声明
Appendix List of Abbreviations
1 Introduction
2Review of literature
2.1Antibiotics and antibiotic resistance
2.1.1Antibiotic and its historical perspective
2.1.2Importance of antibiotics
2.1.3Emergence of Antibiotic Resistance
2.1.4Mechanismsof antibiotic resistance
2.1.5Co-selection of antibiotic resistance genes and metals
2.2Heavy metals resistant Cupriavidus metallidurans BS1
2.3Aims and Objectives
3Co-Selection of Antibiotic Resistance Genes, and Mobile Genetic Elements in the presence of Heavy Metals
3.1Material and method
3.1.1Sampling sites and sample collection
3.2Method development and validation for antibiotics analysis
3.2.1Chemicals and Reagents
3.2.2 Equipment
3.2.3LC–MS/MS conditions
3.2.4 Samples
3.2.5Sample spiking
3.3Method optimization
3.3.1 Extraction
3.3.2 Cleanup
3.3.3Simultaneous extraction and clean-up method
3.3.4Method performance and validation
3.4Metal analysis
3.4.1Sample preparation
3.4.2Digestion method
3.4.3ICP-MS measurements
3.5Bacterial Community Analysis
3.5.1DNA extraction
3.5.2Sequencing and16SrRNA community analysis
3.6Antibiotic resistance genes and cluster analysis
3.6.1High-throughput qPCR
3.6.2ARGs analysis and correlation analysis
3.6.3Procrustes analysis
3.6.4Redundancy analysis (RDA)and Variance partitioning analysis (VPA)
3.7 Results
3.7.1Method optimization
3.7.2Method Validation
3.7.3 Metals Analysis
3.7.4Cluster analysis of ARGs and MGEs
3.8 Discussion
3.8.1Optimization of the Antibiotic extraction method
3.8.2Heavy Metal Analysis
3.8.3Co-occurrence analysis of resistome,microbiome, metals and antibiotics
4Comparative insights into the complete genome sequence
4.1Materials and Methods
4.1.1Bacterial isolation
4.1.2Minimal inhibitory concentration (MIC)
4.1.3Growth conditions, genomic DNA preparation and molecular identification
4.1.4 Phylogenetic analysis
4.1.5Genome annotation and characterization of Cupriavidus metallidurans BS1
4.1.6Nucleotide Sequence Accession Number
4.2Results and Discussion
4.2.1Morphology, Growth and physiology
4.2.2Comparative genome annotation and properties
4.2.3Comparative genome plasticity
4.2.4Determinants of metal homeostasis and genomic resistance superclusters
4.2.5Comparative overview of the encoded heavy metal resistance systems on the genomes of C.metallidurans BS1 and CH34
4.2.6P-type ATPases
4.2.7CDF proteins
4.2.8The RND pumps
4.2.9Gold-copper detoxification systems of C. metallidurans BS1 and CH34
4.2.10The Czc–the main resistance determinants for zinc, cobalt, and cadmium
4.2.11The Cnr,Chr and Ncc–the main resistance determinants for cobalt, nickel and chromium
4.2.12Mercury and arsenic resistance determinants
4.2.13Megaplasmid pBS1 in BS1
5 Conclusion
参考文献
Supporting Information
Published papers
致谢
福建农林大学;
