Dumpster diving for diatom plastid 16S rRNA genes

PeerJ

article

Krista L. Bonfantine¹  Stacey M. Trevathan-Tackett¹  Ty G. Matthews¹  AnaNeckovic²  Han Ming Gan¹ 

[1] Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University;School of Life and Environmental Sciences, Deakin University;GeneSEQ Sdn Bhd

关键词: 16S rRNA;    Metabarcoding;    Algae;    Biofilm;    Bioindicator;    Cyanobacteria;    Bacillariophyta;    Diatom;   

DOI  :  10.7717/peerj.11576

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia.

【 授权许可】

CC BY