Culture-dependent bacteria in commercial fishes: Qualitative assessment and molecular identification using 16S rRNA gene sequencing

Fish contamination has been extensively investigated along the Saudi coasts, but studies pertaining to bacterial pathogens are scarce. We conducted qualitative assessment and molecular identification of culture-dependent bacteria in 13 fish species from three coastal sites and a local fish market in Jeddah, Saudi Arabia. Bacterial counts of gills, skin, gut and muscle were examined on agar plates of Macconkey’s (Mac), Eosin Methylene Blue (EMB) and Thiosulfate Citrate Bile Salts (TCBS) culture media. Bacterial counts significantly differed between species, sources and feeding habits of examined fishes. Mugil cephalus exhibited higher counts on TCBS (all body parts), Mac (gills, muscle and gut) and EMB (gills and muscle). Fishes from Area I had higher bacterial loads, coinciding with those in seawater and sediment from the same site, indicating direct association between habitat conditions and the levels of bacterial contamination. By feeding habit, detritivorous fish harbored higher counts than herbivorous and carnivorous species. Bacterial counts of skin were higher in fish from market than field sites, and positively correlated with other body parts indicating the relation of surface bacterial load on the overall quality of fish. Rahnella aquatilis (Enterobacteriaceae) and Photobacterium damselae (Vibrionaceae) were among the dominant species from fish muscle based on 16S rRNA sequencing. These species are known human pathogens capable of causing foodborne illness with severe antibiotic resistance. Opportunistic pathogens, e.g. Hafnia sp. (Enterobacteriaceae) and Pseudomonas stutzeri (Pseudomonadaceae) also occurred in fish muscle. The inclusion of bacterial contamination in future monitoring efforts is thus crucial. Keywords: Marine environment, Fish, Bacterial contamination, Population count, Molecular identification, Sanger sequencin

Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora

Sponge diseases have been widely reported, yet the causal factors and major pathogenic microbes remain elusive. In this study, two individuals of the sponge Crella cyathophora in total that showed similar disease-like characteristics were collected from two different locations along the Red Sea coast separated by more than 30 kilometers. The disease-like parts of the two individuals were both covered by green surfaces, and the body size was much smaller compared with adjacent healthy regions. Here, using high-throughput pyrosequencing technology, we investigated the prokaryotic communities in healthy and disease-like sponge tissues as well as adjacent seawater. Microbes in healthy tissues belonged mainly to the Proteobacteria, Cyanobacteria and Bacteroidetes, and were much more diverse at the phylum level than reported previously. Interestingly, the disease-like tissues from the two sponge individuals underwent shifts of prokaryotic communities and were both enriched with a novel clade affiliated with the phylum Verrucomicrobia, implying its intimate connection with the disease-like Red Sea sponge C. cyathophora. Enrichment of the phylum Verrucomicrobia was also considered to be correlated with the presence of algae assemblages forming the green surface of the disease-like sponge tissues. This finding represents an interesting case of sponge disease and is valuable for further study

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

<div><p>In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.</p></div

Mineral components of a sediment core from the Atlantis II Deep of the Red Sea.

<p>The core (A) was obtained from the Atlantis II Deep (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140766#pone.0140766.g001" target="_blank">Fig 1</a>). The layers of interests were selected based on naked eye observation (B). XRD analysis shows that the major components were anhydrite, halite and sphalerite (C). The abundance and distribution of the other minor components FeS₂, CaCO₃, BaSO₄ and SiO₂ were indicated by + (<10%), ++ (10%-30%) and +++ (>30%), with halite content discounted (C). Minor components that could not be detected were labeled as 'n.d.'.</p

Pyrosequencing results of 16S rDNA amplicons.

<p>The sediment samples were obtained from the Atlantis II Deep (ABS) and Discovery Deep (DBS) in 2010 cruise. The depths of the samples were inferred from the number (cm) in the sample IDs. Effective numbers of the 16S rDNA pyrosequencing reads were determined with barcodes on them. The number of OTUs was calculated based on a 3% dissimilarity among the aligned reads.</p><p>Pyrosequencing results of 16S rDNA amplicons.</p

Geographic locations of two deep sea brine pools in the Red Sea.

<p>The sediment cores from Atlantis II (ABS) and Discovery (DBS) were sectioned for microbial studies. A barite crust was identified between 152 cm and 169 cm by mineral analysis on the ABS. The core of 268 KS was sampled in 1982 by Thisse et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140766#pone.0140766.ref019" target="_blank">19</a>]. The barite crust in the Atlantis II Deep was discovered by Sval'nov et al. (1984) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0140766#pone.0140766.ref010" target="_blank">10</a>].</p

Porosity and carbon sources in the ABS sediment layers.

<p>The sediment layers were obtained from the Atlantis II Deep (ABS). DOC represents dissolved organic carbon; IC refers to inorganic carbon. Nitrite and nitrate were undetectable.</p><p>Porosity and carbon sources in the ABS sediment layers.</p