Differential induction, isolation, physicochemical and molecular characterization of temperate phages of environmental Vibrio cholerae as evidence of phage mediated Horizontal Gene Transfer

The resurgence of the enteric pathogen Vibrio cholerae, the causative organism of epidemic cholera, remains a major health problem in many developing countries like India. The southern Indian state of Kerala is endemic to cholera. The outbreaks of cholera follow a seasonal pattern in regions of endemicity. Marine aquaculture settings and mangrove environments of Kerala serve as reservoirs for V. cholerae. The non-O1/non-O139 environmental isolates of V. cholerae with incomplete ‘virulence casette’ are to be dealt with caution as they constitute a major reservoir of diverse virulence genes in the marine environment and play a crucial role in pathogenicity and horizontal gene transfer. The genes coding cholera toxin are borne on, and can be infectiously transmitted by CTXΦ, a filamentous lysogenic vibriophages. Temperate phages can provide crucial virulence and fitness factors affecting cell metabolism, bacterial adhesion, colonization, immunity, antibiotic resistance and serum resistance. The present study was an attempt to screen the marine environments like aquafarms and mangroves of coastal areas of Alappuzha and Cochin, Kerala for the presence of lysogenic V. cholerae, to study their pathogenicity and also gene transfer potential. Phenotypic and molecular methods were used for identification of isolates as V. cholerae. The thirty one isolates which were Gram negative, oxidase positive, fermentative, with or without gas production on MOF media and which showed yellow coloured colonies on TCBS (Thiosulfate Citrate Bile salt Sucrose) agar were segregated as vibrios. Twenty two environmental V. cholerae strains of both O1 and non- O1/non-O139 serogroups on induction with mitomycin C showed the presence of lysogenic phages. They produced characteristic turbid plaques in double agar overlay assay using the indicator strain V. cholerae El Tor MAK 757. PCR based molecular typing with primers targeting specific conserved sequences in the bacterial genome, demonstrated genetic diversity among these lysogen containing non-O1 V. cholerae . Polymerase chain reaction was also employed as a rapid screening method to verify the presence of 9 virulence genes namely, ctxA, ctxB, ace, hlyA, toxR, zot,tcpA, ninT and nanH, using gene specific primers. The presence of tcpA gene in ALPVC3 was alarming, as it indicates the possibility of an epidemic by accepting the cholera. Differential induction studies used ΦALPVC3, ΦALPVC11, ΦALPVC12 and ΦEKM14, underlining the possibility of prophage induction in natural ecosystems, due to abiotic factors like antibiotics, pollutants, temperature and UV. The efficiency of induction of prophages varied considerably in response to the different induction agents. The growth curve of lysogenic V. cholerae used in the study drastically varied in the presence of strong prophage inducers like antibiotics and UV. Bacterial cell lysis was directly proportional to increase in phage number due to induction. Morphological characterization of vibriophages by Transmission Electron Microscopy revealed hexagonal heads for all the four phages. Vibriophage ΦALPVC3 exhibited isometric and contractile tails characteristic of family Myoviridae, while phages ΦALPVC11 and ΦALPVC12 demonstrated the typical hexagonal head and non-contractile tail of family Siphoviridae. ΦEKM14, the podophage was distinguished by short non-contractile tail and icosahedral head. This work demonstrated that environmental parameters can influence the viability and cell adsorption rates of V. cholerae phages. Adsorption studies showed 100% adsorption of ΦALPVC3 ΦALPVC11, ΦALPVC12 and ΦEKM14 after 25, 30, 40 and 35 minutes respectively. Exposure to high temperatures ranging from 50ºC to 100ºC drastically reduced phage viability. The optimum concentration of NaCl required for survival of vibriophages except ΦEKM14 was 0.5 M and that for ΦEKM14 was 1M NaCl. Survival of phage particles was maximum at pH 7-8. V. cholerae is assumed to have existed long before their human host and so the pathogenic clones may have evolved from aquatic forms which later colonized the human intestine by progressive acquisition of genes. This is supported by the fact that the vast majority of V. cholerae strains are still part of the natural aquatic environment. CTXΦ has played a critical role in the evolution of the pathogenicity of V. cholerae as it can transmit the ctxAB gene. The unusual transformation of V. cholerae strains associated with epidemics and the emergence of V. cholera O139 demonstrates the evolutionary success of the organism in attaining greater fitness. Genetic changes in pathogenic V. cholerae constitute a natural process for developing immunity within an endemically infected population. The alternative hosts and lysogenic environmental V. cholerae strains may potentially act as cofactors in promoting cholera phage ‘‘blooms’’ within aquatic environments, thereby influencing transmission of phage sensitive, pathogenic V. cholerae strains by aquatic vehicles. Differential induction of the phages is a clear indication of the impact of environmental pollution and global changes on phage induction. The development of molecular biology techniques offered an accessible gateway for investigating the molecular events leading to genetic diversity in the marine environment. Using nucleic acids as targets, the methods of fingerprinting like ERIC PCR and BOX PCR, revealed that the marine environment harbours potentially pathogenic group of bacteria with genetic diversity. The distribution of virulence associated genes in the environmental isolates of V. cholerae provides tangible material for further investigation. Nucleotide and protein sequence analysis alongwith protein structure prediction aids in better understanding of the variation inalleles of same gene in different ecological niche and its impact on the protein structure for attaining greater fitness of pathogens. The evidences of the co-evolution of virulence genes in toxigenic V. cholerae O1 from different lineages of environmental non-O1 strains is alarming. Transduction studies would indicate that the phenomenon of acquisition of these virulence genes by lateral gene transfer, although rare, is not quite uncommon amongst non-O1/non-O139 V. cholerae and it has a key role in diversification. All these considerations justify the need for an integrated approach towards the development of an effective surveillance system to monitor evolution of V. cholerae strains with epidemic potential. Results presented in this study, if considered together with the mechanism proposed as above, would strongly suggest that the bacteriophage also intervenes as a variable in shaping the cholera bacterium, which cannot be ignored and hinting at imminent future epidemics.

