Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1016/j.mimet.2013.05.006
Title (Primary) Recovery of soil unicellular eukaryotes: an efficiency and activity analysis on the single cell level
Author Lentendu, G.; Hübschmann, T.; Müller, S.; Dunker, S.; Buscot, F.; Wilhelm, C.
Source Titel Journal of Microbiological Methods
Year 2013
Department UMB; BOOEK; iDiv
Volume 95
Issue 3
Page From 463
Page To 469
Language englisch
Keywords Soil unicellular eukaryotes; Cell recovery; Flow cytometry; Cell sorting; Low abundant microorganisms
UFZ wide themes RU1

Eukaryotic unicellular organisms are an important part of the soil microbial community, but they are often neglected in soil functional microbial diversity analysis, principally due to the absence of specific investigation methods in the special soil environment. In this study we used a method based on high-density centrifugation to specifically isolate intact algal and yeast cells, with the aim to analyze them with flow cytometry and sort them for further molecular analysis such as deep sequencing. Recovery efficiency was tested at low abundance levels that fit those in natural environments (104 to 106 cells per g soil). Five algae and five yeast morphospecies isolated from soil were used for the testing. Recovery efficiency was between 1.5 to 43.16% and 2 to 30.2%, respectively, and was dependent on soil type for three of the algae. Control treatments without soil showed that the majority of cells were lost due to the method itself (58% and 55.8% respectively). However, the cell extraction technique did not much compromise cell vitality because a fluorescein di-acetate assay indicated high viability percentages (73.3% and 97.2% of cells, respectively). The low abundant algae and yeast morphospecies recovered from soil were cytometrically analyzed and sorted. Following, their DNA was isolated and amplified using specific primers. The developed workflow enables isolation and enrichment of intact autotrophic and heterotrophic soil unicellular eukaryotes from natural environments for subsequent application of deep sequencing technologies.

Persistent UFZ Identifier
Lentendu, G., Hübschmann, T., Müller, S., Dunker, S., Buscot, F., Wilhelm, C. (2013):
Recovery of soil unicellular eukaryotes: an efficiency and activity analysis on the single cell level
J. Microbiol. Methods 95 (3), 463 - 469 10.1016/j.mimet.2013.05.006