Methods to Study Litter Decomposition: A Practical Guide

Preface

Foreword

Part 1. Litter dynamics

1.      Litter Input (Arturo Elosegi & Jesús Pozo)

2.      Leaf Retention (Arturo Elosegi)

3.      Manipulating Litter Retention in Streams (Michael Dobson)

4.      Coarse Benthic Organic Matter (Jesús Pozo & Arturo Elosegi)

5.      Leaching (Felix Bärlocher)

6.      Leaf Mass Loss Estimated by the Litter-Bag Technique (Felix Bärlocher)

7.      Determining Litter Mass Loss by the Plant Tagging Approach (Kevin A. Kuehn & Mark O. Gessner)

8.      Wood Decomposition (Arturo Elosegi, Maite Arroita & Libe Solagaistua)

9.      Decomposition of Fine Particulate Organic Matter (Yoshimura Chihiro)

Part 2. Chemical and Physical Leaf Properties

11.  Total Phosphorus, Nitrogen, and Carbon in Leaf Litter (Mogens R. Flindt, Ana I. Lillebø, Javier Pérez & Verónica Ferreira)

12.  Total Protein (Mark O. Baerlocher)

13.  Free Amino Acids (Shawn D. Mansfield & Mark O. Baerlocher)

14.  Determination of Total Carbohydrates (Shawn D. Mansfield)

15.  Determination of Soluble Carbohydrates (Letitia da Ros, Faride Unda, Shawn D. Mansfield)

16.  Total Lipids (Mark O. Gessner & Paul T. M. Neumann)

17.  Polyunsaturated Fatty Acids in Decomposing Leaf Litter (Eric Von Elert)

18.  Total Phenolics (Felix Bärlocher & Manuel A.S. Graça)

19.  Radial Diffusion Assay for Tannins (Manuel A.S. Graça & Felix Bärlocher)

20.  Acid Butanol Assay to Determine Bulk Concentrations of Condensed Tannins (Mark O. Gessner & Daniel Steiner)

21.  Lignin and Cellulose (Mark O. Gessner)

22.  Physical Litter Properties: Leaf Toughness and Tensile Strength (Manuel A.S. Graça & Martin Zimmer)

Part 3. Microbial Decomposers

23.  Techniques for Handling Ingoldian Fungi (Enrique Descals)

24.  Maintenance of Aquatic Hyphomycete Cultures (Ludmila Marvanová)

25.  An Illustrated Key to the Common Temperate Species of Aquatic Hyphomycetes (Vladislav Gulis, Ludmila Marvanová & Enrique Descals)

26.  Sporulation by Aquatic Hyphomycetes (Felix Bärlocher)

27.  Ergosterol as a Measure of Fungal Biomass (Mark O. Gessner)

28.  Fungal Growth Rates and Production (Keller Suberkropp, Mark O. Gessner & Kevin A. Kuehn)

29.  Bacterial Abundance and Biomass Determination in Plant Litter by Epifluorescence Microscopy (Nanna Buesing & Mark O. Gessner)

30.  Growth and Production of Litter-Associated Bacteria (Nanna Buesing, Mark O. Gessner & Kevin A. Kuehn)

31.  Isolation of Cellulose-Degrading Bacteria (Jürgen Marxsen)

32.  ATP as a Measure of Microbial Biomass (Manuela Abelho)

33.  Respiration of Litter-Associated Microbes and Invertebrates (Manuel A.S. Graça & Manuela Abelho)

Part 4. Molecular Microbial Community Analyses

34.  Terminal Restriction Fragment Length Polymorphism (T-Rflp) to Estimate Fungal Diversity (Liliya G. Nikolcheva & Felix Bärlocher)

35.  Denaturing Gradient Gel Electrophoresis (DGGE) to Estimate Fungal Diversity (Liliya G. Nikolcheva & Felix Bärlocher)

37.  Metabarcoding of Litter-associated Fungi and Bacteria (Sofia Duarte, Christian Wurzbacher & Sahadevan Seena)

38.  Identifying Active Members of Litter Fungal Communities by Precursor rRNA (Martina Stursová & Petr Baldrian)

39.  Gene Expression Analysis of Litter-Associated Fungi Using RNA-Seq (Elizabeth C. Bourne, Paul R. Johnston, Elisabeth Funk & Michael T. Monaghan)

40.  Metaproteomics of Litter-associated Fungi (Katharina M. Keiblinger & Katharina Riedel)

Part 5. Enzymatic Capabilities

41.  Extractellular Fungal Hydrolytic Enzyme Activity (Shawn D. Mansfield)

42.  Cellulases (Martin Zimmer)

43.  Viscosimetric Determination of Endocellulase Activity (Björn Hendel & Jürgen Marxsen)

44.  Fluorometric Determination of The Activity of beta-Glucosidase and other Extracellular Hydrolytic Enzymes (Björn Hendel & Jürgen Marxsen)

45.  Pectin-degrading Enzymes: Polygalacturonase and Pectin Lyase (Keller Suberkropp)

46.  Lignin-degrading Enzymes: Phenoloxidase and Peroxidase (Björn Hendel, Robert L. Sinsabaugh & Jürgen Marxsen)

47.  Phenol Oxidation (Martin Zimmer)

48.  Proteinase Activity: Azocoll and Thin-layer Enzyme Assay (Manuel A.S. Graça & Felix Bärlocher)

Part 6. Litter Consumers

49.  Processing of Aquatic Invertebrates Colonizing Decomposing Litter (John S. Richardson)

51.  Shredder Feeding and Growth Rates (Manuel A.S. Graça & José M. González)

52.  Feeding Preferences (Cristina Canhoto, Manuel A.S. Graça & Felix Bärlocher)

53.  Energy Budget of Shredders (Manuel A.S. Graça)

54.  The Role of Shredders in Litter Dynamics at Stream Scale (José M. González & Manuel A.S. Graça)

Part 7. Litter Manipulations

55.  Manipulation of Leaf Litter Stoichiometry (Julio Arce-Funck, Vincent Felten, Michael Danger)

56.  Isotopic Labelling of Leaf-litter Nitrogen (Bernd Zeller, Severine Bienaimé & Etienne Dambrine)

57.  Decomposition and Consumption Tablets (DECOTABSs) (Gea H. van Der Lee, Ellard R. Hunting, J. Arie Vonk & Michiel H.S. Kraak)

58.  Inoculation of Leaf Litter with Aquatic Hyphomycetes (Eric Chauvet)

Part 8. Data Analyses

59.  A Primer for Statistical Analysis (Felix Bärlocher)

60.  Determining Temperature-normalized Decomposition Rates (Mark O. Gessner & Frank Peeters)

61.  Biodiversity Analysis (Felix Bärlocher)

62.  A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-associated Fungi and Bacteria (Sahadevan Seena, Sofia Duarte & Christian Wurzbacher)