Methods to Study Litter Decomposition

Felix Bärlocher is a Research Professor at Mt. Allison University, Sackville, New Brunswick, Canada. He retired from teaching in 2016. He has pioneered and published landmark studies on the ecology of aquatic hyphomycetes, a polyphyletic group of fungi that dominate the decomposition of riparian tree leaves in streams. Additional central research interests are the taxonomy and evolution of aquatic hyphomycetes, molecular approaches to characterize these fungi and trophic interactions with litter-consuming invertebrates. Mark O. Gessner is Department Head at the Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) and Professor at the Berlin Institute of Technology (TU Berlin) in Germany. Trained as an aquatic ecosystem scientist, he is widely recognized for his work over 30 years on ecosystem processes, particularly many facets of the decomposition of plant litter in freshwaters, including the role of fungi, bacteria and detritivorous invertebrates, as wellas the importance of changing environmental conditions, biodiversity and human activities in controlling decomposition rates.Manuel A.S. Graça is a Researcher at MARE (Marine & Environmental Sciences Centre) and Professor at the University of Coimbra, Portugal. His extensive work for more than 30 years in Mediterranean and tropical climates has focused on shaded headwater streams, where he investigates particularly the trilogy of leaf litter – microbial decomposers – litter-consuming detritivores and their role in detrital food webs. Studies on anthropogenic impacts on streams and benthic stream invertebrates are also a major long-standing research interest.

• Part 1. Litter dynamics: chapter 1.  Litter Input (Arturo Elosegi & Jesús Pozo).- Chapter 2. Leaf Retention (Arturo Elosegi).- chapter 3. Manipulating Litter Retention in Streams (Michael Dobson).- chapter 4. Coarse Benthic Organic Matter (Jesús Pozo & Arturo Elosegi).- chapter5. Leaching (Felix Bärlocher).- Chapter 6. Leaf Mass Loss Estimated by the Litter-Bag Technique (Felix Bärlocher).- Chapter7. Determining Litter Mass Loss by the Plant Tagging Approach (Kevin A. Kuehn & Mark O. Gessner).- Chapter 8. Wood Decomposition (Arturo Elosegi, Maite Arroita & Libe Solagaistua).- Chapter9. Decomposition of Fine Particulate Organic Matter (Yoshimura Chihiro).- Chapter10. Coarse Particulate Organic Matter Budgets (Jesús Pozo & Jon Molinero).- Part 2. Chemical and Physical Leaf Properties. Chapter11. Total Phosphorus, Nitrogen, and Carbon in Leaf Litter (Mogens R. Flindt, Ana I. Lillebø, Javier Pérez & Verónica Ferreira).- Chapter12. Total Protein (Mark O. Baerlocher).- Chapter13. Free Amino Acids (Shawn D. Mansfield & Mark O. Baerlocher).- chapter14. Determination of Total Carbohydrates (Shawn D. Mansfield).- chapter15. Determination of Soluble Carbohydrates (Letitia da Ros, Faride Unda, Shawn D. Mansfield).- Chapter16. Total Lipids (Mark O. Gessner & Paul T. M. Neumann).- Chapter17.  Polyunsaturated Fatty Acids in Decomposing Leaf Litter (Eric Von Elert).- Chapter18.  Total Phenolics (Felix Bärlocher & Manuel A.S. Graça).- Chapter19. Radial Diffusion Assay for Tannins (Manuel A.S. Graça & Felix Bärlocher).- Chapter20.   Acid Butanol Assay to Determine Bulk Concentrations of Condensed Tannins (Mark O. Gessner & Daniel Steiner).- Chapter21.    Lignin and Cellulose (Mark O. Gessner).- Chapter22. Physical Litter Properties: Leaf Toughness and Tensile Strength (Manuel A.S. Graça & Martin Zimmer).- Part 3. Microbial Decomposers. Chapter23. Techniques for Handling Ingoldian Fungi (Enrique Descals).- Chapter24.     Maintenance of Aquatic Hyphomycete Cultures (Ludmila Marvanová).- Chapter 25.  An Illustrated Key to the Common Temperate Species of Aquatic Hyphomycetes (Vladislav Gulis, Ludmila Marvanová & Enrique Descals).- Chapter26. Sporulation by Aquatic Hyphomycetes (Felix Bärlocher).- Chapter 27. Ergosterol as a Measure of Fungal Biomass (Mark O. Gessner).- Chapter 28. Fungal Growth Rates and Production (Keller Suberkropp, Mark O. Gessner & Kevin A. Kuehn).