scholarly journals Optimization of eDNA metabarcoding methodology for the biomontoring of the ichthyofauna in the Eastern Mediterranean Sea

2021 ◽  
Vol 4 ◽  
Author(s):  
Panagiotis Kasapidis ◽  
Christina Karli
Keyword(s):  
Mediterranean Sea ◽  
Water Column ◽  
Eastern Mediterranean ◽  
Habitat Type ◽  
Species Level ◽  
Reference Database ◽  
Soft Substrate ◽  
Eastern Mediterranean Sea ◽  
The Mediterranean ◽  
Oligotrophic Ecosystems

Environmental DNA (eDNA) metabarcoding is a relatively new methodology for the detection of organisms in an environmental sample, with emerging applications in the fields of ecology, conservation, invasive biology, biomonitoring and more. Several studies are using eDNA nowadays, yet in the Mediterranean marine ecosystems, its use is limited mostly on plankton studies so far. The icthyofauna of the Eastern Mediterranean is undergoing major changes due to biological invasions, mainly form the Red Sea, in combination with the climate change, and a reliable high-throughput biomonitoring tool is essential to monitor these changes. The main goal of this study was to develop a reliable eDNA metabarcoding protocol to study and monitor fish biodiversity in the oligotrophic ecosystems of the Eastern Mediterranean. The study had two parts: a) standardization of the method by testing two different sets of primers in aquaria with known fish species assemblages, and b) estimation of the heterogeneity of fish eDNA distribution in different habitats within a coastal area, in order to determine the most efficient sampling strategy. In both cases, samples were analysed through Next Generation Sequencing on a Illumina MiSeq platform. To standardize the method, we sampled and filtered water from two tanks of the 'Cretaquarium'. We tested two different sets of primers, one for 16S rRNA and the MiFish primers of Miya et al. (2015) for 12S rRNA, in order to estimate their efficiency in assessing species' composition both qualitatively and semi-quantitatively. Both primer sets performed well and most taxa in both tanks were detected up to species level, with 16S marker exhibiting higher resolution. A rather weak correlation was also detected between actual fish biomass and relative abundance as estimated by eDNA metabarcoding. To estimate the eDNA heterogeneity in natural ecosystems, we sampled water in a coastal ecosystem over three distinct types of habitats: hard substrate, soft substrate, Posidonia meadows, as well as in the mid of the water column. Three samples per habitat were collected, two PCRs per DNA extract were performed and results were obtained only for the 16S marker. A total of 69 taxa were detected, with 55 of them distinguished at the species level, while in each sample the number of taxa detected ranged from 13 to 27. Posidonia meadows and the water column samples showed the greatest heterogeneity, in contrast to the hard and soft substrate samples that showed little differentiation both within and between habitat type. Based on these results, an improved protocol should include more technical PCR replicates per sample (at least 3 PCRs), at least one sample per habitat in each area, and a larger volume of water filtered per sample or alternatively, more samples mixed together in order to achieve better representation of the community. Moreover, it was apparent the need of a more complete and curated reference database for the Mediterranean fishes for the aforementioned markers, in order to be able to reliably identify fishes of the Mediterranean ecosystems at species level. In conclusion, the method seems to work well, and with some small improvements, as well as with the complementation of the respective reference databases, it can be used as a reliable tool for the study of biodiversity and biomonitoring of fish communities of the oligotrophic ecosystems of the Eastern Mediterranean Sea.

scholarly journals On the Circulation and Thermohaline Properties of the Eastern Mediterranean Sea

2021 ◽  
Vol 8 ◽  
Author(s):  
Milena Menna ◽  
Riccardo Gerin ◽  
Giulio Notarstefano ◽  
Elena Mauri ◽  
Antonio Bussani ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Water Column ◽  
Mixed Layer ◽  
Eastern Mediterranean ◽  
Mixed Layer Depth ◽  
Eastern Mediterranean Sea ◽  
Salt Fingers ◽  
Main Circulation ◽  
Satellite Altimetry Data

