Metagenomic comparison of microbial communities inhabiting confined and unconfined aquifer ecosystems

Abstract

A metagenomic analysis of two aquifer systems located under a dairy farming region was performed to examine to what extent the composition and function of microbial communities varies between confined and surface-influenced unconfined groundwater ecosystems. A fundamental shift in taxa was seen with an overrepresentation of Rhodospirillales, Rhodocyclales, Chlorobia and Circovirus in the unconfined aquifer, while Deltaproteobacteria and Clostridiales were overrepresented in the confined aquifer. A relative overrepresentation of metabolic processes including antibiotic resistance (β-lactamase genes), lactose and glucose utilization and DNA replication were observed in the unconfined aquifer, while flagella production, phosphate metabolism and starch uptake pathways were all overrepresented in the confined aquifer. These differences were likely driven by differences in the nutrient status and extent of exposure to contaminants of the two groundwater systems. However, when compared with freshwater, ocean, sediment and animal gut metagenomes, the unconfined and confined aquifers were taxonomically and metabolically more similar to each other than to any other environment. This suggests that intrinsic features of groundwater ecosystems, including low oxygen levels and a lack of sunlight, have provided specific niches for evolution to create unique microbial communities. Obtaining a broader understanding of the structure and function of microbial communities inhabiting different groundwater systems is particularly important given the increased need for managing groundwater reserves of potable water.

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

“…In conclusion, this work expands our understanding of microbial diversity in karst aquifers and emphasizes the importance of evaluating and quantifying active microbial processes that could affect carbonate weathering in the subsurface. The results have important implications for investigations related to carbon sequestration and storage (see, e.g., Mitchell et al, 2009;Kirk, 2011) and groundwater and drinking water resources (see, e.g., Stein et al, 2010;Smith et al, 2011). Accordingly, to fully appreciate diverse microbial communities and carbonate geochemistry, more experimental research is needed from freshwater segments of karst aquifers and caves, and the potential role of microbes in affecting karst aquifer hydraulic properties (for example, porosity, transmissivity) should also be considered.…”

“…Karst aquifer modification can be affected by external mechanisms like climate change that alter the flux of meteoric water into the system (see, e.g., Loáiciga et al, 2000;Loáiciga, 2009), or from internal processes like chemical reactions and microbial activity (see, e.g., Engel et al, 2004). Although microbes have been shown to affect water quality and biogeochemical and ecosystem-level processes in other types of aquifers (Griebler and Lueders, 2009;Kato et al, 2009;Stein et al, 2010;Smith et al, 2011), there has been limited research to define microbial activities that affect aquifer karstification.…”

Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef

“…The SEED is organised into three hierarchical levels for metabolism and six levels for taxonomy [37][38][39]. Matches with a E-value of <0.05 were considered significant with a minimum alignment of 50 bp [31,[39][40][41][42][43][44][45][46]. All data was normalised to sequencing effort by dividing by the total number of hits.…”

Linking Microbial Community Structure to Function in Representative Simulated Systems

“…This approach allows for the study of microorganisms in their natural environmental settings and has produced a wealth of data on microbial communities in the human microbiome (6)(7)(8)(9)(10) and in aquatic systems (11)(12)(13)(14). However, there is no realistic capacity to control parameters within in vivo systems.…”