Distribution and diversity of autotrophic bacteria in groundwater systems based on the analysis of RuBisCO genotypes

University of Innsbruck, Institute of Ecology, Technikerstrasse 25, 6020 Innsbruck, Austria.
Systematic and Applied Microbiology (Impact Factor: 3.28). 04/2009; 32(2):140-50. DOI: 10.1016/j.syapm.2008.11.005
Source: PubMed


A molecular approach, based on the detection of ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) large subunit genes, was applied to investigate the distribution and diversity of autotrophic bacteria in groundwater systems. DNA extracts from 48 sampling stations, including a variety of pristine and polluted, shallow and deep-subsurface groundwater samples obtained from Germany and Austria, served as a template for the PCR amplification of form I (cbbL) and form II (cbbM) large subunit RubisCO genes. The majority of the samples (>80%) contained two different forms of RubisCO. In 17 samples, all three forms of RubisCO were identified. PCR products from four selected groundwater habitats containing all three forms of RubisCO were used to construct clone libraries. Based on restriction fragment length polymorphism (RFLP) analysis, 109 RubisCO-clone-inserts were subjected to sequencing and phylogenetic analysis. With the exception of a form IA RubisCO sequence cluster obtained from deep subsurface samples, which was identical to the RubisCO genes described for Ralstonia metallidurans CH34, most sequences were distantly related to a variety of RubisCO species in chemolithoautotrophic Proteobacteria. Several sequences occurred in isolated lineages. These findings suggest that autotrophic bacteria with the capability to assimilate CO2 via the Calvin Cycle pathway are widespread inhabitants of groundwater systems.

