Draft whole-genome sequence of Sphingobium sp. 22B, a polycyclic aromatic hydrocarbon- degrading bacterium from semiarid Patagonia, Argentina

Sphingobium sp. 22B is a polycyclic aromatic hydrocarbon-degrading strain isolated from Patagonia, Argentina, with capabilities to withstand the environmental factors of that semiarid region. The draft genome shows the presence of genes related with responses to carbon starvation and drying environmental conditions.Fil: Madueño, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Macchi, Marianela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Morelli, Irma Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Coppotelli, Bibiana Marina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Draft whole-genome sequence of Sphingobium sp. 22B, a polycyclic aromatic hydrocarbon- degrading bacterium from semiarid Patagonia, Argentina

Sphingobium sp. 22B is a polycyclic aromatic hydrocarbon-degrading strain isolated from Patagonia, Argentina, with capabilities to withstand the environmental factors of that semiarid region. The draft genome shows the presence of genes related with responses to carbon starvation and drying environmental conditions.Centro de Investigación y Desarrollo en Fermentaciones Industriale

Insights into the mechanisms of desiccation resistance of the Patagonian PAH-degrading strain Sphingobium sp. 22B

Aim: To analyze the physiological response of Sphingobium sp. 22B to water stress. Methods and results:The strain was grown under excess of carbon source and then submitted to low (60RH) and high (18RH) water stress conditions for 96 h. Quantification of trehalose, glycogen, polyhydroxybutyrate (PHB), and transmission electron microscopy (TEM) was studied. Genes linked with desiccation were searched in Sphingobium sp. 22B and Sphingomonas "sensu latu" genomes and their transcripts were quantified by Real-Time PCR. Results showed that, in absence of water stress, strain 22B accumulated 4.76± 1.41% of glycogen, 0.84± 1.62% of trehalose and 44.9± 6.4% of PHB per cellular dry weight. Glycogen and trehalose were mobilized in water stresses conditions, this mobilization was significantly higher in 60RH in comparison to 18RH. Gene treY was upregulated 6-fold change in 60RH relative to 18RH. TEM and quantification of PHB revealed that PHB was mobilized under 60RH condition accompanied by the downregulation of the phbB gene. TEM images showed an extracellular amorphous matrix in 18RH and 60RH. Major differences were found in the presence of aqpZ and trehalose genes between strain 22B and Sphingomonas genomes. Conclusion: Strain 22B showed a carbon conservative metabolism capable of accumulation of three types of endogenous carbon sources. The strain responds to water stress by changing the expression pattern of genes related with desiccation, formation of an extracellular amorphous matrix and mobilization of the carbon sources according to the degree of water stress. Trehalose, glycogen and PHB may have multiple functions in different degrees of desiccation. The robust endowment of molecular responses to desiccation shown in Sphingobium sp. 22B could explain its survival in semiarid soil.Significance and Impact of the studyUnderstanding the physiology implicated in the toleration of the PAH-degrading strain Sphingobium sp 22B to environmental desiccation may improve the bioaugmentation technologies in semiarid hydrocarbons contaminated soils.Centro de Investigación y Desarrollo en Fermentaciones Industriale

Insights into the mechanisms of desiccation resistance of the Patagonian PAH-degrading strain Sphingobium sp. 22B

AimTo analyze the physiological response of Sphingobium sp. 22B to water stress.Methods and resultsThe strain was grown under excess of carbon source and then submitted to low (60RH) and high (18RH) water stress conditions for 96 h. Quantification of trehalose, glycogen, polyhydroxybutyrate (PHB), and transmission electron microscopy (TEM) was studied. Genes linked with desiccation were searched in Sphingobium sp. 22B and Sphingomonas ?sensu latu? genomes and their transcripts were quantified by Real-Time PCR. Results showed that, in absence of water stress, strain 22B accumulated 4.76± 1.41% of glycogen, 0.84± 1.62% of trehalose and 44.9± 6.4% of PHB per cellular dry weight. Glycogen and trehalose were mobilized in water stresses conditions, this mobilization was significantly higher in 60RH in comparison to 18RH. Gene treY was upregulated 6-fold change in 60RH relative to 18RH. TEM and quantification of PHB revealed that PHB was mobilized under 60RH condition accompanied by the downregulation of the phbB gene. TEM images showed an extracellular amorphous matrix in 18RH and 60RH. Major differences were found in the presence of aqpZ and trehalose genes between strain 22B and Sphingomonas genomes.ConclusionStrain 22B showed a carbon conservative metabolism capable of accumulation of three types of endogenous carbon sources. The strain responds to water stress by changing the expression pattern of genes related with desiccation, formation of an extracellular amorphous matrix and mobilization of the carbon sources according to the degree of water stress. Trehalose, glycogen and PHB may have multiple functions in different degrees of desiccation. The robust endowment of molecular responses to desiccation shown in Sphingobium sp. 22B could explain its survival in semiarid soil.Significance and Impact of the studyUnderstanding the physiology implicated in the toleration of the PAH-degrading strain Sphingobium sp 22B to environmental desiccation may improve the bioaugmentation technologies in semiarid hydrocarbons contaminated soils.Fil: Madueño, Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Coppotelli, Bibiana Marina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Festa, Sabrina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Alvarez, H. M.. Universidad Nacional de la Patagonia "San Juan Bosco". Instituto de Biociencias de la Patagonia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Biociencias de la Patagonia; ArgentinaFil: Morelli, Irma Susana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; Argentin