The circulation of the Eastern Mediterranean Sea is characterized by numerous recurrent or permanent anticyclonic structures, which modulate the pathway of the main currents and the exchange of the water masses in the basin. This work aims to describe the main circulation structures and thermohaline properties of the Eastern Mediterranean with particular focus on two anticyclones, the Pelops and the Cyprus gyres, using in-situ (drifters and Argo floats) and satellite (altimetry) data. The Pelops gyre is involved in the circulation and exchange of Levantine origin surface and intermediate waters and in their flow toward the Ionian and the Adriatic Sea. The Cyprus Gyre presents a marked interannual variability related to the presence/absence of waters of Atlantic origin in its interior. These anticyclones are characterized by double diffusive instability and winter mixing phenomena driven by salty surface waters of Levantine origin. Conditions for the salt finger regime occur steadily and dominantly within the Eastern Mediterranean anticyclones. The winter mixing is usually observed in December–January, characterized by instability conditions in the water column, a gradual deepening of the mixed layer depth and the consequent downward doming of the isohalines. The mixing generally involves the first 200 m of the water column (but occasionally can affect also the intermediate layer) forming a water mass with well-defined thermohaline characteristics. Conditions for salt fingers also occur during mixing events in the layer below the mixed layer.

scholarly journals New Fisheries-related data from the Mediterranean Sea (October 2015)

2015 ◽  
Vol 16 (3) ◽  
pp. 703 ◽  
Author(s):  
K. TSAGARAKIS ◽  
A. BAŞUSTA ◽  
N. BAŞUSTA ◽  
F. BIANDOLINO ◽  
D. BOSTANCI ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Eastern Mediterranean ◽  
Length Distribution ◽  
Central Mediterranean ◽  
Eastern Mediterranean Sea ◽  
Related Data ◽  
Solea Solea ◽  
Commercially Important ◽  
The Mediterranean ◽  
Polyprion Americanus

In this third Collective Article, with fisheries-related data from the Mediterranean Sea, we present the historical length distribution of Lophius budegassa in the catch of commercial trawlers in the Greek seas; length-weight and length-length relationships of five flatfish species (Lepidorhombus boscii, L. whiffiagonis, Platichthys flesus, Pegusa lascaris and Solea solea) from different coastal areas of Turkey (Black Sea and Eastern Mediterranean Sea); growth of settled Polyprion americanus and length-weight relationships of this species and of Deltentosteus quadrimaculatus, Capros aper and three commercially important groupers in the Eastern Mediterranean Sea; the age, growth and mortality of Zosterisessor ophiocephalus in the Eastern Adriatic Sea; the length-weight relationship and condition factor of Atherina boyeri in a Central Mediterranean semi-isolated lagoon, and also the length-weight and length-length relationships of three Alburnus species from different inland waters in Turkey.

scholarly journals Thalassospira sp. Isolated from the Oligotrophic Eastern Mediterranean Sea Exhibits Chemotaxis toward Inorganic Phosphate during Starvation

2011 ◽  
Vol 77 (13) ◽  
pp. 4412-4421 ◽  
Author(s):  
Annemarie Hütz ◽  
Karin Schubert ◽  
Jörg Overmann
Keyword(s):  
Mediterranean Sea ◽  
Water Column ◽  
Inorganic Phosphate ◽  
Phosphate Uptake ◽  
Eastern Mediterranean ◽  
Phosphate Limitation ◽  
Soluble Phosphate ◽  
Free Living ◽  
Eastern Mediterranean Sea ◽  
Content Type

