Microcolony Cultivation on a Soil Substrate Membrane System Selects for Previously Uncultured Soil Bacteria

Traditional microbiological methods of cultivation recover less than 1% of the total bacterial species, and the culturable portion of bacteria is not representative of the total phylogenetic diversity. Classical cultivation strategies are now known to supply excessive nutrients to a system and therefore select for fast-growing bacteria that are capable of colony or biofilm formation. New approaches to the cultivation of bacteria which rely on growth in dilute nutrient media or simulated environments are beginning to address this problem of selection. Here we describe a novel microcultivation method for soil bacteria that mimics natural conditions. Our soil slurry membrane system combines a polycarbonate membrane as a growth support and soil extract as the substrate. The result is abundant growth of uncharacterized bacteria as microcolonies. By combining microcultivation with fluorescent in situ hybridization, previously “unculturable” organisms belonging to cultivated and noncultivated divisions, including candidate division TM7, can be identified by fluorescence microscopy. Successful growth of soil bacteria as microcolonies confirmed that the missing culturable majority may have a growth strategy that is not observed when traditional cultivation indicators are used

Cultivating previously uncultured soil bacteria using a soil substrate membrane system

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Microcolony Cultivation on a Soil-substrate Membrane System (SSMS)combined with FISH for Detection selects for hitherto Uncultured Soil Bacteria

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Methane Oxidising Bacteria as Environmental Indicators

This report focuses on methane oxidising bacteria (methanotrophs). The key function of methanotrophs as methane consumers and degraders of halogenated hydrocarbons bring them in the perspective of being useful indicators of environmental perturbations. Effects of climate on diversity and temperature adaptation as well as the capacity of different methanotrophs to degrade two atmospheric pollutants (chlorofluoromethanes) was investigated. None of the methanotrophs were found to be adapted for growth at permanently low temperatures although type I methanotrophs grew better at lower temperatures than the type II methanotrophs. Some of the methanotrophs were able to degrade dichlorofluoromethane while chlorodifluoromethane degradation was not demonstrated. No correlation was found between the degradation capacity and the origin of the isolates (landfill or wetland soil), or characteristics of their methane monooxygenase enzymes.The project did not identify a simple correlation between climatic variation or environmental stress and the variation in composition of the methanotroph community. More knowledge about temperature dependent interactions between type I and type II methanotrophs is needed before the composition of methanotrophs can be implemented as an indicator revealing ecological consequences of e.g. changes in climate

Spatial variability in bacterioplankton community composition at the Skagerrak-Kattegat Front

13 pages, 5 figures, 2 tablesThe distribution of bacterial heterotrophic production and cell concentrations in the world oceans is well documented. Nevertheless, information on the distribution of specific bacterial taxa and how this is influenced by environmental factors in separate sea areas is sparse. Here we report on bacterial community structure across the Skagerrak-Kattegat front. The front separates North Sea water from water with a Baltic Sea origin. We documented community differences across the front using denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified bacterial 16S ribosomal DNA and whole-genome DNA hybridization towards community DNA. Analysis of the community 'fingerprints' by DGGE revealed clustering of samples according to side of the front and depth. Consistent with these results, whole-genome DNA hybridization for 28 bacterial species isolated from the sampling region indicated that bacteria related to the Roseobacter clade and Bacteroidetes as well as prosthecate bacteria (e.g. Hyphomonas) showed distinct distribution patterns on each side of the front, and also with depth. Differences in bacterioplankton species composition across the frontal area were paralleled by differences in quantitative variables such as phytoplankton biomass (chl a), dissolved organic carbon, and bacterial production. Furthermore, we observed differences in more descriptive variables such as salinity range, bacterial growth-limiting nutrients and phytoplankton composition. We suggest that not only quantitative but also qualitative differences in variables that affect bacterial growth are required to cause divergence in bacterioplankton community composition between marine regionsPeer Reviewe