1. Macrofauna associated with a bank of Cladocora caespitosa (Anthozoa, Scleractinia) in the Gulf of Trieste (northern Adriatic)Valentina Pitacco, Martina Orlando-Bonaca, Borut Mavrič, Lovrenc Lipej, 2014, izvirni znanstveni članek Povzetek: The Mediterranean stony coral Cladocora caespitosa (Linnaeus, 1767) is a native colonial, zooxanthellate, shallow water coral, particularly sensitive to global changes and anthropogenic activities. Due to its shape and size, it is able to host a diversifi ed faunal assemblage, which is still relatively unknown. A recently discovered bank of C. caespitosa, discovered close to Cape Ronek (Gulf of Trieste, Slovenia), was investigated in November 2010. Altogether 121 invertebrate taxa, belonging to 9 different phyla were found. Taxa composition in colonies differed markedly from the surrounding areas within the bank. Only 5 taxa (4 % of the total) were found both within and without C. caespitosa colonies. Our results confi rm the role of C. caespitosa as a habitat builder and indicate the importance of the studied bank for biodiversity
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2. Mixtures of Chemical Pollutants at European Legislation Safety Concentrations: How Safe are They?Raquel Negrão Carvalho, Augustine Aruqwe, Selim Ait-Aissa, Anne Bado-Nilles, Stefania Balzamo, Anders Baun, Shimshon Belkin, Ludek Blaha, Francois Brion, Daniela Conti, Vesna Flander-Putrle, Valentina Turk, 2014, izvirni znanstveni članek Povzetek: The risk posed by complex chemical mixtures in the environment to wildlife and humans is increasingly debated, but has been rarely tested under environmentally relevant scenarios. To address this issue, two mixtures of 14 or 19 substances of concern (pesticides, pharmaceuticals, heavy metals, polyaromatic hydrocarbons, a surfactant, and a plasticizer), each present at its safety limit concentration imposed by the European legislation, were prepared and tested for their toxic effects. The effects of the mixtures were assessed in 35 bioassays, based on 11 organisms representing different trophic levels. A consortium of 16 laboratories was involved in performing the bioassays. The mixtures elicited quantifiable toxic effects on some of the test systems employed, including i) changes in marine microbial composition, ii) microalgae toxicity, iii) immobilization in the crustacean Daphnia magna, iv) fish embryo toxicity, v) impaired frog embryo development, and vi) increased expression on oxidative stress-linked reporter genes. Estrogenic activity close to regulatory safety limit concentrations was uncovered by receptor-binding assays. The results highlight the need of precautionary actions on the assessment of chemical mixtures even in cases where individual toxicants are present at seemingly harmless concentrations.
Ključne besede: morje, analizna kemija, biologija, evtrofikacija, hranilne snovi, fitoplankton, onesnaževanje, Piranski zaliv
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3. Loop-mediated isothermal amplification of specific endoglucanase gene sequence for detection of the bacterial wilt pathogen Ralstonia solanacearumRok Lenarčič, Dany Morisset, Manca Pirc, Pablo Llop, Maja Ravnikar, Tanja Dreo, 2014, izvirni znanstveni članek Povzetek: The increased globalization of crops production and processing industries also promotes the side-effects of more rapid and efficient spread of plant pathogens. To prevent the associated economic losses, and particularly those related to bacterial diseases where their management relies on removal of the infected material from production, simple, easy-to-perform, rapid and cost-effective tests are needed. Loop-mediated isothermal amplification (LAMP) assays that target 16S rRNA, fliC and egl genes were compared and evaluated as on-site applications. The assay with the best performance was that targeted to the egl gene, which shows high analytical specificity for diverse strains of the betaproteobacterium Ralstonia solanacearum, including its non-European and non-race 3 biovar 2 strains. The additional melting curve analysis provides confirmation of the test results. According to our extensive assessment, the egl LAMP assay requires minimum sample preparation (a few minutes of boiling) for the identification of pure cultures and ooze from symptomatic material, and it can also be used in a high-throughput format in the laboratory. This provides sensitive and reliable detection of R. solanacearum strains of different phylotypes.
