Most of the available freshwater is underground as groundwater. Pure groundwater ecosystems are classified as oligotrophic settings because they support a variety of well adapted species with limited energy yield, activity, growth, and reproduction. Thus, structural changes in groundwater species communities reflect declines in groundwater quality and quantity. Despite growing awareness of this issue, the only basis for current assessment methodologies for groundwater ecosystems is the evaluation of abiotic characteristics. However, to identify changes in microbial communities and their associated metabolic processes, this technique is insufficient. Our understanding of the diversity and makeup of microbial communities in various contexts has significantly improved in recent years as a result of the advent of culture-independent molecular tools to investigate bacteria. By allowing the identification of a single bacterial species in a sample, High-Throughput Sequencing (HTS) techniques offer a high resolution of the diversity and composition of microbial communities in varied contexts. Additionally, the taxonomic data obtained enables the prediction of a community's metabolic functions. Although labour- and money-intensive, the procedure isn't always the best option for assessing a large number of samples. While species identification in a community is not achievable, DNA-fingerprinting is a less complex and more affordable technology that may identify changes in microbial communities. As such, it is a useful complement to HTS. By directly comparing the results of DNAfingerprinting and HTS, the current paper aims to provide information regarding the usability of this technology as a monitoring tool against this background. Results of both approaches were favourably correlated, despite the fact that the analysis of bacterial communities employing HTS obtained noticeably higher diversity estimates in our study. Additionally, DNAfingerprinting caught patterns of community composition that were comparable to those obtained by HTS, despite the fact that HTS gave more precise and in-depth results describing the composition and diversity of bacterial communities. As a result, we may recommend DNA fingerprinting as an affordable substitute for estimating diversity and gauging community size, particularly as a viable methodological strategy for environmental tests.
