Exploring past environments with microbial biomarkers: a molecular approach using sedimentary DNA and 3-Hydroxy fatty acids

Thorpe, Amy C. ORCID: 0000-0003-0210-2767 (2023). Exploring past environments with microbial biomarkers: a molecular approach using sedimentary DNA and 3-Hydroxy fatty acids. University of Birmingham. Ph.D.

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Abstract

Palaeoclimate records are crucial for understanding the causes and rates of past climate change and informing predictions of future climate change. Palaeoenvironmental records of microbial communities are important for understanding the ecological impacts of climatic and environmental change due to their position near the base of many food webs, roles in biogeochemical cycling, and ability to act as indicators of change. Producing detailed and reliable palaeoclimate records and reconstructions of past microbial communities depends on the application of organic molecules preserved in temporally stratified sedimentary archives as biomarkers of change. This thesis explores the use of two promising novel microbial biomarkers: sedimentary DNA (sedDNA) to reconstruct past microbial communities, and bacterial 3-hydroxy fatty acids (3-OH FAs) to reconstruct past climates.
Analysis of sedDNA is becoming more frequently used to reconstruct past microbial communities and can be applied with a relatively high taxonomic resolution. However, the taphonomy of DNA in lakes is poorly understood, and the reliability of sedDNA-based reconstructions of microbial communities is largely unknown. To reconstruct past bacterial and eukaryotic microbial communities, 16S rRNA and 18S rRNA gene amplicon sequencing were carried out on sediment cores collected from Esthwaite Water (English Lake District) spanning approximately 100 years. To assess the reliability of these reconstructions, the sedDNA records were compared against concurrent, long-term microscopy-based monitoring of cyanobacteria and eukaryotic algae in the surface water, revealing comparable broad-scale temporal shifts in community composition in response to eutrophication. However, a decline in the concentration of 16S rRNA genes and proportion of DNA likely originating from the water column down-core suggested that the reliability of reconstructions may be reduced in older sediments. These results demonstrate that sedDNA is a valuable tool to reconstruct past microbial communities, but further study is needed to better understand the extent and rate of DNA deposition and degradation in lake sediments to enhance its development as a reliable biomarker.
Proxies based on 3-OH FAs show significant potential as palaeoclimate biomarkers that can be applied to various environments. However, the identity of 3-OH FA producers and the influence of bacterial community composition on the performance of 3-OH FA proxies in terrestrial environments have yet to be determined. Through paired bacterial 16S rRNA gene amplicon sequencing and 3-OH FA analysis in soils and lake surface sediments collected across large gradients of mean annual air temperature (MAAT), mean annual precipitation (MAP) and soil and lake sediment pH in the U.S., it was suggested that distinct communities of bacteria specific to each environment may be responsible for the production of 3-OH FAs. Therefore, the bacterial community may be an important driver of 3-OH FA distribution in the environment. Furthermore, the culture-based analysis revealed that bacteria from different taxonomic lineages may produce a distinct suite of 3-OH FA isomers. These findings highlight the importance of considering the bacterial producers of 3-OH FAs in the development of reliable 3-OH FA proxies for palaeoclimate reconstructions.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):