Ključne besede: plant pathogens, bacterial diseases
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4. Artificially induced migration of redox layers in a coastal sediment from the Northern AdriaticEduard Metzger, D. Langlet, E. Viollier, Neža Koron, Bettina Riedel, Michael Stachowitsch, Jadran Faganeli, M. Tharaud, E. Geslin, F. Jorissen, 2014, izvirni znanstveni članek Povzetek: Long-term experimental studies suggest that, under transient anoxic conditions, redox fronts within the sediment shift upwards, causing sequential rise and fall of benthic fluxes of reduced species (Mn(II), Fe(II) and S(-II)). Infaunal benthic organisms are associated with different redox fronts as micro-habitats and must be affected by such changes during natural hypoxia events. In order to document the geochemical evolution of the sediment during prolonged anoxia in the framework of an in situ experiment designed to mimic natural conditions, benthic chambers were deployed on the seafloor of the Northern Adriatic and sampled after 9, 30 and 315 days of incubation. Oxygen and sulfide were measured continuously in the early stages (9 days) of the experiment. High-resolution pore water profiles were sampled by DET probes and redox-sensitive species (S(VI), Mn(II) and Fe(II)) and alkalinity were measured.
Starting oxygen saturation was about 80% within the chamber. After 7 days, anoxia was established in the bottom waters within the chambers. Mn(II) and Fe(II) started diffusing towards the anoxic water column until they reached the surficial sediment. Being reoxidized there, Mn and Fe reprecipitated, giving a rusty coloration to the seafloor. Infaunal species appeared at the sediment surface. After 20 days, all macro-organisms were dead. Decomposition of macro-organisms at the sediment–water interface generated S(-II) within the entire height of the chamber, leading to a downward flux of sulfides into the sediment, where they were quickly oxidized by metallic oxides or precipitated as FeS. S(-II) was below detection in the water column and pore waters at the end of the experiment. Our results suggest that S(-II) enrichment in the water column of coastal systems, which are episodically anoxic, is strongly controlled by the biomass of benthic macrofauna and its decay during anoxia, whereas its residence time in the water column is controlled by iron availability (as solid oxides or as dissolved reduced cations) within the sediment, even without water circulation.
Ključne besede: Adriatic Sea, marine sediments, anoxia, Northern Adriatic
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5. GoMapMan : integration, consolidation and visualization of plant gene annotations within the MapMan ontologyŽiva Ramšak, Špela Baebler, Ana Rotter, Matej Korbar, Igor Mozetič, Björn Usadel, Kristina Gruden, 2014, izvirni znanstveni članek Povzetek: GoMapMan (http://www.gomapman.org) is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species. GoMapMan is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis and three crop species (potato, tomato and rice) are included. The main features of GoMapMan are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.
Ključne besede: genes, plants
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7. Temperature dependence of planktonic metabolism in the subtropical North Atlantic OceanL.S. Garcia-Corral, E. Barber, A. Regaudie-de_Gioux, S. Sal, J.M. Holding, S. Agusti, N. Navarro, P. Serret, Patricija Mozetič, Carlos M. Duarte, 2014, izvirni znanstveni članek Povzetek: The temperature dependence of planktonic metabolism in the subtropical North Atlantic Ocean was assessed on the basis of measurements of gross primary production (GPP), community respiration (CR) and net community production (NCP), as well as experimental assessments of the response of CR to temperature manipulations. Metabolic rates were measured at 68 stations along three consecutive longitudinal transects completed during the Malaspina 2010 Expedition, in three different seasons. Temperature gradients were observed in depth and at basin and seasonal scale. The results showed seasonal variability in the metabolic rates, the highest rates being observed during the spring transect. The overall mean integrated GPP / CR ratio was 1.39 ± 0.27 decreasing from winter to summer, and the NCP for the subtropical North Atlantic Ocean during the cruises exhibits net autotrophy (NCP > 0) in about two-thirds (66%) of the total sampled communities. Also, we reported the activation energies describing the temperature dependence of planktonic community metabolism, which was generally higher for CR than for GPP in the subtropical North Atlantic Ocean, as the metabolic theory of ecology predicts. Furthermore, we made a comparison of activation energies describing the responses to in situ temperature in the field (EaCR = 1.64 ± 0.36 eV) and those derived experimentally by temperature manipulations (EaCR = 1.45 ± 0.6 eV), which showed great consistency.
