Impacts of Biodegradable Polymers on Microbial Communities and Function across Diverse Ecosystems
- 주제(키워드) 생분해 , 생물정보학
- 주제(DDC) 547
- 발행기관 아주대학교 일반대학원
- 지도교수 이평천
- 발행년도 2025
- 학위수여년월 2025. 2
- 학위명 박사
- 학과 및 전공 일반대학원 분자과학기술학과
- 실제URI http://www.dcollection.net/handler/ajou/000000034581
- 본문언어 영어
- 저작권 아주대학교 논문은 저작권에 의해 보호받습니다.
초록/요약
Biodegradable polymers have emerged as promising alternatives to traditional non- biodegradable plastics for mitigating environmental pollution. These materials, designed to decompose naturally over time, offer a potential solution for the persistent issue of plastic waste accumulation in ecosystems. However, although their adoption has been increasing in various industries, there remains a significant paucity of in-depth research examining how these biodegradable polymers interact with and affect microbial communities in different environmental settings. This study aimed to address this critical knowledge gap by conducting a comprehensive investigation into the impact of biodegradable polymers on microbial populations across diverse environments. By focusing on ambient topsoil and industrial composting conditions, this study seeks to provide valuable insights into the complex interactions between these materials and the microorganisms responsible for their degradation. Initially, Antarctic Ocean seawater samples were used for validation and optimization of the microbiome analysis protocols. This study employed metagenomic analysis to investigate the microbial diversity and carotenoid biosynthesis pathways in the Antarctic Ocean, focusing on seawater samples collected at depths of 16 and 25 m near King Sejong Station. The analysis revealed diverse carotenoid-related genes, including those involved in C40 (e.g., astaxanthin, myxol, and spirilloxanthin), C30 (e.g., staphyloxanthin), and C50 (e.g., bacterioruberin) biosynthesis, with depth-specific variations in gene prevalence. This successful refinement will establish a foundation for analyzing shifts in microbial communities during polymer decomposition. The research subsequently focuses on examining the biodegradation of standard biodegradable polybutylene adipate terephthalate (normal-PBAT) and their ionic aggregates (PBAT-Zn2+), with an emphasis on polymer-microbe interactions. This study investigated the biodegradation of normal PBAT and PBAT-Zn²⁺ in soil, highlighting the significant differences in microbial and functional responses. PBAT-Zn²⁺ exhibited enhanced CO₂ generation and distinct shifts in microbial community composition, including increased abundance of taxa associated with rhizosphere activity and aromatic compound metabolism. Differential abundance analyses revealed significant functional changes, including elevated levels of polyester-degrading enzymes and aromatic compound degradation pathways in the PBAT-Zn²⁺ samples. Microbial network analyses demonstrated structural differences, with the PBAT-Zn²⁺ fostering more modular and cohesive networks. Metagenomic and meta-amplicon sequencing analyses corroborated these findings, whereas MAG analysis identified key taxa contributing to functional shifts. This study aimed to investigate how the physical and chemical properties of polymers affect microbial activity and biodegradability and to identify specific microbial taxa and functional pathways involved in these processes. Furthermore, this study seeks to explore the interconnected dynamics of monomers and their resulting polyesters to elucidate how monomeric components drive microbial changes during polymer degradation. This study examined the biodegradation of nine polyesters and their six monomers, highlighting differences in microbial and functional responses. Most polymers exhibited high biodegradability, except PL_44, with lower melting (Tm) and crystallization (Tc) temperatures, correlating with increased degradation rates. Monomers, particularly diacids and diols, demonstrate high biodegradability and influence the microbial community composition. Functional analyses revealed distinct metabolic pathways linked to monomers and polymers, with diols contributing significantly to microbial shifts during polymer degradation. Meta- shotgun sequencing identified key taxa, including Rhodococcus and Amycolatopsis, associated with polymer breakdown, and Chitinophagaceae, central to diol degradation. Lastly, this study employed a combination of metagenomic and metatranscriptomic approaches to provide a comprehensive analysis of microbial dynamics during polymer biodegradation. This study investigated the biodegradation of poly(3-hydroxypropionate) [Poly(3HP)] under industrial composting conditions, utilizing combined metagenomic and metatranscriptomic analyses to explore microbial dynamics and functional activity. While metagenomic data revealed significant microbial and functional gene changes, metatranscriptomic analysis indicated a general downregulation of gene expression during the active biodegradation phase. This dual analysis was designed to elucidate both the taxonomic composition and active functional contributions of the microbial communities under industrial composting conditions. The primary objective of this study was to enhance the understanding of microbial interactions with biodegradable polymers and inform the development of sustainable materials and waste management strategies. This comprehensive study has significantly advanced our understanding of biodegradable polymers and their interactions with microbial communities in various environments. Future research on these findings could lead to innovative solutions for addressing plastic pollution and promoting sustainable practices in materials science and environmental management.
