title: A study of iron-oxidising bacteria, their habitats and their associated biogenic iron ochre, sampled from the Greater Glasgow area
Creators: name: Drummond, Adam
Publisher: name: University of Glasgow
Year: 2023

description: Leptothrix ochracea is a species of iron-oxidising bacterium that is frequently found in ferrous iron rich waters throughout the world where it contributes to the production of biogenic iron ochre. When viewed microscopically, biogenic iron ochre produced by L.ochracea is found to comprise hollow microtubular filaments. The ability to produce iron oxide containing microtubes under ambient conditions has led to L.ochracea being an attractive bacterium to study however there is currently no isolated axenic culture of L.ochracea nor is a thorough understanding of the exopolymeric secretions which act as a scaffold for microtubular formation. This research aims to address these areas by studying biogenic iron ochre mats collected from several sample sites surrounding the greater Glasgow area. Chapter 3 provides a provides a characterisation of the sampled biogenic iron ochre, primarily by SEM-EDX and XRD, to confirm the presence of filamentous material and investigate its composition and phase. Further to this there is also the development of a protocol to extract and characterise organic material associated with the samples along with a study of the interaction of thiol containing reducing agents with the material. Chapter 4 provides a characterisation of the bacterial communities present at three of the sample sites via the high-throughput Illumina sequencing of the V3 – V4 region of the 16S rRNA gene. This is an important area of the study as it is essential to understand which other bacteria are found within the biogenic iron ochre mats as this will provide insight to the biogeochemistry occurring. By understanding the other bacteria present and biogeochemistry it may be possible to develop an artificial environment in which to grow and isolate L.ochracea. Chapter 5 provides the development of protocols to isolate various types of bacteria from biogenic iron ochre mats. This chapter begins with the utilisation of solid agar media and solid gellan gum media supplemented with ferrous iron salts to isolate single colonies of bacteria. This chapter then investigates other isolation techniques including liquid enrichment growths and gradient tubes and culminates with the development of a protocol to isolate single filaments of bacteria via a micromanipulator. Isolated bacteria had their genomic DNA extracted which was then amplified by PCR and sequenced via highthroughput Illumina sequencing. Chapter 6 provides a thorough characterisation of the sample sites used throughout this study. Characterisation includes multiple photographs, measurements and descriptions, the physicochemical conditions present, the inorganic species present and the concentration of dissolved inorganic and organic carbon present. Orbitrap mass spectrometry is then used to characterise the organic material present. The recent history and underlying geology of selected sample sites is also investigated to assess whether anthropogenic activity or natural geology have a greater effect on the chemistry occurring within the sample sites. As with Chapter 4, by fully understanding the sample sites and chemistry occurring within them it may be possible to develop artificial media and environments that could be used to grow and isolate L.ochracea.