School of Earth Sciences - Theses
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ItemThe role of soil microorganisms in the solubilisation of secondary lanthanide phosphate minerals in weathered granite( 2022)During the weathering of granite, a major component of Earth’s continental crust, many elements are redistributed from metastable minerals into new, more stable ones, a critical process in soil formation. Microorganisms are key drivers of mineral weathering, but the mechanisms by which they promote mineral dissolution and the connections between microbial metabolisms and element redistribution are poorly understood. Understanding the biogeochemical controls involved in the remobilisation of rare earth elements (REEs, ‘lanthanides’) from relatively insoluble minerals to uptake for cofactors of lanthanide-dependent microbial metabolism is an important and topical area of study. This thesis was developed around investigating highly insoluble secondary lanthanide phosphate mineral formation and dissolution in weathered granite profiles. Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals is critical for releasing phosphate into the biosphere. For decades, a question has prevailed regarding how highly insoluble secondary lanthanide phosphate minerals dissolve during rock weathering. It was hypothesised that microorganisms play a role in this process; however, REEs were considered biologically inert at the time. Recently, following the discovery of a lanthanide-dependent methanotroph, studies have shown that lanthanide-dependent methanol oxidation is common in many environments, including soils, but the mechanisms responsible for lanthanide acquisition and uptake from the environment remain poorly understood. The thesis reviews and discusses the major outstanding questions and mechanisms involved in the biogeochemical mobilisation of lanthanides in weathered granite (Chapter One). Field emission-SEM/EDX (scanning electron microscopy with energy dispersive X-ray) and mass spectrometry were used to study primary and secondary mineral formation and dissolution in granite material while genome-resolved metagenomics, enrichment, isolation and bioleaching were utilised to study the capability of the microbial community to break down REE minerals and utilise lanthanides (Chapter Two). The process of secondary lanthanide phosphate formation and dissolution was investigated in different granite types of variable mineralogy. The phenomenon of REE mobilisation, precipitation of nanocrystalline REE/P minerals, and ultimately REE/P mineral dissolution, during granite weathering was documented in three major granitic types (I-, A-, and S-type). It was documented that the dissolution of highly insoluble secondary REE/P minerals, as well as monazite, can precede soil formation and occurs in soils (Chapter Three). Using genome-resolved metagenomics alongside enrichment and isolation methods, the work aimed to characterise the microbial community of a weathered granite profile, to detect the presence of lanthanide-dependent genes, and to assess their potential REE/P- bioleaching capabilities. One well-developed granite weathering profile in which lanthanum phosphate formation and dissolution were documented was selected for further biological analysis. Genome-resolved metagenomic analyses revealed microbes including Verrucomicrobia, Acidobacteria, Gemmatimonadetes, and Alphaproteobacteria with the capacity to utilise lanthanide-dependent methanol oxidation (XoxF) are prevalent in the region where insoluble lanthanide-phosphate minerals dissolve. Conserved hypothetical proteins and transporters not previously associated with xoxF systems were also identified across diverse phyla suggesting lanthanide usage is prevalent and highlights targets for further investigation. Biosynthetic gene clusters of predicted siderophores containing xoxF systems were identified and may be involved in dissolving REE/P minerals (Chapter Four). Enriched microbial co-cultures capable of producing siderophores were capable of dissolving lanthanum from highly insoluble rhabdophane in the laboratory at essentially circumneutral pH suggesting dissolution mechanisms independent of organic acids (Chapter Five). This study's genome-resolved metagenomic analysis identifies mechanisms in moderately weathered granite that may promote REE/P mineral dissolution and general rock weathering. The study also successfully demonstrates a new in situ sampling approach for enriching and isolating microorganisms capable of solubilising lanthanum from highly insoluble lanthanide phosphate minerals. The findings and methodology of this study have relevance and application suitable for experimental studies looking to describe new lanthanide-based systems, express and characterise novel siderophore gene clusters, improve lanthanide recovery technology, and further describe the microbial controls on mineral weathering prior to soil formation.