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- Kaden, Rene, et al.
(författare)
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Application of the Dynamic Cultivation System for Microorganisms – a new way to culture the unculturables
- 2014
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Ingår i: Clays and clay minerals. - 0009-8604 .- 1552-8367. ; 62:3-4, s. 203-210
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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- Kaden, Rene, et al.
(författare)
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The Dynamic Cultivation System : A new method for the detection of temporal shifts in microbial community structure in clay
- 2012
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Ingår i: Applied Clay Science. - : Elsevier BV. - 0169-1317 .- 1872-9053. ; 65–66:1, s. 53-56
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Tidskriftsartikel (refereegranskat)abstract
- A major problem in the analysis of natural bacterial populations is that probably less than 1% of species were so far cultured and described. In order to overcome this disadvantage, culture independent DNA based methods, such as comparison of PCR-amplified 16S rRNA genes, are used for the description of the bacterial diversity and the identification of various species. Unfortunately, each molecule of DNA, including those of dead organisms and allochthonous genomes, can be detected by PCR-based molecular fingerprint techniques within a sample besides the DNA of native organisms. Hence, an adequate image of the actually active population composition cannot be projected with these methods. An additional challenge is the extraction of DNA from charged particles and the presence of inhibitors for downstream molecular analyses. This study reports the results of a new cultivation approach that allows to overcome these problems and to obtain almost total environmental DNA of microorganisms for subsequent genetic DNA fingerprint techniques.This new approach, the Dynamic Cultivation System (DCS) is characterized by special nutrient availability to simulate the bacterial natural habitat and the cell–cell interaction for various processes, such as collective degradation of compounds.The DCS was applied in combination with the genetic fingerprint technique Denaturing Gradient Gel Electrophoresis (DGGE) to study changes in the population composition during an alteration process of clay. The results indicate a changing bacterial diversity over time which seems to correlate to the changing pH in the clay samples in situ. This effect was most evident after cultivation on the DCS.
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