Dataset Information

Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system (Ria de Aveiro, Portugal).

ABSTRACT: The genus Psychrobacter includes Gram-negative coccobacilli that are non-pigmented, oxidase-positive, non-motile, psychrophilic or psychrotolerant, and halotolerant. Psychrobacter strain ENNN9_III was isolated from water in a polluted temperate estuarine system, contaminated with hydrocarbons and heavy metals. The genome has a G + C content of 42.7%, 2618 open reading frames (ORFs), three copies of the rRNAs operon, and 29 tRNA genes. Twenty-five sequences related to the degradation of aromatic compounds were predicted, as well as numerous genes related to resistance to metals or metal(loid)s. The genome sequence of Psychrobacter strain ENNN9_III provides the groundwork for further elucidation of the mechanisms of metal resistance and aromatic compounds degradation. Future studies are needed to confirm the usefulness of this strain for bioremediation proposes.

SUBMITTER: Gomes JC

PROVIDER: S-EPMC4832037 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system (Ria de Aveiro, Portugal).

Gomes Jaqueline Conceição Meireles JC Azevedo Juliana Simão Nina de JS Veras Adonney Allan de Oliveira AA Alves Jorianne Thyeska Castro JT Henriques Isabel I Correia António A Silva Artur Luiz da Costa da AL Carneiro Adriana Ribeiro AR

Genomics data 20160223

The genus Psychrobacter includes Gram-negative coccobacilli that are non-pigmented, oxidase-positive, non-motile, psychrophilic or psychrotolerant, and halotolerant. Psychrobacter strain ENNN9_III was isolated from water in a polluted temperate estuarine system, contaminated with hydrocarbons and heavy metals. The genome has a G + C content of 42.7%, 2618 open reading frames (ORFs), three copies of the rRNAs operon, and 29 tRNA genes. Twenty-five sequences related to the degradation of aromatic ...[more]

PMID: 27114904

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Project description:BACKGROUND, AIM AND SCOPE: Ria de Aveiro (Portugal) is a shallow coastal lagoon of high economic and ecological importance. Hardly any data on its chemical pollution by polar organic pollutants are available in literature. This study focused on the presence and sources of a series of phenolic endocrine-disrupting compounds (EDCs) in this area, including parabens, alkylphenolic compounds and bisphenol-A (BPA). A number of possible sources of pollution are present in the area, including the large harbours present in the lagoon, the city of Aveiro and the rivers discharging into the area. A recently constructed submarine wastewater outfall, located a few kilometres from the lagoon inlet has also been suggested as a possible source of pollution to Ria de Aveiro in several publications. The aim of the current field study was to investigate the occurrence and main sources of phenolic endocrine disruptors in Ria de Aveiro. MATERIALS AND METHODS: An extensive sampling campaign was performed, with surface water and wastewater grab samples taken at over 50 locations, in duplicate on different days. Samples were treated using solid phase extraction and analysed by liquid chromatography tandem mass spectrometry. RESULTS AND DISCUSSION: Concentrations in lagoon water were generally low: not exceeding 20 ng/L for most analytes. Levels in river water exceeded those in the lagoon by a factor 3 to 500 (o-phenylphenol (PhP) and nonylphenoxy ethoxy acetic acids (A9PEC), respectively), with concentrations up to 700 ng/L for BPA and 7,300 ng/L for A9PEC. Samples from the harbours showed EDC levels similar to those in the rest of the lagoon, but in the city of Aveiro, elevated concentrations were observed for alkylphenol ethoxylates (A9PEO), A9PEC, PhP and BPA. Wastewater effluents showed low levels for parabens, whilst alkylphenolic compounds reached several micrograms per litre. The effluents are discharged into the ocean via a submarine outfall, but as marine water near the outfall showed slightly elevated concentrations only for A9PEO, it does not seem to be a significant source of these EDCs for the area. CONCLUSIONS: All the studied phenolic EDCs were detected in the study area, with high levels found in some of the rivers discharging into the lagoon, and generally low concentrations in the lagoon itself. The main sources for all investigated EDCs were the rivers Caster and Antuã which discharge into the lagoon. The city of Aveiro was identified as a secondary source. As the tidal water exchange volume is much larger than the freshwater input from the rivers, concentrations of phenolic EDCs remained low in the lagoon.

