Microbial communities of upland peat swamps were no different 1 year after a hazard reduction burn

Fire in wetlands is poorly understood, yet hazard reduction burns are a common management practice and bushfires are becoming increasingly prevalent because of climate change. Fire may have long-lasting implications for the microbial component of these wetland ecosystems that regulate carbon and nutrient cycling. The extremely fire-prone Blue Mountains World Heritage Area in south-eastern Australia contains hundreds of endangered peat-forming upland swamps that regularly experience both bushfires and hazard reduction burns. In a before–after control–­impact study, we surveyed the sediment microbial community of these swamps to test the impact of a low-intensity hazard reduction burn. Along with sediment pH, moisture and organic content, we measured gene abundances including those relating to carbon cycling (quantitative PCR (qPCR) of pmoA, mcrA, bacterial 16S rRNA and archaeal 16S rRNA), and bacteria community fingerprint (terminal restriction fragment length polymorphism (T-RFLP)). One year after the hazard reduction burn, there were no significant differences in the gene abundances or microbial community fingerprint that could be attributed to the fire, suggesting that the hazard reduction burn did not have a long-term impact on these microbial communities.

Microbial diversity in grape musts from Austrian and South African grape varieties and regions

Vitis vinifera is one of the most widely planted crops and holds important economic value in South Africa and Austria. Grapes obtained from this plant harbour a complex fungal community which plays a crucial role in the wine fermentation process and influences wine flavour and aroma. For many years the contributions of the natural yeasts has been eclipsed by the use of active dry yeast (ADY) inoculant, mainly of the species Saccharomyces cerevisiae. However, recent studies show a growing interest in deciphering the natural microbial diversity and in promoting its persistence during fermentation in order to enhance wine typicity. The current preliminary study aims to provide a first broad assessment of the fungal community fingerprint of different grape varietals from different wine producing areas in Austria and South Africa through Automated Ribosomal Intergenic Spacer Analysis (ARISA). The ARISA profiles separated the samples according to country of origin, and suggested some regional and varietal separation within each country. Future work will evaluate the contribution of these fungal communities to wine chemical composition and sensorial distinctness.

Web-Based Phylogenetic Assignment Tool for Analysis of Terminal Restriction Fragment Length Polymorphism Profiles of Microbial Communities

ABSTRACT Culture-independent DNA fingerprints are commonly used to assess the diversity of a microbial community. However, relating species composition to community profiles produced by community fingerprint methods is not straightforward. Terminal restriction fragment length polymorphism (T-RFLP) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (T-RF) sizes through the use of web-based resources that predict T-RF sizes for known bacteria. The process quickly becomes computationally intensive due to the need to analyze profiles produced by multiple restriction digests and the complexity of profiles generated by natural microbial communities. A web-based tool is described here that rapidly generates phylogenetic assignments from submitted community T-RFLP profiles based on a database of fragments produced by known 16S rRNA gene sequences. Users have the option of submitting a customized database generated from unpublished sequences or from a gene other than the 16S rRNA gene. This phylogenetic assignment tool allows users to employ T-RFLP to simultaneously analyze microbial community diversity and species composition. An analysis of the variability of bacterial species composition throughout the water column in a humic lake was carried out to demonstrate the functionality of the phylogenetic assignment tool. This method was validated by comparing the results generated by this program with results from a 16S rRNA gene clone library.

Spatial Changes in the Bacterial Community Structure along a Vertical Oxygen Gradient in Flooded Paddy Soil Cores

ABSTRACT Molecular ecology techniques were applied to assess changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores. Microsensor measurements showed that oxygen was depleted from 140 μM at the floodwater/soil interface to nondetectable amounts at a depth of approximately 2.0 mm and below. Bacterial 16S rRNA gene (rDNA)-based community fingerprint patterns were obtained from 200-μm-thick soil slices of both the oxic and anoxic zones by using the T-RFLP (terminal restriction fragment length polymorphism) technique. The fingerprints revealed a tremendous shift in the community patterns in correlation to the oxygen depletion measured with depth. 16S rDNA clone sequences recovered from the oxic or anoxic zone directly corresponded to those terminal restriction fragments which were highly characteristic of the respective zone. Comparative sequence analysis of these clones identified members of the α and β subclasses of Proteobacteria as the abundant populations in the oxic zone. In contrast, members of clostridial cluster I were determined to be the predominant bacterial group in the oxygen-depleted soil. The extraction of total RNA followed by reverse transcription-PCR of the bacterial 16S rRNA and T-RFLP analysis resulted for both oxic and anoxic zones of flooded soil cores in community fingerprint patterns similar to those obtained by the rDNA-based analysis. This finding suggests that the microbial groups detected on the rDNA level are the metabolically active populations within the oxic and anoxic soil slices examined.