Aquifers, springs and other groundwater-dependent ecosystems are threatened by urban land use, which causes water quality deterioration through nutrient loading, sewage infiltration, groundwater extraction and, along coasts, seawater intrusion. The presence of certain microbes in groundwater can indicate that an aquifer is anthropogenically contaminated. Interpretations made from observations of indicator microbes in groundwater are limited because the relationship between the presumably allochthonous indicator microbes and relevant autochthonous microbial communities has not been characterized. This study addressed whether autochthonous aquifer biofilms can influence the presence of presumed microbial indicators in groundwater, and simultaneously used microbial indicators to trace sources of urban contamination at a karst spring of conservation concern. These questions were approached using a 17-month time series analysis of attached biofilm and adjacent unattached bacteria in the submerged karst aquifer conduit associated with this spring. Environmental 16S rRNA gene sequencing was performed to characterize these communities, and community structure data were contextualized with groundwater geochemical and hydrogeological measurements. Linear regression models were developed to explain the relative abundance patterns of indicator microbes and other unattached microbes at this site. The results of this study suggest that dominant aquifer biofilms do not influence the presence of unattached microbial taxa that are presumed to be indicators of groundwater contamination, and generated new information about the origin of coliform bacteria at the study site. These results build confidence in the use of microbial indicators in groundwater-dependent ecosystem conservation strategies and inform future management plans for urban aquifers and springs worldwide. K E Y W O R D S conservation, groundwater-dependent ecosystems, indicator species, land use, microbial biodiversity, urbanization | 325 SCHARPING ANd GAREY 1 | INTRODUC TI ON 1.1 | Conserving groundwater-dependent ecosystems in a changing world Ecosystems that rely on a supply of groundwater to maintain their structure and function, termed groundwater-dependent ecosystems, are both ecologically important and sensitive to environmental changes. This ecosystem type, which includes aquifers, springs, wetlands and many surface water bodies, makes important contributions to the biodiversity of a region by providing habitats for endemic, relict and specialized obligate species (Humphreys, 2006; Kløve, Ala-aho, et al., 2011). Groundwater-dependent ecosystems also provide useful services to people. For example, they support globally significant sources of potable and irrigation water, act as filters for nutrient and toxin loads, generate nursery habitats for economically important game species and are at the core of many recreational activities and cultural sites (Kløve, Allan, et al., 2011; Stinnesbeck et al., 2018). However, because groundwater-dependent ecosystems tend ...