Progress on “Changing coastlines: data assimilation for morphodynamic prediction and predictability”

The task of assessing the likelihood and extent of coastal flooding is hampered by the lack of detailed information on near-shore bathymetry. This is required as an input for coastal inundation models, and in some cases the variability in the bathymetry can impact the prediction of those areas likely to be affected by flooding in a storm. The constant monitoring and data collection that would be required to characterise the near-shore bathymetry over large coastal areas is impractical, leaving the option of running morphodynamic models to predict the likely bathymetry at any given time. However, if the models are inaccurate the errors may be significant if incorrect bathymetry is used to predict possible flood risks. This project is assessing the use of data assimilation techniques to improve the predictions from a simple model, by rigorously incorporating observations of the bathymetry into the model, to bring the model closer to the actual situation. Currently we are concentrating on Morecambe Bay as a primary study site, as it has a highly dynamic inter-tidal zone, with changes in the course of channels in this zone impacting the likely locations of flooding from storms. We are working with SAR images, LiDAR, and swath bathymetry to give us the observations over a 2.5 year period running from May 2003 – November 2005. We have a LiDAR image of the entire inter-tidal zone for November 2005 to use as validation data. We have implemented a 3D-Var data assimilation scheme, to investigate the improvements in performance of the data assimilation compared to the previous scheme which was based on the optimal interpolation method. We are currently evaluating these different data assimilation techniques, using 22 SAR data observations. We will also include the LiDAR data and swath bathymetry to improve the observational coverage, and investigate the impact of different types of observation on the predictive ability of the model. We are also assessing the ability of the data assimilation scheme to recover the correct bathymetry after storm events, which can dramatically change the bathymetry in a short period of time.

Nitrogen fluxes from the landscape are controlled by net anthropogenic nitrogen inputs and by climate

The flux of nitrogen (N) to coastal marine ecosystems is strongly correlated with the “net anthropogenic nitrogen inputs” (NANI) to the landscape across 154 watersheds, ranging in size from 16 km2 to 279 000 km2, in the US and Europe. When NANI values are greater than 1070 kg N km−2 yr−1, an average of 25% of the NANI is exported from those watersheds in rivers. Our analysis suggests a possible threshold at lower NANI levels, with a smaller fraction exported when NANI values are below 1070 kg N km−2 yr−1. Synthetic fertilizer is the largest component of NANI in many watersheds, but other inputs also contribute substantially to the N fluxes; in some regions, atmospheric deposition of N is the major component. The flux of N to coastal areas is controlled in part by climate, and a higher percentage of NANI is exported in rivers, from watersheds that have higher freshwater discharge.