ABSTRACTThe eastern Mediterranean Sea represents an ultraoligotrophic environment where soluble phosphate limits the growth of bacterioplankton. Correspondingly, genes coding for high-affinity phosphate uptake systems and for organophosphonate utilization are highly prevalent in the plankton metagenome. Chemotaxis toward inorganic phosphate constitutes an alternative strategy to cope with phosphate limitation, but so far has only been demonstrated for two bacterial pathogens and an archaeon, and not in any free-living planktonic bacterium. In the present study, bacteria affiliated with the genusThalassospirawere found to constitute a regular, low-abundance member of the bacterioplankton that can be detected throughout the water column of the eastern Mediterranean Sea. A representative (strain EM) was isolated in pure culture and exhibited a strong positive chemotaxis toward inorganic phosphate that was induced exclusively in phosphate-starved cultures. Phosphate-depleted cells were 2-fold larger than in exponentially growing cultures, and 43% of the cells retained their motility even during prolonged starvation over 10 days. In addition,Thalassospirasp. strain EM was chemotactically attracted by complex substrates (yeast extract and peptone), amino acids, and 2-aminoethylphosphonate but not by sugar monomers. Similarly to the isolate from the eastern Mediterranean, chemotaxis toward phosphate was observed in starved cultures of the other two available isolates of the genus,T. lucentensisDSM 14000TandT. profundimarisWP0211T. AlthoughThalassospirasp. represents only up to 1.2% of the total bacterioplankton community in the water column of the eastern Mediterranean Sea, its chemotactic behavior potentially leads to an acceleration of nutrient cycling and may also explain the persistence of marine copiotrophs in this extremely nutrient-limited environment.

scholarly journals High resolution nested model for the Cyprus, NE Levantine Basin, eastern Mediterranean Sea: implementation and climatological runs

2003 ◽  
Vol 21 (1) ◽  
pp. 221-236 ◽  
Author(s):  
G. Zodiatis ◽  
R. Lardner ◽  
A. Lascaratos ◽  
G. Georgiou ◽  
G. Korres ◽  
...  
Keyword(s):  
High Resolution ◽  
Mediterranean Sea ◽  
General Circulation ◽  
Eastern Mediterranean ◽  
Pilot Project ◽  
Ocean Model ◽  
Eastern Mediterranean Sea ◽  
Coastal Shelf ◽  
Forecasting System ◽  
The Mediterranean

Abstract. A high resolution nested flow model for the coastal, shelf and open sea areas of the Cyprus Basin, NE Levantine, eastern Mediterranean Sea is implemented to fulfil the objectives of the Mediterranean Forecasting System Pilot Project, funded by the EU. The Cyprus coastal ocean model is nested entirely within a coarse regional grid model of the eastern Mediterranean Sea, using the MODB climatology for initialisation and the ECMWF perpetual year surface forcing. The nested simulations of the Cyprus model were able to reproduce, with greater detail, flow features similar to those of the coarse grid regional model. The project results show the feasibility of the approach for the development of an operational forecasting system in the Mediterranean Sea, particularly in the Cyprus coastal/shelf sea area. Key words. Oceanography: general (descriptive and regional oceanography; numerical modelling) Oceanography: physical (general circulation)

scholarly journals The effects of decomposing invasive jellyfish on biogeochemical fluxes and microbial dynamics in an ultraoligotrophic sea

2020 ◽  
Author(s):  
Tamar Guy-Haim ◽  
Maxim Rubin-Blum ◽  
Eyal Rahav ◽  
Natalia Belkin ◽  
Jacob Silverman ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Water Column ◽  
Nutrient Dynamics ◽  
Eastern Mediterranean ◽  
Oxygen Demand ◽  
Bacterial Biomass ◽  
Ecosystem Functions ◽  
Water Interface ◽  
Overlying Water ◽  
Eastern Mediterranean Sea

