Variations in Microbial Community Structure through  the Stratified Water Column in the Tyrrhenian Sea  (Central Mediterranean)

Smedile, Francesco; Scarfi, Simona; Domenico, Emilio De; Garel, Marc; Glanville, Helen; Gentile, Gabriella; Cono, Violetta La; Tamburini, Christian; Giuliano, Laura; Yakimov, Michail M.

doi:10.3390/jmse3030845

Cited by 4 publications

(3 citation statements)

References 63 publications

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“…The strains from Puerto Rico salterns originate from the study of Cantrell et al (2006). Seawater and deep sea strains were collected in 2013 during the DEEP-PRES-SURE Cruise on board the R/V Urania (Smedile et al 2015), from water columns 25-2500 m in depth, sampled at four stations in the Mediterranean Sea: Station Vector in the Tyrrhenian Sea (39°32′00.6″N 13°22′28.5″ E, Station KM3 in the Ionian Sea (36°30′61.3″N 15°40′ 59.9″E), and above the anoxic hypersaline lakes L' Atalante (35°18′92″N 21°23′92″E) and Medee (34°24′00″N 22°26′99″E), in the central and south Mediterranean Sea, respectively (de Leo et al 2018). Strains from corals in the Pacific Ocean (China) were isolated by Luo et al (2017).…”

Section: Isolation Of Strains and Sampling Sitesmentioning

confidence: 99%

The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi

et al. 2019

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The polymorphic black yeast Hortaea werneckii (Capnodiales, Ascomycota) is extremely halotolerant (growth from 0 to 30% [w/v] NaCl) and has been extensively studied as a model for halotolerance in Eukaryotes for over two decades. Its most frequent sources are hypersaline environments and adjacent sea-water habitats in temperate, subtropical and tropical climates. Although typically saprobic, H. werneckii can also act as a commensal coloniser on human skin, causing tinea nigra on hands and soles. Here, we report that addition of NaCl to culture media expands the growth range of H. werneckii to 37 °C, which explains its colonisation of human skin, with its increased salinity. The morphological and physiological plasticity/ versatility of H. werneckii indicate that a species complex might be involved. This was investigated in this polyphasic taxonomic analysis based on the global diversity of H. werneckii strains collected from hypersaline environments, and from humans and animals. Analysis of D1/ D2domains of 28S and internal transcribed spacer rDNA revealed 10 and 17 genotypes, respectively, that were not always compliant. The genotypes have global distributions. Human and environmental strains with the same genotypes are intermingled. Due to the limited number of phylogenetically informative characters in the ribosomal DNA dataset, the partial genes encoding for β-tubulin (BTB) and mini-chromosome maintenance protein (MCM7) were also sequenced. The use of these genes was hampered by ambiguous sequences obtained by Sanger sequencing, as a consequence of the diploid and highly heterozygous genome of many H. werneckii strains. Analysis of the BTB and MCM7 genes showed that in some cases two copies of the gene from the same genome are positioned in distant phylogenetic clusters of the intraspecific gene tree. Analysis of whole-genome sequences of selected H. werneckii strains generally confirmed the phylogenetic distances estimated on the basis of ribosomal genes, but also showed substantial reticulation within the phylogenetic history of the strains. This is in line with the hypothesis that the diploid genomes of H. werneckii were formed by hybridizations, which have sometimes occurred between relatively divergent strains.

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Section: Isolation Of Strains and Sampling Sitesmentioning

confidence: 99%

The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi

et al. 2019

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“…Driving mechanisms for shelf-slope exchange processes that influence biological activities can be external, such as processes driven by regional seasonal variation in the mean winds and distant river plumes moving into the area, or internal to the area of interest, such as those that generate fronts due to the interaction between local currents and tides with the changing bathymetry at the shelf break (see Palma et al [3]). To investigate these processes we require high resolution measurements of physical properties such as temperature, salinity, density, as well as ocean circulation model outputs that describe the dynamics of coastal waters, all of which can potentially influence biological dynamics, see for example Baltazar-Soares et al [4] and Smedile et al [5].…”

