Journal of Forensic Pathology

High-throughput Sequencing (HTS) and DNA Fingerprinting (T-RFLP) are Being Compared to Determine the Richness and Makeup of Microbial Communities in Groundwater Ecosystems

Alexander Wilson^{* *}Correspondence: Alexander Wilson, Department of Forensic, Denmark, Email:

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Introduction

94% of the freshwater that may be used is groundwater, demonstrating both its economic and ecological significance. Groundwater is a crucial source of drinking water and is also used in industry and agriculture. The majority of surface aquatic ecosystems (such as lakes, rivers, streams, and wetlands) are quantitatively and/or qualitatively connected to the groundwater, and its ecological function is described as a component of the hydrological cycle. In addition to being a resource, groundwater is also a separate ecosystem with unique environmental traits from those found at the surface.

Pure groundwater ecosystems are classified as oligotrophic settings, meaning that all of their organic and nutrient intake comes from outside sources. Groundwater are home to a large number of highly adapted microbes, protozoans, and metazoans despite the fact that these environmental conditions only permit poor energy yield, activity, development, and reproduction. Therefore, the dynamics, stability, and productivity of the groundwater ecosystem can be directly impacted by the functional diversity of groundwater species, or, more specifically, the variety of metabolic processes. This functional diversity supports and provides ecosystem services, such as the maintenance of excellent groundwater water quality, which is essential for human well-being. Changes in taxonomic diversity are thought to have an impact on ecosystem functioning generally, while it is not clear how much they can affect functional diversity. Anthropogenic activities frequently cause changes in the structure and composition of species communities in groundwater ecosystems, which are linked to the degradation of groundwater quality and quantity. Groundwater's importance for the environment and human health has changed as a result of growing awareness of the detrimental impacts of groundwater pollution on ecosystem services. In light of this, a groundwater ecosystem conservation strategy has been developed under the European Groundwater Directive. The characterization of groundwater ecosystems to date has relied solely on the measurement of chemical and hydrogeological characteristics, in contrast to surface aquatic ecosystems where biological and ecological data are readily used as indicators of system quality. However, and this is significant, using abiotic criteria to evaluate the quality of groundwater ecosystems is an inadequate method for identifying effects on species communities and, consequently, ecosystem functioning. Biomonitoring, which uses specialised species' responses to reflect how environmental stressors affect the community of biota, can provide comprehensive information pointing to anthropogenic effects like contamination. Additionally, it makes it possible to assess how environmental stress affects several levels of biological organisation. However, it has proven difficult to develop groundwater biomonitoring techniques due to the limited accessibility to and low density of higher organisms in groundwater ecosystems. The topic of potential target organisms for groundwater monitoring has been brought up several times. They have the following characteristics that make them particularly suitable as a biological monitoring "toolkit": (1) their great abundance and widespread occurrence in the Earth's subsurface; (2) their dominant role in the processes of mineralization and degradation; and (3) their wide range of physiological functionalities. DNA-based molecular approaches that are not dependent on culture have recently emerged as reliable and repeatable ways to determine the makeup of microbial communities in a variety of situations. DNA fingerprinting, a popular and well-established technique for studying microbial communities, is based on phylogenetic variations of a particular species in the nucleotide composition of a desired target gene. There are several fingerprinting techniques that have been used successfully to evaluate structural changes in microbial communities. One of the most popular fingerprinting techniques is terminal restriction fragment length polymorphism because it offers better resolution and reproducibility than other fingerprinting methods. T-RFLP analyses have the drawback that the total bacterial diversity is frequently underestimated and that the results do not accurately reflect taxonomic information. In contrast, High-Throughput Sequencing (HTS) is a molecular approach that can identify species within a microbial community and more accurately reflects taxonomic diversity. According to Sogin et al., estimates acquired from conventional cloning and capillary sequencing procedures revealed that the microbial diversity in maritime habitats obtained by HTS was significantly higher. HTS is a less time- and cost-effective monitoring technology, especially for large numbers of samples, due to the relatively high costs and labour input compared to DNA-fingerprinting. The sole purpose of this research is to compare T-RFLP and HTS in terms of how well they can replicate the structure and diversity of the groundwater microbial community. In three research locations with various intensities of land use, we repeatedly sampled springs and groundwater wells. We proposed three main hypotheses: (1) bacterial communities reflect differences between study areas and sampling sites; (2) T-RFLP and HTS yield comparable results with regard to the classification of study areas and sampling sites; and (3) both methods can capture the diversity of groundwater bacteria comparably well.