Abstract. Over the past several decades, jellyfish blooms have intensified spatially and temporally, affecting functions and services of ecosystems worldwide. At the demise of a bloom, an enormous amount of jellyfish biomass sinks to the seabed and decomposes. This process entails reciprocal microbial and biogeochemical changes, typically enriching the water column and seabed with large amounts of organic and inorganic nutrients. Jellyfish decomposition was hypothesized to be particularly important in nutrient-impoverished ecosystems, such as the Eastern Mediterranean Sea – one of the most oligotrophic marine regions in the world. Since the 1970s, this region is experiencing the proliferation of a notorious invasive scyphozoan jellyfish, Rhopilema nomadica. In this study, we estimated the short-term decomposition effects of R. nomadica on nutrient dynamics at the sediment-water interface. Our results show that the degradation of R. nomadica has led to increased oxygen demand and acidification of overlying water as well as high rates of dissolved organic nitrogen and phosphate production. These conditions favored heterotrophic microbial activity, bacterial biomass accumulation, and triggered a shift towards heterotrophic bio-degrading bacterial communities, whereas autotrophic pico-phytoplankton abundance was moderately affected or reduced. This shift may further decrease primary production in the water column of the Eastern Mediterranean Sea. Deoxygenation, acidification, nutrient enrichment and microbial community shifts at the sediment-water interface may have a detrimental impact on macrobenthic communities. Based on these findings we suggest that jelly-falls and their decay may facilitate an additional decline in ecosystem functions and services.

scholarly journals Spring distribution of shelled pteropods across the Mediterranean Sea

2020 ◽  
Author(s):  
Roberta Johnson ◽  
Clara Manno ◽  
Patrizia Ziveri
Keyword(s):  
Climate Change ◽  
Mediterranean Sea ◽  
Eastern Mediterranean ◽  
Hot Spot ◽  
Environmental Parameters ◽  
Saturation State ◽  
Eastern Mediterranean Sea ◽  
The Mediterranean ◽  
First Time ◽  
Natural Laboratory

Abstract. Shelled pteropods represent an excellent sentinel for indicating exposure to ocean acidification (OA). Here, for the first time, we characterise spring pteropod distribution throughout the Mediterranean Sea, a region that has been identified as a climate change hot-spot. The presence of a west–east natural biogeochemical gradient makes this region a natural laboratory to investigate how the variability in environmental parameters may affect pteropod distribution. Results show that pteropod abundance is significantly higher in the eastern Mediterranean Sea where there is a higher aragonite saturation state (Ωar), showing that distribution is positively correlated with Ωar. We also observed a resilience of pteropods to higher temperatures and low nutrient conditions, including phosphorous limitation. The higher abundance of pteropods in ultra-oligotrophic conditions (eastern Mediterranean Sea) suggests that this organism can play an important role as the prime calcifying zooplankton within specific oligotrophic regions.

scholarly journals <i>Blastodinium</i> spp. infect copepods in the ultra-oligotrophic marine waters of the Mediterranean Sea

2011 ◽  
Vol 8 (2) ◽  
pp. 2563-2592 ◽  
Author(s):  
C. Alves-de-Souza ◽  
C. Cornet ◽  
A. Nowaczyk ◽  
S. Gasparini ◽  
A. Skovgaard ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Gene Sequence ◽  
Eastern Mediterranean ◽  
Gut Contents ◽  
Sequence Analyses ◽  
Naupliar Stage ◽  
Wide Range ◽  
The Mediterranean ◽  
Successive Generations ◽  
Oligotrophic Ecosystems

