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The Ross Ice Shelf is the Antarctic region that over the last deglaciation experienced the greatest change in areal ice cover. Today, cold, dense and saline water masses (brines) produced in the Ross Sea polynya, flow from the shelf to the deep ocean providing a significant contribution to the propelling of the global ocean circulation regulating the climate. In particular, the Hillary Canyon in the Eastern Ross Sea is the main conduit through which brines descend the slope to reach the deeper ocean and is thus one of the greatest regions of cold, dense water export in the world.A Contourite Depositional System (the ODYSSEA CDS) on the western flank of the Hillary Canyon is inferred to have been generated through several hundred-thousand years by along-slope, contour currents that transported and accumulated the sediments brought down the Hillary Canyon by means of brines. A multi-proxy investigation was conducted on the shallowest part of the ODYSSEA CDS depositional sequences, which we expect to contain i) the record of the brine formation, ii) the indication on contour current strength through time, and iii) their interplay and modulation associated to climate change.Six gravity cores, collected in both the proximal and distal area of the ODYSSEA CDS, were studied through multi-proxy analyses including sediment physical properties (texture, structures, water content, wet bulk density), compositional characteristics (XRF, geochemistry and detrital apatite, zircon, and rutile U-Pb on ice-rafted debris) (Lucchi et al., 2019; Neofitu et al., 2020) and microfossil content (planktonic and benthic foraminifera, calcareous nannofossils and diatoms). An age model has been reconstructed combining palaeomagnetic record, biostratigraphic content, tephrochronology and AMS radiocarbon dating on planktonic foraminifera tests.Inferred variations in dense water formation, contour current strength and ice sheet dynamics are discussed in the light of our data interpretation. Lucchi, R.G., Caburlotto, A., Miserocchi, S., Liu, Y., Morigi, C., Persico, D., Villa, G., Langone, L., Colizza, E., Macrì, P., Sagnotti, L., Conte, R., Rebesco, M., 2019. The depositional record of the Odyssea drift (Ross Sea, Antarctica). Geophysical Research Abstracts, Vol. 21, EGU2019-10409-1, 2019. EGU General Assembly, Vienna (Austria), 7–12, April, 2019 (POSTER).Neofitu, R., Mark, C., Rebesco, M., Lucchi, R.G., Douss, N., Morigi, C., Kelley, S., Daly, J.S., 2020. Tracking Late Quaternary ice sheet dynamics by multi-proxy detrital mineral U-Pb analysis: A case study from the Odyssea contourite, Ross Sea, Antarctica. Geophysical Research Abstracts. EGU General Assembly, Vienna (Austria), 3–8, May, 2020 (POSTER for session CL1.11).

International audience; A new method merges conventional and quantitative biostratigraphic approaches, supported by magnetic polarity data, to develop a chronological framework for sediment core MD03-2595 retrieved on the continental rise off Wilkes Land, East Antarctica before proceeding to paleoceanographic and paleoclimatic analysis. This combined method helped to identify climatic cycles, highlight stratigraphic discontinuities and reworking, and assess regional sedimentological and diatom biostratigraphic evolution. Core MD03-2595 spans the last 0.8 Ma, from the Mid Pleistocene Transition (MPT) to the Early Holocene. A hiatus including Marine Isotope Stages (MIS) 19, 18 and 17 was identified, and a decreasing trend in sediment accumulation rates from MIS 16 to the Holocene was observed. This quantitative diatom biostratigraphic dataset, placed in its own sedimentological and paleomagnetic context, provides new information regarding the paleobiogeographic distribution and ecological responses of biostratigraphically significant diatom species, such as Thalassiosira elliptipora and T. fasciculata, for the Matuyama-Brunhes (M-B) transition, and Actinocyclus ingens, Hemidiscus karstenii and Rouxia spp. for the middle and late Pleistocene diatom biozonation.

Indexación: Scopus. Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless "open" according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids. Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities. https://www.frontiersin.org/articles/10.3389/fmicb.2018.00138/full

Vibrios are Gram-negative bacteria autochthonous of estuarine and coastal marine environments. Several species have been described in association with intestinal or extraintestinal infections in humans, and transmission through seafood has been documented.

