System-level study of metabolisms of a new species, Gordonia ajoucoccus
System-level study of metabolisms of a new species, Gordonia ajoucoccus
- 주제(키워드) Gordonia
- 발행기관 아주대학교
- 지도교수 이평천
- 발행년도 2016
- 학위수여년월 2016. 2
- 학위명 박사
- 학과 및 전공 일반대학원 분자과학기술학과
- 실제URI http://www.dcollection.net/handler/ajou/000000021507
- 본문언어 영어
- 저작권 아주대학교 논문은 저작권에 의해 보호받습니다.
초록/요약
Biodegradation is a viable bioremediation technology for various pollutants. It has long been known that microorganisms degrade environmental pollutants, such as carbzole, crude oil, fluorine and pyrene, in various matrices and environments. Biodegradation is a broad field and involves the use of a wide range of microorganisms to break chemical bonds. The genus Gordonia has attracted much interest in recent years due to their ability to degrading xenobiotics, environmental pollutants or slowly biodegradable natural polymers as well as to transform or synthesize possibly useful compounds. However, there has been little research so far on the ability of microorganisms in the genus Gordonia to degrade and assimilate n-alkanes. Taxonomic studies were performed on a novel carotenoid-producing strain, designated A2T, isolated from crude oil-contaminated soil. The phylogenetic tree of 16S rRNA gene sequence analysis showed that the strain A2T was closely related to Gordonia amicalis KCTC 9940T. DNA-DNA relatedness of strain A2T with respect to its closest phylogenetic neighbors was 65.7% for G. amicalis NBRC 9940T. Based on the phylogenetic, chemotaxonomic, and phenotypic data, strain A2T is concluded to represent a novel species of the genus Gordonia, for which the name Gordonia ajoucoccus sp. nov. is proposed. The type strain is A2T (=KCTC 11900BPT = CECT 8382T). The caronteoid of γ-carotene and keto-γ-carotene is synthezed from G. ajoucoccus A2T. G. ajoucoccus A2T is also capable of assimilating n-alkanes with a broad range of chain lengths (C6, C8–C25). Batch culture containing 1% (v/v) hexadecane or 1% (v/v) commercial diesel yielded 25 mg/L and 2.6 mg/L of carotenoids from G. ajoucoccus A2T in a bioreactor, respectively. Analysis of hexadecane and hexane degradation metabolites using gas chromatography/mass spectrometry (GC/MS) proposed that G. ajoucoccus A2T may possess a primary alcohol terminal oxidation pathway that allows it to utilize n-alkanes and hexane as carbon sources. Metabolites of the metabolic response of G. ajoucoccus A2T grown on various carbon sources were analyzed using GC/MS. Metabolites such as amino acids, sugars, and organic acids could be identified. Thirty-four metabolites were detected in five replicate samples, and score plots of PLS-DA were generated to comparatively evaluate the effects of consumption of various carbon sources on strain A2T. We reported the draft sequence of strain A2T. It has a 5,029,502-base-pair circular chromosome encoding 4,666 genes, and the genome consists of genes that are involved in denitrification, the alkane degradation pathway, the β-oxidation pathway, the butanol biosynthesis pathway, benzoate degradation, molecule transportation, wax ester synthesis, and other processes. In our experiments, phylogenetic and phenotypic analyses purposed that this strain A2T represents a novel species with various pathways. In this study, we have identified novel pathways for the degradation of n-alkane and production of secondary metabolites in G. ajoucoccus A2T.
more목차
Chapter 1. General Introduction 1
1.1 Bioremediation of crude oil-contaminated soil using bacteria 2
1.2 Metabolomics of environmental bacteria 5
1.3 Next generation sequencing of environmental bacteria 8
1.4 Aims of this study 10
1.5 References 12
Chapter 2. Gordonia ajoucoccus sp. nov., an carotenoid-producing species isolated from crude oil-contaminated soil 19
2.1 Abstract 20
2.2 Introduction 21
2.3 Materials and Methods. 22
2.4 Results and Discussion. 37
2.5 References 39
Chapter 3. Carotenoid production from n-alkanes with a broad range of chain lengths by the novel species Gordonia ajoucoccus 45
3.1 Abstract 46
3.2 Introduction. 47
3.3 Materials and Methods 50
3.4 Results and Discussion.. 56
3.5 References 72
Chapter 4. Metabolomics for systems biology in Gordonia ajoucoccus 79
4.1 Abstract. 80
4.2 Introduction 81
4.3 Materials and Methods. 84
4.4 Results and Discussion. 88
4.5 References. 106
Chapter 5. Draft genome sequence of Gordonia ajoucoccus from oil-contamined soil and analysis of genome revealed putative mechanisms 109
5.1 Abstract 110
5.2 Introduction 111
5.3 Materials and Methods. 114
5.4 Results and Discussion. 116
5.5 References 125
Chapter 6. Conclusion 128
Abstract in Korea. 130
Acknolwledgements 132
