Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective
학위논문 (박사)-- 서울대학교 대학원 : 협동과정 바이오엔지니어링전공, 2015. 2. JungHoon,Lee. The effects of human disturbance are increasing rapidly and can be observed in ecosystems in terms of effects on larger organisms. This thesis analyzes three case studies to explore how human disturbances affect the environment at the m...
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서울대학교 대학원
2015
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Online Access: | http://hdl.handle.net/10371/119883 |
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ftseoulnuniv:oai:s-space.snu.ac.kr:10371/119883 |
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Seoul National University: S-Space |
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ftseoulnuniv |
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English |
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carbon nanotubes environment human disturbance logging metagenetic microbial community ocean acidification 660 |
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carbon nanotubes environment human disturbance logging metagenetic microbial community ocean acidification 660 DorsafKerfahi Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective |
topic_facet |
carbon nanotubes environment human disturbance logging metagenetic microbial community ocean acidification 660 |
description |
학위논문 (박사)-- 서울대학교 대학원 : 협동과정 바이오엔지니어링전공, 2015. 2. JungHoon,Lee. The effects of human disturbance are increasing rapidly and can be observed in ecosystems in terms of effects on larger organisms. This thesis analyzes three case studies to explore how human disturbances affect the environment at the microbial scale. The first study examined how land use change affects the structure and diversity of fungal communities in Malaysian tropical forests in Borneo. It was clear that α and β-diversity, as well as community composition differed across different logging histories (unlogged, once-logged and twice-logged), and oil palm plantations. The second study examined how increasing atmospheric CO2 on the ocean impacts the sediment bacterial communities off Vulcano, Italy in the Mediterranean. Bacterial community composition changed with increasing CO2, and bacterial diversity increased with higher CO2. The globally increasing ocean CO2 can be associated with shifts in sediment bacterial community composition, but most of these organisms are resilient. The third study compared the effect of both raw and acid treated (functionalized) multi-walled carbon nanotubes (MWCNTs) on soil bacterial communities, applying different concentrations of MWCNTs (0 µg/g, 50 µg/g, 500 µg/g and 5000 µg/g) to a soil microcosm system. Bacterial diversity was not affected by either type of MWCNT. However, overall soil bacterial community composition for functionalized carbon nanotubes at high concentrations were affected. This last study suggests that fMWCNTs may alter microbial community composition on the timescale of at least weeks to months. In contrast, it appears that raw MWCNTs do not affect soil microbial community composition. These different case studies are examples of the ways in which metagenetic studies can help recognize the impact of human disturbance on the environment, ultimately enabling us to allow effective management decisions in order to protect the environment. ABSTRACT i TABLE OF CONTENTS ii LIST OF FIGURES vi LIST OF TABLES ix GENERAL INTRODUCTION 1 OBJECTIVES OF THE STUDY 3 CHAPTER 1: WHAT IS DISTURBANCE? 4 1.1 Introduction 4 1.2 Defining disturbance 4 1.3 Types of disturbances 5 1.4 Why do we have to study disturbance? 5 1.5 Agents of disturbance 6 1.6 Conclusion 6 CHAPTER 2: THE METAGENOMICS APPROACH 7 2.1 The basic concepts of metagenomics 7 2.2 Historical overview of metagenomics 8 2.3 The need for metagenomics in studying microbial communities 9 2.4 Soil metagenomics 9 2.5 Next-generation DNA sequencing methods 10 2.5.1 454-Pyroseqencing 11 2.5.2 Illumina (Solexa) 12 2.5.3 454-pyroseqencing vs Illumina 13 2.6 Targeted genes 14 2.6.1 16S rRNA 14 2.6.2 ITS region of the fungal ribosomal repeat 15 CHAPTER 3: THE IMPACT OF LOGGING AND FOREST CONVERSION TO OIL PALM ON FUNGAL COMMUNITIES IN BORNEO, MALAYSIA 17 3.1 Introduction 17 3.2 Materials and Methods 19 3.2.1 Study area 19 3.2.2 Soil sampling and DNA extraction 20 3.2.3 PCR amplification and pyrosequencing 21 3.2.4 Sequence processing 21 3.2.5 Soil analyses 22 3.2.6 Statistical analysis 22 3.3 Results 23 3.4 Discussion 30 3.5 Conclusion 32 CHAPTER 4: RESPONSES OF BENTHIC BACTERIAL COMMUNITIES TO NATURAL CO2 GRADIENT IN THE MEDITERRANEAN SEA OFF VULCANO, ITALY 34 4.1 Introduction 34 4.2 Importance of marine microbes 35 4.3 Key ecological services provided by marine microbes 36 4.4 Why is ocean acidification an urgent problem? 