Control of aquifer geology on the spatio-temporal distribution of groundwater prokaryotes in England

Bhattacharyya, Archita and Sorensen, James and Gooddy, Daren and Read, Daniel and Surridge, Ben (2025) Control of aquifer geology on the spatio-temporal distribution of groundwater prokaryotes in England. PhD thesis, Lancaster University.

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Abstract

Groundwater is a source of drinking water for over two billion people globally. Groundwater also harbours vast and under-explored prokaryotic communities essential to subsurface biogeochemical cycling and maintaining drinking water quality. Despite their importance, large-scale national studies to understand the spatio-temporal variation of groundwater prokaryotes are scarce. This is the first systematic study of prokaryotic ecosystems in the groundwater of three major aquifers of England, which is the source of one-third of the public water supply. This research employed modern microbial monitoring technologies, such as flow cytometry and eDNA metabarcoding. Groundwater samples were collected from public supply sources of three major aquifers of England: Permo-Triassic sandstone, Cretaceous chalk, and Jurassic limestone. The research aimed to assess the collective influence of aquifer geology, groundwater recharge and chemistry in shaping the groundwater prokaryotic ecosystems on a national spatial scale. The aquifer geology and surface connectivity were observed to be significant drivers of total bacterioplankton cell concentration (TCC). The karstic limestone aquifers showed almost two times higher TCC than intergranular sandstone and dual porosity chalk aquifers due to more frequent allochthonous prokaryotic input, evident from the higher abundance of animal parasitic DNA in the limestone aquifer. The seasonal recharge seemed to have impacted only the chalk aquifer, where higher groundwater levels were related to a reduction in TCC. The TCC reduction in the chalk aquifer could be a result of dilution by the recharge water from the unsaturated zone of the aquifer, containing a lower bacterial concentration. The sandstone aquifer was enriched in prokaryotic classes such as Gammaproteobacteria, Bacteroidia and OM190, and a higher proportion of chemoheterotrophic and autotrophic functions. In contrast, chalk and limestone aquifers exhibited compositional and functional similarity, characterised by a greater presence of Omnitrophia, Nanoarchaeia, Dehalococcoidia, Gracilibacteria, and Saccharimonadia, and many unknown functions indicating the presence of cryptic functional potentials. The results suggested that the community composition of the two carbonate aquifers could be different from the ferro-silicate sandstone aquifer due to differences in groundwater chemistry, controlled by mineral dissolution from the aquifer matrix. While on the national scale, the prokaryotic communities varied significantly between aquifer types, within individual aquifers, spatial variation seemed to be controlled strongly by total dissolved nitrogen concentrations and overlying strata thickness. A focused study in the sandstone communities revealed that while the communities did not shift seasonally, the recharge age of groundwater was related to community composition. The groundwater with a younger recharge age was higher in dissolved nitrogen and oxygen and originated from shallower zones of the aquifer, hosted heterotrophic and parasitic families, including Omnitrophaceae and Nanoarchaeia. In contrast, the old recharge age groundwater with lower dissolved nitrogen and oxygen concentration originated from deeper parts of the aquifer and hosted autotrophic families such as Gallionellaceae, Rhodocyclaceae, Hydrogenophilaceae and Comamonadaceae. Thus, within individual aquifers, groundwater nutrient chemistry controlled by recharge age had a substantial impact on the community composition. This thesis is a significant contribution to the growing number of national studies on groundwater prokaryotic ecosystems. Unlike many regional studies, this research established that on a large spatial scale, the proximity of sampling sites did not possess prokaryotic ecosystem similarities. Instead, similar prokaryotes were selected collectively by similar geologies and similar levels of surface connectivity. Thus, different aquifer geologies can be used in the future for classifying prokaryotic ecosystem management zones. The datasets from relatively clean drinking water sources can be used as a reference microbial community structure for England’s major aquifers for future monitoring and groundwater management strategies.