High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu.

ABSTRACT

OBJECTIVE: To explore the diversity of glycoside hydrolase family 10 xylanase genes in the sediment of soda lake Dabusu by using high-throughput amplicon sequencing based on the Illumina HiSeq2500 platform. RESULTS: A total of 227,420 clean reads, representing approximately 49.5 M bp, were obtained. Operational taxonomic unit (OTU) classification, with a 95% sequence identity cut-off, resulted in 467 OTUs with 392 annotated as GH10 xylanase, exhibiting 35-99% protein sequence identity with their closest-related xylanases in GenBank. Above 75% of the total OTUs demonstrated less than 80% identity with known xylanases. In addition, xylanases derived from the sediment were found to be affiliated to 12 different phyla, with Bacteroidetes, Proteobacteria, Actinobacteria, Firmicutes, Verrucomicrobia, and Basidiomycota being the dominant phyla. Moreover, barcode sequence had a major effect on abundance with only a minor effect on diversity. CONCLUSIONS: High-throughput amplicon sequencing offers insight into xylanase gene diversity at a substantially higher resolution and lesser cost than library cloning and Sanger sequencing, facilitating a more thorough understanding of xylanase distribution and ecology.