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Impact of Rain Forest Transformation on Roots and Functional Diversity

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Impact of Rain Forest Transformation on Roots and Functional Diversity of Root-Associated Fungal Communities Dissertation zur Erlangung des mathematisch-naturwissenschaftlichen Doktorgrades "Doctor rerum naturalium" der Georg-August-Universit¨atG¨ottingen im Promotionsprogramm "Grundprogramm Biologie" der Georg-August University School of Science (GAUSS) vorgelegt von: Josephine Sahner aus Berlin G¨ottingen,2016 Betreuungsausschuss Prof. Dr. Andrea Polle, Department of Forest Botany and Tree Physiology, B¨usgen- Institute Prof. Dr. Rolf Daniel, Department of Genomic and Applied Microbiology Mitglieder der Pr¨ufungskommission Referentin: Prof. Dr. Andrea Polle, Department of Forest Botany and Tree Physiology, B¨usgen-Institute Korreferent: Prof. Dr. Rolf Daniel, Department of Genomic and Applied Microbiology Weitere Mitglieder der Pr¨ufungskommission: Prof. Dr. Holger Kreft, Biodiversity, Macroecology & Conservation Biogeography Group, Faculty of Forest Sciences and Forest Ecology Prof. Dr. Edzo Veldkamp, Soil Science of Tropical and Subtropical Exosystems, B¨usgen- Institute Prof. Dr. Thomas Friedl, Experimental Phycology and Culture Collection of Algae at the University of G¨ottingen PD Dirk Gansert, Centre of biodiversity and sustainable land use, Section: Biodiversity, ecology and nature conservation Tag der m¨undlichenPr¨ufung:13.12.2016 placeholder Table of Contents List of Figures ix List of Tables xi List of Abbreviations xiii Summary 1 1 General Introduction 6 1.1 Anthropogenic Land Use { a Driver for Global Change . 7 1.2 Deforestation in The Tropics . 7 1.3 Rubber Trees and Oil Palms { Main Actors for Land Use Changes in Indonesia . 8 1.4 The Impact of Land Use Changes on Plant Diversity . 10 1.5 Plants and their Associated Microorganisms . 11 1.6 Plant Root-Associated Fungal Communities . 12 1.6.1 Mycorrhizal Fungi . 13 1.6.2 Plant Pathogenic Fungi . 14 1.6.3 Saprotrophic Fungi . 14 1.7 Metagenomics and Functional Trait-Based Approaches to Investigate Hyper- divers Communities . 15 1.8 Scope of this Thesis . 15 1.9 References . 17 2 Degradation of Root Community Traits as Indicator for Transformation of Tropical Lowland Rain Forests into Oil Palm an Rubber Plantations 27 2.1 Introduction . 27 2.2 Materials and Methods . 29 2.2.1 Site Description . 29 2.2.2 Sampling and Export Permission . 29 2.2.3 Sampling Design . 31 2.2.4 Sample Preparation . 32 2.2.5 Analysis of Root Vitality and Ectomycorrhizal Colonization . 33 2.2.6 Arbuscular Mycorrhizal Colonization . 33 iv TABLE OF CONTENTS 2.2.7 Determination of Arbuscular Mycorrhizal Spore Abundance . 34 2.2.8 Element Analysis in Plant and Soil fractions . 35 2.2.9 Determination of Soil pH . 36 2.2.10 Maps of the Sampling Site . 36 2.2.11 Data Analysis . 36 2.2.12 Data Deposition and Availability . 37 2.3 Results . 37 2.3.1 Root Community-Weighed Traits are Massively Affected by the Land Use System . 37 2.3.2 Root Community-Weighed Traits Indicate Transformation Intensity . 38 2.3.3 Transformation Intensity is Linked with Ecosystem Properties . 42 2.4 Discussion . 46 2.4.1 Root Community-Weighed Traits and Soil Properties Vary with Forest Transformation . 46 2.4.2 Degradation of Root Health is Related to Accumulation of Plant Toxic Elements . 48 2.5 Acknowledgments . 50 2.6 Author Contributions . 50 2.7 References . 51 3 The Impact on Roots and Functional Diversity of Root-Associated Fungal Communities 57 3.1 Introduction . 58 3.2 Material and Methods . 61 3.2.1 Sites . 61 3.2.2 Sampling . 62 3.2.3 Sampling and Export Permission . 63 3.2.4 Calculation of Land Use Intensity Index . 65 3.2.5 DNA Extraction from Root Communities . 65 3.2.6 Amplicon Library Preparation for Illumina Sequencing . 66 3.2.7 Sequencing Processing . 68 3.2.8 Statistical Analysis . 69 3.3 Results . 72 v TABLE OF CONTENTS 3.3.1 Diversity and Composition of Root-Associated Fungal Communities in Four Different Land Use Systems . 72 3.3.2 Taxonomic Composition of Root-Associated Fungal Communities . 79 3.3.3 Land Use Intensity of the Investigated Core Plots . 81 3.3.4 Dissimilarities of Root-Associated Fungal Communities Referring to Land Use . 83 3.3.5 Assignment of Root-Associated Fungal OTUs to Guilds and Functional Groups . 85 3.3.6 Contribution of Specific Fungal Genera Assigned to an Ecological Guild to Dissimilarities Among Root-associated Fungal Communities From Different Land Use Systems . 