To date, ~1% of all bacteria that occur in environmental ecosystems such as soil, sedimentary rocks, and groundwater have been described. Comprehensive explanation of ecological interactions on a microscale level is thus almost impossible. The Dynamic Cultivation System (DCS) was developed in order to detect more microbial taxa than with common cultivation approaches, as well as previously undescribed bacterial species. The DCS is a quick and easy in situ method for the cultivation of numerous bacterial taxa in support of the description of microbial colonized ecosystems. To investigate the bacterial populations within a clay-maturation process after mining the raw material, the DCS was used to increase the microbial biomass for further molecular analysis. Two different methods were applied to extract the bacteria from the DCS and these were compared in terms of efficiency at detection of large numbers of different taxa and in terms of applicability to the detection of previously undescribed species in raw clays. A collection of different undescribed species was detected with sequencing. While direct picking of bacterial colonies leads to the detection of different genera, species mainly of the genus Arthobacter were proved in the phosphate-buffered saline-suspended biomass. Thus, a combination of the approaches mentioned above is recommended to increase the number of detectable species. The DCS will help to describe better the microbial content of ecosystems, especially soils that contain charged particles.

Sea ice microalgae actively contribute to the pool of dissolved organic matter (DOM) available for bacterial metabolism, but this link has historically relied on bulk correlations between chlorophyll a (a surrogate for algal biomass) and bacterial abundance. We incubated microbes from both the bottom (congelation layer) and surface brine region of Antarctic fast ice for nine days. Algal-derived DOM was manipulated by varying the duration of irradiance, restricting photosynthesis with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) or incubating in the dark. The bacterial response to changes in DOM availability was examined by performing cell counts, quantifying bacterial metabolic activity and examining community composition with denaturing gradient gel electrophoresis. The percentage of metabolically active bacteria was relatively low in the surface brine microcosm (10–20% of the bacterial community), the treatment with DCMU indirectly restricted bacterial growth and there was some evidence for changes in community structure. Metabolic activity was higher (35–69%) in the bottom ice microcosm, and while there was no variation in community structure, bacterial growth was restricted in the treatment with DCMU compared to the light/dark treatment. These results are considered preliminary, but provide a useful illustration of sea ice microbial dynamics beyond the use of ‘snapshot’ biomass correlations.

We report here a comparative analysis of the growth, acidification capacity, and chemical and microbiologic composition between kefir grains after 20 subcultures in whey at 20, 30, and 37°C and the original kefir grains coming from milk along with a determination of the microbiological composition of the fermented whey as compared with that of traditional fermented milk.

When fermentation was carried out repeatedly at 30 or 37°C, kefir grains changed their kefir-like appearance, exhibited reduced growth rates, had a lower diversity of yeasts and water content, and a higher protein-to-polysaccharide ratio compared with the original kefir grains. In contrast, at 20°C kefir grains could remain in whey for prolonged periods without altering their acidification capacity, growth rate, macroscopic appearance or chemical and microbiologic composition—with the only difference being a reduction in certain yeast populations after 20 subcultures in whey. At this incubation temperature, the presence of Lactobacillus kefiranofaciens, Lb. kefir, Lb. parakefir, Lactococcus lactis, Kluyveromyces marxianus, Saccharomyces unisporus, and Sac. cerevisiae was detected in kefir grains and in fermented whey by denaturing-gradient-gel electrophoresis (DGGE). In whey fermented at 20°C the number of lactic-acid bacteria (LAB) was significantly lower (P<0·05) and the number of yeast significantly higher (P<0·05) than in fermented milk. Since the DGGE profiles were similar for both products, at this temperature the microbiologic composition of fermented whey is similar to that of fermented milk. We therefore suggest a temperature of 20°C to preserve kefir grains as whey-fermentation starters.

