scholarly journals Building a high-quality reference genome assembly for the the eastern Mediterranean Sea invasive sprinter Lagocephalus sceleratus (Tetraodontiformes, Tetraodontidae)

2020 ◽  
Author(s):  
Theodoros Danis ◽  
Alexandros Tsakogiannis ◽  
Jon B. Kristoffersen ◽  
Daniel Golani ◽  
Dimitris Tsaparis ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Genome Assembly ◽  
Eastern Mediterranean ◽  
Western Mediterranean ◽  
High Quality ◽  
Total Size ◽  
Western Mediterranean Sea ◽  
Invasive Biology ◽  
The Family ◽  
Lagocephalus Sceleratus

ABSTRACTThe Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. However, the genomic resources and especially reference assemblies are sparse for the members of the family. In this study, we focus on the silver-cheeked toadfish (Lagocephalus sceleratus) a well-known ‘invasive sprinter’ that has invaded and spread throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal within a decade. We sequenced the genome of L. sceleratus using a single MinION flow cell for the main assembly, and Illumina reads for polishing the assembly. The resulted assembly consisted of 241 contigs (N50 = 11,3 Mb) with a total size of 360 Mb and yielded 98% BUSCO completeness. The high-quality genome assembly built here is expected to set the ground for future studies on this focal species’ invasive biology.

scholarly journals Parasites of the head of Scomber colias (Osteichthyes: Scombridae) from the western Mediterranean Sea

2014 ◽  
Vol 59 (1) ◽  
Author(s):  
Salvatore Mele ◽  
Maria Pennino ◽  
Maria Piras ◽  
José Bellido ◽  
Giovanni Garippa ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Eastern Mediterranean ◽  
Western Mediterranean ◽  
Parasite Fauna ◽  
Point Of View ◽  
Published Data ◽  
Multivariate Techniques ◽  
Western Mediterranean Sea ◽  
Scomber Colias ◽  
Non Parametric

AbstractThe metazoan parasite assemblage of the head of 30 specimens of the Atlantic chub mackerel (Scomber colias) from the western Mediterranean Sea was analysed. Eight species of parasites were found, four mazocraeid monogeneans: Grubea cochlear (prevalence = 10%), Kuhnia scombercolias (59%), K. scombri (52%), Pseudokuhnia minor (86%); three didymozoid trematodes: Nematobothrium cf. faciale (21%), N. filiforme (41%), N. scombri (7%); and one laerneopodid copepod: Clavelissa scombri (7%). Results were compared with previously published data from 14 localities of the eastern Mediterranean Sea and the Atlantic Ocean, using non-parametric univariate and multivariate analyses, and the whole parasite fauna of S. colias was compared with that of the congeners (S. australasicus, S. japonicus and S. scombrus). Parasites showed to reflect the biogeographical and phylogenetic history of host. From a methodological point of view, the use of both non-parametric univariate and multivariate techniques proved to be effective tools to detect dissimilarities between parasite assemblages.

Feeding Habits of Alepocephalus Rostratus (Pisces: Alepocephalidae) in the Western Mediterranean Sea

1998 ◽  
Vol 78 (4) ◽  
pp. 1295-1306 ◽  
Author(s):  
M. Carrassón ◽  
J. Matallanas
Keyword(s):  
Mediterranean Sea ◽  
Prey Item ◽  
Narrow Range ◽  
Feeding Habits ◽  
Western Mediterranean ◽  
Western Mediterranean Sea ◽  
The Family ◽  
Different Seasons ◽  
Scarcity Of Resources ◽  
Important Fish

The present study examines the feeding habits of Alepocephalus rostratus, the only species of the family Alepocephalidae in the Mediterranean Sea and the second most important fish species, in terms of biomass, inhabiting the deep slope of the Catalan Sea. Samples were obtained at depths between 1000–2250 m. Diet was analysed for two different size-classes (immature and mature specimens) at three different bathymetric strata during two different seasons. The feeding habits of A. rostratus included a narrow range of mobile macroplanktonic organisms (e.g. Pyrosoma atlanticum and Chelophyes appendiculata) and some material of benthic origin. Pyrosoma atlanticum was the preferred prey item in spring at 1000–1425 m, being very scarce in summer at the same depth as a consequence of its scarcity in the environment during this season. There were some ontogenic differences in the diet of A. rostratus at 1425–2250 m. Adults ingested more and larger prey than juvenile specimens. The scarcity of resources below 1200–1400 m fostered a more diversified diet, as well as passive predation of sedimented material.