Project description:BackgroundThe cockle is available to numerous fishing villages in Europe, especially Portugal. In the Ria de Aveiro, there is a lack of a fisheries management program and the need for new ecological studies on cockle biology, ecology, and conservation. We shared local ecological knowledge (LEK) highlights about the cockle-Cerastoderma edule (Linnaeus 1758) in the Ria de Aveiro in favor of adaptive management of this bioresource.MethodsSemi-structured interviews with sixty shellfishers in this coastal lagoon were carried out during April and May 2021. LEK data on the biology and ecology of the cockle were analyzed using an ethical-emic approach and the model of integration of different individual skills. These informal data were compared with previously published data for the species, the Fish Base, and GBIF databases.Results and discussionThe average minimum size of the cockle for capture was 23.4 mm, and the average capture per tide was 137.12 kg. The areas with the highest productivity and the most shellfish were RIAV1 and RIAV2. Cockles inhabit areas of sand and mud at an average depth of 2.71 cm. Feeds are mainly small particles, plankton, mud, and algae. The main predators were crabs, European plaice, and bird species. Cockles spawn primarily in late spring and summer. As of 2010, there was a slight decrease in cockle stocks in the Ria de Aveiro due to overfishing, increased rainfall, and changes in the sediment. Considering and analyzing this knowledge is essential for a better understanding of the environmental context the cockles thrive in the view of users of the natural resource.ConclusionInformal data shared by shellfishers in the Ria de Aveiro were typical of filter-feeding bivalves. LEK may assist in planning future management plans for cockles, and unrefuted data may serve as untestable hypotheses. Ethnobiological studies in the Ria de Aveiro lagoon with other species may improve the management of this system since multiple fisheries are carried out in this coastal area.

Project description:From June 2004 to December 2007, samples were weekly collected at a fixed station located at the mouth of Ria de Aveiro (West Iberian Margin). We examined the seasonal and inter-annual fluctuations in composition and community structure of the phytoplankton in relation to the main environmental drivers and assessed the influence of the oceanographic regime, namely changes in frequency and intensity of upwelling events, over the dynamics of the phytoplankton assemblage. The samples were consistently handled and a final subset of 136 OTUs (taxa with relative abundance > 0.01%) was subsequently submitted to various multivariate analyses. The phytoplankton assemblage showed significant changes at all temporal scales but with an overriding importance of seasonality over longer- (inter-annual) or shorter-term fluctuations (upwelling-related). Sea-surface temperature, salinity and maximum upwelling index were retrieved as the main driver of seasonal change. Seasonal signal was most evident in the fluctuations of chlorophyll a concentration and in the high turnover from the winter to spring phytoplankton assemblage. The seasonal cycle of production and succession was disturbed by upwelling events known to disrupt thermal stratification and induce changes in the phytoplankton assemblage. Our results indicate that both the frequency and intensity of physical forcing were important drivers of such variability, but the outcome in terms of species composition was highly dependent on the available local pool of species and the timing of those events in relation to the seasonal cycle. We conclude that duration, frequency and intensity of upwelling events, which vary seasonally and inter-annually, are paramount for maintaining long-term phytoplankton diversity likely by allowing unstable coexistence and incorporating species turnover at different scales. Our results contribute to the understanding of the complex mechanisms of coastal phytoplankton dynamics in relation to changing physical forcing which is fundamental to improve predictability of future prospects under climate change.

Dataset Information

Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system (Ria de Aveiro, Portugal).

Publications

Draft genome sequence of Psychrobacter sp. ENNN9_III, a strain isolated from water in a polluted temperate estuarine system (Ria de Aveiro, Portugal).

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