Statistical differences between relative quantitative molecular fingerprints from microbial communities

Differentiation and quantification of the ochratoxin A producers Aspergillus ochraceus and Aspergillus westerdijkiae using PCR-DGGE

Ochratoxin A (OTA) is a nephrotoxic, teratogenic, immunotoxic, and carcinogenic mycotoxin which is produced in tropical zones mainly by Aspergillus carbonarius, A. niger, A. ochraceus, and A. westerdijkiae. A. ochraceus and A. westerdijkiae species are phenotypically and genomically very close but A. westerdijkiae produce OTA at a very higher level than A. ochraceus. These species have been differentiated recently. The DNA primer pairs which were drawn so far are not specific and a genomic region of the same size is amplified for both species or they are too specific, and in this case, the DNA of a single species is amplified. To help preventing OTA contamination of foodstuffs, the PCR-DGGE (Denaturing Gradient Gel Electrophoresis) method was used to discriminate between A. ochraceus and A. westerdijkiae DNA fragments of the same size but with different sequences and thus faster access to a diagnosis of the toxigenic potential of the fungal microflora. The proposed methodology was able to differentiate A. westerdijkiae from A. ochraceus with only one primer pairs in a single run. A calibration based on initial DNA content was obtained from image analysis of the DGGE gels and a method of quantification of the two strains was proposed.

Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential

(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.

Kinetics of Indigenous Nitrate Reducing Sulfide Oxidizing Activity in Microaerophilic Wastewater Biofilms

Nitrate decreases sulfide release in wastewater treatment plants (WWTP), but little is known on how it affects the microzonation and kinetics of related microbial processes within the biofilm. The effect of nitrate addition on these properties for sulfate reduction, sulfide oxidation, and oxygen respiration were studied with the use of microelectrodes in microaerophilic wastewater biofilms. Mass balance calaculations and community composition analysis were also performed. At basal WWTP conditions, the biofilm presented a double-layer system. The upper microaerophilic layer (~300 μm) showed low sulfide production (0.31 μmol cm^-3 h^-1) and oxygen consumption rates (0.01 μmol cm^-3 h^-1). The anoxic lower layer showed high sulfide production (2.7 μmol cm^-3 h^-1). Nitrate addition decreased net sulfide production rates, caused by an increase in sulfide oxidation rates (SOR) in the upper layer, rather than an inhibition of sulfate reducing bacteria (SRB). This suggests that the indigenous nitrate reducing-sulfide oxidizing bacteria (NR-SOB) were immediately activated by nitrate. The functional vertical structure of the biofilm changed to a triple-layer system, where the previously upper sulfide-producing layer in the absence of nitrate split into two new layers: 1) an upper sulfide-consuming layer, whose thickness is probably determined by the nitrate penetration depth within the biofilm, and 2) a middle layer producing sulfide at an even higher rate than in the absence of nitrate in some cases. Below these layers, the lower net sulfide-producing layer remained unaffected. Net SOR varied from 0.05 to 0.72 μmol cm^-3 h^-1 depending on nitrate and sulfate availability. Addition of low nitrate concentrations likely increased sulfate availability within the biofilm and resulted in an increase of both net sulfate reduction and net sulfide oxidation by overcoming sulfate diffusional limitation from the water phase and the strong coupling between SRB and NR-SOB syntrophic relationship.

Bacterial distribution along a 50 °C temperature gradient reveals a parceled out hot spring environment

Understanding the distribution of bacteria is a major goal of microbial ecology which remains to be fully deciphered. In this study, a model 50 °C temperature gradient at a Northern Thailand hot spring was analyzed to determine how the bacterial communities were structured in the environment. Communities were examined through 16S rRNA gene amplification, denaturing gradient gel electrophoresis, and sequencing. The two major phyla, Cyanobacteria and Chloroflexi, showed characteristic distributions along the temperature gradient. Different clades were allocated at specific portions of the gradient. Comparisons of the bacterial communities along the temperature gradient showed sharp decreases of similarity at increasing temperature difference. Peaks of maximum richness were observed at 50 and 70 °C. This study contributes to explain how environmental conditions and microbial interactions can influence the distribution of specific bacterial clades and phyla shaping the structure of microbial communities in nature.

