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Application of the Dynamic Cultivation System for Microorganisms — A New Way to Culture the Unculturables

Published online by Cambridge University Press:  01 January 2024

René Kaden ,
Eve Menger-Krug ,
Katja Emmerich ,
Kerstin Petrick  and
Peter Krolla-Sidenstein
René Kaden*
Affiliation:
Department of Medical Sciences, Uppsala University, Dag Hammarskjöldsväg 17, 75185, Uppsala, Sweden
Eve Menger-Krug
Affiliation:
Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Herrmann-von-Helmholtz-Platz 1, 76131, Eggenstein-Leopoldshafen, Germany
Katja Emmerich
Affiliation:
Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Herrmann-von-Helmholtz-Platz 1, 76131, Eggenstein-Leopoldshafen, Germany
Kerstin Petrick
Affiliation:
Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Herrmann-von-Helmholtz-Platz 1, 76131, Eggenstein-Leopoldshafen, Germany
Peter Krolla-Sidenstein
Affiliation:
Karlsruhe Institute of Technology (KIT), Institute of Functional Interfaces (IFG), Herrmann-von-Helmholtz-Platz 1, 76131, Eggenstein-Leopoldshafen, Germany
*
*E-mail address of corresponding author: [email protected]
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Abstract

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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.

Keywords

ClayDGGEDCSEcologyMicrobial DiversitySequencing
Type
Article
Information
Clays and Clay Minerals , Volume 62 , Issue 3 , June 2014 , pp. 203 - 210
Copyright
Copyright © Clay Minerals Society 2014

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