Cataloguing the bacterial community of the Great Salt Plains, Oklahoma using 16S rRNA based metagenomics pyrosequencing

Abstract

The Great Salt Plains of Oklahoma (GSP) is an extreme region, a hypersaline environment from marine origin and a unique area of the Salt National Wild Refuge in the north-central region of Oklahoma. In this study we analyzed the diversity and distribution of bacteria in two habitats; vegetated areas (GAB) and salt flat areas (GAS) in the sediments of GSP using the high-throughput techniques of 16S rRNA gene amplicon (V1-V2 regions) metagenomics-454 pyrosequencing. The filtered sequences resulted to a total of 303,723 paired end reads were generated, assigned into 1646 numbers of OTUs and 56.4% G + C content for GAB, and a total of 144,496 paired end reads were generated, assigned into 785 numbers of OTUs and 56.7% G + C content for GAS. All the resulting 16S rRNA was of an average length ~ 187 bp, assigned to 37 bacterial phyla and candidate divisions. The abundant OTUs were affiliated with Proteobacteria (36.2% in GAB and 31.5% in GAS), Alphaproteobacteria (13.3% in GAB and 8.7% in GAS), Gammaproteobacteria (13% in GAB and 14.2% in GAS), Deltaproteobacteria (6.5% in GAB and 6.1% in GAS), Betaproteobacteria (2.6% in GAB and 1.14% in GAS), Bacteroidetes (16.8% in GAB and 24.3% in GAS), Chloroflexi (8.7% in GAB and 6% in GAS), Actinobacteria (8.5% in GAB and 5.8% in GAS) and Firmicutes (6.5% in GAB and 6.6% in GAS). This is the first study of a high resolution microbial phylogenetic profile of the GSP and the findings stipulate evidence of the bacterial heterogeneity that might be originated by surface and subsurface environments and better understanding of the ecosystem dynamics of GSP. Metagenome sequence data are available at NCBI with accession numbers; LT699840-LT700186.

Estudio del papel de las amebas de vida libre como reservorio de Helicobacter pylori y otras bacterias patógenas en aguas y alimentos mediante técnicas moleculares

“…Los estudios de las comunidades microbianas permiten conocer en profundidad la diversidad de los ecosistemas e incluso llegar a entender procesos microbiológicos complejos (Vanwonterghem et al, 2014). En los últimos años ha habido un gran incremento en el uso de estrategias de metagenómica de secuenciación dirigida para determinar la diversidad microbiana de diversos ambientes (Caporaso et al, 2012;Bhattacharjee et al, 2017;Gad, 2017). Uno de los pasos más críticos para llevar a cabo un buen análisis de amplicones del gen rRNA es la elección de los iniciadores (Klindworth et al, 2013).…”