scholarly journals Intriguing diversity among diazotrophic picoplankton along a Mediterranean transect: a dominance of rhizobia

2011 ◽  
Vol 8 (3) ◽  
pp. 827-840 ◽  
Author(s):  
M. Le Moal ◽  
H. Collin ◽  
I. C. Biegala
Keyword(s):  
Mediterranean Sea ◽  
16S Rdna ◽  
Eastern Mediterranean ◽  
Western Mediterranean ◽  
Central Mediterranean ◽  
Surface Distribution ◽  
Western Mediterranean Sea ◽  
Diazotrophic Cyanobacteria ◽  
The Mediterranean ◽  
Marine Areas

Abstract. The Mediterranean Sea is one of the most oligotrophic marine areas on earth where nitrogen fixation has formally believed to play an important role in carbon and nitrogen fluxes. Although this view is under debate, the diazotrophs responsible for this activity have still not been investigated in the open sea. In this study, we characterised the surface distribution and species richness of unicellular and filamentous diazotrophs across the Mediterranean Sea by combining microscopic counts with size fractionated in situ hybridization (TSA-FISH), and 16S rDNA and nifH genes phylogenies. These genetic analyses were possible owing to the development of a new PCR protocol adapted to scarce microorganisms that can detect as few as 1 cell ml−1 in cultures. Low concentrations of diazotrophic cyanobacteria were detected and this community was dominated at 99.9% by picoplankton hybridized to the Nitro821 probe, specific for unicellular diazotrophic cyanobacteria (UCYN). Among filamentous cyanobacteria only 0.02 filament ml−1 of Richelia were detected in the eastern basin, while small (0.7–1.5 μm) and large (2.5–3.2 μm) Nitro821-targeted cells were recovered at all stations with a mean concentration of 3.5 cell ml−1. The affiliation of the small Nitro821-targeted cells to UCYN-A was confirmed by 16S and nifH phylogenies in the western Mediterranean Sea. In the central and the eastern Mediterranean Sea no 16S rDNA and nifH sequence from UCYN was obtained as cells concentration were close to, or below PCR detection limit. Bradyrhizobium sequences dominated nifH clone libraries from picoplanktonic size fractions. A few sequences of γ-proteobacteria were also detected in the central Mediterranean Sea. While low phosphate and iron concentrations could explain the absence of Trichodesmium sp., the factors that prevent the development of UCYN-B and C remain unknown. We also propose that the dominating picoplankters probably developed specific strategies, such as associations with protists or particles, and/or photosynthetic activity, to acquire carbon for sustaining diazotrophy.

scholarly journals Host- microbiome interactions in a changing sea: the gill microbiome of an invasive oyster under drastic changes in temperature

2020 ◽  
Author(s):  
Yahala Rina-Dor ◽  
Yehuda Benayahu ◽  
Leah Reshef ◽  
Uri Gophna
Keyword(s):  
Mediterranean Sea ◽  
Eastern Mediterranean ◽  
Seawater Temperature ◽  
Gill Tissue ◽  
Amplicon Sequencing ◽  
Western Mediterranean ◽  
Rrna Gene ◽  
Western Mediterranean Sea ◽  
Series Of Experiments ◽  
Health Deterioration

The gill tissue of bivalve mollusks hosts rich symbiotic microbial communities that may contribute to the host wellbeing. Spondylus spinosus is a Lessepsian invasive oyster to the eastern Mediterranean Sea that has become highly abundant, while constantly expending its range northwestward. Using 16S rRNA gene amplicon sequencing we examined how temperature affects the gill microbiota of S. spinosus, and the oysters themselves, in a series of experiments: exposing the oysters to the current annual seawater temperature range; to the colder temperature of the western Mediterranean Sea; and to elevated temperature as predicted under global warming scenarios. The bacterial genus Endozoicomonas dominated the communities of the S. spinosus, mainly upon exposure to winter-like temperatures. Exposure to elevated seawater temperature resulted in a significant change in the bacterial communities, while the oysters maintained normal functioning, suggesting that the oyster may survive a seawater warming scenario. Exposure to colder winter temperature typical to the western Mediterranean Sea resulted in health deterioration of the oysters, emergence of opportunistic pathogens, and a decline in the relative abundance of Endozoicomonas, suggesting that S. spinosus might not survive in the cold western Mediterranean Sea. The findings indicate that gill bacteria are greatly affected by temperature, which could consequently restrict the range expansion of this and other invasive oysters.