Deception Island, an active stratovolcano located in the South Shetland Islands, Antarctica, provides excellent conditions for the thermophilic bacteria growth because of high ground temperatures in specific areas, such as Fumarole Bay where the temperatures are above the mesophilic range. Denaturing Gradient Gel Electrophoresis (DGGE) was used with the 16S ribosomal gene to analyse cultures of thermophilic bacteria from a soil sample taken from Fumarole Bay. Nine bands were sequenced and analysed from DGGE and they indicated the presence of bacteria from the genera Geobacillus, Bacillus, Brevibacillus, Thermus and uncultured sulphate reducing bacteria. Some of which have been reported in other Antarctic geothermal sites. Geobacillus, Bacillus and Brevibacillus genera were successfully cultivated in an enriched medium. A pure culture of one thermophilic Geobacillus bacterium was obtained closely related to Geobacillus jurassicus.

This study assessed the impact of Pinus radiata (D. Don) genetically modified (GM) by biolistic insertion of the LEAFY and nptII genes on rhizosphere microbial communities of field grown trees. Rhizosphere soil was sampled quarterly for two consecutive years. A culture-independent approach was used to characterise the microbial communities based on PCR and denaturing gradient gel electrophoresis (DGGE) of 16S/18S rDNA gene fragments, and internal transcribed spacer (ITS) fragments amplified from total rhizosphere DNA. Trees from two independent transformation events were sampled, together with non-modified control trees of the same parental genotype. DGGE profiles of rhizosphere general Bacteria did not differ between GM and control trees with one exception (summer 2006 sample). For Alphaproteo- and Actinobacteria, significant differences between treatments were detected in one out of eight samplings. Small seasonal shifts could be detected in all bacterial communities. General fungal and ectomycorrhizal communities did not differ significantly between GM and control trees with the exception of summer 2006, when ectomycorrhizal communities associated with GM trees from one transformation event differed from those associated with control trees. Small seasonal shifts of general fungal and ectomycorrhizal communities were seen over the two-year sampling period. More detailed analysis of microbial communities at one sampling date (using amplified rDNA restriction analysis (ARDRA) and 16S/18S rDNA sequencing) revealed significant differences in four ARDRA groups between one GM treatment and the control (bacteria), and significant differences in one ARDRA group between the two GM treatments (fungi). When data from all sampling dates are considered together, the low incidence of statistical differences in the microbial communities associated with the genetically modified and control trees suggests that there was no significant impact of this genetic modification on rhizosphere microbial communities.

With the rapid development of nanotechnology, the security of nanomaterials has been an increasing cause for concern. In this study, the impact of titanium dioxide nanoparticles (nano-TiO2) on the phyllosphere bacterial community were analysed by both a culturable-dependent method and a polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) method. The quantity of culturable phyllosphere bacteria was significantly reduced with an increased concentration of nano-TiO2. With increasing concentrations from 0.002 to 20 mg/ml of nano-TiO2, the quantity of culturable phyllosphere bacteria decreased from 1.8×106 to 3.1×105 cfu/g. The phyllosphere bacteria community was analysed by PCR-DGGE, and when the concentrations of nano-TiO2 were higher than 0.02 mg/ml, the DGGE bands were significantly lower than in the control. Sequencing results of the bands from the DGGE gel showed that there were at least seven genera in the phyllosphere bacteria. Only one uncultured bacterium was unaffected by the concentration of nano-TiO2.

In the rumen, plant particles are colonised and degraded by the rumen micro-organisms. Although numerous important findings about fibre-associated bacterial community were obtained using traditional or molecular techniques, little information is available on the dynamics of bacteria associated with feed particles during incubation in the rumen. In the present study, ryegrass leaf, ryegrass stem and rice straw, representing different carbohydrate compositions, were used as substrates and placed in the rumen of goats by using nylon bags, and PCR/DGGE (denaturing gradient gel electrophoresis) with subsequent sequence analysis were used to monitor the dynamics of and identify bacteria associated with the substrates during 24 h of incubation. DGGE results showed that substrate samples collected from 10 min to 6 h had similar DGGE patterns, with up to 24 predominant bands to each sample, including 14 common bands to all samples, suggesting a rapid and stable colonisation by a highly diverse bacterial community. Substrate samples collected at 12 and 24 h showed similar DGGE patterns but had great difference in DGGE patterns from those collected at 10 min to 6 h, suggesting an apparent shift in bacterial community. Sequence analysis indicated that most substrate-associated bacteria were closely related to fibrolytic bacteria. In conclusion, a highly diverse and similar rumen bacterial community could immediately colonise to different substrates and remained stable during the initial 6 h of incubation, but experienced a marked change after 12 h of incubation. Italian ryegrass leaf, Italian ryegrass stem and rice straw were colonised with a similar bacterial community.

