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Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.

Llorens-Marès T, Yooseph S, Goll J, Hoffman J, Vila-Costa M, Borrego CM, Dupont CL, Casamayor EO - ISME J (2015)

Bottom Line: Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium.We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments.Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

View Article: PubMed Central - PubMed

Affiliation: Integrative Freshwater Ecology Group, Center of Advanced Studies of Blanes-Spanish Council for Research (CEAB-CSIC), Blanes, Girona, Spain.

ABSTRACT
Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

No MeSH data available.


Related in: MedlinePlus

Vertical profiles of physicochemical data for Lake Banyoles basin C-III and Lake Cisó. Metagenomic analyses were carried out at two selected depths (dotted lines): the oxic–anoxic interface (shadowed areas indicate the redoxcline zone) and the anoxic and sulfurous (euxinic) hypolimnia.
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fig1: Vertical profiles of physicochemical data for Lake Banyoles basin C-III and Lake Cisó. Metagenomic analyses were carried out at two selected depths (dotted lines): the oxic–anoxic interface (shadowed areas indicate the redoxcline zone) and the anoxic and sulfurous (euxinic) hypolimnia.

Mentions: Lake Cisó and basin III of Lake Banyoles (Banyoles C-III) are in the Banyoles karstic area, northeastern Spain (42°8'N, 2°45'E), and the microbial communities inhabiting these water bodies have been extensively studied by limnologists and microbial ecologists (see, for example, Guerrero et al., 1980; Garcia-Gil and Abellà, 1992; Pedrós-Alió and Guerrero, 1993). The lakes were sampled on 8–9 May 2010. Vertical profiles of temperature, conductivity, oxygen and redox potential were measured in situ with a multiparametric probe OTT-Hydrolab MS5 (Hatch Hydromet, Loveland, CO, USA). The different water compartments (oxic epilimnion, metalimnion with the oxic–anoxic interface and anoxic hypolimnion) were determined for each lake according to the physicochemical profiles recorded in situ (Figure 1). For sulfide analyses, 10 ml of subsamples were collected in screw-capped glass tubes and immediately alkalinized by adding 0.1 ml of 1 M NaOH and fixed by adding 0.1 ml of 1 M zinc acetate. Sulfide was analyzed in the laboratory according to Trüper and Schlegel (1964). For pigments, water samples were processed as described by Guerrero et al. (1985) and analyzed by HPLC as previously reported (Borrego et al., 1999). Iron (Fe+2) concentrations were obtained from Garcia-Gil (1990).


Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics.

Llorens-Marès T, Yooseph S, Goll J, Hoffman J, Vila-Costa M, Borrego CM, Dupont CL, Casamayor EO - ISME J (2015)

Vertical profiles of physicochemical data for Lake Banyoles basin C-III and Lake Cisó. Metagenomic analyses were carried out at two selected depths (dotted lines): the oxic–anoxic interface (shadowed areas indicate the redoxcline zone) and the anoxic and sulfurous (euxinic) hypolimnia.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4478705&req=5

fig1: Vertical profiles of physicochemical data for Lake Banyoles basin C-III and Lake Cisó. Metagenomic analyses were carried out at two selected depths (dotted lines): the oxic–anoxic interface (shadowed areas indicate the redoxcline zone) and the anoxic and sulfurous (euxinic) hypolimnia.
Mentions: Lake Cisó and basin III of Lake Banyoles (Banyoles C-III) are in the Banyoles karstic area, northeastern Spain (42°8'N, 2°45'E), and the microbial communities inhabiting these water bodies have been extensively studied by limnologists and microbial ecologists (see, for example, Guerrero et al., 1980; Garcia-Gil and Abellà, 1992; Pedrós-Alió and Guerrero, 1993). The lakes were sampled on 8–9 May 2010. Vertical profiles of temperature, conductivity, oxygen and redox potential were measured in situ with a multiparametric probe OTT-Hydrolab MS5 (Hatch Hydromet, Loveland, CO, USA). The different water compartments (oxic epilimnion, metalimnion with the oxic–anoxic interface and anoxic hypolimnion) were determined for each lake according to the physicochemical profiles recorded in situ (Figure 1). For sulfide analyses, 10 ml of subsamples were collected in screw-capped glass tubes and immediately alkalinized by adding 0.1 ml of 1 M NaOH and fixed by adding 0.1 ml of 1 M zinc acetate. Sulfide was analyzed in the laboratory according to Trüper and Schlegel (1964). For pigments, water samples were processed as described by Guerrero et al. (1985) and analyzed by HPLC as previously reported (Borrego et al., 1999). Iron (Fe+2) concentrations were obtained from Garcia-Gil (1990).

Bottom Line: Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium.We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments.Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

View Article: PubMed Central - PubMed

Affiliation: Integrative Freshwater Ecology Group, Center of Advanced Studies of Blanes-Spanish Council for Research (CEAB-CSIC), Blanes, Girona, Spain.

ABSTRACT
Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems.

No MeSH data available.


Related in: MedlinePlus