The original article briefly discusses Microviridae viruses found in the metagenomes in the Abstract (Results), Results (Metagenome derived insights into Chlorobiales populations), Discussion (New species of green sulfur bacteria and possible viral predation), and Conclusions.Since the article's publication it has come to light that the sequences associated with the Microviridae viruses belong to PhiX 174 (Genbank Accession Number NC_001422), a member of Microviridae family.
We compared methods for extracting interstitial water from stratified sediments in Lake Geneva and Lake Zurich. Microbial metabolites (NH 4 + , NO 3 ‒ , NO 2 ‒ , SO 4 2‒ , Mn 2+ , Fe 2+ , PO 4 3‒ , DOC), pH, conductivity, and VFA (volatile fatty acids such as acetate and propionate) as well as more conservative chemical species (Na + , K + , Ca 2+ , Mg 2+ , and H 4 SiO 4 ) were analyzed in pore‐water samples collected with a high‐pressure squeezing‐filtration method and an in situ equilibrium diffusion technique. Both methods are useful if the limitations of their applicability are appreciated. Among the nonvolatile compounds, squeezing leads to increased concentrations of Na + , K + , HPO 4 2‒ , H 4 SiO 4 , NO 2 ‒ , and DOC. Intracellular metabolites from only partially lysed or still living sediment organisms may be released into the aqueous extract under the influence of very high pressures. The squeezing technique needs to be optimized for pressures that yield pore‐water sample volumes large enough for the required analyses but do not disrupt cells.
Fuschna Spring in the Swiss Alps (Engadin region) is a bicarbonate iron(II)-rich, pH-neutral mineral water spring that is dominated visually by dark green microbial mats at the side of the flow channel and orange iron(III) (oxyhydr)oxides in the flow channel. Gradients of O(2), dissolved iron(II), and bicarbonate establish in the water. Our goals were to identify the dominating biogeochemical processes and to determine to which extent changing geochemical conditions along the flow path and seasonal changes influence mineral identity, crystallinity, and microbial diversity. Geochemical analysis showed microoxic water at the spring outlet which became fully oxygenated within 2.3 m downstream. X-ray diffraction and Mössbauer spectroscopy revealed calcite (CaCO(3)) and ferrihydrite [Fe(OH)(3)] to be the dominant minerals which increased in crystallinity with increasing distance from the spring outlet. Denaturing gradient gel electrophoresis banding pattern cluster analysis revealed that the microbial community composition shifted mainly with seasons and to a lesser extent along the flow path. 16S rRNA gene sequence analysis showed that microbial communities differ between the flow channel and the flanking microbial mat. Microbial community analysis in combination with most-probable-number analyses and quantitative PCR (qPCR) showed that the mat was dominated by cyanobacteria and the channel was dominated by microaerophilic Fe(II) oxidizers (1.97 × 10(7) ± 4.36 × 10(6) 16S rRNA gene copies g(-1) using Gallionella-specific qPCR primers), while high numbers of Fe(III) reducers (10(9) cells/g) were identified in both the mat and the flow channel. Phototrophic and nitrate-reducing Fe(II) oxidizers were present as well, although in lower numbers (10(3) to 10(4) cells/g). In summary, our data suggest that mainly seasonal changes caused microbial community shifts, while geochemical gradients along the flow path influenced mineral crystallinity.
We collected the culturable heterotrophic bacteria from oligotrophic high mountain lake habitats and tested their capability to induce ice formation. Direct plating was carried out using low-nutrient medium at a temperature of between 3 and 4°C. As many as 84 isolates were recovered from glacial ice and natural biofilm growing on granite rocks surface. Six out of 84 isolates were capable of expressing the ice-nucleation phenotype. After autoclaving the cell suspension at 121°C for 15 min, isolate J78 was still able to retain the ability for ice formation. Heat-stable ice nuclei produced by ice-nucleating active bacteria have potential applications in biotechnology. Characterization of INA bacteria was performed employing live-dead Gram staining and molecular methods. Universal primers for Bacteria (S-D-Bact-0008-b-S-20 and S-D-Bact-1524-a-A-18) were used for PCR to amplify almost the full length of the 16S rRNA genes of selected INA isolates. Restriction fragment length polymorphism analysis resulted in 2 unique patterns, as represented by J43 and J83, respectively. Based on DNA sequencing of 16S rRNA gene, isolate J43 (GeneBank accession no. AJ864852) was closely related to Pseudomonas mephitica (99.2% sequence similarity) and Janthinobacterium lividum (99% similarity), whereas isolate J83 (GeneBank accession no. AJ864859) showed 100% sequence identity to Pseudomonas fluorescens.