scholarly journals Thalassobaculum salexigens sp. nov., a new member of the family Rhodospirillaceae from the NW Mediterranean Sea, and emended description of the genus Thalassobaculum

2010 ◽  
Vol 60 (1) ◽  
pp. 209-213 ◽  
Author(s):  
Laurent Urios ◽  
Valérie Michotey ◽  
Laurent Intertaglia ◽  
Françoise Lesongeur ◽  
Philippe Lebaron
Keyword(s):  
Mediterranean Sea ◽  
Reductase Activity ◽  
Fatty Acid Content ◽  
Western Mediterranean ◽  
Rrna Gene ◽  
The North ◽  
Western Mediterranean Sea ◽  
The Family ◽  
Emended Description ◽  
Nw Mediterranean

A novel Gram-negative bacteria, named CZ41_10aT, was isolated from coastal surface waters of the north-western Mediterranean Sea. Cells were motile, pleomorphic rods, 1.6 μm long and 0.7 μm wide and formed cream colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol%. Phylogenetic analysis of 16S rRNA gene sequences placed the new isolate in the genus Thalassobaculum, a member of the family Rhodospirillaceae, class Alphaproteobacteria. Unlike Thalassobaculum litoreum CL-GR58T, its closest relative, strain CZ41_10aT was unable to grow anaerobically and did not exhibit nitrate reductase activity. On the basis of DNA–DNA hybridization, fatty acid content and physiological and biochemical characteristics, this isolate represents a novel species for which the name Thalassobaculum salexigens sp. nov. is proposed. The type strain is CZ41_10aT (=DSM 19539T=CIP 109064T=MOLA 84T). An emended description of the genus Thalassobaculum is also given.

scholarly journals Directional bilateral asymmetry in otolith morphology may affect fish stock discrimination based on otolith shape analysis

2018 ◽  
Vol 76 (1) ◽  
pp. 232-243 ◽  
Author(s):  
Kélig Mahé ◽  
Djamila Ider ◽  
Andrea Massaro ◽  
Oussama Hamed ◽  
Alba Jurado-Ruzafa ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Shape Analysis ◽  
Eastern Mediterranean ◽  
Western Mediterranean ◽  
Fish Stock ◽  
Stock Identification ◽  
Bilateral Asymmetry ◽  
Otolith Shape ◽  
Otolith Shape Analysis ◽  
Western Mediterranean Sea

Abstract Otolith shape analysis is an efficient fish stock identification tool. However, most applications used left and right otoliths or only one of them arbitrarily chosen without testing for biases resulting from potential directional bilateral asymmetry (DA) in otolith shape, i.e. a unimodal population-level deviation form bilateral symmetry between right and left otolith shapes. In this study, 560 bogues (Boops boops) were sampled from 11 geographical locations from the Canary Islands to the Aegean Sea and elliptical Fourier descriptors were used to describe their otoliths’ shape. First, a significant otolith DA was observed at the global scale with an average amplitude of 2.77%. However, at the scale of sampling locations, DA was not always significant and varied in amplitude and direction. Second, population structure was investigated using the shape of either right otoliths or left otoliths or both together. Analyses based on right otoliths or both otoliths together, suggested three stock units: a North-Western Mediterranean Sea stock, an Eastern Mediterranean Sea stock, and a Central-Eastern Atlantic Ocean and South-Western Mediterranean Sea stock. In contrast, no coherent geographical pattern was found based on left otoliths. Our results highlight the importance of accounting for potential otolith DA in otolith shape-based stock identification.

Novel insights on the diversity and ecology of the Family Lumbrineridae (Polychaeta) along the Iberian Peninsula coasts

2015 ◽  
Vol 96 (7) ◽  
pp. 1427-1435 ◽  
Author(s):  
S.C. García Gómez ◽  
Luis F. Carrera-Parra ◽  
Ferran Alsina Mas ◽  
Rosa Freitas ◽  
Roberto Martins
Keyword(s):  
New Species ◽  
Continental Shelf ◽  
Iberian Peninsula ◽  
Mediterranean Sea ◽  
Western Mediterranean ◽  
Western Mediterranean Sea ◽  
Continental Shelves ◽  
The Family ◽  
Surrounding Areas ◽  
New Occurrences

