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«By KIMBERLY Y. EPPS A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE ...»

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LINKING SPECIES RICHNESS, LITTER CHEMICAL DIVERSITY AND SOIL CARBON

DYNAMICS IN THE ATLANTIC FOREST, BAHIA, BRAZIL

By

KIMBERLY Y. EPPS

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

© 2009 Kimberly Y. Epps To Vera Jean and Omar Jamal, in whose hearts no bitterness could take root

ACKNOWLEDGMENTS

Little can be accomplished in solitude. From its inception to its completion, this work is beholden to a cast of thousands. Foremost, I thank my mother, Yvonne D. Epps, for her steadfast encouragement and unconditional love, my family consisting of the Shareef-EppsMinter-Perkins-Justice-Runge Units, and its drafted members Joyce Dow, Toni Greene-Garner, and Edith Yamanoha.

My life of science began at my kindergarten discovery that stars were fiery balls of gas.

Since then I have been fortunate to have been influenced by phenomenal teachers and mentors along the years. I express sincere gratitude to Mrs. Rosenthal (3rd grade) and Mrs. Millet (4th grade) of P.S. 95Q; Mrs. Proimos (6th grade) and Mr. Ytuarte (7th grade) of the Immaculate Conception School of Jamaica; Mme. Gerton (French), Mr. Gordon (Physics), Mr. Greenberg (Geometry), and Mr. Kelly (English) of Bronx Science; Prof. Shirlynn Spacapan (Psychology) and Prof. Art Benjamin (“Fun Math”) of HMC; Dr. Paul Marcotte (International Agricultural Development), Dr. Bill Rains (Agronomy), and Dr. Kate Scow (Soil Microbiology) of U.C.

Davis. For training my eyes, ears, head and hands, I thank Sheila Pinkel (Photography, Pomona), Marti Kanin and Julie Hochman (‘Cello). For unparalleled training in field grit and economy, I am indebted to Dr. Eliska Rejmankova of U.C. Davis.

Here at my current home in Gator Country, I thank my doctoral committee for expanding my horizons while tightening my scientific investigation skills: Wendell Cropper for introducing me to the wonders of open source code and to the genius of Ramon Margalef; Willie Harris for being a model thinker and professor; Quintino Araújo for my immersion in the scientific and artistic culture of cacao; and P.K. Nair and Nigel Smith for grounding my inquiries in application and human need. Adding to the embarrassment of riches have been my “behind-the-scenes” advisors, Jim Reeves (USDA); Nairam Barros (UFV), Jack Ewel (UF); Al Medvitz (UCD);

Mark Van Horn (UCD); Arlicélio de Queiroz Paiva (UESC); Rosana Higa (EMBRAPA Floresta), George Sodrê (CEPLAC); Yuncong Li (UF); and Virupax Baligar (USDA) with whom it would be a pleasure and honor to consider future research plans.

For bringing me up to speed on soil microbiology and the wonders of Biolog, I thank Cory Krediet and Max Teplitski. For my crash course in the Atlantic Rain Forest I am grateful for the technical orientation of André M. Amorim and José Limão da Paixão of the CEPLAC Herbarium as well as to my dear friend, right hand, and mateiro superior, Agnaldo Oliveira da Silva. I acknowledge the support of the community of the Assentamento Frei Vantuy and in particular, the leadership of Maïsa Fontana and Marlene Rebouças. The expertise and daily efforts of Dr.

Helena Serôdio, José Nelson Machado, Celso, Claudionou, Osmario of CEPLAC-CEPEC;

Edilson Fernando da Silva, “Seu” José Alberto, Luis Claudio de Almeida Barbosa, Antônio Lelis Pinheiro, Verónica, and Aldemir at the Federal University of Viçosa were indispensible to my work, as were the time and tutelage of the inimitable DRIFTS-Squad, Barry Francis and Tanesha Simmons of USDA-EMBUL.

For their willingness to brave dangers ranging from vigilante wasps and busted boots to siever’s lung, pipettor’s thumb and dishpan hands, I thank my Brothers and Sisters in Soil past and present: Dalton Abdala, Kahlil Apuzen-Ito, Elena Azuaje, Christine Bliss, Lizette Borges Gómez, Oldair Vinhas Costa, Eric Carvalho, Joy Futrell, Antônio and Emanuela GamaRodrigues, Sarah Johnson, Francisco Lópes Neto, Isabel Lopez-Zamora, Melissa Martin, Edson Márcio Matiello, Marina Morales, Deoyani Sarkhot, Shinjiro Sato, Sharon Schnabel, Lauren Serra, Lisa Stanley, Aja Stoppe, Dashuai Sun, Ken van Rees, Marcela Quintero, and especially, Barbara Cade-Menun for leading the way down the dirt path.

