Diversity of Prokaryotic Community at a Shallow Marine Hydrothermal Site Elucidated by Illumina Sequencing Technology

Abstract

To investigate the prokaryotic community structure and composition in an active hydrothermal site, named Black Point, off Panarea Island (Eolian Islands, Italy), we examined sediment and fluid samples, differing in temperature, by a massive parallel sequencing (Illumina) technique targeting the V3 region of the 16S rRNA gene. The used technique enabled us to detect a greater prokaryotic diversity than that until now observed and to reveal also microorganisms occurring at very low abundance (≤0.01 %). Most of sequences were assigned to Bacteria while Archaea were a minor component of the microbial community in both low- and high-temperature samples. Proteobacteria (mainly consisting of Alpha-, Gamma-, and Epsilonproteobacteria) dominated among all samples followed by Actinobacteria and Bacteroidetes. Analyzed DNA obtained from samples taken at different temperatures indicated the presence of members of different dominant genera. The main differences were observed between sediment samples where Rhodovulum and Thiohalospira prevailed at high temperature, while Thalassomonas and Sulfurimonas at low temperature. Chlorobium, Acinetobacter, Sulfurimonas, and Brevundimonas were abundant in both low- and high-temperature fluid samples. Euryarchaeota dominated the archaeal community in all samples. Classes of Euryarchaeota embracing hyperthermophilic members (Thermococci and Thermoplasmata) and of Crenarchaeota (Thermoprotei) were more abundant in high-temperature samples. A great number of sequences referred to Bacteria and Archaea still remained unaffiliated, indicating that Black Point site represents a rich source of so-far uncharted prokaryotic diversity.

Presence of diverse Candidatus Methylomirabilis oxyfera -like bacteria of NC10 phylum in agricultural soils

“…; Lentini et al . ). In the present study, the 2 × 300 bp paired‐end protocol that developed by Fadrosh et al .…”

“…The high diversity of NC10 phylum bacterial 16S rRNA genes observed in the examined soil cores could be attributed to the high-throughput sequencing technology applied in this study. As compared with the clone libraries using the specific primers, the Illumina MiSeq system using the universal primers has high depth coverage of microbial diversity and can detect both abundant and rare microbes in diverse environments (Bartram et al 2011;Gaporaso et al 2012;Lentini et al 2014). In the present study, the 2 9 300 bp paired-end protocol that developed by Fadrosh et al (2014) was applied, and the average length of the recovered 16S rRNA gene sequences was 400-500 bp by using this protocol.…”

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

“…Illumina-based sequencing has found applications in characterizing the bacterial community in various natural and man-made environments, such as drinking water biofilter (Liao et al 2014), biofilm on drinking water distribution pipe (Wu et al 2014), anaerobic digestion sludge (Yang et al 2014), tropical rainforest leaf litter , river water (Staley et al 2013), soil (Rubin et al 2013), and mangrove wetland sediment (Jiang et al 2013). In addition, Illumina-based sequencing has also had several applications to characterize archaeal community in natural and man-made environments, such as fluid and sediment at a shallow marine hydrothermal site (Lentini et al 2014), biogas-producing and phenol-degrading bioreactor (Ju and Zhang 2014), and reservoir sediment (Zhang and Huang 2013). However, information on Illumina MiSeq sequencing of microbial community in lake water or sediment is still very limited.…”

High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA

“…In contrast, the nonfunctional 16S rRNA gene is ubiquitous, does not have this limitation, and, hence, may be better for assessment of aerobic methanotroph diversity in natural environments. Through the use of barcoded PCR primers targeting the V3 region of microbial 16S rRNA gene, the Illumina ® MiSeq multiplex NGS platform has high depth coverage of microbial diversity and can detect both abundant and rare microbes in diverse environments [ 33 , 34 , 35 , 36 ]. NGS (Next-Generation Sequencing) technology allows the assessment of microbiota both qualitatively (to determine diversity) and quantitatively (to determine abundance based on the frequency of sequences detected) to reveal and contrast microbial communities between habitats.…”