Sting jets in intense winter North-Atlantic windstorms

Extratropical cyclones dominate autumn and winter weather over western Europe. The strongest cyclones, often termed windstorms, have a large socio-economic impact due to the strong surface winds and associated storm surges in coastal areas. Here we show that sting jets are a common feature of windstorms; up to a third of the 100 most intense North Atlantic winter windstorms over the last two decades satisfy conditions for sting jets. The sting jet is a mesoscale descending airstream that can cause strong near-surface winds in the dry slot of the cyclone, a region not usually associated with strong winds. Despite their localized transient nature these sting jets can cause significant damage, a prominent example being the storm that devastated southeast England on 16 October 1987. We present the first regional climatology of windstorms with sting jets. Previously analysed sting jet cases appear to have been exceptional in their track over northwest Europe rather than in their strength.

Transport impacts on atmosphere and climate: shipping

Emissions of exhaust gases and particles from oceangoing ships are a significant and growing contributor to the total emissions from the transportation sector. We present an assessment of the contribution of gaseous and particulate emissions from oceangoing shipping to anthropogenic emissions and air quality. We also assess the degradation in human health and climate change created by these emissions. Regulating ship emissions requires comprehensive knowledge of current fuel consumption and emissions, understanding of their impact on atmospheric composition and climate, and projections of potential future evolutions and mitigation options. Nearly 70% of ship emissions occur within 400 km of coastlines, causing air quality problems through the formation of ground-level ozone, sulphur emissions and particulate matter in coastal areas and harbours with heavy traffic. Furthermore, ozone and aerosol precursor emissions as well as their derivative species from ships may be transported in the atmosphere over several hundreds of kilometres, and thus contribute to air quality problems further inland, even though they are emitted at sea. In addition, ship emissions impact climate. Recent studies indicate that the cooling due to altered clouds far outweighs the warming effects from greenhouse gases such as carbon dioxide (CO2) or ozone from shipping, overall causing a negative present-day radiative forcing (RF). Current efforts to reduce sulphur and other pollutants from shipping may modify this. However, given the short residence time of sulphate compared to CO2, the climate response from sulphate is of the order decades while that of CO2 is centuries. The climatic trade-off between positive and negative radiative forcing is still a topic of scientific research, but from what is currently known, a simple cancellation of global mean forcing components is potentially inappropriate and a more comprehensive assessment metric is required. The CO2 equivalent emissions using the global temperature change potential (GTP) metric indicate that after 50 years the net global mean effect of current emissions is close to zero through cancellation of warming by CO2 and cooling by sulphate and nitrogen oxides.

Sting jets in intense winter North-Atlantic windstorms

Extratropical cyclones dominate autumn and winter weather over western Europe. The strongest cyclones, often termed windstorms, have a large socio-economic impact due to the strong surface winds and associated storm surges in coastal areas. Here we show that sting jets are a common feature of windstorms; up to a third of the 100 most intense North Atlantic winter windstorms over the last two decades satisfy conditions for sting jets. The sting jet is a mesoscale descending airstream that can cause strong near-surface winds in the dry slot of the cyclone, a region not usually associated with strong winds. Despite their localized transient nature these sting jets can cause significant damage, a prominent example being the storm that devastated southeast England on 16 October 1987. We present the first regional climatology of windstorms with sting jets. Previously analysed sting jet cases appear to have been exceptional in their track over northwest Europe rather than in their strength.

Robust future changes in temperature variability under greenhouse gas forcing and the relationship with thermal advection

Recent temperature extremes have highlighted the importance of assessing projected changes in the variability of temperature as well as the mean. A large fraction of present day temperature variance is associated with thermal advection, as anomalous winds blow across the land-sea temperature contrast for instance. Models project robust heterogeneity in the 21st century warming pattern under greenhouse gas forcing, resulting in land-sea temperature contrasts increasing in summer and decreasing in winter, and the pole-to-equator temperature gradient weakening in winter. In this study, future monthly variability changes in the 17 member ensemble ESSENCE are assessed. In winter, variability in midlatitudes decreases while in very high latitudes and the tropics it increases. In summer, variability increases over most land areas and in the tropics, with decreasing variability in high latitude oceans. Multiple regression analysis is used to determine the contributions to variability changes from changing temperature gradients and circulation patterns. Thermal advection is found to be of particular importance in the northern hemisphere winter midlatitudes, where the change in mean state temperature gradients alone could account for over half the projected changes. Changes in thermal advection are also found to be important in summer in Europe and coastal areas, although less so than in winter. Comparison with CMIP5 data shows that the midlatitude changes in variability are robust across large regions, particularly high northern latitudes in winter and mid northern latitudes in summer.