37 4.5 Benthic biogeochemistry 38 4.6 Materials and methods 39 4.6.1 Study site 39 4.6.2 Marine sediment sampling and DNA extraction 42 4.6.3 PCR amplification and pyrosequencing 42 4.6.4 Analysis of pyrosequencing data 43 4.6.5 Statistical processing and analysis of results 43 4.7 Results 44 4.7.1 Effect of seawater pCO2 on bacterial community composition 46 4.7.2 Effect on bacterial community diversity 47 4.7.3 Effect of pCO2 on relative abundance of dominant taxa 48 4.7.4 Relationship between seawater pCO2 and sediment properties 50 4.8 Discussion 51 4.9 Conclusion 55 CHAPTER 5: EFFECTS OF MULTI WALLED CARBON NANOTUBES ON SOIL BACTERIAL COMMUNITIES 56 5.1 Introduction 56 5.2 Structure of carbon nanotubes 59 5.3 Properties of carbon nanotubes 61 5.4 Applications of carbon nanotubes 62 5.4.1 Peptide delivery by carbon nanotubes 62 5.4.2 Cellular uptake of carbon nanotubes 62 5.4.3 Nucleic acid delivery by carbon nanotubes 65 5.4.4 Drug delivery with carbon nanotubes 66 5.5 Materials and methods 66 5.5.1 Soil sampling 66 5.5.2 Preparation and characterization of MWCNTs 67 5.5.3 Characterization of MWCNTs 68 5.5.4 Soil incubation 69 5.5.5 DNA extraction and sequencing 69 5.5.6 Quantitative PCR analysis 70 5.5.7 Data analysis 70 5.5.8 Statistical analysis 71 5.6 Results 71 5.6.1 MWCNTs characterization 72 5.6.2 Effect of MWCNTs on bacterial community diversity 74 5.6.3 Effect of MWCNTs on bacterial community composition 74 5.6.4 Effect of MWCNTs on bacterial community abundance 78 5.7 Discussion 83 5.8 Conclusion 85 GENERAL CONCLUSIONS 86 References 89 APPENDIX 116 Doctor |
author2 |
JungHoon,Lee 공과대학 협동과정 바이오엔지니어링전공 |
format |
Thesis |
author |
DorsafKerfahi |
author_facet |
DorsafKerfahi |
author_sort |
DorsafKerfahi |
title |
Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective |
title_short |
Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective |
title_full |
Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective |
title_fullStr |
Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective |
title_full_unstemmed |
Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective |
title_sort |
effects of human disturbance on the environment: a microbial ecology perspective |
publisher |
서울대학교 대학원 |
publishDate |
2015 |
url |
http://hdl.handle.net/10371/119883 |
genre |
Ocean acidification |
genre_facet |
Ocean acidification |
op_relation |
000000024992 http://hdl.handle.net/10371/119883 |
_version_ |
1766159570913198080 |
spelling |
ftseoulnuniv:oai:s-space.snu.ac.kr:10371/119883 2023-05-15T17:52:12+02:00 Effects of Human Disturbance on the Environment: A Microbial Ecology Perspective 미생물 생태학적인 시각으로 바라본 인간에 의한 교란이 환경에 미치는 영향 DorsafKerfahi JungHoon,Lee 공과대학 협동과정 바이오엔지니어링전공 2015-02 application/pdf 2791938 bytes http://hdl.handle.net/10371/119883 en eng 서울대학교 대학원 000000024992 http://hdl.handle.net/10371/119883 carbon nanotubes environment human disturbance logging metagenetic microbial community ocean acidification 660 Thesis 2015 ftseoulnuniv 2019-11-15T01:24:09Z 학위논문 (박사)-- 서울대학교 대학원 : 협동과정 바이오엔지니어링전공, 2015. 2. JungHoon,Lee. The effects of human disturbance are increasing rapidly and can be observed in ecosystems in terms of effects on larger organisms. This thesis analyzes three case studies to explore how human disturbances affect the environment at the microbial scale. The first study examined how land use change affects the structure and diversity of fungal communities in Malaysian tropical forests in Borneo. It was clear that α and β-diversity, as well as community composition differed across different logging histories (unlogged, once-logged and twice-logged), and oil palm plantations. The second study examined how increasing atmospheric CO2 on the ocean impacts the sediment bacterial communities off Vulcano, Italy