We collected the culturable heterotrophic bacteria from oligotrophic high mountain lake habitats and tested their capability to induce ice formation. Direct plating was carried out using low-nutrient medium at a temperature of between 3 and 4°C. As many as 84 isolates were recovered from glacial ice and natural biofilm growing on granite rocks surface. Six out of 84 isolates were capable of expressing the ice-nucleation phenotype. After autoclaving the cell suspension at 121°C for 15 min, isolate J78 was still able to retain the ability for ice formation. Heat-stable ice nuclei produced by ice-nucleating active bacteria have potential applications in biotechnology. Characterization of INA bacteria was performed employing live-dead Gram staining and molecular methods. Universal primers for Bacteria (S-D-Bact-0008-b-S-20 and S-D-Bact-1524-a-A-18) were used for PCR to amplify almost the full length of the 16S rRNA genes of selected INA isolates. Restriction fragment length polymorphism analysis resulted in 2 unique patterns, as represented by J43 and J83, respectively. Based on DNA sequencing of 16S rRNA gene, isolate J43 (GeneBank accession no. AJ864852) was closely related to Pseudomonas mephitica (99.2% sequence similarity) and Janthinobacterium lividum (99% similarity), whereas isolate J83 (GeneBank accession no. AJ864859) showed 100% sequence identity to Pseudomonas fluorescens.
SUMMARY: Lake Geneva is a large, holomictic, eutrophic lake with a maximum depth of about 300 m. The sediments in the central basin have a pillow-like appearance. The soft elevations containing the major portion of the recently sedimented detritus are separated by trenches of 5 to 15 cm depth in which the top sediment layers seem to be missing. Bottom-dwelling fishes (Lota lota) prefer the trenches as their habitat and might partly be responsible for the turbation of the trench sediment layers. Thus, within distances of 10 to 30 cm two sediment types can clearly be distinguished. They differ with respect to morphology and chemical stratification. Concentration depth profiles of nitrate, manganese(II), iron(II), sulphate, and methane dissolved in the interstitial water reveal the location within the sediment of microbially catalysed redox processes. The redox transition zone (RTZ) from aerobic to anaerobic is located only a few millimetres below the sediment surface in the pillow sediments, which contain the bulk of the organic detritus. The RTZ is at a depth of approximately 6 cm in the trench sediments, which are poor in oxidizable organic matter. The same thermodynamic sequence of microbially catalysed redox reactions can be observed in both sediment types. As a consequence, microbial activities as well as diffusion fluxes of dissolved substances in and out of the different sediment regions vary greatly. This leads to small-scale horizontal differences in the sediment's abilities to supply nutrients to the bottom water, which is probably a major controlling factor for sediment-borne eutrophication of this lake.
During the last two decades, more than 100 cattle deaths have been reported from 11 alpine sites in south-eastern Switzerland. Pathological findings and the histological examination of their organs strongly indicated acute hepatotoxicosis. Clinical symptoms suggestive of neurotoxicity were also observed in some cases. To elucidate the etiology of these poisonings, different water bodies in one of the affected alpine pastures were investigated for cyanobacterial toxins. The waters were highly oligotrophic, cold and turbid, and the ice-free period was limited to 3–4 months. The algal community in these waters consisted mostly of benthic cyanobacteria forming dense mats on the surface of sediments and on submerged rocks. Oscillatoria limosa and Phormidium konstantinosum (=Oscillatoria tenuis) dominated these populations, but occasionally other species of Oscillatoria, Phormidium, Tychonema and Pseudanabaena also occurred in the mats. Samples from the cyanobacterial mats yielded positive results in a protein phosphatase inhibition assay, reacted with antibodies against microcystins in an enzyme-linked immunosorbent assay and were hepatotoxic in a mouse bioassay. The same cyanobacterial material also included neurological effects in mice. High-performance liquid chromatography was used to identify a microcystin, in these cyanobacterial samples as well as in the corresponding lake water. To our knowledge, this is the first documented example of hepatotoxicity associated with benthic cyanobacteria, and the first report of toxic cyanobacteria from the remote, oligotrophic alpine environment.
The rates of microbial and abiotic iron oxidation were determined in a variety of cold (T = 9–12 °C), circumneutral (pH = 5.5–9.0) environments in the Swiss Alps. These habitats include iron–bicarbonate springs, iron–arsenic–bicarbonate springs, and alpine lakes. Rates of microbial iron oxidation were measured up to a pH of 7.4, with only abiotic processes detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39–89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where biological iron oxidation was measured. Geochemical sampling suites accompanying each experiment include field data (temperature, pH, conductivity, dissolved oxygen, and redox sensitive solutes), solute concentrations, and sediment composition. Dissolved inorganic carbon concentrations indicate that bicarbonate and carbonate are typically the most abundant anions in these systems. Speciation calculations reveal that ferrous iron typically exists as FeCO3(aq), FeHCO3+, FeSO4(aq), or Fe2+ in these systems. The abundance of ferrous carbonate and bicarbonate species appears to lead to a dramatic increase in the abiotic rate of reaction compared to the rate expected from chemical oxidation in dilute solution. This approach, integrating geochemistry, rates, and community composition, reveals locations and geochemical conditions that permit microbial iron oxidation and locations where the abiotic rate is too fast for the biotic process to compete.
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