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Endospore-enriched sequencing approach reveals unprecedented diversity of Firmicutes in sediments Endospore-forming enrichment

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Wunderlin Tina, Junier Thomas, Roussel-Delif Ludovic, Jeanneret Nicole, Junier Pilar,
Project Metabolic capabilities of spore-forming microorganisms
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Original article (peer-reviewed)

Journal Environmental Microbiology Reports
Volume (Issue) 6(6)
Page(s) 631 - 639
Title of proceedings Environmental Microbiology Reports
DOI 10.1111/emi4.2014.6.issue-6

Abstract

We present a method for the physical isolation of endospores from environmental samples allowing the specific targeting of endospore-forming bacteria for sequencing (endospore-enriched community). The efficiency of the method was tested on lake sediment samples. After 16S rRNA gene amplicon sequencing, the composition in the endospore-enriched community was compared with the community from untreated control samples (whole community). In the whole community, Firmicutes had a relative abundance of 8% and 19% in the two different lake sediments. In contrast, in the endospore-enriched community, Firmicutes abundance increased to 90.6% and 83.9%, respectively, confirming the efficiency of the endospore enrichment. The relative abundance of other microbial groups that form spore-like resisting states (i.e. actinobacteria, cyanobacteria and myxococcales) was below 2% in the endospore-enriched community, indicating that the method is adapted to true endospores. Representatives from two out of the three known classes of Firmicutes (Bacilli and Clostridia) were detected and supposedly asporogenic groups (e.g. Ethanoligenes and Trichococcus) could be detected. The method presented here is a leap forward for ecological studies of endospore-forming Firmicutes. It can be applied to other types of samples in order to reveal the diversity and metabolic potential of this bacterial group in the environment.
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