest of the
Biosphere 2 system.










Some of the rain and irrigation water percolated through the entire soil
profile. This sub-soil water, carrying substances leached from the soils, was

collected and stored in a storage tank for future use. The subsoil water in the
Biosphere was reused either as-is or after removal of dissolved solids by a
reverse osmosis system. The remaining rain and irrigation water was either
held in the soil pores by matric forces, taken up by plants and retained, or
diffused back into the atmosphere via evaporation and transpiration. The
average monthly relative humidity was over 65% year-round in the
rainforest biome, with daily minima above 50%.

Air handling, temperature, and humidity control system
Seven air handlers in the rainforest basement were operated to
regulate temperatures, extract condensate from the air, and to create air
movement. Temperature was controlled by a heat exchange between a water
coil and circulating air in the handler. Three temperature classes of water
originating externally to the Biosphere were circulated in the coils of the

system: heating water, cooling tower water, and chilled water which reached
the lowest temperatures. The rate of the air flow through an air handler was
controlled by opening or closing an 'econodisc' located inside each of the air
handlers. Though normally controlled remotely, they were also controlled
manually from inside the air handler. Air from the air handlers circulated
through a system of plenums, ducts and openings from the basement into the
rainforest. The air returned through gratings on the west and northwest
periphery of the rainforest, where it entered the basement and was again
pulled through the air handlers and over the heating coils.










Human Intervention

During the 2 year closure of the system (1991-1993) certain herbaceous
plants in the rainforest biome were extensively pruned for two reasons. The

first reason was to arrest primary succession. Early successional species were
pruned so that the later successional species would survive. Pruning of vines

occurred when they appeared to be heavily shading the trees and understory
and when vines had grown into the tree canopies. Both vines and ginger belt
herbs were pruned when they pressed against the glass causing algal growth
on the glass surface. These selective harvests decreased the competitive

advantage of high net-producers (e.g., Ipomoea and Passiflora vines) over

species important for the long-term structure of the rainforest, particularly
the larger trees. The second reason for harvest was an attempt to increase

sequestration of CO, and to increase 02 production. High levels of CO2 were
thought to be decreasing the ocean pH, and oxygen concentrations eventually
decreased to the point of affecting the health of the human inhabitants. To

meet these goals, plants were propagated in an attempt to cover vertical
surfaces with photosynthetic biomass. Growth of high net-producing species
(Ipomoea sp., Passiflora edulis) and herbaceous plant species in the
circumferential ginger belt habitat was encouraged by judicious pruning in
areas where they would not overwhelm other species, given the constraint of
diversity maintenance.

The pruned biomass was removed from the rainforest, dried to retard
respiration, and stacked in the basement. A small percentage of the material
was used for fodder for domestic livestock. Of the three terrestrial wilderness
biomes, the rainforest required the most time to manage for regulation of the
atmosphere, while seeking to maintain species richness. Estimates of the










amount of biomass removed through pruning were made from weekly

records of time used for each task and from field journals.


Plant Mapping and Identifications


Initial Mapping and Identifications: 1990-1991

By September 1991, over 1800 individual plants had been planted in the
rainforest mesocosm. Every plant was marked with a pink flag that had a

unique number written on it which tracked it in the database, linking its
location in the rainforest with size measurements and other information,
including its origin, when available. Thus a history of every plant in the
Biosphere 2 rainforest could be tracked through time. Specimens of many

accessions are maintained in herbarium cabinets on location at the Biosphere
2 Center, and some were placed in the herbarium of the New York Botanical
Gardens. Some plants have not been identified, and many identifications
that were made have not been verified.


Species Additions and Removals

During the first 2-year closure, Sept. 1991-Sept. 1993, additional papayas,
bananas, malanga, and canna were planted in the rainforest for food

production. These were mapped and logged into the database after the first
closure. Additionally, some plants that had been planted before the first
closure had been omitted from the original survey, and the corrections were
made.










During the beginning of the period (Nov. 1993-Dec. 1993) between the
first and second closures an additional 339 individuals were planted in the

rainforest. The Leucaena trees that had been planted for initial shade of the

key rainforest species were removed and weighed for subsequent estimates of
biomass.


Field Measurements

The first survey was the record made at the time of planting, shown in
Figure A-1.


