Thesis
Structural and Comparative Genomics of Microvirga and Methylobacterium Rhizobial Strains
Honours, Murdoch University
2024
Abstract
The legume genus Listia includes perennial herbaceous species identified as potential pasture legumes in southern Australia. Species within Listia form highly specific nitrogen-fixing symbioses with rhizobial strains of pigmented methylobacteria and Microvirga species. The molecular basis for this symbiotic specificity has yet to be established. Previous studies have identified these methylobacteria as belonging to a separate taxon; however, they have yet to be named and described as a new species, and no finished rhizobial Microvirga genome is currently available. Therefore, the Microvirga lotononidis strain WSM3557T and six Methylobacterium strains isolated from diverse Listia species were sequenced via nanopore sequencing and assembled with Flye. Methylobacterium sp. WSM2598 and Mv. lotononidis WSM3557T assemblies were refined using existing Illumina reads and Pilon. The WSM3557T assembly indicated a potential symbiotic plasmid containing the nod, nif, fix and type 3 secretion system genes. For the Methylobacterium strains, the average nucleotide identity (ANI) and digital DNA-DNA hybridisation (dDDH) results confirmed that they belonged to a novel Methylobacterium species, with genetic diversity between strains. Whole genome sequence and 16S rRNA phylogenies indicated that Listia-nodulating Methylobacterium species formed a clade with the rhizobial Methylobacterium nodulans and non-rhizobial Methylobacterium isbiliense. The 15 essential nif genes in Azorhizobium caulinodans were present in the seven assembled strains, indicating a potential for ex-planta nitrogen fixation. A copy of the ahpCD genes, encoding alkyl hydroperoxide reductase, was present in Methylobacterium strains but not WSM3557T, and might be necessary for maintaining a microoxic nodule environment. The data obtained from this study will be used to name and describe the new Methylobacterium species and will be important for determining the molecular basis of symbiotic specificity in these Listia-symbioses.
Details
- Title
- Structural and Comparative Genomics of Microvirga and Methylobacterium Rhizobial Strains
- Authors/Creators
- Emma Holder
- Contributors
- Julie Ardley (Supervisor) - Murdoch University, School of Medical, Molecular and Forensic SciencesWayne Reeve (Supervisor) - Murdoch University, Centre for Sustainable Farming Systems
- Awarding Institution
- Murdoch University; Honours
- Identifiers
- 991005731486407891
- Murdoch Affiliation
- School of Medical, Molecular and Forensic Sciences
- Resource Type
- Thesis
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