Microbial weathering of shale rock in natural and historic industrial environments
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Date
02/07/2018Author
Samuels, Toby Stephen
Metadata
Abstract
The weathering of shales is a globally important process affecting both natural and
built environments. Shales form roughly 70 % of worldwide sedimentary rock
deposits and therefore the weathering of these rocks has substantial effects on the
geochemical cycling of elements such as carbon, iron and sulfur. Microbes have been
shown to play a key role in weathering shales, primarily through the oxidation of the
iron and sulfur of embedded pyrite and the resultant production of sulfuric acid.
Despite significant interest in the microbial weathering of shales within industrial
sectors such as biohydrometallurgy and civil engineering, comparatively few studies
have investigated microbial shale weathering in natural environments. Furthermore,
the role of microbes in natural shale weathering processes beyond iron oxidation has
largely remained unexplored.
In this thesis, the weathering capabilities of microbial communities from natural
weathered shale was investigated. The North Yorkshire coastline was used as a study
location, due to the abundance and diversity of natural cliffs and historic, disused
industrial sites. Cliff erosion and recession on the North Yorkshire coastline is a
major concern for local authorities and is the focus of current research. The aim of
this work has been to evaluate microbial shale weathering processes within these
environments, and hypothesise the possible contribution they may have to erosive
processes.
Phenotypic plate assays inoculated with weathered shale material were used to obtain
rock weathering bacterial isolates that tested positive for a specific weathering
phenotype, such as iron oxidation or siderophore production. Subsequent 16S rRNA
sequencing enabled genera level identification, revealing 15 genera with rock
weathering capabilities with several being associated with multiple weathering
phenotypes including Aeromonas sp., Pseudomonas sp. and Streptomyces sp.. Shale
enrichment liquid cultures were incubated with shale rock chips to simulate natural
biological weathering conditions, and the concentration of rock-leached elements in
the fluid measured. No evidence of microbially-enhanced leaching was found
consistently for any element, however the significant reduction in leachate iron
concentration under biological conditions indicates that iron precipitation occurred
via microbial iron oxidation.
Enrichment cultures inoculated with weathered shale and containing organic matter
(OM) rich rocks in water or M9 medium, both liquids lacking an organic carbon
source, were grown over several months. The cultures yielded microbial isolates that
could utilise rock bound OM sources and one bacterial isolate, Variovorax
paradoxus, was taken forward for ecophysiological study. The shale rock that the
organism was isolated from, along with other OM rich rocks (mudstones and coals),
elicited complex responses from V. paradoxus including enhanced growth and
motility.
Finally, mineral microcosms in vitro and mesocosms in situ investigated microbial
colonization and weathering of shale-comprising minerals (albite, calcite, muscovite,
pyrite and quartz). Microcosms were established using iron oxidizing enrichment
cultures, as based on the results of the simulated rock weathering experiments, while
the in situ mesocosms were buried within weathered shale scree within a disused
mine level. Levels of colonization significantly varied between minerals within the
microcosms (pyrite>albite, muscovite>quartz>calcite). Although differences in
mineral colonization were seen in the mesocosms, they did not match those in the
microcosms and were not statistically significant. Pyrite incubated in the microcosms
became significantly weathered, with extensive pit formation across the mineral
surface that is consistent with microbial iron oxidation. In the mesocosms, pit
formation was not identified on pyrite surfaces but dark etchings into the pyrite
surface were found underneath fungi hyphal growth.
The results of this thesis highlights that a range of microbial rock weathering
mechanisms are abundant across weathered shale environments. Microbial iron
oxidizing activity was a dominant biogeochemical process that altered rock-fluid
geochemistry and weathered pyrite surfaces. However, the impact on rock or mineral
weathering of other microbial mechanisms was not elucidated by this work. Given
the known capabilities of these mechanisms, the conditions under which they are
active may not have been met within the experimental setup used. Microbial iron oxidation in shale and shale-derived materials has previously been
demonstrated to weaken rock structure through acid production and secondary
mineral formation. From the results of this thesis, it is clear that microbial iron
oxidation is an active process within some of the weathered shale environments
studied, including cliff surfaces. Therefore, it can be hypothesised that microbial
activity could play a role in structurally weakening shale rock within cliffs and
accelerate their erosion. Future work should attempt to quantify the rate and extent of
microbial iron oxidizing activity within shale cliff environments and investigate its
contribution to erosive processes.