more목차
Chapter 1. General introduction 1
1.1. Introduction 1
1.2. Biodegradation 2
1.3. Bioinformatics for environmental microorganisms 4
1.4. Aims of this study 6
Chapter 2. Validation of environmental microbiome analysis tools using Antarctic Ocean samples 9
2.1. Abstract 9
2.2. Introduction 10
2.3. Materials and methods 12
2.3.1. Sample information 12
2.3.2. DNA extraction and Illumina shotgun sequencing 12
2.3.3. Quality control and data preprocessing 12
2.3.4. Metagenomic assembly and annotation with SqueezeMeta 13
2.3.5. Statistical analysis 13
2.4. Results and discussion 15
2.4.1. Metagenomic analysis of microbial diversity in the Antarctic Ocean 15
2.4.2. Diversity of carotenoid-producing enzymes in the Antarctic Ocean uncovered through metagenomic study 17
2.4.3. C40 carotenoid biosynthetic pathways in the Antarctic Ocean as revealed by metagenomic analysis 20
2.4.4. C30 and C50 carotenoid biosynthetic pathways of Antarctic Ocean microbial communities 26
2.4.5. Discussion 29
Chapter 3. Biodegradation-induced changes in soil microbial communities: A comparative study of ionic aggregates of PBAT and 9 polyesters with their monomers 31
3.1. Abstract 31
3.2. Introduction 33
Case I: Ionic aggregates of PBAT 35
3.3. Materials and methods 35
3.3.1. Biodegradation experiments 35
3.3.2. DNA extraction and Illumina sequencing 36
3.3.3. Analysis for 16S rRNA meta-amplicon sequencing 36
3.3.4. Analysis for meta shotgun sequencing 37
3.4. Results and discussion 38
3.4.1. Biodegradation experiments 38
3.4.2. 16S meta-amplicon analysis 40
3.4.2.1. Comparison of microbial relative abundance 40
3.4.2.2. Comparison of gene abundances 45
3.4.2.3. Differential abundance analysis of MetaCyc pathway 50
3.4.2.4. Microbial network analysis 55
3.4.3. Meta-shotgun sequencing analysis 64
3.4.3.1. Microbial relative abundance 64
3.4.3.2. Comparison of gene abundances 67
3.4.3.3. Comparison of MAGs and their MetaCyc pathways 72
Case II: 9 polyesters and their monomers 77
3.5. Materials and methods 77
3.5.1. Biodegradation experiments 77
3.5.2. DNA extraction and Illumina shotgun sequencing 79
3.5.3. Analysis for 16S rRNA meta-amplicon sequencing 79
3.5.4. Analysis for meta shotgun sequencing 80
3.6. Results and discussion 81
3.6.1. Biodegradation experiments for 9 polymers 81
3.6.2. Biodegradation experiments for 6 monomers 86
3.6.3. Comparison of microbial relative abundance 88
3.6.4. Comparative analysis of microbial abundance in 16S meta-amplicon and meta-shotgun sequencing data 94
3.6.5. Comparative analysis of KEGG Orthology (KO) abundance in 16S meta-amplicon and meta-shotgun sequencing data 100
3.6.6. MetaCyc pathway abundance comparison in 16S meta-amplicon sequencing data 110
3.6.7. Cross-condition KO effect size correlation analysis 116
3.6.8. MAG Analysis 120
Chapter 4. Integrated metagenomic and metatranscriptomic insights into Poly(3HP) biodegradation under composting conditions 123
4.1. Abstract 123
4.2. Introduction 125
4.3. Materials and methods 127
4.3.1. Biodegradation experiments 127
4.3.2. Nucleic acid extraction and Illumina sequencing 127
4.3.3. Examination of meta-shotgun and transcriptome sequencing data 128
4.4. Results and discussion 129
4.4.1. Biodegradability of poly(3HP) in industrial compost conditions 129
4.4.2. Comparison of microbial relative abundance between metagenomic and metatranscriptomic sequencing 131
4.4.3. Integrated metagenomic and metatranscriptomic insights into microbial dynamics and functional pathways during biodegradation 134
5. Conclusion 141
6. References 144
ABSTRACT IN KOREAN 159