Decadal predictability of the Atlantic meridional overturning circulation and climate in the IPSL-CM5A-LR model

This study explores the decadal potential predictability of the Atlantic Meridional Overturning Circulation (AMOC) as represented in the IPSL-CM5A-LR model, along with the predictability of associated oceanic and atmospheric fields. Using a 1000-year control run, we analyze the prognostic potential predictability (PPP) of the AMOC through ensembles of simulations with perturbed initial conditions. Based on a measure of the ensemble spread, the modelled AMOC has an average predictive skill of 8 years, with some degree of dependence on the AMOC initial state. Diagnostic potential predictability of surface temperature and precipitation is also identified in the control run and compared to the PPP. Both approaches clearly bring out the same regions exhibiting the highest predictive skill. Generally, surface temperature has the highest skill up to 2 decades in the far North Atlantic ocean. There are also weak signals over a few oceanic areas in the tropics and subtropics. Predictability over land is restricted to the coastal areas bordering oceanic predictable regions. Potential predictability at interannual and longer timescales is largely absent for precipitation in spite of weak signals identified mainly in the Nordic Seas. Regions of weak signals show some dependence on AMOC initial state. All the identified regions are closely linked to decadal AMOC fluctuations suggesting that the potential predictability of climate arises from the mechanisms controlling these fluctuations. Evidence for dependence on AMOC initial state also suggests that studying skills from case studies may prove more useful to understand predictability mechanisms than computing average skill from numerous start dates.

Projected changes in medicanes in the HadGEM3 N512 high-resolution global climate model

Medicanes or “Mediterranean hurricanes” represent a rare and physically unique type of Mediterranean mesoscale cyclone. There are similarities with tropical cyclones with regard to their development (based on the thermodynamical disequilibrium between the warm sea and the overlying troposphere) and their kinematic and thermodynamical properties (medicanes are intense vortices with a warm core and even a cloud-free eye). Although medicanes are smaller and their wind speeds are lower than in tropical cyclones, the severity of their winds can cause substantial damage to islands and coastal areas. Concern about how human-induced climate change will affect extreme events is increasing. This includes the future impacts on medicanes due to the warming of the Mediterranean waters and the projected changes in regional atmospheric circulation. However, most global climate models do not have high enough spatial resolution to adequately represent small features such as medicanes. In this study, a cyclone tracking algorithm is applied to high resolution global climate model data with a horizontal grid resolution of approximately 25 km over the Mediterranean region. After a validation of the climatology of general Mediterranean mesoscale cyclones, changes in medicanes are determined using climate model experiments with present and future forcing. The magnitude of the changes in the winds, frequency and location of medicanes is assessed. While no significant changes in the total number of Mediterranean mesoscale cyclones are found, medicanes tend to decrease in number but increase in intensity. The model simulation suggests that medicanes tend to form more frequently in the Gulf of Lion–Genoa and South of Sicily.

Steric sea level variability (1993-2010) in an ensemble of ocean reanalyses and objective analyses