The relationship between Vibrio parahaemolyticus strains isolated from the aquatic environment and those isolated from cases of infection in humans is poorly understood due to the low prevalence of tdh - and/or trh -positive strains in the environment. To address this concern, it would be useful to analyse the genetic relationships among environmental and food strains and with reference to clinical isolates, also applying molecular typing methods. The aim of this study was to evaluate the prevalence of toxigenic V. parahaemolyticus in Italian coastal waters and seafood, to examine intra-species variability and to identify, using serotyping and pulsed-field gel electrophoresis (PFGE), relationships among strains from different sources, geographical origin and period of isolation. Of the 192 V. parahaemolyticus strains isolated in different Italian areas and examined in this study, 25 (13.0%) proved to carry the trh gene while none of the strains proved positive to the search by PCR for tdh and Group-Specific-toxRS genes. The prevalence of toxigenic strains in the Tyrrhenian Sea was significantly lower than that calculated for the Ligurian coasts. Regarding the sources of isolation, the higher prevalence of trh-positive V. parahaemolyticus was revealed in fish, followed by clams, plankton, oysters, mussels and lastly seawater. Within the toxigenic strains, 16 serotypes and 20 distinct PFGE patterns were identified. Two clusters, which included a total of 8 V. parahaemolyticus strains, were specifically associated with the North Adriatic Sea area and were stable over time. Our results demonstrate that trh-positive V. parahaemolyticus strains circulated in Italy in the period 2002–2009 with a prevalence higher than that reported from other European and extra-European countries, confirming that toxigenic V. parahaemolyticus is an emerging public health concern in Italy, regardless of its pandemic potential.

Most Vibrio species in autochthonous marine microbial communities, such as Vibrio alginolyticus, Vibrio harveyi, Vibrio anguillarum among others, are considered nonpathogenic for humans. However, because many bacterial virulence genes are located in mobile genetic elements, the acquisition of mobile DNA could mediate the appearance of virulent or more virulent strains even in a species defined as nonpathogenic. In this study, we screened a collection of marine nonpathogenic Vibrio strains isolated in the area of the Venetian Lagoon for the presence of virulence and fitness genes usually present in Vibrio cholerae and Vibrio parahaemolyticus clinical isolates. More than one-third of the strains tested positive for the presence of at least one of the potential virulence/fitness genes with the gene encoding the V. cholerae neuraminidase the most frequently detected. Moreover, 13 of the environmental strains carried modified versions of the V. cholerae pathogenicity island VPI-2, and four of them also contained partial fragments of the V. parahaemolyticus Vp-PAI. The data obtained support the view of nonpathogenic Vibrio strains as a significant reservoir of virulence and fitness genes. The emergence of environmental bacteria with new virulence traits might constitute a direct concern for public health and a risk for human health.

In the marine environment, the persistence and abundance of Vibrio are related to a number of environmental parameters. The influence of the different environmental variables in determining the Vibrio occurrence could be different in the specific geographic areas around the world. Moreover, oceanographic parameters are generally interdependent and should not be considered separately when their influence on bacterial presence and concentration is tested. In this study, an integrated approach was used to identify key parameters determining the abundance of Vibrio spp in marine samples from the Venetian Lagoon in Italy, which is an important area for fish farming and tourism. Multivariate techniques have been adopted to analyze the dataset: using PCA, it was shown that a relatively high proportion of the total variance in this area was mainly due to two independent variables, namely salinity and temperature. Using cluster analysis, it was possible to categorize different groups with homogeneous features as regards space ("stations") and time ("seasons") distribution, as well as to quantify the values of environmental variables and the Vibrio abundances in each category. Furthermore, integrating key environmental factors and bacterial concentration values, it was possible to identify levels of salinity and sea surface temperature which were optimal for Vibrio concentration in water, plankton, and sediment samples. The identification of key environmental variables conditioning Vibrio occurrence should facilitate ocean monitoring, making it possible to predict unexpected variations in marine microflora which determine possible public health risks in coastal areas.

Vibrio parahaemolyticus is a natural inhabitant of marine environments and constitutes part of the autochthonous microbial communities, but is also associated with human gastroenteritis, wound infections and septicemia. Recently, a number of clinical cases of infection due to ingestion of seafood contaminated with V. parahaemolyticus and potentially pandemic marine strains isolated from water and plankton have been reported in Europe. To identify the source of virulent strains and to analyze the possible persistence, in time and space, of particular clones, the molecular typing of Vibrio strains is of high epidemiological interest. In this study, we applied pulsed-field gel electrophoresis and two PCR-based techniques (enterobacterial repetitive intergenic consensus- and repetitive extragenic palindromic-PCR) to establish the DNA fingerprints for the analysis of genetic variability among the environmental V. parahaemolyticus strains isolated in the area of the Venetian Lagoon. A temporal distribution of the environmental strains in the studied geographical area and, in some cases, a strong association between a certain genetic profile and a specific source have been evidenced. A number of genetic clusters/clones seem to persist over time, reappearing in the marine environment for subsequent months and also at a 1-year gap. The use of multiple typing methods allowed a more accurate characterization of the environmental strain genetic profiles and the identification of clones hardly revealed through common techniques.