Ključne besede: morje, plankton, fitoplankton, klorofil, trofični status, anoksije
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8. Meiofauna winners and losers of coastal hypoxia: case study harpacticoid copepodsMateja Grego, Bettina Riedel, Michael Stachowitsch, Marleen De Troch, 2014, izvirni znanstveni članek Povzetek: The impact of anoxia on meiobenthic copepod species was assessed by means of a field experiment. Four plexiglass chambers were deployed in situ in 24 m depth to simulate an anoxic event of 9 days, 1 month, 2 months and 10 months. From normoxic to anoxic conditions, we recorded a drop in copepod density and species richness. With increasing duration of anoxia the relative abundance of the individuals of the family Cletodidae increased, and they survived the 1 month and 2 month anoxia, the latter with few specimens. They were the true "winners" of the experimentally induced anoxia. Dominance did not increase in the deployments because not one, but several species from this family were tolerant to anoxia. The overall rate of survival was the same for males and females, but no juvenile stages of copepods survived in anoxia. During a recovery phase of 7 days after a short-term anoxia of 9 days, harpacticoid copepod density did not increase significantly, and there was only a slight increase in species diversity. We concluded that no substantial colonisation from the surrounding sediment took place. The survivors, however, showed a high potential for recovery according to the number of gravid females, whose number increased significantly once the oxygen was available again. These findings imply that substantial energy is allocated to reproduction in the recovery phase.
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9. Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potatoŠpela Baebler, Kamil Witek, Marko Petek, Katja Stare, Magda Tušek-Žnidarič, Maruša Pompe Novak, Jenny Renaut, K. Szajko, D. Strzelczyk-Żyta, W. Marczewski, Karolina Morgiewicz, Kristina Gruden, Jacek Hennig, 2014, izvirni znanstveni članek Povzetek: The purpose of the study was to investigate the role of salicylic acid (SA) signalling in Ny-1-mediated hypersensitive resistance (HR) of potato (Solanum tuberosum L.) to Potato virus Y (PVY). The responses of the Ny-1 allele in the Rywal potato cultivar and transgenic NahG-Rywal potato plants that do not accumulate SA were characterized at the cytological, biochemical, transcriptome, and proteome levels. Analysis of noninoculated and inoculated leaves revealed that HR lesions started to develop from 3 d post inoculation and completely restricted the virus spread. At the cytological level, features of programmed cell death in combination with reactive oxygen species burst were observed. In response to PVY infection, SA was synthesized de novo. The lack of SA accumulation in the NahG plants led to the disease phenotype due to unrestricted viral spreading. Grafting experiments show that SA has a critical role in the inhibition of PVY spreading in parenchymal tissue, but not in vascular veins. The whole transcriptome analysis confirmed the central role of SA in orchestrating Ny-1-mediated responses and showed that the absence of SA leads to significant changes at the transcriptome level, including a delay in activation of expression of genes known to participate in defence responses. Moreover, perturbations in the expression of hormonal signalling genes were detected, shown as a switch from SA to jasmonic acid/ethylene signalling. Viral multiplication in the NahG plants was accompanied by downregulation of photosynthesis genes and activation of multiple energy-producing pathways.
Ključne besede: plant-pathogen interactions, Potato virus Y, salicylic acid, whole transcriptome analysis
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