Diversity of gene cassettes and the abundance of the class 1 integron-integrase gene in sediment polluted by metals

• Published in: Extremophiles : life under extreme conditions Vol. 20; no. 3; pp. 283 - 289
• Main Authors: Oliveira-Pinto, Clarisse, Costa, Patrícia S., Reis, Mariana P., Chartone-Souza, Edmar, Nascimento, Andréa M. A.
• Format: Journal Article
• Language: English
• Published: Tokyo Springer Japan 01-05-2016; Springer Nature B.V
• Subjects: Antibiotic resistance; Arsenic - analysis; Bacteria; Bacteroidetes - genetics; Bacteroidetes - isolation & purification; Biochemistry; Biomedical and Life Sciences; Biotechnology; Contaminated sediments; Deoxyribonucleic acid; DNA; Dry season; Environmental Pollution; Genes, Bacterial; Genetic diversity; Genetic Variation; Geologic Sediments - chemistry; Geologic Sediments - microbiology; Heavy metals; Integrases - genetics; Iron - analysis; Life Sciences; Microbial Ecology; Microbiology; Microbiota; Original Paper; Proteobacteria - genetics; Proteobacteria - isolation & purification; Rainy season; Seasons; Sediment pollution; Space life sciences; Gene cassette; Arsenic; gene; Class 1 integron; qPCR; Iron; Metal; Freshwater sediment; intI gene
• ISSN: 1431-0651; 1433-4909
• DOI: 10.1007/s00792-016-0820-3

The integron-gene cassette system has typically been associated with antibiotic-resistant pathogens. However, the diversity of gene cassettes and the abundance of class 1 integrons outside of the clinical context are not fully explored. Primers targeting the conserved segments of
attC
recombination sites were used to amplify gene cassettes from the sediment of the Mina stream, which exhibited a higher degree of stress to metal pollution in the dry season than the rainy season. Of the 143 total analyzed sequences, 101 had no matches to proteins in the database, where cassette open reading frames could be identified by homology with database entries. There was a predominance of sequences encoding essential cellular functions. Each season that was sampled yielded a specific pool of gene cassettes. Real-time PCR revealed that 8.5 and 41.6 % of bacterial cells potentially harbored a class 1 integron in the rainy and dry seasons, respectively. In summary, our findings demonstrate that most of the gene cassettes have no ascribable function and, apparently, historically metal-contaminated sediment favors the maintenance of bacteria containing the
intI1
gene. Thus, the diversity of gene cassettes is far from being fully explored deserving further attention.