Vibrio parahaemolyticus is a natural inhabitant of estuarine and marine environments constituting part of the autochthonous microflora. This species is associated with human gastroenteritis caused by ingestion of contaminated water and undercooked seafood. During the past several years, the number of V. parahaemolyticus gastroenteritis cases have increased worldwide, causing over half of all food-poisoning outbreaks of bacterial origin. Vibrio populations in water are known to be influenced by environmental factors. Notably, it has been shown that in different parts of the world the distribution of V. parahaemolyticus in the marine environment is related to the water temperature. In this study, we identified environmental determinants affecting distribution of V. parahaemolyticus in the Venetian Lagoon, in the Italian North Adriatic Sea. Data obtained revealed that sea surface temperature constitutes the key factor influencing occurrence of V. parahaemolyticus, but salinity and chlorophyll concentration are also important. Serotyping of a collection of V. parahaemolyticus environmental isolates revealed high serodiversity, with serotypes O3:KUT and O1:KUT, belonging to the 'pandemic group', occurring with higher frequency. From our results, we conclude that there is no correlation between serotype and specific geographic site or season of the year. However, certain serotypes were isolated in the Lagoon during the entire 18 months of the study, strongly suggesting persistence in this environment.

Infections due to the pathogenic human vibrios, Vibrio parahaemolyticus, Vibrio cholerae and Vibrio vulnificus, are mainly associated with consumption of raw or partially cooked bivalve molluscs. At present, little is known about the presence of Vibrio species in crustaceans and the risk of vibriosis associated with the consumption of these products. The aim of the present study was to evaluate the prevalence and concentration of the main pathogenic Vibrio spp. in samples of crustaceans (n=143) commonly eaten in Italy, taking into account the effects of different variables such as crustacean species, storage conditions and geographic origin. Subsequently, the potential pathogenicity of V. parahaemolyticus strains isolated from crustaceans (n=88) was investigated, considering the classic virulence factors (tdh and trh genes) and four genes coding for relevant proteins of the type III secretion systems 2 (T3SS2α and T3SS2β). In this study, the presence of V. cholerae and V. vulnificus was never detected, whereas 40 samples (28%) were positive for V. parahaemolyticus with an overall prevalence of 41% in refrigerated products and 8% in frozen products. The highest prevalence and average contamination levels were detected in Crangon crangon (prevalence 58% and median value 3400 MPN/g) and in products from the northern Adriatic Sea (35%), with the samples from the northern Venetian Lagoon reaching a median value of 1375 MPN/g. While genetic analysis confirmed absence of the tdh gene, three of the isolates contained the trh gene and, simultaneously, the T3SS2β genes. Moreover three possibly clonal tdh-negative/trh-negative isolates carried the T3SS2α apparatus. The detection of both T3SS2α and T3SS2β apparatuses in V. parahaemolyticus strains isolated from crustaceans emphasised the importance of considering new genetic markers associated with virulence besides the classical factors. Moreover this study represents the first report dealing with Vibrio spp. in crustaceans in Italy, and it may provide useful information for the development of sanitary surveillance plans to prevent the risk of vibriosis in seafood consumers.

Insignia is a novel DNA computational system which uses highly efficient algorithms to compare bacterial genomes and to identify specific DNA signatures to distinguish a target bacterium, or group of bacteria, from all other known bacterial species. It is currently being validated using different bacterial groups, including Vibrio spp. In this study, the genomic analysis by Insignia was conducted on Vibrio parahaemolyticus, a halophilic gram-negative bacteria which constitutes a leading cause of seafood-borne disease. Insignia was used to identify 37 V. parahaemolyticus-specific signatures and to design PCR assays to validate the representative signature sequences by TaqMan essays. The 37 assays targeted loci distributed around the genome and detected genes coding for hypothetical proteins and for proteins involved in adhesion, starvation and virulence. A panel of V. parahaemolyticus environmental strains isolated from the North Adriatic Sea (Italy) and from the Black Sea (Georgia) was used to validate the selected signatures. The signature assays revealed both sensitive and specific and the method allowed a more accurate identification of the tested bacterial strains at the species level when compared to biochemical and PCR standard methods. Using Insignia, it was possible to distinguish two different groups among the strains previously identified as V. parahaemolyticus: most of the strains were included in a "V. parahaemolyticus-like group" showing nearly all of the signatures assayed while a small group of 10 strains contained only a few of the signatures tested. By sequencing the 16S rDNA of this latter group, it was confirmed that they were not V. parahaemolyticus but in fact belonged to other Vibrio species. No significant genome-wide differences were detected between the strains isolated in Italy and in Georgia though the very different geographical origin.