86 3.3.7 Shifts Among Functional Groups Referring to Different Land Use Systems 90 3.3.8 Dissimilarities Within the Communities of Different Functional Groups . 93 3.4 Discussion . 95 3.4.1 Research on Fungal Diversity Conducted in Tropical Region . 95 3.4.2 Differences of Fungal OTU Richness Across Land Use Systems . 96 3.4.3 Different Patterns in OTU Richness of Root-Associated Fungal Com- munities in Land Use Systems of the Two Landscapes . 97 3.4.4 Root-Associated Fungal Community Composition was Affected by Land Use Change . 98 3.4.5 Ecological Fungal Guilds: Abundances in and Shift Between Land Use Systems . 99 3.5 References . 102 4 Comparisons of Illumina Sequencing and 454 Pyrosequencing on Fungal Community Samples 110 4.1 Introduction . 111 4.2 Materials and Methods . 116 4.2.1 Study Sites and Sampling . 116 4.2.2 DNA Extraction . 117 4.2.3 Primer Choice for 454 Pyrosequencing and Illumina MiSeq Sequencing 117 4.2.4 Amplicon Library Preparation for 454 Pyrosequencing . 118 4.2.5 Amplicon Library Preparation for Illumina MiSeq Sequencing . 120 vi TABLE OF CONTENTS 4.2.6 Sequence Processing . 120 4.2.7 Data Analyses . 121 4.3 Results . 123 4.3.1 Higher OTU Richness and Sequence Richness of Root-Associated Fun- gal Communities Analyzed by Illumina Sequencing . 123 4.3.2 Alpha and Beta-Diversity of Root-Associated Fungal Communities are not Influenced by the Applied NGS Technique and Related Differential Barcoding of Fungal DNA . 129 4.3.3 Taxonomic Composition of Root-Associated Fungal Communities were Similar Between Root Community Samples Analyzed by Illumina Se- quencing and 454 Pyrosequencing . 132 4.3.4 The Applied NGS Technique had no Influence on the Relative Abun- dance of Selected Fungal Orders and Genera . 135 4.4 Discussion . 138 4.4.1 Effect of Applied NGS Technique and Related Sequenced Fungal Bar- code on Obtained Results on Fungal OTU and Sequence Richness . 138 4.4.2 Effects of the Applied NGS Techniques and Related Differing Sequenced Fungal Barcode Regions on Alpha- and Beta-Diversity . 139 4.4.3 The Detection of the Taxonomic Composition of Root-Associated Fun- gal Communities is Affected by the Applied NGS Techniques and Dif- ferent DNA Barcode Regions . 140 4.4.4 Taxonomic Overlap and Distinctness of Root-Associated Fungal Com- munities Investigated by Two Different NGS Techniques . 141 4.4.5 Validation of Data on Relative Abundances of Fungal OTUs Belonging to Selected Fungal Genera with a Proven Ecological Function . 142 4.5 References . 143 5 Synthesis 148 5.1 The Broader Frame of this Thesis . 149 5.2 Relationship Between Root Community Traits, Fungal OTU Richness and Eco- logical Functions . 150 5.3 Conclusion and Outlook . 155 5.4 References . 156 vii TABLE OF CONTENTS 6 Supplements xiv Declaration of the Authors Own Contributions xxxiv Acknowledgments xxxv Curriculum Vitae xxxvii Eidestattliche Erkl¨arung xxxviii viii List of Figures 1.2.1 Changes in Land Coverage with Forest and Deforestation in Sumatra. 8 1.3.1 Extensive and Intensive Rubber Cultivation in Sumatra . 9 1.3.2 Oil Palm Cultivation in Sumatra . 10 1.5.1 Plants and their Associated Microorganisms . 12 2.2.1 Maps of the Province Jambi (A) with the Landscapes Bukit12 (B) and Harapan (C) on Sumatra (Indonesia) . 30 2.3.1 Chemical Composition of Roots in Different Land Use Systems . 40 2.3.2 Performance Parameters of Roots in Different Land Use Systems . 41 2.3.3 Principle Component Analysis of Root Community-Weighed Traits . 42 2.3.4 Non-Metric Multidimensional Scaling (NMDS) of Root Community-Weighed Traits . 44 3.2.1 Maps of the Province of Jambi (A) with the Bukit12 (B) and Harapan (C) landscapes on Sumatra (Indonesia) . 62 3.2.2 Setup for Freeze Drying and Storage of Fine Root Material . 64 3.3.1 Richness of Rarified Fungal Sequences and OTUs on Land Use Landscape Level . 75 3.3.2 Rarefaction Curve on Core Plot Level Rarified to 12.789 Sequences in the Two Different Landscapes . 76 3.3.3 Fungal OTU Richness of Samples Rarified to 12.789 Sequences . 77 3.3.4 Venn Diagram of Shared and Unique Shared Fungal OTUs Among the Four Different Land Use Systems . 78 3.3.5 Relative Abundances of Fungal Phyla (A) and Orders (B) in Four Different Land Use Systems . 80 3.3.6 Land Use Intensity of the Four Investigated Different Land Use Systems . 83 3.3.7 Non-Metric Multidimensional Scaling (NMDS) of Fungal OTU Communities Based on Bray Curtis Distance Matric . 84 3.3.8 Relative Abundances of Fungal Genera Assigned to Ecological Guilds in Four Different Land Use Systems . 87 3.3.9 Contribution of Fungal Genera to the Dissimilarity of Whole Fungal Com- munities in the Four Different Land Use Systems . ..