Second Survey: Transition Period, 1993-1994

Base maps used for the second survey were made from the original
CAD-generated survey maps completed in 1991. The complete map of the
rainforest was divided into cells, each covering approximately 10.6 m x 7 m at

a scale of 1:24. Thirty-five complete or partial cells provided total coverage of
the rainforest.

Each plant found from the original survey was marked with a black
plastic tag (approx. 5 by 8 cm) with its unique number etched in white. The

tags were fixed around the base of plants with plastic cable ties. Data forms
that were computer-generated for each plant specified the measurements that

were to be taken for the plant. Data recorded on the forms were entered into a
data base, and the paper forms stored at the Biosphere 2 Center. Plants that
had not been mapped before the 1991 closure were tagged and added to the
original maps. Additionally, plants that were introduced during the period of
the survey were tagged and noted on the map.











Third Survey: June-August 1996

The third plant survey was made in 1996 using blueline base maps
copied from the original maps that had been modified during the 1993-1994

resurvey. We searched for every plant indicated on the base maps and for all
plants that were listed in the database provided by Biosphere 2 Center. Each of
the 35 cells had a form listing all of the species within the cell. We assigned
one of three status categories to each plant: alive, dead or not found. When a
tag was located with no plant next to it at the mapped location, the plant was
classified as 'dead' and the tag was removed. When neither tag nor plant was
found at the mapped location, the plant was considered 'not found'. In most
cases, the 'not found' category plants were dead, though since we had neither
evidence of correct location by finding the tag nor a live plant we created this
category to indicate uncertainty (plant tags are easily lost in or were
previously removed from this site). When a living plant of the same species
listed in the database was found in the location of the survey point, it was
classified liveses.

When the identification listed on the forms was incorrect or suspect, it
was corrected or questioned on the field forms. On less than 10 occasions, a
plant classified as 'dead' or 'not found' in the previous survey was found
alive in the 1996 survey. When we were unable to locate the tag on a plant,
we tied survey flagging tape to it with the original survey number and Latin
binomial written in waterproof ink so that replacement tags could be made
and attached at a later time. Collections of plants in flower were made and
pressed for later identification.










New numbers were assigned to plants that were in one of the
following categories: plants (excluding tiny seedlings with only cotyledons or

the first few leaves) recruited from seeds produced inside the Biosphere (e.g.

Pachira aquatica); plants that had wandered to a new location but were clearly

once located at a numbered survey point (e.g., Dieffenbachia sp.); plants that
did not appear on the maps and did not have a tag, but clearly were

intentionally planted at one point (e.g., Eucharis grandiflora).

Problems with the survey method

Clonal or creeping understory species and climbing plants and canopy
vines were not mapped and total number of individuals for viney species
that root at the nodes was not quantified during this period due to the

uncertainty of delimiting an individual. This included Scindapsus aureus,
Syngonium podophyllum, Passiflora coriacea, Ipomoea sp., Cyperus
alternifolius, Tradescantia sp., Calissia fragrans. Likewise, the spread of clonal
ginger belt species was not mapped. These plants were simply identified as
alive, dead, or not found.

Not all of the planter pockets on the mountain could be accessed, and
assumptions were made, in some cases with only limited visibility, that since
there was no longer a functioning irrigation system to the pockets that the

originally placed plants were dead. This included fewer than 20 individual
plants.


Species lists and assembly of data

For the total species count, individuals within a genus that were
unidentified to species were counted as a separate species only if there were
no other species within the genus. If there were other species in the genus,










the unidentified individuals were considered unknown, since they could

have overlapped with species already counted. Unknown species were not

included in species abundance figures or growth form spectra. Species that

were classified as "not found" in a survey were considered dead for purposes

of this study.


Surveys of Species Found per 1000 Individuals Counted


Biosphere 2 rainforest

A count of the cumulative number of species found per cumulative
number of individuals was made in the Biosphere 2 lowland rainforest
habitat in April, 1998. Plants were identified and recorded in 1.5 m belt

transects covering the entire lowland rainforest and the east-facing ginger

belt. As each individual was identified, it was recorded in a column with the

proper species label until there were a certain number of individuals per

column, starting with 1 in the first column, 10 in the next, and about 100 in

the subsequent columns. All of the plants in the lowland rainforest area were

counted. A diagram of the transects was drawn and transferred onto a map of
the area so that similar counts could be made using maps from previous
years.