For reminding me that life is not a one-note samba, but rather a frevo, forró and at times a choro, I thank Abby Lóces; Ana Amelia Guimarães Araujo; Anthony Heric; Arceli Trindade da Silva; Ayesha Nibbe; Carol Souza; Charlotte Norris; David Giles; David Healy; Flora Piasentin;

Francisco “Chico” de Vale; Glória Fidelis da Paixão; Jina Kim; Justine Di Fiore; Katie Painter;

Kipp Sutton; Larry Dieterich; the “Rainha das Aguas”, Maria Apareçida; Maria Mariano; Maura Barros; Michelle Young; Morena Maia; Neyde Alice Pereira; “ O Paulozão”; Prashanth Ak;

Rozeli Shiroma; Scott Looney; and Sylvia Ward. I am grateful for those who kept my heart and belly fed – Renata Santiago, Judite de Ilhéus; Regina Alvez Ferreira; Jean Rissman; Karen van Epen; Danielle Calin; Paty Guerra; Gustavo Dantas; Ana Elisa Del’Arco; Cecilia and Wilton Carvalho; Halter Maia; Ivani de Brito; Sônia Sampaio, and Gina Gonçalves dos Santos.





This work was performed under the authorization of CNPq and IBAMA Permit No. RMC I am grateful to the kind attentiveness of Dr. Francisco Guerra who led us along the way to authorization. For their financial support, I thank the generous contributions of the University of Florida Alumni Fellowship; the Graduate Women in Science-Nell I. Mondy Award; the Ford Foundation Pre-Doctoral Diversity Fellowship and the Epps-Tadross-Minter-Painter Student Emergency Funds.

Above all, I welcome the opportunity to once again express my deep gratitude for the otherworldly patience, good humor, cheerleadership and translation abilities of my advisor and role model, Nicholas B. Comerford.

Lastly, for giving me the home of my spirit, a second mother tongue, and a very, very fine dog, I thank Bahia, herself.

–  –  –

ACKNOWLEDGMENTS

LIST OF TABLES

LIST OF FIGURES

ABSTRACT

CHAPTER

1 INTRODUCTION

2 CHEMICAL DIVERSITY – HIGHLIGHTING A SPECIES RICHNESS AND

ECOSYSTEM FUNCTION DISCONNECT

Introduction

Materials and Methods

Characterization of Leaf Tissue

Mathematical Treatment of Spectral Data

Results and Discussion

Experimental Ramifications of Chemical Diversity

Conclusion

3 THE EFFECT OF CHEMICAL IDENTITY AND CHEMICAL DIVERSITY ON THE

DECOMPOSITION OF TROPICAL LEAF MIXTURES

Introduction

Materials and Methods

Leaf Material Collection and Characterization

Calculation of Chemical Diversity

Incubation Study

Microbial Community-Level Physiological Profiling

Statistics

Results

Species Identity on Carbon Mineralization of Mixtures

Chemical Identity on Carbon Mineralization of Mixtures

Identification of Functional Chemical Traits

Microbial Functional Diversity and Non-additive Effects

Discussion

Importance of Species Identity and Chemical Identity on Carbon Mineralization.........54 Which Traits?

Microbial Underpinnings of Non-Additive Effects

Conclusion

4 TREE SPECIES DIVERSITY AND NUTRIENT CYCLING POTENTIALS OF

SMALL-SCALE CACAO PRODUCTION SYSTEMS AND SECONDARY FOREST

FRAGMENTS IN SOUTHERN BAHIA, BRAZIL

Introduction

Materials and Methods

Site Selection and Characterization

Species Inventory and Tree Diversity

Forest Floor

Litterfall Production

Soil Nutrient Status

Statistical Analysis

Results and Discussion

Tree Density and Species Inventory

Litter Production, Standing Biomass

Nutrient Inflows through Litterfall

Soil Nutrient Status

Conclusion

5 OVERVIEW AND SYNTHESIS

APPENDIX

A USING INFRARED SPECTROSCOPY TO DETERMINE THE RELATIVE

CONTRIBUTION OF ORGANIC INPUTS TO SURFACE SOIL ORGANIC

MATTER

Introduction

Materials and Methods

Study Site and Sampling

Single-species stands

Mixed-species stands

Sample Preparation

Spectral Analysis and Isotopic Carbon Analysis

Statistical Analysis

Results and Discussion

Relative Importance of Above- and Belowground Inputs

Interpretation

Conclusion

LIST OF REFERENCES

BIOGRAPHICAL SKETCH

–  –  –

2-1 Published mineral nutrition studies reporting total nutrient concentrations used to investigate the chemical diversity (CDQ) and species richness relationship.