Quantifying the effect of the seawater density changes on sea level variability is of crucial importance for climate change studies, as the sea level cumulative rise can be regarded as both an important climate change indicator and a possible danger for human activities in coastal areas. In this work, as part of the Ocean Reanalysis Intercomparison Project, the global and regional steric sea level changes are estimated and compared from an ensemble of 16 ocean reanalyses and 4 objective analyses. These estimates are initially compared with a satellite-derived (altimetry minus gravimetry) dataset for a short period (2003–2010). The ensemble mean exhibits a significant high correlation at both global and regional scale, and the ensemble of ocean reanalyses outperforms that of objective analyses, in particular in the Southern Ocean. The reanalysis ensemble mean thus represents a valuable tool for further analyses, although large uncertainties remain for the inter-annual trends. Within the extended intercomparison period that spans the altimetry era (1993–2010), we find that the ensemble of reanalyses and objective analyses are in good agreement, and both detect a trend of the global steric sea level of 1.0 and 1.1 ± 0.05 mm/year, respectively. However, the spread among the products of the halosteric component trend exceeds the mean trend itself, questioning the reliability of its estimate. This is related to the scarcity of salinity observations before the Argo era. Furthermore, the impact of deep ocean layers is non-negligible on the steric sea level variability (22 and 12 % for the layers below 700 and 1500 m of depth, respectively), although the small deep ocean trends are not significant with respect to the products spread.

Biogeography of Glandulocaudinae (Teleostei : Characiformes : Characidae) revisited: phylogenetic patterns, historical geology and genetic connectivity

The biogeography of the Glandulocaudinae ( former Glandulocaudini) is reviewed. The major pattern of diversification presented by this group of freshwater fishes can be clearly associated to the main aspects of the tectonic evolution of the southern portion of the Cis-Andean South American Platform. The phylogenetic relationships within the group suggest that the clade represented by Lophiobrycon is the sister-group of the more derived clade represented by the genus Glandulocauda and Mimagoniates. Lophiobrycon and Glandulocauda occur in areas of the ancient crystalline shield of southeastern Brazil and their present allopatric distribution is probably due to relict survival and tectonic vicariant events. Populations of Glandulocauda melanogenys are found in contiguous drainages in presently isolated upper parts of the Tiete, Guaratuba, Itatinga, and Ribeira de Iguape basins and this pattern of distribution is probably the result of river capture caused by tectonic processes that affected a large area in eastern and southeastern Brazil. The species of Mimagoniates are predominantly distributed along the eastern and southeastern coastal areas, but M. microlepis is additionally found in the rio Iguacu and Tibagi basins. Mimagoniates barberi occurs in both SW margin of the upper rio Parana basin and the lower Paraguay and Mimagoniates sp. occurs in the upper Paraguay river basin. Tectonic activations of the Continental Rift of Southeastern Brazil along the eastern margin of the Upper Parana basin promoted population fragmentation responsible of the present day distribution presented by Glandulocauda melanogenys. We hypothesize that occurrence of Mimagoniates along the lowland area around the Parana basin was due to a single or a multiple fragmentation of populations along the W-SW border of the upper Parana Basin, probably due to the major tectonic origin of the Chaco-Pantanal wetland foreland basins since the Miocene as well as Cenozoic tectonic activity along the borders of the upper Parana basin, such as in the eastern Paraguay, in the Asuncion Rift. Distributional pattern of Mimagoniates suggests that its initial diversification may be related to the tectonic evolution of the Chaco-Pantanal foreland basin system and a minimum age of 2.5 M.Y are proposed for this monophyletic group. Previous hypotheses on sea level fluctuations of the late Quaternary as being the main causal mechanism promoting cladogenesis and speciation of the group are critically reviewed. Phylogeographic studies based on molecular data indicate significant differences among the isolated populations of M. microlepis. These findings suggest that a much longer period of time and a paleogeographic landscape configuration of the Brazilian southeastern coastal region explain the present observed phylogenetic and biogeographic patterns.

O Litoral e a metrópole dinâmica imobiliária, turismo e expansão urbana na região metropolitana de Natal-RN