As a result of the recent application of DNA based technology to the investigation of maritime Antarctic freshwater lakes, patterns have begun to emerge in the bacterioplankton communities that dominate these systems. In this study, the bacterioplankton communities of five Antarctic and five Arctic freshwater lakes were assessed and compared with existing data in the literature, to determine whether emerging patterns in Antarctic lakes also applied to Arctic systems. Such a bipolar comparison is particularly timely, given the current interest in biogeography, the global distribution of microorganisms and the controversy over the global ubiquity hypothesis. In addition, it has recently been discovered that commonly encountered bacterial sequences, often originating from uncultivated bacteria obtained on different continents, form coherent phylogenetic freshwater clusters. In this study we encountered both identical sequences and sequences with a high degree of similarity among the bacterioplankton in lake water from both poles. In addition, Arctic freshwater lakes appeared to be dominated by some of the same groups of bacterioplankton thought to be dominant in Antarctic lakes, the vast majority of which represented uncultivated groups.

Both bacterial culture and molecular approaches were used to investigate the bacterial diversity inside the Chinese Antarctic Great Wall Station and in its adjacent area. Heterotrophic bacteria were isolated from the samples using a direct plating method. γ-Proteobacteria, Actinobacteria, Flavobacteria and Firmicutes were isolated from these samples. In the three water samples, Pseudomonas species were dominant. In soil samples, Flavobacterium, Bacillus or Arthrobacter species dominated. Escherichia coli strains were isolated only in two samples from inside the station. Total cell counts in the six soil samples were semi-quantified by Quantitative Competitive-PCR of the 16S rRNA gene copies. The soil samples contained 105 to 109 cells g−1. Denaturing gradient gel electrophoresis (DGGE) was used further to investigate the bacterial diversity in the soil samples. A wider range of bacterial diversity including α-Proteobacteria, β-Proteobacteria, δ-Proteobacteria, γ-Proteobacteria, Flavobacteria, Actinobacteria and unclassified bacteria was discovered.

Fungi can be found in almost any environment, and play important roles in ecosystem processes such as nutrient cycling and degradation. Despite their importance, the vast majority of fungi have not yet been isolated and identified. Due to the difficulties inherent in culture-based methods, fungal ecologists have turned to community fingerprinting techniques, which utilise signal molecules to profile the fungal members of an environmental sample without culturing. Commonly used signal molecules include chitin, ergosterol, membrane lipids and nucleic acids. Several DNA-based fingerprinting methods have been successfully applied to fungal communities, including D/TGGE (denaturing/temperature gradient gel electrophoresis), SSCP (single-stranded conformational polymorphism), RISA (ribosomal intergenic spacer analysis), and T-RFLP (terminal restriction length fragment polymorphism). These techniques allow the fungal ecologist to rapidly profile fungal populations in an ecosystem, without the need for laborious culturing or cloning.

Tams1 is the polymorphic immunodominant merozoite-piroplasm surface protein of Theileria annulata. Evidence for selection of divergent forms of Tams1 has been obtained recently. This study was performed to address whether selection takes place during persistent infection of the bovine host or during passage through the Hyalomma tick vector. Four calves were infected with a T. annulata isolate representing multiple parasite genotypes. The development of the parasite population was analysed by denaturing gradient gel electrophoresis (DGGE) using the Tams1 gene as a marker. In addition, the parasitaemia was measured by a semi-quantitative reverse line blot hybridization assay in order to correlate Tams1 variation to changes in parasitaemia. It was found that both parasitaemia and parasite population displayed limited variation during persistent infection. Ticks were allowed to acquire T. annulata during 2 periods of the bovine infection. Tams1 alleles detected in ticks fed during acute infection were identical to the population in the bovine host. However, ticks fed during the carrier status acquired parasites showing a single Tams1 isotype that represented, in several cases, a minor population in the bovine host at the time of infestation. Although only a limited number of ticks were studied, these preliminary data suggest that specific parasite genotypes may be selected during tick transmission from a carrier animal.