in the Mediterranean. Bacterial community composition changed with increasing CO2, and bacterial diversity increased with higher CO2. The globally increasing ocean CO2 can be associated with shifts in sediment bacterial community composition, but most of these organisms are resilient. The third study compared the effect of both raw and acid treated (functionalized) multi-walled carbon nanotubes (MWCNTs) on soil bacterial communities, applying different concentrations of MWCNTs (0 µg/g, 50 µg/g, 500 µg/g and 5000 µg/g) to a soil microcosm system. Bacterial diversity was not affected by either type of MWCNT. However, overall soil bacterial community composition for functionalized carbon nanotubes at high concentrations were affected. This last study suggests that fMWCNTs may alter microbial community composition on the timescale of at least weeks to months. In contrast, it appears that raw MWCNTs do not affect soil microbial community composition. These different case studies are examples of the ways in which metagenetic studies can help recognize the impact of human disturbance on the environment, ultimately enabling us to allow effective management decisions in order to protect the environment. ABSTRACT i TABLE OF CONTENTS ii LIST OF FIGURES vi LIST OF TABLES ix GENERAL INTRODUCTION 1 OBJECTIVES OF THE STUDY 3 CHAPTER 1: WHAT IS DISTURBANCE? 4 1.1 Introduction 4 1.2 Defining disturbance 4 1.3 Types of disturbances 5 1.4 Why do we have to study disturbance? 5 1.5 Agents of disturbance 6 1.6 Conclusion 6 CHAPTER 2: THE METAGENOMICS APPROACH 7 2.1 The basic concepts of metagenomics 7 2.2 Historical overview of metagenomics 8 2.3 The need for metagenomics in studying microbial communities 9 2.4 Soil metagenomics 9 2.5 Next-generation DNA sequencing methods 10 2.5.1 454-Pyroseqencing 11 2.5.2 Illumina (Solexa) 12 2.5.3 454-pyroseqencing vs Illumina 13 2.6 Targeted genes 14 2.6.1 16S rRNA 14 2.6.2 ITS region of the fungal ribosomal repeat 15 CHAPTER 3: THE IMPACT OF LOGGING AND FOREST CONVERSION TO OIL PALM ON FUNGAL COMMUNITIES IN BORNEO, MALAYSIA 17 3.1 Introduction 17 3.2 Materials and Methods 19 3.2.1 Study area 19 3.2.2 Soil sampling and DNA extraction 20 3.2.3 PCR amplification and pyrosequencing 21 3.2.4 Sequence processing 21 3.2.5 Soil analyses 22 3.2.6 Statistical analysis 22 3.3 Results 23 3.4 Discussion 30 3.5 Conclusion 32 CHAPTER 4: RESPONSES OF BENTHIC BACTERIAL COMMUNITIES TO NATURAL CO2 GRADIENT IN THE MEDITERRANEAN SEA OFF VULCANO, ITALY 34 4.1 Introduction 34 4.2 Importance of marine microbes 35 4.3 Key ecological services provided by marine microbes 36 4.4 Why is ocean acidification an urgent problem? 37 4.5 Benthic biogeochemistry 38 4.6 Materials and methods 39 4.6.1 Study site 39 4.6.2 Marine sediment sampling and DNA extraction 42 4.6.3 PCR amplification and pyrosequencing 42 4.6.4 Analysis of pyrosequencing data 43 4.6.5 Statistical processing and analysis of results 43 4.7 Results 44 4.7.1 Effect of seawater pCO2 on bacterial community composition 46 4.7.2 Effect on bacterial community diversity 47 4.7.3 Effect of pCO2 on relative abundance of dominant taxa 48 4.7.4 Relationship between seawater pCO2 and sediment properties 50 4.8 Discussion 51 4.9 Conclusion 55 CHAPTER 5: EFFECTS OF MULTI WALLED CARBON NANOTUBES ON SOIL BACTERIAL COMMUNITIES 56 5.1 Introduction 56 5.2 Structure of carbon nanotubes 59 5.3 Properties of carbon nanotubes 61 5.4 Applications of carbon nanotubes 62 5.4.1 Peptide delivery by carbon nanotubes 62 5.4.2 Cellular uptake of carbon nanotubes 62 5.4.3 Nucleic acid delivery by carbon nanotubes 65 5.4.4 Drug delivery with carbon nanotubes 66 5.5 Materials and methods 66 5.5.1 Soil sampling 66 5.5.2 Preparation and characterization of MWCNTs 67 5.5.3 Characterization of MWCNTs 68 5.5.4 Soil incubation 69 5.5.5 DNA extraction and sequencing 69 5.5.6 Quantitative PCR analysis 70 5.5.7 Data analysis 70 5.5.8 Statistical analysis 71 5.6 Results 71 5.6.1 MWCNTs characterization 72 5.6.2 Effect of MWCNTs on bacterial community diversity 74 5.6.3 Effect of MWCNTs on bacterial community composition 74 5.6.4 Effect of MWCNTs on bacterial community abundance 78 5.7 Discussion 83 5.8 Conclusion 85 GENERAL CONCLUSIONS 86 References 89 APPENDIX 116 Doctor Thesis Ocean acidification Seoul National University: S-Space |