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    Chen et al. BMC Plant Biol (2021) 21:389 https://doi.org/10.1186/s12870-021-03125-z RESEARCH Open Access Transcriptomics of diferent tissues of blueberry and diversity analysis of rhizosphere fungi under cadmium stress Shaopeng Chen1*, QianQian Zhuang1, XiaoLei Chu2, ZhiXin Ju1, Tao Dong1 and Yuan Ma1 Abstract Blueberry (Vaccinium ssp.) is a perennial shrub belonging to the family Ericaceae, which is highly tolerant of acid soils and heavy metal pollution. In the present study, blueberry was subjected to cadmium (Cd) stress in simulated pot culture. The transcriptomics and rhizosphere fungal diversity of blueberry were analyzed, and the iron (Fe), manga- nese (Mn), copper (Cu), zinc (Zn) and cadmium (Cd) content of blueberry tissues, soil and DGT was determined. A correlation analysis was also performed. A total of 84 374 annotated genes were identifed in the root, stem, leaf and fruit tissue of blueberry, of which 3370 were DEGs, and in stem tissue, of which 2521 were DEGs. The annotation data showed that these DEGs were mainly concentrated in a series of metabolic pathways related to signal transduction, defense and the plant–pathogen response. Blueberry transferred excess Cd from the root to the stem for storage, and the highest levels of Cd were found in stem tissue, consistent with the results of transcriptome analysis, while the lowest Cd concentration occurred in the fruit, Cd also inhibited the absorption of other metal elements by blueberry. A series of genes related to Cd regulation were screened by analyzing the correlation between heavy metal content and transcriptome results. The roots of blueberry rely on mycorrhiza to absorb nutrients from the soil.
  • Fungal Allergy and Pathogenicity 20130415 112934.Pdf

    Fungal Allergy and Pathogenicity 20130415 112934.Pdf

    Fungal Allergy and Pathogenicity Chemical Immunology Vol. 81 Series Editors Luciano Adorini, Milan Ken-ichi Arai, Tokyo Claudia Berek, Berlin Anne-Marie Schmitt-Verhulst, Marseille Basel · Freiburg · Paris · London · New York · New Delhi · Bangkok · Singapore · Tokyo · Sydney Fungal Allergy and Pathogenicity Volume Editors Michael Breitenbach, Salzburg Reto Crameri, Davos Samuel B. Lehrer, New Orleans, La. 48 figures, 11 in color and 22 tables, 2002 Basel · Freiburg · Paris · London · New York · New Delhi · Bangkok · Singapore · Tokyo · Sydney Chemical Immunology Formerly published as ‘Progress in Allergy’ (Founded 1939) Edited by Paul Kallos 1939–1988, Byron H. Waksman 1962–2002 Michael Breitenbach Professor, Department of Genetics and General Biology, University of Salzburg, Salzburg Reto Crameri Professor, Swiss Institute of Allergy and Asthma Research (SIAF), Davos Samuel B. Lehrer Professor, Clinical Immunology and Allergy, Tulane University School of Medicine, New Orleans, LA Bibliographic Indices. This publication is listed in bibliographic services, including Current Contents® and Index Medicus. Drug Dosage. The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any change in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug. All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means electronic or mechanical, including photocopying, recording, microcopy- ing, or by any information storage and retrieval system, without permission in writing from the publisher.