The 1991 count of cumulative species per cumulative individuals was
completed from the original map and species list from 1991. The 1.5 m wide
belt transects drawn on the maps were sampled in the same order as they
were sampled on the ground in 1998. The center of each plant was included
only if the surveyed center of the plant (as recorded on the map) was
encountered within the transect; overlaps were not counted. In addition,










species/individual counts were made for the ginger belt, bamboo belt, cloud

bowl, virzea, and mountain terraces on the 1991 map.

Puerto Rico rainforest

The same field method was used in Puerto Rico on a landslide near the
El Verde Field Station, but the belt transect zig-zagged across the landslide
area. All plants greater than 0.5 m tall within a 1 meter distance on either

side of the observer were counted and identified. Where there was

uncertainty as to whether or not 2 plants were the same, collections were

made and checked later with local botanical technicians. Considerable care

was taken to stay within the boundary of the 11-year-old landslide area. In
addition, databases were sampled for number of species per 1000.


Leaf Area Index

Leaf area index in the Biosphere 2 rainforest lowland habitat was
estimated from counts of vertical leaf overlap using a 50-foot extendable rod
expanded upwards from a ground point. The interception of every leaf above

the ground point was counted. A record of the number of leaf interceptions

per ground point was made for 30 points in the lowland forest habitat of the
Biosphere 2 rainforest biome over a ground area of approximately 300 m2.


Number of Seedlings per 0.54 m2

Thirty 0.54 m2 circular plots were located 10 paces apart in the rainforest
lowland habitat in April 1998. The plots were defined with a plastic hoop and
were searched for seedlings. The counts were made over a ground area of
approximately 370 m2.











Percent of Holes in Leaves

A visual estimate was made of the percent of holes in leaf blades.

Holes were counted if they appeared to have been caused by consumers, and

were not counted if they appeared to be the result of mechanical injury from

wind or human activities. The leaves that were selected were within the

range of view of the ground-based observer. Ten leaves on each of twenty

trees were counted using the following percentage categories: 0, <1, 1-5, 5-10.

There were no leaves that had more than 10% of the blade consumed.


Number of Green or Yellow Fallen Leaves per 0.54 m2

The 0.54 m2 circular plots used for seedling counts were also used for

counts of the number of green or yellow fallen leaves per 0.54 m2. Each plot

was searched for yellow or green leaves. A leaf that was 100% green was

recorded as green. A leaf that had any amount of yellowing was recorded as

yellow. If over 50% of the leaf was brown, it was considered brown and not

recorded.


Calculations


Diversity Index

The Shannon-Wiener index of diversity, H' = -2 p, In pi where p, is
the proportion of individuals found in the ith species, was calculated using
the rainforest survey data for 1991, 1993, and 1996. Calculations were made to
follow the plants from the first planting through all three sampling dates.











Biomass Estimates

Three estimates of biomass have been made: one for Nov. 1990, the

second for July 1991 just prior to the first closure, and one in 1993 reflecting

changes during the first 2 years of closure. The 1990 and 1991 estimates were

made by personnel from Yale University School of Forestry and

Environmental Studies (Haberstock 1991). Estimates were made from size

attributes measured for individual plants inside the Biosphere such as height

and diameter at breast height, using equations for trees from the literature

(woody trees except forLeucaena from Scatena et al. 1993) and an equation for

the 'Musa' type developed by Haberstock based on small destructive sampling

at Biosphere 2.

For the 1990 estimate, every plant in the Biosphere 2 rainforest was
measured. For the 1991 estimate, every large woody tree, about 1/2 of the

'Musa' category, and 10% of most other categories were measured.

Measurements were made on randomly selected subsets of plant categories
other than trees.

The July 1993 estimate (Bierner 1993) was extrapolated from a subset of
tree measurements, using the equations cited above. The subset included 81
big trees, which were compared with their previous measurements to

calculate a percent increase in biomass. That increase was assumed to be the
same for all growth forms in the rainforest, and was applied to original
biomass estimates to arrive at the 1993 estimate.











