期刊
BIOLOGY DIRECT
卷 10, 期 -, 页码 -出版社
BMC
DOI: 10.1186/s13062-015-0065-6
关键词
Archaea; Thermoproteales; Introns; 16S rRNA; Geothermal; Metagenomics
类别
资金
- DOE-Pacific Northwest National Laboratory [112443]
- Department of Energy (DOE)-Joint Genome Institute Community Sequencing Program [CSP 787081]
- NSF IGERT Program [DGE 0654336]
- Genomic Science Program, Office of Biological and Environmental Research, U.S. DOE
Background: Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which universal archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Results: Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. Conclusions: The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different universal 16S rRNA primers employed in environmental microbial community analysis.
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