The dynamic interaction between microbial biodiversity, biogeochemical activity and sedimentary geomorphology in the Severn Estuary

Williams, Angharad S. 2015. The dynamic interaction between microbial biodiversity, biogeochemical activity and sedimentary geomorphology in the Severn Estuary. PhD Thesis, Cardiff University. Item availability restricted.

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Abstract

The Severn Estuary, UK is an important model estuarine environment due to its hyper-tidal range, leading to dynamic sediment environments. This work investigated the diversity and relationship with geochemistry of Severn Estuary sediment prokaryotic communities, which have not been previously described in detail. Focus was placed on the diversity and distribution of the largely uncultivated Chloroflexi, which were detected in high abundance in the deep subsurface but previous work has failed to address the diversity of subdivisions in dynamic surface sediments. Three geophysically different sampling sites were analysed from intertidal, shallow water and deep water areas of the Severn Estuary. Molecular profiling methods using the 16S ribosomal RNA (rRNA) gene, such as denaturing gradient gel electrophoresis (DGGE), ribosomal intergenic spacer analysis (RISA), quantitative PCR (qPCR) and 454 pyrosequencing were used. Novel qPCR and pyrosequencing methods were designed to target Chloroflexi subdivisions. Each of the sampling sites was characterised by differing prokaryotic communities depending on sediment turbidity and geochemistry, though the most abundant phyla, Proteobacteria, Firmicutes and Chloroflexi, were constant. The novel methods revealed surprising abundance and diversity of Chloroflexi subdivisions in Severn Estuary sediments, dominated by Anaerolineae, on a more detailed scale than previously reported in the literature. Further experiments described how sediment prokaryotic community structure and function changed over a wide temperature range and over 100 days. Slurries of Severn Estuary intertidal sediments were incubated between 1 - 80oC. A critical temperature window of 43oC indicated a shift in the bacterial community to thermophilic spore-forming Firmicutes and from heterotrophic to autotrophic sulphate reduction. In the Archaea community, methanogenesis shifted from chemoorganotrophic to chemolithotrophic dependent metabolism. These results extend our knowledge of the geochemical changes in temperature dependent sediment communities, which is important for the modelling of climate susceptible habitats, such as coastal sediments.

Item Type:	Thesis (PhD)
Status:	Unpublished
Schools:	Biosciences
Subjects:	Q Science > QR Microbiology
Uncontrolled Keywords:	Microbial ecology; Severn Estuary; Estuarine sediment; Chloroflexi; Prokaryotic diversity; Hyper-tidal; Sediment biogeochemistry
Date of First Compliant Deposit:	30 March 2016
Last Modified:	19 Mar 2016 23:53
URI:	https://orca.cardiff.ac.uk/id/eprint/70294

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