High-throughput amplicon sequencing demonstrates extensive diversity of xylanase genes in the sediment of soda lake Dabusu
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.
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.
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.
KeywordsAmplicon sequencing Gene diversity High-throughput Metagenomics Soda lake Xylanase
This work was supported by the National Natural Science Foundation of China (31301406), the Marine Biological Engineering Platform for Innovative Services (2014FJPT02), and the China Scholarship Council (2017-3059).
Supplementary Figure 1—Length polymorphism of GH 10 xylanase fragments derived from the sediment of soda lake Dabusu.
Supplementary Figure 2—The top 10 abundant phyla of the GH10 fragment sequences derived from the sediment of soda lake Dabusu.
Supplementary Table 1—GH10 xylanase gene fragments and their closest relatives based on amino acid sequence identity.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
- Pelikan C, Herbold CW, Hausmann B, Muller AL, Pester M, Loy A (2016) Diversity analysis of sulfite- and sulfate-reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community-optimized bioinformatics. Environ Microbiol 18:2994–3009. https://doi.org/10.1111/1462-2920.13139 CrossRefGoogle Scholar
- Trindade-Silva AE, Rua CP, Andrade BG, Vicente AC, Silva GG, Berlinck RG, Thompson FL (2013) Polyketide synthase gene diversity within the microbiome of the sponge Arenosclera brasiliensis, endemic to the Southern Atlantic Ocean. Appl Environ Microbiol 79:1598–1605. https://doi.org/10.1128/aem.03354-12 CrossRefGoogle Scholar