Section: Introductionmentioning

confidence: 99%

Vertical Structure of the Water Column at the Virgin Islands Shelf Break and Trough

Seijo-Ellis

David

Salmun

2019

JMSE

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The steep US Virgin Islands Shelf Break (VISB) and the Virgin Islands Trough (VIT) at the Northeastern Caribbean Sea comprise a dynamic region of the Atlantic Ocean. In situ oceanographic data collected in the region during April 2017 were used to examine the spatial variability in temperature, density, salinity, and relative Chlorophyll-a. Analysis of data from the upper 300 m of the water column, that include deep and shallow water stations in the shelf break region, shows strong stratification of the water column. Stations shallower than 800 m along the shelf break are more variable in temperature, density, and salinity than those that are deeper than 800 m along the trough. For shallow stations, the mixed layer depth deepens along-shelf from West to East while at the deep stations the opposite occurs. Salinity maxima exhibit more variability in depth and range of values in the shallow stations compared to deep stations. Six different types of water masses that contribute to the strong stratification in the region were identified in our study: Caribbean Surface Water, Subtropical Underwater, Sargasso Sea Water, Tropical Atlantic Central Water, Antarctic Intermediate Water, and North Atlantic Deep Water. The upper level Caribbean Surface Water, Subtropical Underwater, and Sargasso Sea Water are present in shallow stations, indicating potential meridional intrusions from the VIT to the VISB which may not be resolved by current ocean circulation models and are not captured in satellite data. The analysis presented here indicates that competing physical processes may be controlling the vertical structure of the water column in the region and merit further examination.

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“…These organisms were first described in 16S rRNA gene clone libraries from marine sponges, and subsequently were found in marine plankton (Thiel, 2006 ; Thiel et al, 2007a , b ). In a depth profile from the central Mediterranean, E01-9C-26 clones were the only Gammaproteobacteria group found at every depth in both DNA and RNA-based clone libraries (Smedile et al, 2015 ). E01-9C-26 was also reported to be a major contributor to both DNA and RNA libraries from the water column in the Adriatic Sea and was present to a lesser degree in marine snow libraries from the same site (Vojvoda et al, 2014 ).…”

Section: Resultsmentioning

confidence: 99%

Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface

et al. 2018

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Optofluidic single-cell genome amplification was used to obtain genome sequences from sub-micron cells collected from the euphotic and mesopelagic zones of the northwestern Sargasso Sea. Plankton cells were visually selected and manually sorted with an optical trap, yielding 20 partial genome sequences representing seven bacterial phyla. Two organisms, E01-9C-26 (Gammaproteobacteria), represented by four single cell genomes, and Opi.OSU.00C, an uncharacterized Verrucomicrobia, were the first of their types retrieved by single cell genome sequencing and were studied in detail. Metagenomic data showed that E01-9C-26 is found throughout the dark ocean, while Opi.OSU.00C was observed to bloom transiently in the nutrient-depleted euphotic zone of the late spring and early summer. The E01-9C-26 genomes had an estimated size of 4.76–5.05 Mbps, and contained “O” and “W”-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes. Metabolic reconstruction indicated E01-9C-26 are likely versatile methylotrophs capable of scavenging C1 compounds, methylated compounds, reduced sulfur compounds, and a wide range of amines, including D-amino acids. The genome sequences identified E01-9C-26 as a source of “O” and “W”-type monooxygenase genes related to methane and ammonium monooxygenases that were previously reported from ocean metagenomes, but are of unknown function. In contrast, Opi.OSU.00C genomes encode genes for catabolizing carbohydrate compounds normally associated with eukaryotic phytoplankton. This exploration of optofluidics showed that it was effective for retrieving diverse single-cell bacterioplankton genomes and has potential advantages in microbiology applications that require working with small sample volumes or targeting cells by their morphology.

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Variations in Microbial Community Structure through the Stratified Water Column in the Tyrrhenian Sea (Central Mediterranean)

Cited by 4 publications

References 63 publications

The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi

The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi

Vertical Structure of the Water Column at the Virgin Islands Shelf Break and Trough

Optofluidic Single-Cell Genome Amplification of Sub-micron Bacteria in the Ocean Subsurface

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