Publication Details

Category Text Publication
Reference Category Journals
DOI 10.3390/biology10070569
Licence creative commons licence
Title (Primary) Identifying hidden viable bacterial taxa in tropical forest soils using amplicon sequencing of enrichment cultures
Author Sansupa, C.; Wahdan, S.F.M.; Disayathanoowat, T.; Purahong, W.
Source Titel Biology
Year 2021
Department BOOEK
Volume 10
Issue 7
Page From art. 569
Language englisch
Topic T5 Future Landscapes
Keywords eDNA; enrichment culture; amplicon sequencing; soil bacteria; bacterial community; culture-dependent; culture-independent; bacterial function
Abstract This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.
Persistent UFZ Identifier
Sansupa, C., Wahdan, S.F.M., Disayathanoowat, T., Purahong, W. (2021):
Identifying hidden viable bacterial taxa in tropical forest soils using amplicon sequencing of enrichment cultures
Biology-Basel 10 (7), art. 569 10.3390/biology10070569