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γ-Hexachlorocyclohexane (γ-HCH) persists in the environment and is recalcitrant to microbial degradation. To determine the extent of the microbial potential for the degradation of γ-HCH the diversity of bacteria from 12 soil samples collected around insecticide- and pesticide-producing factories in Egypt were assessed and compared with biofilm communities grown on γ-HCH microcrystals. From all samples, highly diverse microbes were isolated, able to grow on γ-HCH as sole source of carbon. The same soil samples were used to inoculate γ-HCH microcrystals on a substratum in microcosms to grow biofilm communities. All soil samples formed multispecies biofilms on γ-HCH. Biofilms stained with Nile Red showed distinct cell clusters of high hydrophobicity, and it is speculated that these aggregates have a substantial role in the degradation of the hydrophobic substrate. While many Bacillus species were isolated, this group was almost absent in the different biofilm communities. The finding of cells with highly hydrophobic envelopes together with the differences in species composition between isolates and interacting microbial communities points to fundamental differences in the interaction with hydrophobic substrates of single strains and microbial communities. [ABSTRACT FROM AUTHOR]

Methanotrophs in the rhizosphere of rice field ecosystems attenuate the emissions of CH4 into the atmosphere and thus play an important role for the global cycle of this greenhouse gas. Therefore, we measured the activity and composition of the methanotrophic community in the rhizosphere of rice microcosms. Methane oxidation was determined by measuring the CH4 flux in the presence and absence of difluoromethane as a specific inhibitor for methane oxidation. Methane oxidation started on day 24 and reached the maximum on day 32 after transplantation. The total methanotrophic community was analysed by terminal restriction fragment length polymorphism (T-RFLP) and cloning/sequencing of the pmoA gene, which encodes a subunit of particulate methane monooxygenase. The metabolically active methanotrophic community was analysed by stable isotope probing of microbial phospholipid fatty acids (PLFA-SIP) using 13C-labelled CH4 directly added to the rhizospheric region. Rhizospheric soil and root samples were collected after exposure to 13CH4 for 8 and 18 days. Both T-RFLP/cloning and PLFA-SIP approaches showed that type I and type II methanotrophic populations changed over time with respect to activity and population size in the rhizospheric soil and on the rice roots. However, type I methanotrophs were more active than type II methanotrophs at both time points indicating they were of particular importance in the rhizosphere. PLFA-SIP showed that the active methanotrophic populations exhibit a pronounced spatial and temporal variation in rice microcosms. [ABSTRACT FROM AUTHOR]

A moorland soil site polluted with PCB showed a high diversity of metabolically active bacteria. Beside frequent types of 16S rRNA sequences similar to those of the species of Sphingomonas and the Acidobacterium phylum an unusual high number of sequences from the genus Burkholderia were found. Burkholderia was also the main genus in isolates enriched on biphenyl or various chlorobenzoates. In microcosm experiments sterilized surfaces exposed to PCB polluted soil always showed the presence of clay aggregates formed by bacteria attached to the substratum. The bacteria use the PCB loaded clay colloids as transport medium for the water insoluble substrate to get access to the carbon source. This is a novel mechanism of how bacteria deal with hydrophobic substrates. [ABSTRACT FROM AUTHOR]

Microbial consortia of composite biofilms, grown in surface water of acidic mining lakes near Lauchhammer, Germany, were investigated. The red-brown colored lake water was acidic (pH 2.5), had high concentrations of Fe(III), Al(III), and sulphate and low concentrations of dissolved organic matter. As a result the abundance of bacteria in the lake is with 104 cells mL-1 rather low. One input of organic material into the lake are autumnal leaves from trees, growing in the lakeside area. From aliquots of unfixed birch leave biofilms the 16S rRNA genes were amplified by PCR and community fingerprints were determined by single-strand conformation polymorphism (SSCP) analysis. Specific bands within the fingerprints were extracted from SSCP gels and sequenced for the taxonomical affiliation.These results were compared with those from the second type of biofilms which were grown on sterile substrata, floating submersed in surface waters of the lakes. By excising the bands from the gel and sequencing the individual bands bacterial taxa, common to both types of biofilms, were found but also some, which were only present in one type of biofilm. Ultrathin sectioned biofilms often showed bacteria associated with electron dense particles as main inorganic constituents. Elemental microanalysis by energy dispersive X-ray analysis (EDX) revealed them to contain iron, sulfur and oxygen as main elemental fractions and electron diffraction ring pattern analysis classified them to be schwertmannite. These bacteria and their interactions with each other as well as with the inorganic minerals formed in this lake generally is of great interest, in order to use these results for bioremediation applications. [ABSTRACT FROM AUTHOR]