Growth Form Spectra

The symbols used to represent the rainforest plants on the original
maps were changed for this study. Nine growth forms are used to describe

the plants, as follows: tree (T), arborescent palm and palmlike plant (P), shrub

(S), giant-leaved herb (G), herb (H), graminoid (R), woody graminoid, such as
bamboo (A), climber (C), and epiphyte (E). Discrimination between giant-
leaved herbs (Musa, Strelitzia) and herbs (Calathea, Maranta) was somewhat
arbitrary, but generally giant-leaved herbs have the form of herbaceous trees.

All herbaceous and woody vines and lianas were lumped into the climber

category. All bromeliads and orchids were considered epiphytes if a

description of the species was not found to the contrary. Since these
categories do not always agree with those of other studies, certain categories
were lumped when comparisons were made with other published data. In
particular, the following growth forms were lumped: Herb = Herb + Giant-
leaved herb + Graminoid; Tree = Tree + Arborescent palm + Woody

graminoid.


Poisson Distribution

A grid of squares was printed onto transparencies, with each square
representing a ground area of 2 m by 2 m. The transparency was placed over
the map of plants in the rainforest biome, and the number of plants in each
square was counted and recorded on the transparency. The entire rainforest
biome was counted with the exception of squares containing concrete slabs,
water bodies, or other features that would have prevented planting. A total
of 389 squares were counted, or about 80% of the rainforest surface area.










The total number of squares containing the same number of plants was
tabulated, and the mean number of plants per square was calculated. From
this, a Poisson distribution was generated for comparison with the actual
distribution. A chi-square test was used to make the determination.

The ratio of the variance to the mean was calculated to compare with
the same ratio of the Poisson distribution, which is equal to one. A ratio
greater than one would imply contagious distribution; less than one,
regularity (Whittaker 1975).


Simulation Method

The simulation method used in this dissertation is described in detail
by Odum and Odum (in press). The first step of the method is to draw a
diagram of the system being studied using symbols of the energy systems
language (Table 1-2). The study system is delineated inside the border of a
window to include material and information storage in their hierarchical
order, energy flows, feedbacks, and energy drains. External energy sources are
shown flowing in from outside across the system border. Next, rate equations
are written from the diagrams. The method is explained with a simple
example.

The diagram and equations in Figure 2-2 represent the species diversity
on islands as described by MacArthur and Wilson (1967) and interpreted and
drawn by Beyers and Odum (1993) using energy systems symbols. Here
diversity (Q) is the result of the constant inflow of seeds, spores, and other

propagules immigrating from outside the system and the outflow from the
system due to linear extinction. The number of species already established on
an island system as shown creates a backforce against colonization by new










species. The backforce is represented diagrammatically by the pathway
between P and S, which lacks an directional flow arrow; and mathematically
in the equations which show the rate of flow as dependent on the difference
between P and S.

Figure 2-3 shows a simple, one-tank model of biodiversity, where Q is
the species diversity of the system; J is the constant flow of species from

outside the system (seeds, spores, other propagules) immigrating into the
system; K1 is the pathway coefficient for the rate of extinction, which is
described with a quadratic drain representing extinctions in proportion to self
interactions such as interspecies competition. K2 is the coefficient for linear
extinction in proportion to species present. The inflow of species in this
model is independent of the number of species already present, as shown by

the constant flow of species P to the system storage Q.

For calibration, values of storage and flows are placed on the diagram
to help visualize consistency. Then a calibration table is made to calculate
the pathway coefficients. Table 2-4 calculates pathway coefficients for the
model shown in Figure 2-4 when the biodiversity at steady state is 60 species.

An EXCEL spreadsheet was used to run the simple biodiversity
simulation. Results of the simulation when started with different values of
diversity are shown in Figure 2-5.


Emergy Evaluation

Emergy evaluations of Biosphere 2 construction and rainforest
development were made according to the method of Odum (1996), as
summarized below:

















S S = S (P-S)-PS
Species
Present S = Soe-(X+A)t +

-P (1- e-(X+P)t)
9IS Linear extinction






Figure 2-2. Diagram and equations for species diversity on
an island as described by MacArthur and Wilson (1967)
and drawn by Beyers and Odum (1993).