Lumbrinerids are amongst the most abundant and diverse polychaete families in worldwide continental shelves, and have received attention recently through the description of several new species and new occurrences. Herein, a total of four lumbrinerid species are firstly reported in the eastern and southern Spanish continental shelf, extending their biogeographic distribution to the western Mediterranean Sea and increasing up to 25 the number of species known in the Iberian Peninsula coasts. New insights on taxonomy, ecological and biogeographic preferences and an updated taxonomic key for Iberian coasts and surrounding areas are also provided.

scholarly journals Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader

2021 ◽  
Vol 12 ◽  
Author(s):  
Theodoros Danis ◽  
Vasileios Papadogiannis ◽  
Alexandros Tsakogiannis ◽  
Jon B. Kristoffersen ◽  
Daniel Golani ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Western Mediterranean ◽  
Gene Family Evolution ◽  
Rapid Expansion ◽  
Phylogenomic Analysis ◽  
Western Mediterranean Sea ◽  
Evolution Analysis ◽  
Genomic Landscape ◽  
Lagocephalus Sceleratus ◽  
Successful Invader

The Tetraodontidae family encompasses several species which attract scientific interest in terms of their ecology and evolution. The silver-cheeked toadfish (Lagocephalus sceleratus) is a well-known “invasive sprinter” that has invaded and spread, in less than a decade, throughout the Eastern and part of the Western Mediterranean Sea from the Red Sea through the Suez Canal. In this study, we built and analysed the first near-chromosome level genome assembly of L. sceleratus and explored its evolutionary landscape. Through a phylogenomic analysis, we positioned L. sceleratus closer to T. nigroviridis, compared to other members of the family, while gene family evolution analysis revealed that genes associated with the immune response have experienced rapid expansion, providing a genetic basis for studying how L. sceleratus is able to achieve highly successful colonisation. Moreover, we found that voltage-gated sodium channel (NaV 1.4) mutations previously connected to tetrodotoxin resistance in other pufferfishes are not found in L. sceleratus, highlighting the complex evolution of this trait. The high-quality genome assembly built here is expected to set the ground for future studies on the species biology.

scholarly journals Silica cycling in the ultra-oligotrophic eastern Mediterranean Sea

2014 ◽  
Vol 11 (15) ◽  
pp. 4211-4223 ◽  
Author(s):  
M. D. Krom ◽  
N. Kress ◽  
K. Fanning
Keyword(s):  
Mediterranean Sea ◽  
Silicic Acid ◽  
Deep Water ◽  
Phytoplankton Bloom ◽  
Eastern Mediterranean ◽  
Water Concentration ◽  
Western Mediterranean ◽  
Eastern Mediterranean Sea ◽  
Western Mediterranean Sea

Abstract. Although silica is a key plant nutrient, there have been few studies aimed at understanding the Si cycle in the eastern Mediterranean Sea (EMS). Here we use a combination of new measurements and literature values to explain the silicic acid distribution across the basin and to calculate a silica budget to identify the key controlling processes. The surface water concentration of ∼1 μM, which is unchanging seasonally across the basin, was due to the inflow of western Mediterranean Sea (WMS) water at the Straits of Sicily. It does not change seasonally because there is only a sparse population of diatoms due to the low nutrient (N and P) supply to the photic zone in the EMS. The concentration of silicic acid in the deep water of the western Ionian Sea (6.3 μM) close to the S Adriatic are an of formation was due to the preformed silicic acid (3 μM) plus biogenic silica (BSi) from the dissolution of diatoms from the winter phytoplankton bloom (3.2 μM). The increase of 4.4 μM across the deep water of the EMS was due to silicic acid formed from in situ diagenetic weathering of aluminosilicate minerals fluxing out of the sediment. The major inputs to the EMS are silicic acid and BSi inflowing from the western Mediterranean (121 × 109 mol Si yr−1 silicic acid and 16 × 109 mol Si yr−1 BSi), silicic acid fluxing from the sediment (54 × 109 mol Si yr−1) and riverine (27 × 109 mol Si yr−1) and subterranean groundwater (9.7 × 109 mol Si yr−1) inputs, with only a minor direct input from dissolution of dust in the water column (1 × 109 mol Si yr−1). This budget shows the importance of rapidly dissolving BSi and in situ weathering of aluminosilicate minerals as sources of silica to balance the net export of silicic acid at the Straits of Sicily. Future measurements to improve the accuracy of this preliminary budget have been identified.

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