Microbial Signatures in Deep CO2-Saturated Miocene Sediments of the Active Hartoušov Mofette System (NW Czech Republic)

The Hartoušov mofette system is a natural CO₂ degassing site in the central Cheb Basin (Eger Rift, Central Europe). In early 2016 a 108 m deep core was obtained from this system to investigate the impact of ascending mantle-derived CO₂ on indigenous deep microbial communities and their surrounding life habitat. During drilling, a CO₂ blow out occurred at a depth of 78.5 meter below surface (mbs) suggesting a CO₂ reservoir associated with a deep low-permeable CO₂-saturated saline aquifer at the transition from Early Miocene terrestrial to lacustrine sediments. Past microbial communities were investigated by hopanoids and glycerol dialkyl glycerol tetraethers (GDGTs) reflecting the environmental conditions during the time of deposition rather than showing a signal of the current deep biosphere. The composition and distribution of the deep microbial community potentially stimulated by the upward migration of CO₂ starting during Mid Pleistocene time was investigated by intact polar lipids (IPLs), quantitative polymerase chain reaction (qPCR), and deoxyribonucleic acid (DNA) analysis. The deep biosphere is characterized by microorganisms that are linked to the distribution and migration of the ascending CO₂-saturated groundwater and the availability of organic matter instead of being linked to single lithological units of the investigated rock profile. Our findings revealed high relative abundances of common soil and water bacteria, in particular the facultative, anaerobic and potential iron-oxidizing Acidovorax and other members of the family Comamonadaceae across the whole recovered core. The results also highlighted the frequent detection of the putative sulfate-oxidizing and CO₂-fixating genus Sulfuricurvum at certain depths. A set of new IPLs are suggested to be indicative for microorganisms associated to CO₂ accumulation in the mofette system.

Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity

Widespread antibiotic resistance among bacterial pathogens is providing the impetus to explore novel sources of antimicrobial agents. Recently, the potent antibacterial activity of certain clay minerals has stimulated scientific interest in these materials. One such example is Kisameet glacial clay (KC), an antibacterial clay from a deposit on the central coast of British Columbia, Canada. However, our understanding of the active principles of these complex natural substances is incomplete. Like soils, clays may possess complex mixtures of bacterial taxa, including the Actinobacteria, a clade known to be rich in antibiotic-producing organisms. Here, we present the first characterization of both the microbial and geochemical characteristics of a glacial clay deposit. KC harbors surprising bacterial species richness, with at least three distinct community types. We show that the deposit has clines of inorganic elements that can be leached by pH, which may be drivers of community structure. We also note the prevalence of Gallionellaceae in samples recovered near the surface, as well as taxa that include medically or economically important bacteria such as Actinomycetes and Paenibacillus. These results provide insight into the microbial taxa that may be the source of KC antibacterial activity and suggest that natural clays may be rich sources of microbial and molecular diversity.

Identifying and characterizing the resident microbial populations (bacteria, viruses, protozoa, and fungi) is key to understanding the ecology, chemistry, and homeostasis of virtually all sites on Earth. The Kisameet Bay deposit in British Columbia, Canada, holds a novel glacial clay with a history of medicinal use by local indigenous people. We previously showed that it has potent activity against a variety of antibiotic-resistant bacteria, suggesting it could complement our dwindling arsenal of antibiotics. Here, we have characterized the microbiome of this deposit to gain insight into what might make the clay antibacterial. Our analyses suggest that the deposit contains a surprising diversity of bacteria, which live in at least three distinct environments. In addition, the clay harbors bacteria that may have interesting potential as biocontrol/bioremediation agents or producers of novel bioactive compounds.

Biodegradation of chlorobenzene and nitrobenzene at interfaces between sediment and water

Plumes of contaminated groundwater often pass through an oxic/anoxic interface when they discharge into surface water bodies. We tested the hypothesis that contaminants recalcitrant under anaerobic conditions but degradable under aerobic conditions can be biodegraded at the interface resulting in the protection of the overlying water. Flow-through columns containing sediment and water were used to evaluate degradation of synthetic organic compounds at the thin organic layer at the sediment/water interface. Sediment samples collected from several sites contaminated with nitrobenzene (NB) or chlorobenzene (CB) were tested for their biodegradation capacities in the columns. The biodegradation capacities of sediment in the columns were 2-4.2 g CB·m(-2)·d(-1) and 6.5 g NB·m(2)·d(-1). Bacteria able to carry out rapid and complete biodegradation of CB or NB were detected in the sediments prior to the experiments, which suggested the presence of an active microbial community at the contaminated sites. The results revealed robust biodegradation of toxic compounds migrating across the sediment/water interface and indicate that the biodegradation capacities were sufficient to eliminate transport of the contaminants to the overlying water in the field.

Influence of seasonal and geochemical changes on the geomicrobiology of an iron carbonate mineral water spring

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.

The iron-oxidizing proteobacteria

The ‘iron bacteria’ are a collection of morphologically and phylogenetically heterogeneous prokaryotes. They include some of the first micro-organisms to be observed and described, and continue to be the subject of a considerable body of fundamental and applied microbiological research. While species of iron-oxidizing bacteria can be found in many different phyla, most are affiliated with the Proteobacteria. The latter can be subdivided into four main physiological groups: (i) acidophilic, aerobic iron oxidizers; (ii) neutrophilic, aerobic iron oxidizers; (iii) neutrophilic, anaerobic (nitrate-dependent) iron oxidizers; and (iv) anaerobic photosynthetic iron oxidizers. Some species (mostly acidophiles) can reduce ferric iron as well as oxidize ferrous iron, depending on prevailing environmental conditions. This review describes what is currently known about the phylogenetic and physiological diversity of the iron-oxidizing proteobacteria, their significance in the environment (on the global and micro scales), and their increasing importance in biotechnology.

Investigation of mineral water springs of Miercurea Ciuc (Csíkszereda) region (Romania) with cultivation-dependent microbiological methods

Water samples of ten mineral water springs at Miercurea Ciuc (Csíkszereda) region (Romania) were examined during 2005-2006 using cultivation-dependent microbiological methods. The results of standard hygienic bacteriological tests showed that the Hargita Spring had perfect and five other springs had microbiologically acceptable water quality (Zsögöd-, Nagy-borvíz-, Taploca-, Szentegyháza- and Lobogó springs). The water of Borsáros Spring was exceptionable (high germ count, presence of Enterococcus spp.).Both standard bacteriological and molecular microbiological methods indicated that the microbiological water quality of the Szeltersz-, Nádasszék- and Délo springs was not acceptable. Bad water quality resulted from inadequate spring catchment and hygiene (low yield, lack of runoff, negligent usage of the springs, horse manure around the spring).The 16S rRNA gene-based identification of strains isolated on standard meat-peptone medium resulted in the detection of typical aquatic organisms such as Shewanella baltica, Aeromonas spp., Pseudomonas veronii, Psychrobacter sp,. Acinetobacter spp. and allochthonous microbes, like Nocardia, Streptomyces, Bacillus, Microbacterium , and Arthrobacter strains indicating the impact of soil. Other allochthonous microbes, such as Staphylococcus spp., Micrococcus sp., Lactococcus sp., Clostridium butyricum, Yersinia spp., Aerococcus sp., may have originated from animal/human sources.