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Analysis of microbial diversity in an extreme environment: White Island, New Zealand

thesis
posted on 29.03.2022, 00:52 by Raquel Ibáñez-Peral
White island, the most active volcano in New Zealand, is a poorly studied environment that represents an ideal site for the investigation of acidophilic thermophiles. The microorganisms present on here are continually exposed to extreme environmental conditions as they are surrounded by steamy sulphurous fumaroles and acidic streams. The sediment temperature ranges from 38°C to 104°C whilst maintaining pH values below 3. A survey of the volcanic hydrothermal system of White Island was undertaken in order to gain insights onto the microbial diversity using culture-dependant techniques and molecular and phylogenetic analyses. A novel liquid medium based on "soil-extract" was designed which supported growth of bacterial and archaeal mixed cultures. Molecular analyses revealed that the dominant culturable bacterial species belong to the Bacteroidetes, Firmicutes and α-Proteobacteria groups. Several previously uncultured archaeal species were also present in the mixed cultures. The knowledge gained from these studies was intended to help in the development of a novel microbial detection technique suitable for community analysis. -- Conventional molecular techniques used to study microbial biodiversity in environmental samples are both time-consuming and expensive. A novel bead-based assay employing Quantum dots (QDs) was considered to have many advantages over standard molecular techniques. These include high detection speeds, sensitivity, specificity, flexibility and the capability for multiplexed analysis. QDs are inorganic semiconductor nanoparticles made up of crystals about the size of proteins. It has been claimed that the physical and chemical properties of the QDs have significant advantages compared to organic dyes, including brighter fluorescence and resistance to photo-bleaching. Their optical properties facilitate the simultaneous imaging of multiple colours due to their flexible excitation and narrow band emission. Functionalised QDs are able to bind to different biological targets such as DNA, allowing high-throughput analysis for rapid detection and quantification of genes and cells. -- The optical and physical characteristics of the QDs as well their interaction with biomolecules are shown to be suitable for the development of a novel bead-based technique able to target the key microbial species and identify them by flow cytometric measurements (FCM). The broad absorption and narrow emission spectra of the QDs, as well as their fluorescence intensity and specify to target biomolecules, was compared to other organic fluorophores. The potential advantages and limitations of QDs as a fluorophores for biological applications are discussed. -- The data acquired during this study provides a broad overview of the microbial diversity and ecology of the volcanically-active hydrothermal systems of White Island and constitutes the baseline for the development of a novel bead-based technique based on QDs.

History

Table of Contents

Literature review -- Materials and methods -- Sampling sites and sampling material -- Enrichment cultures and molecular analyses -- Optical and binding characterisation of the QDs -- Applications of the QDs -- Concluding remarks.

Notes

Bibliography: p. 227-259 "June, 2008".

Awarding Institution

Macquarie University

Degree Type

Thesis PhD

Degree

Thesis (PhD), Macquarie University, Division of Environmental & Life Sciences, Dept. of Chemistry & Biomolecular Sciences

Department, Centre or School

Dept. of Chemistry and Biomolecular Sciences

Year of Award

2009

Principal Supervisor

Peter L. Bergquist

Additional Supervisor 1

Malcolm Walter

Additional Supervisor 2

Belinda Ferrari

Rights

Copyright disclaimer: http://www.copyright.mq.edu.au Copyright Raquel Ibá́ñez-Peral 2009.

Language

English

Jurisdiction

New Zealand

Extent

xvii, 259 p. ill. (some col.)

Former Identifiers

mq:6278 http://hdl.handle.net/1959.14/44764 1348256