Microbial biodiversity in groundwater ecosystems

Abstract

Summary 1. Groundwater ecosystems offer vast and complex habitats for diverse microbial communities. Here we review the current status of groundwater microbial biodiversity research with a focus on Bacteria and Archaea and on the prospects of modern techniques for enhancing our understanding of microbial biodiversity patterns and their relation to environmental conditions. 2. The enormous volume of the saturated terrestrial underground forms the largest habitat for microorganisms on earth. Up to 40% of prokaryotic biomass on earth is hidden within this terrestrial subsurface. Besides representing a globally important pool of carbon and nutrients in organisms, these communities harbour a degree of microbial diversity only marginally explored to date. 3. Although first observations of groundwater microbiota date back to Antonie van Leeuwenhoek in 1677, the systematic investigation of groundwater microbial biodiversity has gained momentum only within the last few decades. These investigations were initiated by an increasing awareness of the importance of aquifer microbiota for ecosystem services and functioning, including the provision of drinking water and the degradation of contaminants. 4. The development of sampling techniques suitable for microbiological investigations as well as the application of both cultivation‐based and molecular methods has yielded substantial insights into microbial communities in contaminated aquifers, whereas knowledge of microbial biodiversity in pristine habitats is still poor at present. 5. Several novel phylogenetic lineages have been described from groundwater habitats, but to date no clearly ‘endemic’ subsurface microbial phyla have been identified. The future will show if the rather low diversity generally found in pristine oligotrophic aquifers is a fact or just a result of low abundances and insufficient resolution of today’s methods. Refined approaches complemented by statistically rigorous applications of biodiversity estimates are urgently needed. 6. Factors identified to control microbial diversity in aquifers include spatial heterogeneity, temporal variability and disturbances such as pollution with chemical anthropogenic contaminants. Although first insights into the importance of individual biogeochemical processes may be obtained from surveys of microbial diversity within functional groups, direct links to groundwater ecosystem functioning have rarely been established so far.

Thermal effects on microbial composition and microbiologically induced corrosion and mineral precipitation affecting operation of a geothermal plant in a deep saline aquifer

“…These reactions are related to the degradation of organic matter (Parkes et al 1994(Parkes et al , 2000Whitman et al 1998;Wellsbury et al 2002), rock and mineral weathering and alteration (Rogers et al 1998;Bennett et al 2001;Shock 2009;Gadd 2010), quality of groundwater (Goldscheider et al 2006;Wilson et al 2006;Griebler and Lueders 2009), and failures in engineered subsurface systems caused by corrosion and scaling (Van Hamme et al 2003;Valdez et al 2009;Javaherdashti 2011). Geothermal gradients in the terrestrial crust range from approximately 10°C km -1 to 60°C km -1 (Philpotts 1990).…”

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

“…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.…”

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor

“…Syntrophs specifically form obligate mutualistic interactions with methanogens to metabolize organic compounds whose degradation otherwise rapidly becomes thermodynamically unfavorable (DG40) as by-products accumulate (Schink, 1997;Schink and Stams, 2006). Despite such low-energy conditions, engineered and natural methanogenic environments harbor a wide diversity of uncharacterized microorganisms from known phyla and candidate phyla without cultivated representatives (microbial dark matter; Rinke et al, 2013; also see Juottonen et al, 2005;Nemergut et al, 2008;Griebler and Lueders, 2009;Riviere et al, 2009;Glockner et al, 2010;Kong et al, 2010;Kim et al, 2011;Lykidis et al, 2011;Nelson et al, 2011;Rinke et al, 2013). Their presence indicates many undiscovered microbial niches and interactions.…”