3-1 Initial foliar total nutrient concentrations of 10 tropical tree species used in the incubation study.

3-2 Species composition and abbreviation codes of the 21 leaf mixtures observed in the incubation study.

3-3 Chemical diversity indices of leaf mixtures according to the mode of chemical characterization of material: total nutrient concentration (Total), mid-infrared (MIR) and near-infrared spectroscopy (NIR).

3-4 Kendall’s Tau correlation coefficient of total nutrient concentrations with decomposition responses of leaf-mixtures

3-5 Summary of repeated measures ANOVA for effects of mixture composition on net respired CO2 of 21 leaf mixtures at Day 80

3-6 Summary of factorial ANOVA for effects of mixture composition on the carbon mineralization rate constant, a, of 21 leaf mixtures

3-7 Expected and observed carbon mineralization rates and non-additive effect of paired litter treatments in incubation study

3-8 Summary of factorial ANOVA for effects of mixture composition on interactions of net CO2, I net CO2, and the C mineralization rate constant, I a, of 21 leaf mixtures............70 Summary of selected successful models† relating chemical identity (1/λ) to net 3-9 evolved CO2 and C mineralization rate of 21 leaf mixtures.

Summary of successful models† relating chemical identity (1/λ) and chemical 3-10 diversity (CDQ) on C mineralization rate of 21 leaf mixtures.

Summary of successful models† of the relationship of chemical identity and chemical 3-11 diversity on the decomposition responses of INGA leaf mixtures (n=7).

Summary of successful models† of the relationship of chemical identity and chemical 3-12 diversity on the decomposition responses of EMBA leaf mixtures (n=7)

Summary of successful models† of the relationship of chemical identity and chemical 3-13 diversity on the decomposition responses of PAUM leaf mixtures (n=7)

3-14 Discriminant analysis of non-additive effects observed in the C mineralization rates of 21 leaf mixtures, performed on the first four PCA factor scores of the spectra of key and companion species

3-15 Spectral traits of key species (MIR) contributing to successful models of leaf-mixture decomposition processes and their potential physiochemical interpretation

3-16 Kendall’s Tau correlation between microbial functional diversity (Gini coefficient) and mean substrate use of 31 EcoPlate substrates and the decomposition responses of mixed leaf treatments

4-1 Soil chemical properties and particle size distribution of cacao and secondary forest study sites in the Assentamento Frei Vantuy, Ilhéus, Bahia, Brazil.

4-2 Summary of the floristic diversity of four cabruca sites (0.25 ha) located in the Frei Vantuy Settlement, Ilhéus, Bahia, Brazil

4-3 Summary of the floristic diversity of four secondary forest sites (0.25 ha) located in the Frei Vantuy Settlement, Ilhéus, Brazil

4-4 Phytosociological parameters (excluding cacao) of cabrucas in southern Bahia observed in other studies

4-6 Tree species (≥ 5 cm DBH) identified in the selected study areas of cabruca and secondary forest in the Assentamento Frei Vantuy, Ilhéus, Bahia, Brazil.

4-7 Mean total nutrient concentrations of surface soil (0-10cm) and litter and total annual input of nutrients through litterfall in traditional cacao systems and adjacent secondary forest sites in the Assentamento Frei Vantuy, Ilhéus, Bahia, Brazil..............118

–  –  –

2-1 Chemical diversity (CDQ) as a function of species richness of eight litter species native to the Atlantic Forest region of southern Bahia.

2-2 The effect of the removal of species from a mixture on chemical diversity under assumption of equal species abundance, and DRIFTS characterization of the assemblage in Fig. 2-1.

2-3 The relationship of foliar CDQ diversity with species richness of two different temperate forest communities..

2-4 The idiosyncrasy of additive studies

3-1 Diffuse reflectance infrared spectra of 10 litter species

3-2 Chemical diversity (normalized to the maximum value) of all possible mixtures of 10 selected tropical species as a function of species richness, as characterized by total nutrient concentrations.

3-3 Chemical diversity (normalized to the maximum value) of all possible mixtures of 10 selected tropical species as a function of species richness, as characterized by midinfrared spectroscopy (MIR).

3-4 Chemical diversity (normalized to the maximum value) of all possible mixtures of 10 selected tropical species as a function of species richness, as characterized by nearinfrared spectroscopy (NIR).

3-5 Carbon mineralization of ten individual tropical species and the control treatment........81 3-6 The effect of key species on decomposition responses after 80 days

3-7 Dynamic nature of non-additive effects on cumulative evolved CO2 between litter pairs over the course of incubation.



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