Feasibility of sunflower oil cake degradation with three different anaerobic consortia

Sunflower oil cake (SuOC) is the solid by-product from the sunflower oil extraction process and an important pollutant waste because of its high organic content. For the anaerobic digestion of SuOC three different industrial reactors were compared as inoculum sources. This was done using a biochemical methane production (BMP) test. Inoculum I was a granular biomass from an industrial reactor treating soft-drink wastewaters. Inoculum II was a flocculent biomass from a full-scale reactor treating biosolids generated in an urban wastewater treatment plant. Inoculum III was a granular biomass from an industrial reactor treating brewery wastes. The highest kinetic constant for methane production was achieved using inoculum II. The inoculum sources were analyzed through PCR amplification of 16S rRNA genes and fingerprinting before (t = 0) and after the BMP test (t = 12 days). No significant differences were found in the bacterial community fingerprints between the beginning and the end of the experiments. The bacterial and archaeal communities of inoculum II were further analyzed. The main bacteria found in this inoculum belong to Alphaproteobacteria and Chloroflexi. Of the Archaea detected, Methanomicrobiales and Methanosarcinales made up practically the whole archaeal community. The results showed the importance of selecting an appropriate inoculum in short term processes due to the fact that the major microbial constituents in the initial consortia remained stable throughout anaerobic digestion.

Moonmilk deposits originate from specific bacterial communities in Altamira Cave (Spain)

The influence of bacterial communities on the formation of carbonate deposits such as moonmilk was investigated in Altamira Cave (Spain). The study focuses on the relationship between the bacterial communities at moonmilk deposits and those forming white colonizations, which develop sporadically throughout the cave. Using molecular fingerprinting of the metabolically active bacterial communities detected through RNA analyses, the development of white colonizations and moonmilk deposits showed similar bacterial profiles. White colonizations were able to raise the pH as a result of their metabolism (reaching in situ pH values above 8.5), which was proportional to the nutrient supply. Bacterial activity was analyzed by nanorespirometry showing higher metabolic activity from bacterial colonizations than uncolonized areas. Once carbonate deposits were formed, bacterial activity decreased drastically (down to 5.7% of the white colonization activity). This study reports on a specific type of bacterial community leading to moonmilk deposit formation in a cave environment as a result of bacterial metabolism. The consequence of this process is a macroscopic phenomenon of visible carbonate depositions and accumulation in cave environments.

Microbial community fingerprinting by differential display-denaturing gradient gel electrophoresis

Complex microbial communities exhibit a large diversity, hampering differentiation by DNA fingerprinting. Herein, differential display-denaturing gradient gel electrophoresis is proposed. By adding a nucleotide to the 3' ends of PCR primers, 16 primer pairs and fingerprints were generated per community. Complexity reduction in each partial fingerprint facilitates sample comparison.

Three different phototrophic microbial communities colonizing a single natural shelter containing prehistoric paintings

Three different cases of deterioration were identified in a single natural shelter containing prehistoric paintings. The microbial communities induced by run-off water, a black crust covering a portion of the shelter, and a cryptoendolithic microbial community, were studied. Molecular analyses based both on DNA and RNA were performed to identify the major components of these microbial communities present and metabolically active, respectively, at the studied location. While similar microbial communities were expected due to the proximity of the studied sites, clearly different communities were detected suggesting that specific microorganisms adapt to different micro-environments. Phototrophic microorganisms represented the major portion of total RNA and DNA in the studied microbial communities. Run-off water induced the presence of a large proportion of putative photosynthetic bacteria belonging to Chloroflexi. Different groups of bacteria were associated to phototrophs and were represented by Alpha, Beta, Delta, and Gammaproteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Planctomycetes. The present study confirms a need for careful monitoring of microbial communities associated to distinct cases of deterioration even within a single location, underlining the interest of phototrophic microorganisms as indicators of colonization on cultural heritage at natural shelters.

Sulfate-reducing bacteria are common members of bacterial communities in Altamira Cave (Spain)

The conservation of paleolithic paintings such as those in Altamira Cave (Spain) is a primary objective. Recent molecular studies have shown the existence of unknown microbial communities in this cave including anaerobic microorganisms on cave walls. Herein, we analyzed an anaerobic microbial group, the sulfate-reducing bacteria (SRB), from Altamira Cave with potential negative effects on painting conservation. In the present work, the communities of bacteria and SRB were studied through PCR-DGGE analysis. Data suggest that SRB communities represent a significant, highly diverse bacterial group in Altamira Cave. These findings represent a first report on this physiological group on caves with paleolithic paintings and their potential biodegradation consequences. Expanding our knowledge on microbial communities in Altamira Cave is a priority to design appropriate conservation strategies.