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Available from: Carsten Vogt, Aug 03, 2015
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    • "Real-time quantitative PCR Form IA/B, IC, and ID cbbL genes were quantified using primer sets cbbLG-1F/cbbLG-1R (Selesi et al. 2005), IC-F/ IC-R (Alfreider et al. 2009), and ID-F/ID-R (Paul et al. 2000), respectively, using a LightCycler480 (Roche Diagnostics Ltd, USA). These primer sets were designed to specifically target microbial autotrophs in diverse environments and exclude those from plants. "
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    ABSTRACT: Soil microbial autotrophs play a significant role in CO2 fixation in terrestrial ecosystem, particularly in vegetation-constrained ecosystems with environmental stresses, such as the Tibetan Plateau characterized by low temperature and high UV. However, soil microbial autotrophic communities and their driving factors remain less appreciated. We investigated the structure and shift of microbial autotrophic communities and their driving factors along an elevation gradient (4400-5100 m above sea level) in alpine grassland soils on the Tibetan Plateau. The autotrophic microbial communities were characterized by quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning/sequencing of cbbL genes, encoding the large subunit for the CO2 fixation protein ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). High cbbL gene abundance and high RubisCO enzyme activity were observed and both significantly increased with increasing elevations. Path analysis identified that soil RubisCO enzyme causally originated from microbial autotrophs, and its activity was indirectly driven by soil water content, temperature, and NH4 (+) content. Soil autotrophic microbial community structure dramatically shifted along the elevation and was jointly driven by soil temperature, water content, nutrients, and plant types. The autotrophic microbial communities were dominated by bacterial autotrophs, which were affiliated with Rhizobiales, Burkholderiales, and Actinomycetales. These autotrophs have been well documented to degrade organic matters; thus, metabolic versatility could be a key strategy for microbial autotrophs to survive in the harsh environments. Our results demonstrated high abundance of microbial autotrophs and high CO2 fixation potential in alpine grassland soils and provided a novel model to identify dominant drivers of soil microbial communities and their ecological functions.
    Applied Microbiology and Biotechnology 06/2015; 99(20). DOI:10.1007/s00253-015-6723-x · 3.34 Impact Factor
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    • "Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the enzyme responsible for CO 2 fixation among certain hydrogenotrophic microbes, was detected in various groundwater systems. It has been shown that this metabolism is widespread in microorganisms living in groundwater systems (Alfreider et al., 2009). "
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    ABSTRACT: Leakage of CO2 or brine coming from CO2 geological storage sites constitutes a risk for overlying fresh groundwater resources. One of the main risks is the potential alteration of groundwater quality by the intrusion of contaminants such as trace elements. This paper reviews studies that address the potential impacts of CO2 geological storage leakage on fresh groundwater quality.Leakage can directly modify the chemical properties of fresh water (pH, redox potential, chemical composition) and, as a result, indirectly modify the effect of biogeochemical processes controlling trace element availability. The ability of a CO2 or brine leak to introduce or mobilize trace elements and potentially degrade the quality of water in an overlying aquifer depends on the composition and quantity of the leaking fluids, the nature of the solid phases making up the aquifer (buffering and scavenging capacity) and the concentrations of undesirable or toxic elements that can be mobilized following any such modification. Furthermore, hydrogeological conditions will control the potential dissemination into groundwater. To date, studies have shown that trace elements can be significantly mobilized without necessarily exceeding quality thresholds. In a few cases where aquifers are naturally rich in trace elements (i.e. whose natural concentrations in groundwater are already high), CO2 is able to mobilize these trace elements (e.g. Fe, Mn, Ni, As, Ba, U) and increase concentrations up to or exceeding threshold values.This literature review provides a return on experience essential for both assessing biogeochemical risks prior to the installation of future CO2 geological storage sites and designing and installing fresh groundwater quality monitoring networks.
    International Journal of Greenhouse Gas Control 03/2014; 22:165–175. DOI:10.1016/j.ijggc.2013.12.019 · 3.95 Impact Factor
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    • "Analyses of 16S rRNA gene phylogeny combined with the detection and phylogenetic analyses of genes encoding key enzymes of specific metabolic pathways (such as autotrophic carbon fixation pathways, and sulfur and methane cycles) has been crucial in the study of some subsurface microbial habitats (Campbell et al., 2003; Campbell and Cary, 2004; Blazejak et al., 2006; Brazelton et al., 2006; 2011; 2012; Lin et al., 2006; Nakagawa and Takai, 2008; Alfreider et al., 2009). This approach enables to predict which geochemical energy sources are powering the ecosystem and which biochemical processes are sustaining the microbial community (Nealson et al., 2005; Hoehler, 2007; Cardace and Hoehler, 2009). "
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    ABSTRACT: Microbial and functional diversity were assessed, from a serpentinization-driven subterrestrial alkaline aquifer - Cabeço de Vide Aquifer (CVA) in Portugal. DGGE analyses revealed the presence of a stable microbial community. By 16S rRNA gene libraries and pyrosequencing analyses, a diverse bacterial composition was determined, contrasting with low archaeal diversity. Within Bacteria the majority of the populations were related to organisms or sequences affiliated to class Clostridia, but members of classes Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Deinococci, Gammaproteobacteria and of the phyla Bacteroidetes, Chloroflexi and Nitrospira were also detected. Domain Archaea encompassed mainly sequences affiliated to Euryarchaeota. Only form I RuBisCO - cbbL was detected. Autotrophic carbon fixation via the rTCA, 3-HP and 3-HP/4H-B cycles could not be confirmed. The detected APS reductase alpha subunit - aprA sequences were phylogenetically related to sequences of sulfate-reducing bacteria belonging to Clostridia, and also to sequences of chemolithoautothrophic sulfur-oxidizing bacteria belonging to Betaproteobacteria. Sequences of methyl coenzyme M reductase - mcrA were phylogenetically affiliated to sequences belonging to Anaerobic Methanotroph group 1 (ANME-1). The populations found and the functional key markers detected in CVA suggest that metabolisms related to H2 , methane and/or sulfur may be the major driving forces in this environment.
    Environmental Microbiology 06/2013; 15(6):1687-706. DOI:10.1111/1462-2920.12034 · 6.20 Impact Factor
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