The metropolitan regions of Northeast Brazil are being gradually included in a scenario of international investments, which are motivated by the restructuring of both touristic and real-estate sectors. The new capital, real-estate developers and space configurations that result from this process indicate the need for the creation and implementation of public tools which should, at least, allow the mitigation of the urban impacts and environmental losses resulting from this situation. The effects on landscape and on the socio-spatial configuration result from the intensification caused by the dynamism of the "real estate-tourism" sector. There is a regional integration as an expression of the urban expansion of the metropolitan area of Natal. This study investigates the uniqueness of the restructuring and territorial integration of coastal areas and the strategies of the circuit of capital accumulation formed by linking the real estate to tourism. It is intended to increase the understanding about the strategies of tourism, real estate and public policy agents involved in this territorial reconfiguration and in the fund-raising needed for the investments, to understand the existing social and environmental effects and their future trends and also to understand the forms of spatial production as results from the practices of approaching the land transformation and the tourism valorization of the landscape, in a synchronous manner, first in the Northeast region and, as a focal study, in the Metropolitan Area of Natal. Likewise, it is intended to apprehend the current processes of metropolization of the eastern coast of Rio Grande do Norte, in addition to indicate its physical-territorial transformation and the types of projects/developments promoted by the market in the recent period. Based upon analysis undertaken for the Metropolitan Region of Natal RN, this piece of work presents some considerations on possible legal instruments that can be adjusted to the municipalities which are experiencing the impact of this peculiar and recent phenomenon in the region, caused by the arrival of the real estate-touristic capital. It is also intended to point out basic proposals to the forms of public intervention, in a speculative way, starting from a Metropolitan Planning project within a medium and long term

A produção do mobiliário urbano nos espaços públicos :o desenho do mobiliário urbano nos projetos de reordenamento das orlas do Rio Grande do Norte

This work aims to analyze and evaluate the Urban furniture designed to public areas according to the Revitalization planning for Rio Grande do Norte coastland, defining visual relations among urban elements in the landscape of revitalized public urban areas with cultural, paisagistic and touristic values and the design process used for developing urban furniture to those areas, observing the incoming consequences use to that process in a specific urban context which alters use, functions, cultural images as well as social values attributed to each particular place. Environmental perceptions, legibility of local cultural references and their representation through the design of urban elements, act in a positive or negative manner over the inhabitants cognition process of some particular revitalized area, determining new use and attributions to those areas. Designs for coastal urban interventions try excessively to standardize technical media, construction materials and planning configurations, creating artificial sceneries that segregates users, imposing new structures and usage, generating, consequently, the so called non-places and burlesque regionalism. The research is divided into 4 chapters: 1) Theoretical support (Industrial design; Urban furniture; Public urban spaces; Urban image and environmental perception; Urban occupation and interventions in coastland areas); 2) Methodological procedures and data collection; 3) Analysis of Rio Grande do Norte coastal areas and their urban interventions; 4) Final considerations and Industrial Design contributions to the subject

Projeto raia de fogo: aspectos populacionais da raia de fogo (Dasyatis marianae Gomes, Rosa & Gadig, 2000) e pesca de elasmobrânquios no complexo recifal do Parracho de Maracajaú

The species Dasyatis marianae inhabits coastal areas associated with coral reefs, considered endemic to the northeast of Brazil, occurring from the State of Maranhão to the south of Bahia. Specimens of this species are commonly sighted by divers and fishermen in the area of Maracajaú reefs, a complex reef that is part of the Environmental Protection Area of Coral Reefs (EPACR), which was developed in this study about the ecology and biology of the D. marianae, in order to characterize aspects of population structure in the area of the reef complex of Parracho de Maracajaú. We analyzed 120 specimens caught by artisanal fishing site of the size, weight, sex, stage of maturity and stomach contents. Most subjects were adult males (1.7:1) and was more abundant for rays with lengths between 25 and 29cm of LD, where females reach larger sizes, a feature common to other rays. The largest specimens were captured in the area of seagrass, which is preferred for the species. The distribution of species in the area showed an ontogenetic and sexual segregation, where the youthful occur near the beach, which is a likely area for nursery and growth of the adult females prevail in the seagrass, which apparently has a high prey availability, and Adult males are more distant, a higher proportion occurring in outlying areas, suggesting a habit more exploratory than the females. The evaluation of the reproductive system indicated 3 reproductive cycles per year, one young per pregnancy, and showed that the mature males were smaller than females. The cubs of D. marianae size at birth 12 to 15cm LD. As for diet, the species was characterized as carnivorous crustacean specialist. The performance of visual censuses in different localities allowed to evaluate the density of D. marianae in different environments of the complex. The species occurs in greater numbers in seagrass, environment very important for the conservation of the species. 100 individuals of D. marianae marked in reef complex area enrolled in a recapture rate of 3%. Some behavioral aspects were evaluated, as diurnal pattern of activity, interaction with cleaning and fish Pomacanthus paru followers as Lutjanus analis and Carangoides bartholomaei. Overall, much of the information obtained should be used for management of the species