\ species \



dQ/dt= J- Kl*Q*Q K2*Q


Figure 2-3. Single tank model of biodiversity as a
balance of steady inflow and linear and quadratic
extinction showing storage and pathway coefficients.






















Flows in species per year


Figure 2-4. Single tank model of biodiversity with
calibration values for flows and storage.







Table 2-4. Spreadsheet used to calculate coefficients for single tank
biodiversity model in Figure 2-3, calibrated at steady state.


Storage or flow


Steady state value Coefficient calculation


Storage
Number of species Q = 60
Flow
Yearly species additions J = 1
Quadratic species KI*Q*Q = 0.9 K1 = 0.00025
extinction
Linear species K2*Q = 0.1 K2 = 0.001667
extinction















140

120

S100

S80

o 60
^ ^ -- ^ ==----------:=
40 -
z
20 -

0
0 10 20 30 40 50 60 70 80 90

Time, years

Figure 2-5. Simulation of number of species Q for different
starting values using the single storage model in Figure 2-3.










First, a diagram of the system was drawn showing the elements that
were to be included in the analysis. Second, the emergy evaluation table was

constructed, including columns for the attribute of the system being
measured and their energy values, transformity values, and emergy values.
Others, such as emvalue, may be added if relevant to the analysis being made.
The first column of each table is a note number, referring the reader to the
notes following the table which explain the origin of the values and/or the
calculations used to derive the values. The table was then filled in with
available or calculated data.

The emergy analysis of the developing rainforest of Biosphere 2
included a summation of everything that went into creating the structure and
ecosystems prior to the first material closure. A percentage of the total value
in proportion to the relative size of the rainforest within the Biosphere was
calculated, giving the total cost for the rainforest only. The final analysis was
then used to compare to the tabonuco rainforest system of Puerto Rico.













CHAPTER 3
RESULTS


Data and analyses are presented for Biosphere 2 and the rainforest at El
Verde in Puerto Rico.


Characterization of the Rainforest in Biosphere 2


Soil

The rainforest soils were relatively homogeneous in vertical profile
after placement. Some textural discontinuities resulted from uneven mixing
of the soil materials during their placement, creating sandier and rockier soils
in parts of the lowland rainforest where the soil is a coarse sandy loam or

coarse very sandy pebbly loam throughout the vertical profile (Scarborough
1994). Various soils used for potting mixes of individual plants became part
of the rainforest topsoil after planting. Several of the larger trees had nearly a

cubic meter of soil and root volume. In addition, clay aggregates in the soil
mixture tended to maintain their structure as 'peds' from about 1-12 cm

diameter (Scarborough 1994).

Measurements made by Scott (1999) for December 1993 and those
reported by Lin et al. (1998) for later dates are shown in Table 3-1. Vertical
development of the rainforest soils in the lowland and ginger belt habitats
was apparent in December 1993, after 3 years of emplacement. Scott (1999)
reports an accumulation of some elements (C, N, K, Ca, Mg) in the upper

72









Table 3-1. Characteristics of Biosphere 2 rainforest soils from samples
From Scott (1999) and Lin et al. (1998 and 1999).


taken on different dates.


Depth 1-Dec 19-Dec 25-Jan 31-May 16-Jun 15-Jul
Characteristic (cm) 1993" 1995b 1996b No date 1996d 1996d 1996d
pH 0-10 7.63 -


OM (% dw)



C (% dw)




N03-N (mg g-')


N (% dw)




C/N


1020
0-20
20-40
40-60

0-20
20-40
40-60

0-10
1020
20-40
40-60

0-20
20-40

0-10
1020
20-40
40-60

0-10
1020
0-20
20-40
40-60


7.53

7.51
7.52


7.34+ 0.10
7.36+0.04


3.62+0.49
3.260.26


7.38+0.21
7.50+0.01


4.08+0.47
2.920.39


7.68+0.07

7.98+0.10

4.16+0.42

3.88+0.39


3.09
2.35
2.25
2.35


22.4+5.3
21.4+6.0


26.2+2.3
19.6+3.3


0.29
0.22
0.22
0.24

10.6
10.2

10.2
10.2


11.4+2.9


11.0+3.3


8.2+1.3


7.68+0.07

12.3+1.4












Table 3-1--continued.
Depth 1-Dec 19-Dec 25-Jan No date 31-May 16-Jun 15-Jul
Characteristic (cm) 1994 1995b 1996b 1996d 1996d 1996d
K (mg g-) 0-20 789+189 650+153 561+127 602+145 692+162
0-10 1298
10-20 1009
20-40 856 533+132 523+89 -
40-60 974

