학위논문 (박사)-- 서울대학교 대학원 자연과학대학 생명과학부, 2017. 8. Jonathan Adams.Microorganisms are the major component of global biodiversity, and it is found in the various habitats of terrestrial ecosystems. However, their ecological roles in nature and the patterns of microbial diversity are still poorly understood. Also the dominant factors regulating soil microbial community composition and diversity variation within these ecosystems are still unknown. In this study, the extent of soil microbial diversity was investigated in both experimental and Mountain ecosystem and the way microbial communities are affected by disturbance and environmental gradients, as well as the extent to which ecological processes or other environmental factors contribute to structuring the soil microbial communities.
Firstly, I tested fungal community responses to disturbance gradients in a laboratory environment (Microcosms). Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been experimentally little studied and remained unknown about the responsiveness of soil fungal community structure to disturbance although there is a long history of the effects of disturbance on community structure in larger organisms. I subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. A soil microcosm is subjected to physical disturbance, sterilizing 90% of the soil volume each time, at a range of frequencies. The fungal community structure was analyzed using Illumina HiSeq sequencing of the ITS1 region. It was found that fungal diversity decline with the increasing disturbance frequencies, with no sign of the humpback pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance – which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.
Also, bacterial community responses to environmental gradients were tested in Mt.Norikura, Japan. Little is known about the factors affecting the relative influence of stochastic and deterministic processes on environmental gradients. The investigation on the community assembly, phylogenetic diversity and the relative role of both deterministic (niche-based) process and stochastic process may play in delimiting the bacterial phylogenetic community structure was conducted. Soil DNA from samples collected at a range of elevations was sequenced using Illumina MiSeq of the 16S rRNA gene. Mt. Norikura showed no increase in phylogenetic clustering in upper elevations, suggesting that this may not be a general pattern in elevational systems, no greater role of stochasticity towards upper elevations. However, the strength of phylogenetic clustering and the role of stochasticity was strongly related pH, with structuring and determinism being strongest at lower pH. This pattern follows that found in an earlier study of successional environments, where pH also dominates community structuring. The possibility that pH is a dominant factor in bacterial community structure, as well as in diversity, should be considered.ABSTRACT…………………………………………………………………………………...i
TABLE OF CONTENTS…………………………………………………………………....iii
ABBREVIATION……………………………………………………………………………vi
LIST OF FIGURES…………………………………………………………………………vii
LIST OF TABLES……………………………………………………………………………x
CHAPTER 1. SOIL MICROBIAL DIVERSITY AND RECENT TRENDS IN MICROBIAL ECOLOGY: AN INTRODUCTION………………………………………...1
1.1. The extent of Soil microbial diversity and its pattern in ecosystem……………….2
1.2. What makes soil microbial communities different?................................................4
1.2.1. Disturbance effects on soil microbial communities……………………4
1.2.2. Environmental gradients structuring soil microbial communities……..6
1.3. A general procedure of soil microbial diversity and community analysis………...7
1.3.1. Metagenomic approaches in Soil microbial study……………………..7
1.3.2. Microbial community analysis procedure……………………………..9
1.3.2.1. Initial processing and sequence quality control……………..9
1.3.2.2. Sequence alignment, pre-clustering, chimera removal and taxonomic classification…………………………………………...10
1.3.2.3. OTU based and phylogenetic analysis…………………….11
1.4. Objectives of this study………………………………………………………….13
CHAPTER 2. CHANGES IN SOIL FUNGAL COMMUNITY STRUCTURE WITH INCREASING DISTURBANCE FREQUENCY…………………………………………14
2.1. Introduction……………………………………………………………………..15
2.2. Materials and Methods………………………………………………………….21
2.2.1. Soil microcosm……………………………………………………….21
2.2.2. Disturbance and Growth regimen…………………………………….23
2.2.3. Autoclaving and Validation of Sterility and DNA Destruction………28
2.2.4. PCR Amplification and Sequencing of ITS1 Region…………………28
2.2.5. qPCR for Fungal ITS1 Region……………………………………….29
2.2.6. Statistical Analyses…………………………………………………..30
2.3. Results…………………………………………………………………………..31
2.3.1. Effect of Disturbance frequency on fungal abundance by qPCR…….31
2.3.2. Fungal diversity and community composition in relation to disturbance frequency…………………………………………………………………...33
2.3.3. Phylum-level pattern of fungal community in relation to disturbance frequency…………………………………………………………………...38
2.3.4. Ecological relevance of functional groups of fungal community in relation to disturbance frequency…………………………………………...39
2.4. Discussion………………………………………………………………………42
CHAPTER 3. SOIL PH RATHER THAN ELEVATION DOMINATES BACTERIAL PHYLOGENETIC COMMUNITY ASSEMBLY ON MT. NORIKURA, JAPAN………56
3.1. Introduction……………………………………………………………………..57
3.2. Materials and Methods………………………………………………………….60
3.2.1. Site description and Vegetation………………………………………60
3.2.2. Soil Sampling ………………………………………………………..67
3.2.3. DNA extraction, PCR amplification and sequencing………………...68
3.2.4. Sequencing processing and taxonomic analysis……………………...68
3.2.5. Phylogenetic analysis………………………………………………...69
3.2.6. Statistical analysis……………………………………………………72
3.3. Results…………………………………………………………………………..73
3.3.1. Bacterial community composition……………………………………73
3.3.2. Phylogenetic signal and Phylogenetic diversity……………………...78
3.4. Discussion………………………………………………………………………88
CHAPTER 4. GENERAL CONCLUSIONS………………………………………………92
REFERENCES……………………………………………………………………………...97
APPENDIX………………………………………………………………………………...115
국문초록 (Abstract in Korean)…………………………………………………………...117Docto