Vibrio parahaemolyticus is an inhabitant of estuarine and marine environments that causes seafood-borne gastroenteritis worldwide. Recently, a type 3 secretion system (T3SS2) able to secrete and translocate virulence factors into the eukaryotic cell has been identified in a pathogenicity island (VP-PAI) located on the smaller chromosome. These virulence-related genes have previously been detected only in clinical strains. Classical virulence genes for this species ( tdh , trh ) are rarely detected in environmental strains, which are usually considered to lack virulence potential. However, during screening of a collection of environmental V. parahaemolyticus isolates obtained in the North Adriatic Sea in Italy, a number of marine strains carrying virulence-related genes, including genes involved in the T3SS2, were detected. In this study, we investigated the pathogenic potential of these marine V. parahaemolyticus strains by studying their adherence ability, their cytotoxicity, their effect on zonula occludin protein 1 (ZO-1) of the tight junctions, and their effect on transepithelial resistance (TER) in infected Caco-2 cells. By performing a reverse transcription-PCR, we also tested the expression of the T3SS2 genes vopT and vopB2 , encoding an effector and a translocon protein, respectively. Our results indicate that, similarly to clinical strains, marine V. parahaemolyticus strains carrying vopT and vopB2 and that other genes included in the VP-PAI are capable of adhering to human cells and of causing cytoskeletal disruption and loss of membrane integrity in infected cells. On the basis of data presented here, environmental V. parahaemolyticus strains should be included in coastal water surveillance plans, as they may represent a risk for human health.

In 2005, pandemic Vibrio parahaemolyticus was reported to have been introduced in Europe: O3:K6 strains were isolated from clinical cases in France and Spain, and were found to be associated with consumption of contaminated seafood. On the contrary, pandemic strains were not isolated from seafood or from the environment itself. Analysis of two V. parahaemolyticus strains isolated in May 2007 from Northern Italy seawater and plankton samples revealed the presence of the virulence gene tdh and the pandemic-specific markers orf8 and toxRS/new sequence (group-specific PCR). The two strains showed serotypes not included in the 'pandemic group', but their molecular typing proved that they represent a single clone showing a genetic profile very similar to that of pandemic O3:K6 reference isolates. Moreover, the two marine strains carried three virulence-related genes associated with clinical strains and, to date, hardly ever or never detected in environmental strains. The presence, in strains isolated from the marine environment, of genetic pandemic markers and virulence genes normally associated with clinical isolates proves that marine strains might constitute a public health concern.

Vibrio parahaemolyticus-mediated disease has traditionally been associated with two virulence factors, thermostable direct haemolysin (TDH) and TDH-related haemolysin (TRH), which are present in most clinical isolates. Recently, it has been suggested that other virulence-related factors, such as some type III secretion system (T3SS) proteins, urease and DNA-methyltransferase, among others, might also play a role in disease caused by this bacterial species and have been shown to be carried by clinical, but not by environmental strains. Screening for a number of virulence and virulence-related genes in a collection of V. parahaemolyticus strains isolated from the Italian Adriatic coast indicates that in addition to the trh-positive strains isolated (6%), a significant percentage (18%) of these strains contain one or more genes with a possible role in pathogenicity. Specifically, some of the V. parahaemolyticus strains described in this study are the first environmental strains ever detected carrying T3SS2 genes. Data obtained by reverse transcription-PCR on environmental strain RNA indicate that at least some of these genes are functional. On the basis of the results obtained, it is suggested that such strains might constitute an environmental reservoir of genes possibly contributing to V. parahaemolyticus pathogenicity and to the spread, in the marine environment, of virulence-related genes usually found in clinical strains.

Vibrio parahaemolyticus is a halophilic bacterium capable of causing food- and waterborne gastroenteritis, wound infections, and septicaemia in humans. The wide distribution of V. parahaemolyticus in the marine and estuarine environments is known to depend on the water temperature: it has been suggested that the bacterium might survive in sediments during the winter and be released into the water column in late spring or early summer when the temperature rises to 15°C or higher [1]. .

Enterococci may survive in adverse environments including the human body where bacteriocins, antibiotics, iron-limitation and immune response represent stressing conditions for bacteria that cause division block. In those conditions, bacteria present in the human body would hardly be in an exponentially growing phase but would mostly be in physiological states such as starvation or the viable but nonculturable (VBNC) state. The possibility that the starved and VBNC bacteria can maintain their ability to adhere to living and inanimate substrates is the first mandatory step for them potentially to cause an infection process. In this study it is shown that starved and stationary enterococcal cells are able to form biofilms on plastic material albeit with reduced efficiency as compared to growing cells. Moreover, although VBNC enterococcal forms are not capable of forming biofilms, Enterococcus faecalis and other enterococcal species of medical interest maintain their ability to synthesize the polymeric matrix for a limited period of time under adverse environmental conditions. The data presented, together with those regarding the maintenance of the division recovery potential already proved in nonculturable bacteria, further support the possibility for the VBNC and other nondividing bacterial forms to have a role as infectious agents and to constitute a risk to human health.