Ca (mg g') 0-10 5497 -
1020 5210 -
20-40 4967 -
40-60 4841 -

Mg (mg g-') 0-10 509 -
1020 440 -
20-40 425 -
40-60 441 -

PO4-P (mg g-) 0-20 117+25 111+24 64.5+11.5 67.4+10.8 60.9+9.8
20-40 121+25 99+21 -

Fe (mg g') 0-20 251+45 190+16 161+27 144+16 162+17
20-40 207+44 215+31 -


' Scott (1999). n=6, ave. of eineer belt and lowland habitats. Data for K, Ca, Me were converted from
meq/100g to mg/g to make them easier to compare with other data presented.
b Lin et al. (1998). (Table 1, n=5) (location of samples not given)
Lin et al. (1999). (Table 1 date of samples not given)
d Lin et al. (1999). (Table 2, n=5)











stratum (0 10 cm) of the rainforest soils during this period. Similar trends
were reported by Lin et al. (1998) in Jan. 1996 for percent organic matter and

NO3-N, though in the same study the accumulation was not apparent just
one month earlier. Over a short time (Dec. 95-July 96) the same study reports
a clear decrease in concentrations of NO,-N, PO,-P, and Fe in the 0-20 cm
stratum (the only layer for which data are available for both dates, n=5).

The pH values reported from Dec. 93 through Jan. 96 along a vertical
profile are slightly alkaline, ranging from 7.34+0.10 to 7.98+0.10. Scarborough
(1994) noted a "tendency towards precipitation of soil carbonate minerals in
the rainforest soils, based upon several water chemistry signatures", and that
the water routinely used for irrigation during the first 2 years was enriched
with bicarbonate ions.

Soil bulk density in Dec. 1993 of the 0-10 cm stratum was 1.10 g cm3 for
the lowland and 1.05 g cm3 for the gingerbelt (Scott 1999), Table 3-2. Bulk
density was higher in all of the other strata (to 1.32 in lowland and 1.11 in
ginger belt), but no further patterns were evident. Per cent volume of coarse
fragments increased with depth.

Anoxic areas were reported by Scarborough (1994) after three years of
soil development. He also reported "a great [deal] of soil homogenization of
the upper 12-16 inches due to worm activity," and a gray surficial layer 0-7.5
cm deep forming in the NE quadrant of the lowland habitat that he attributed
to worm activity. Soil fauna as described by Scott (1999) included worms to a
depth of 40 cm, but not in the surface litter which he attributes to predation by
and avoidance of ants. Other macrofauna counted by Scott were isopods,
cockroaches, and millipedes.











Table 3-2. Soil bulk density and percentage coarse fragments
in Biosphere 2 rainforest from samples made in November 1993.
From Scott (1999).

Depth Bulk density Coarse fragment
Location cm g cm3 vol., %
Biosphere 2'
Lowland rainforest 0-10 1.10 8.23
10-20 1.26 12.88
20-40 1.32 15.22
40-80 1.18 15.54
Ginger belt 0-10 0.94 10.94
10-20 1.11 14.60
20-40 1.03 16.75
40-80 1.10 21.13
" Data from Scott (1999), n=3.












Plants

There were two periods of plant introductions to the Biosphere 2
rainforest. The first was from April 1990 to September 1991; the second from

October 1993 to March 1994. The number of individual plants and species are
summarized in Table 3-3.

At the start of the 1991 closure of the Biosphere, 1890 individual plants
were recorded in the rainforest. Of the original plants recorded, 316 species (or

monospecific genera) were recognized in 99 families, with 315 of the original
1890 plants not identified to species.

