Methods to Study Litter Decomposition: A Practical Guide

ISBN-13: 9783030305147 / Angielski / Twarda / 2020 / 604 str.

Felix Barlocher; Mark O. Gessner; Manuel A. S. Graca

Spis treści

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)

10.  Coarse Particulate Organic Matter Budgets (Jesús Pozo & Jon Molinero)

 

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)

36.  Quantitative Real-Time PCR (qPCR) to Estimate Molecular Fungal Abundance (Christiane Baschien & J. Steffen C. Carl)

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 Štursová & 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 β-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)

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)

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)

63.  A Primer for Meta-Analysis (Verónica Ferreira & Felix Bärlocher)

O autorze

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 well as 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.

Blurb

This edited volume is an extensive collection of methods for investigating plant litter dynamics in ecosystems. Particular emphasis is placed on litter decomposition in streams and rivers. The presented methods range from analyses of chemical and physical litter properties to the taxonomic and functional characterization of microbial decomposers, both fungi and bacteria, assessments of litter-consuming invertebrates, and procedures to determine litter dynamics at the stream ecosystem level. Several chapters addressing general topics of data analysis are also included. 

This second edition of the book has been greatly expanded. Its now 63 chapters cover both well-established and recently elaborated techniques, some of which have not yet been applied to decomposing litter in streams. Modern molecular techniques ranging from next-generation sequencing to proteomics receive special attention among the 20 chapters that are entirely new. Numerous methods on characterizing litter consumers have also been added to fill an evident gap of the first edition. However, the basic original concept and all of the previous chapters have been retained, although most of them have been thoroughly updated. 

Typical contributions provide step-by-step protocols that are preceded by brief reviews of the ecological significance and the principles underlying the method. Where available, short compilations of published data have been added in overview tables to provide background information on the range of results to expect. Useful hints, a discussion of potential weaknesses, and key references are provided at the end. Hands-on material useful to implement several of the presented methods (e.g. computer code, calculation sheets) is available online. 

The book is written for students embarking on studies of plant litter dynamics and for established researchers wishing to expand the scope of their methodological toolbox to study litter decomposition and the microbial decomposers and invertebrates involved in the process. The primary intended audience is aquatic ecologists, since many of the methods presented in the book focus on streams and stream organisms. However, the great majority of the protocols can be easily adapted or even directly applied to coastal and terrestrial ecosystems. Consequently, they should be of equal interest to scientists investigating plant litter dynamics in habitats such as mangroves and salt-marshes, terrestrial grasslands and forests.