Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean

Abstract

Cobalt-rich crusts are important metallic mineral resources with great economic potential, usually distributed on seamounts located in the Pacific Ocean. Microorganisms are believed to play a role in the formation of crusts as well as in metal cycling. To explore the microbial diversity related to cobalt-rich crusts, 16S ribosomal RNA gene clone libraries were constructed from three consecutive sediment layers. In total, 417 bacterial clones were obtained from three bacterial clone libraries, representing 17 distinct phylogenetic groups. Proteobacteria dominated in the bacterial communities, followed by Acidobacteria and Planctomycetes. Compared with high bacterial diversity, archaea showed a remarkably low diversity, with all 137 clones belonging to marine archaeal group I except one novel euryarchaeotal clone. The microbial communities were potentially involved in sulfur, nitrogen and metal cycling in the area of cobalt-rich crusts. Sulfur oxidation and metal oxidation were potentially major sources of energy for this ecosystem. This is the first reported investigation of microbial diversity in sediments associated with cobalt-rich crusts, and it casts fresh light on the microbial ecology of these important ecosystems.

Microbial electrolysis cells with biocathodes and driven by microbial fuel cells for simultaneous enhanced Co(II) and Cu(II) removal

“…7(a)). This agreed with the previous study in cobalt-rich deep-sea sediment [35]. Other major bacterial phyla included Firmicutes (14.0%), Bacteroidetes (6.1%), Tenericutes (2.5%), Lentisphaerae (1.4%), Synergistetes (1.0%), and other 8 minor phyla (0.7%).…”

“…Other major bacterial phyla included Firmicutes (14.0%), Bacteroidetes (6.1%), Tenericutes (2.5%), Lentisphaerae (1.4%), Synergistetes (1.0%), and other 8 minor phyla (0.7%). Despite the ubiquitous majority of these phyla in BESs, the phyla Firmicutes and Bacteroidetes were more abundant than those in conventional cobalt-rich sites [35], implying the providence of a good environment for these phyla. Besides the classified phyla, 6.5% of the total reads was unclassified on the phylum level.…”

Archaea in Organic-Lean and Organic-Rich Marine Subsurface Sediments: An Environmental Gradient Reflected in Distinct Phylogenetic Lineages

“…Some oligotrophic sediments are problematic since their microbial community structure and geochemical characteristics overlap with those of hydrothermal sediments (Inagaki et al, 2001; Nercessian et al, 2005; Li et al, 2008) and the deep-water column. Several studies of oligotrophic abyssal sediments (Wang et al, 2004; Xu et al, 2005; Gillan and Danis, 2007) sampled only surficial sediments and recovered the same archaeal phylum, the Marine Group I Crenarchaeota, that is presumed dominant in the overlying water column (e.g., Karner et al, 2001; Church et al, 2003; Agogué et al, 2008; Durbin and Teske, 2010).…”

“…Relatively few studies have surveyed the archaeal diversity of abyssal or ocean gyre sediments to date. A more or less comprehensive list includes: Vetriani et al, 1999; Inagaki et al, 2001; Sørensen et al, 2004; Wang et al, 2004; Nercessian et al, 2005; Wang et al, 2005; Xu et al, 2005; Gillan and Danis, 2007; Li et al, 2008; Tao et al, 2008; Roussel et al, 2009; Wang et al, 2010a, Liao et al, 2011; Durbin and Teske, 2010, 2011. Most of these studies are limited to shallow sediments (<1 m deep) or to few depth intervals.…”

eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses

“…Such diagrams have also been used in various other disciplines, such as: neuroscience [17]; biosciences [18]; microbiology [19]; botany [20]; ecology [21]; public health [22]; museum conservation [23]; criminology [24]; information search and filtering [25]. Scientific work that specifically focuses on the generation of an area-proportional Venn diagram for the quantification of the relationships between studied data sets is also available (e.g., [26]–[28]).…”