All of the plants growing in the rainforest by September, 1991 were
mapped. Every plant was drawn on the map with a symbol representing its

growth form and with a unique survey number. Canopy widths were

mapped to scale. Figure 3-1 shows a section of the map. All of the map is
shown in 20 sections in Figure A-1. Every survey point with its individual
plant identification, growth form, and inventory status for 1991, 1993, and
1996 is listed in Table B-1.

During the second planting period at the end of 1993, 339 individuals
were added in at least 92 species (or monospecific genera), 50 species of which
were new to the rainforest.

In 1996 an additional 48 individual plants in 15 species were recorded.
All of these plants appeared to have been self-propagated, some from seed
(such asPachira aquatica and Coffea arabica) and others clonally (such
asColocasia).





78




Table 3-3. Total number of species and individual
plants seeded in the Biosphere 2 rainforest.

Approximate Number of Number of
dates of planting individuals species
4/90-9/91 1890 316
11/93-2/94 339 92/50a
Total 2229 366
aOf the 92 species, 50 were new to the Biosphere.



















































S17507
17506


Figure 3-1. Map section #3 showing location, growth form, and canopy size
of individual plants in the Biosphere 2 rainforest in September 1991. The
twenty map sections are given in Figure A-1. Approximate scale: 1 cm = 0.6 m.











Plant survey results, first planting

At the end of 1993, a total of 872 (46%) of the original plants (first
planting) were still alive. In 1996, 529 (28%) of the original plants were
found. Table B-2 shows the number of individuals within each species at the
time of closure in 1991, along with the subsequent inventories for 1993 and
1996.

In the 1993 inventory, 194 (61%) of the original species persisted and by
1996, 137 (43%) of the original species remained. The distribution of plants
within species for both inventory years shows a decline in both numbers of
species as well as number of individuals per species, as summarized in
Table 3-4.

All or most of the plants in the following groups from the first
planting died during the first 2 year study period: Adiantaceae (ferns),
Aspleniaceae (ferns), Blechnaceae (ferns), Cyatheaceae (tree ferns),
Orchidaceae, Polypodiaceae (ferns), Selaginellaceae (fern allies), and most
Bromeliaceae (mostly epiphytes); Sagittaria, Pontederia, Typha, Nymphaea,
and Lycopodium. This included almost all of the herbaceous and tree ferns,
fern allies, epiphytes and aquatic plants. The large herbaceous species planted
largely in the peripheral ginger belt thrived, spreading clonally. The most
successful taxa in terms of maintaining large populations were all clonal
species including the following taxa: Musaceae, Marantaceae, Zingiberaceae,
and Strelitziaceae.










Table 3-4. Number of individual plants and species recorded in
1991, 1993, and 1996 surveys of Biosphere 2 rainforest. The first
number in each entry includes plants from the 1991 planting, the
second number from the 1993 planting, and third is plants that
have self-propagated. Species reported are for species new
to the rainforest.


Survey Number of Number of
date individuals species
1991 1890 316
1993 872/339 194/50
1996 529/86/48 137/20/0











Plant survey results, second planting

In 1996, 41% of the second planting species and 25% of the individuals
remained. Table A-3 lists the plants that were added to the rainforest after

September 1993, and their subsequent inventory for 1996. In contrast to the
first planting, many of the Bromeliaceae, largely epiphytes, survived. Most of
the plants in the following families died: Orchidaceae, Arecaceae (palms),
Aspleniaceae (ferns), and Polypodiaceae (ferns).

Abundance and distribution of plants within species

The change in the number of plants within species over 5 years is
shown for the plants from the 1991 planting in Figure 3-2. For all years, there
were relatively few common species and many rare species. In 1991, 90

species were represented by only one individual, whereas only about 15
species were each represented by more than 15 individuals. About 45% of the
species in 1991 had only 1 or 2 individuals, which represented 11% of the
plants. By 1993, both number of species and numbers of individuals within
species had declined, and 56% of the species had only 1 or 2 individuals,
representing only 15% of the individuals, a pattern repeated again in 1996.

Individual and species decline

The mortality rate of individuals and extinction of species was higher
for the second planting than the first over the period 1993-1996 as shown in
Figures 3-3 and 3-4. Seventy-five percent of the second planting individuals
died, whereas only 39% of the first planting individuals died; and about 60%
of the species from the second planting and 30% of the species from the first
planting went extinct over the same period.




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