Pioneering particle-based strategy for isolating viable bacteria from multipart soil samples compatible with Raman spectroscopy
The study of edaphic bacteria is of great interest, particularly for evaluating soil remediation and recultivation methods. Therefore, a fast and simple strategy to isolate various bacteria from complex soil samples using poly(ethyleneimine) (PEI)-modified polyethylene particles is introduced. The research focuses on the binding behavior under different conditions, such as the composition, pH value, and ionic strength, of the binding buffer, and is supported by the characterization of the surface properties of particles and bacteria. The results demonstrate that electrostatic forces and hydrophobicity are responsible for the adhesion of target bacteria to the particles. Distinct advantages of the particle-based isolation strategy include simple handling, enrichment efficiency, and the preservation of viable bacteria. The presented isolation method allows a subsequent identification of the bacteria using Raman microspectroscopy in combination with chemometrical methods. This is demonstrated with a dataset of five different bacteria (Escherichia coli, Bacillus subtilis, Pseudomonas fluorescens, Streptomyces tendae, and Streptomyces acidiscabies) which were isolated from spiked soil samples. In total 92% of the Raman spectra could be identified correctly.
KeywordsBacteria adhesion Isolation of bacteria Identification of bacteria Soil samples Raman spectroscopy Poly(ethyleneimine) functionalization Polyethylene particles
We would like to thank Jan und Andrea Dellith (IPHT Jena) for performing the SEM measurements, Prof. Erika Kothe and Martin Reinicke (Friedrich Schiller University, Institute of Microbiology) for providing Streptomyces spp. cultures, and Tanja Bus (Friedrich Schiller University, Institute for Organic and Macromolecular Chemistry) for assistance with the Zeta potential measurements. Funding of the research projects MikroPlex (PE113-1) within the federal program “ProExzellenz” and BioInter (13022-715) by the Development Bank of Thuringia and the European Union (EFRE) is gratefully acknowledged. Furthermore, we thank the Federal Ministry of Education and Research (BMBF), Germany, for their financial support of InfectoGnostics (13GW0096F) and the InnoProfile-Transfer research group JBCI2.0 (03IPT513Y, Unternehmen Region).
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflicts of interest.
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