A Novel Manganese Oxidising Bacterium: Characterisation and Genomic Evaluation

Abstract

The production of manganese oxide minerals is predominantly mediated by microbes, resulting in the formation of highly redox active minerals which influence the geochemical cycling of many elements; including carbon, nitrogen, sulphur and many metals. This thesis describes the characterisation and genomic evaluation of a novel manganese oxidising Burkholderiales isolate, JOSHI_001, with a focus on gaining insight into the manganese depositing behaviour and ecological significance of this bacterium. This bacterium is believed to be responsible for the formation of manganese-enriched ring structures, termed anelli, present within urban stream biofilms. The results of this research are detailed within three chapters (Chapters 3 – 5). Chapter 3 addresses Aim 1: To investigate the occurrence of JOSHI_001, and like organisms, within urban freshwater systems; describing a field study which investigated the distribution of anelli within urban streams across the Auckland region. A correlation was found between the presence of these structures within biofilms and the level of anthropogenic impact to the site’s catchment area. Chapter 4 addresses Aim 2: To characterise JOSHI_001, as a novel manganese depositing organism; describing a polyphasic characterisation of JOSHI_001, including description of phenotypic, genomic and phylogenetic characters. This characterisation indicates that JOSHI_001 represents a novel genus and species, and we propose the name Siderocapsa amnicola. Finally, Chapter 5 addresses Aim 3: To investigate the mechanism and purpose of manganese deposition by JOSHI_001, and identify candidate manganese oxidation genes; describing an evaluation of the manganese depositing behaviour of this bacterium, using growth experiments and genomic analyses. This resulted in the identification of four candidate manganese oxidase genes of the multicopper oxidase class, tentatively designated mnxG123 and mofA on the basis of homology with these genes within the manganese oxidising bacteria Pseudomonas putida GB-1, Leptothrix cholodnii SP-6 and Leptothrix discophora SS-1. Empirical analyses indicated that manganese oxidation results from the action of an exported soluble factor, which appears to require extracellular activation. An association was found between manganese deposition, exopolymer formation and the nutritional environment, although the specific details of this association require further investigation. The purpose of manganese oxidation was also investigated, indicating that the proposed role for manganese oxides in protection of JOSHI_001 from heavy metal contaminants, which are prevalent within the urban stream environment from which this bacterium was isolated, is unlikely. This research will springboard future research to provide empirical validation of the candidate manganese oxidase genes and has provided a basis for targeted experiments to establish the purpose of this behaviour in JOSHI_001 and potentially other manganese oxidising bacteria.