- Chapter 29.  Bacterial Abundance and Biomass Determination in Plant Litter by Epifluorescence Microscopy (Nanna Buesing & Mark O. Gessner).- Chapter 30. Growth and Production of Litter-Associated Bacteria (Nanna Buesing, Mark O. Gessner & Kevin A. Kuehn).- Chapter 31.     Isolation of Cellulose-Degrading Bacteria (Jürgen Marxsen).- Chapter 32. ATP as a Measure of Microbial Biomass(Manuela Abelho).- Chapter 33. Respiration of Litter-Associated Microbes and Invertebrates (Manuel A.S. Graça & Manuela Abelho).- Part 4. Molecular Microbial Community Analyses. Chapter34. Terminal Restriction Fragment Length Polymorphism (T-Rflp) to Estimate Fungal Diversity (Liliya G. Nikolcheva & Felix Bärlocher).- Chapter 35.  Denaturing Gradient Gel Electrophoresis (DGGE) to Estimate Fungal Diversity (Liliya G. Nikolcheva & Felix Bärlocher).- Chapter36.  Quantitative Real-Time PCR (qPCR) to Estimate Molecular Fungal Abundance (Christiane Baschien & J. Steffen C. Carl).- Chapter 37.      Metabarcoding of Litter-associated Fungi and Bacteria (Sofia Duarte, Christian Wurzbacher & Sahadevan Seena).- Chapter 38.   Identifying Active Members of Litter Fungal Communities by Precursor rRNA (Martina Štursová & Petr Baldrian).- Chapter 39.      Gene Expression Analysis of Litter-Associated Fungi UsingRNA-Seq (Elizabeth C. Bourne, Paul R. Johnston, Elisabeth Funk & Michael T. Monaghan).- Chapter 40. Metaproteomics of Litter-associated Fungi (Katharina M. Keiblinger & Katharina Riedel).- Part 5. Enzymatic Capabilities. Chapter 41. Extractellular Fungal Hydrolytic Enzyme Activity (Shawn D. Mansfield).- chapter 42. Cellulases (Martin Zimmer).- Chapter 43. Viscosimetric Determination of Endocellulase Activity (Björn Hendel & Jürgen Marxsen).- Chapter 44. Fluorometric Determination of The Activity of β-Glucosidase and other Extracellular Hydrolytic Enzymes (Björn Hendel & Jürgen Marxsen).- Chapter 45. Pectin-degrading Enzymes: Polygalacturonase and Pectin Lyase (Keller Suberkropp).- chapter 46. Lignin-degrading Enzymes: Phenoloxidase and Peroxidase (Björn Hendel, Robert L. Sinsabaugh & Jürgen Marxsen).- Chapter 47. Phenol Oxidation (Martin Zimmer).- Chapter 48. Proteinase Activity: Azocoll and Thin-layer Enzyme Assay (Manuel A.S. Graça &Felix Bärlocher).- Part 6. Litter Consumers. Chapter 49. Processing of Aquatic Invertebrates Colonizing Decomposing Litter (John S. Richardson).- chapter 50. Identifying Stream Invertebrates as Plant Litter Consumers (Luz Boyero, Richard G. Pearson, Ricardo J. Albariño, Marcos Callisto, Francisco Correa-Araneda, Andrea C. Encalada, Marcelo Moretti, Alonso Ramírez, April Sparkman, Christopher M. Swan, Catherine M. Yule & Manuel A.S. Graça).- chapter 51. Shredder Feeding and Growth Rates (Manuel A.S. Graça & José M. González).- chapter 52. Feeding Preferences (Cristina Canhoto, Manuel A.S. Graça & Felix Bärlocher).- chapter 53. Energy Budget of Shredders (Manuel A.S. Graça).- chapter 54. The Role of Shredders in Litter Dynamics at Stream Scale (José M. González & Manuel A.S. Graça).- Part 7. Litter Manipulations. Chapter 55. Manipulation of Leaf Litter Stoichiometry (Julio Arce-Funck, Vincent Felten, Michael Danger).- Chapter 56. IsotopicLabelling of Leaf-litter Nitrogen (Bernd Zeller, Severine Bienaimé & Etienne Dambrine).- Chapter 57. Decomposition and Consumption Tablets (DECOTABSs) (Gea H. van Der Lee, Ellard R. Hunting, J. Arie Vonk & Michiel H.S. Kraak).- chapter 58. Inoculation of Leaf Litter with Aquatic Hyphomycetes (Eric Chauvet).- Part 8. Data Analyses. Chapter 59. A Primer for Statistical Analysis (Felix Bärlocher).- Chapter 60. Determining Temperature-normalized Decomposition Rates (Mark O. Gessner & Frank Peeters).- Chapter 61. Biodiversity Analysis (Felix Bärlocher).- Chapter 62. A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-associated Fungi and Bacteria (Sahadevan Seena, Sofia Duarte & Christian Wurzbacher).- Chapter 63. A Primer for Meta-Analysis (Verónica Ferreira & Felix Bärlocher).