Abstract. Blastodinium are chloroplast-containing dinoflagellates which infect a wide range of copepods. They develop inside the gut of their host, where they produce successive generations of sporocytes that are eventually expelled through the anus of the copepod. Here, we report on copepod infections in the oligotrophic to ultra-oligotrophic waters of the Mediterranean Sea sampled during the BOUM cruise. Based on a DNA-stain screening of gut contents, 16% of copepods were possibly infected in samples from the Eastern Mediterranean, with up to 51% of Corycaeidae, 33% of Calanoida, but less than 2% of Oithonidae and Oncaeidae. Parasites were classified into distinct morphotypes, with some tentatively assigned to species B. mangini, B. contortum, and B. cf. spinulosum. Based upon the SSU rDNA gene sequence analyses of 15 individuals, the genus Blastodinium was found to be polyphyletic, containing at least three independent clusters. The first cluster grouped all sequences retrieved from parasites of Corycaeidae and Oncaeidae during this study, and included sequences of Blastodinium mangini (the "mangini" cluster). Sequences from cells infecting Calanoida belonged to two different clusters, one including B. contortum (the "contortum" cluster), and the other uniting all B. spinulosum-like morphotypes (the "spinulosum" cluster). Cluster-specific oligonucleotidic probes were designed and tested by FISH in order to assess the distribution of dinospores, the Blastodinium dispersal and infecting stage. Probe-positive cells were all small thecate dinoflagellates, with lengths ranging from 7 to 18 μm. Maximal abundances of Blastodinium dinospores were detected at the Deep Chlorophyll Maximum (DCM) or slightly below. This was in contrast to distributions of autotrophic pico- and nanoplankton, microplanktonic dinoflagellates, and nauplii which showed maximal concentrations above the DCM. The distinct distributions of dinospores and nauplii argues against infection during the naupliar stage. Blastodinium, described as autotrophic in the literature, may escape the severe nutrient limitation of ultra-oligotrophic ecosystems by living inside copepods.

scholarly journals Integrated survey of elemental stoichiometry (C, N, P) from the western to eastern Mediterranean Sea

2011 ◽  
Vol 8 (4) ◽  
pp. 883-899 ◽  
Author(s):  
M. Pujo-Pay ◽  
P. Conan ◽  
L. Oriol ◽  
V. Cornet-Barthaux ◽  
C. Falco ◽  
...  
Keyword(s):  
Mediterranean Sea ◽  
Water Column ◽  
Eastern Mediterranean ◽  
Western Basin ◽  
Nutrient Sources ◽  
P Limitation ◽  
Elemental Stoichiometry ◽  
Deep Layers ◽  
Redfield Ratios ◽  
The Mediterranean

Abstract. This paper provides an extensive vertical and longitudinal description of the biogeochemistry along an East-West transect of 3000 km across the Mediterranean Sea during summer 2008 (BOUM cruise). During this period of strong stratification, the distribution of nutrients, particulate and dissolved organic carbon (DOC), nitrogen (DON) and phosphorus (DOP) were examined to produce a detailed spatial and vertically extended description of the elemental stoichiometry of the Mediterranean Sea. Surface waters were depleted in nutrients and the thickness of this depleted layer increased towards the East from about 10 m in the Gulf of Lion to more than 100 m in the Levantine basin, with the phosphacline deepening to a greater extent than that for corresponding nitracline and thermocline depths. We used the minimum oxygen concentration through the water column in combination with 2 fixed concentrations of dissolved oxygen to distinguish an intermediate layer (Mineralization Layer; ML) from surface (Biogenic Layer; BL), and deep layers (DL). Whilst each layer was represented by different water masses, this approach allowed us to propose a schematic box-plot representation of the biogeochemical functioning of the two Mediterranean basins. Despite the increasing oligotrophic nature and the degree of P-depletion along the West to East gradient strong similarities were encountered between eastern and western ecosystems. Within the BL, the C:N:P ratios in all pools largely exceeded the Redfield ratios, but surprisingly, the nitrate vs. phosphate ratios in the ML and DL tended towards the canonical Redfield values in both basins. A change in particulate matter composition has been identified by a C increase relative to N and P along the whole water column in the western basin and between BL and ML in the eastern one. Our data showed a noticeable stability of the DOC:DON ratio (12–13) throughout the Mediterranean Sea. This is in good agreement with a P-limitation of microbial activities but in contradiction of the accepted concept that N is recycled faster than C. The western and eastern basins had similar or close biological functioning. Differences come from variability in the allochtonous nutrient sources in terms of quantity and quality, and to the specific hydrodynamic features of the Mediterranean basins.

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