Draft whole-genome sequence of Sphingobium sp. 22B, a polycyclic aromatic hydrocarbon- degrading bacterium from semiarid Patagonia, Argentina

Sphingobium sp. 22B is a polycyclic aromatic hydrocarbon-degrading strain isolated from Patagonia, Argentina, with capabilities to withstand the environmental factors of that semiarid region. The draft genome shows the presence of genes related with responses to carbon starvation and drying environmental conditions.Centro de Investigación y Desarrollo en Fermentaciones Industriale

Assigning ecological roles to the populations belonging to a phenanthrene-degrading bacterial consortium using omic approaches

The present study describes the behavior of a natural phenanthrene-degrading consortium (CON), a synthetic consortium (constructed with isolated strains from CON) and an isolated strain form CON (Sphingobium sp. AM) in phenanthrene cultures to understand the interactions among the microorganisms present in the natural consortium during phenanthrene degradation as a sole carbon and energy source in liquid cultures. In the contaminant degradation assay, the defined consortium not only achieved a major phenanthrene degradation percentage (> 95%) but also showed a more efficient elimination of the intermediate metabolite. The opposite behavior occurred in the CON culture where the lowest phenanthrene degradation and the highest HNA accumulation were observed, which suggests the presence of positive and also negative interaction in CON. To consider the uncultured bacteria present in CON, a metagenomic library was constructed with total CON DNA. One of the resulting scaffolds (S1P3) was affiliated with the Betaproteobacteria class and resulted in a significant similarity with a genome fragment from Burkholderia sp. HB1 chromosome 1. A complete gene cluster, which is related to one of the lower pathways (meta-cleavage of catechol) involved in PAH degradation (ORF 31–43), mobile genetic elements and associated proteins, was found. These results suggest the presence of at least one other microorganism in CON besides Sphingobium sp. AM, which is capable of degrading PAH through the meta-cleavage pathway. Burkholderiales order was further found, along with Sphingomonadales order, by a metaproteomic approach, which indicated that both orders were metabolically active in CON. Our results show the presence of negative interactions between bacterial populations found in a natural consortium selected by enrichment techniques; moreover, the synthetic syntrophic processing chain with only one microorganism with the capability of degrading phenanthrene was more efficient in contaminant and intermediate metabolite degradation than a generalist strain (Sphingobium sp. AM).Centro de Investigación y Desarrollo en Fermentaciones Industriale

La biorremediación en la era post-genómica

La biorremediación tiene hoy en día gran aceptación como una estrategia efectiva para la recuperación de suelos contaminados, sin embargo la falta de información sobre los factores que rigen el funcionamiento metabólico de las comunidades microbianas en los ambientes contaminados hace que, aún en la actualidad, los procesos de biorremediación tengan resultados impredecibles. Las técnicas moleculares basadas en el estudio del DNA, han permitido la identificación de numerosos genes catabólicos abriendo nuevas oportunidades en el desarrollo de los procesos de biorremediación. En esta nueva era post-genómica, las emergentes metatranscriptómica, metaproteómica y metabolómica resultan promesas notables como herramientas para estudiar los mecanismos implicados en la regulación de las vías de degradación, lo que en un futuro nos permitirá desarrollar modelos predictivos sobre la actividad degradadora de la comunidad microbiana del suelo en función de los distintos parámetros bióticos y abióticos, y establecer criterios específicos y claros sobre la elección y evaluación de las estrategias de biorremediación.Bioremediation is nowadays widely accepted as an effective strategy for the recovery of contaminated soils; however the lack of information about the factors that govern the metabolic functioning of microbial communities in contaminated environments means that, still at present, the bioremediation processes have unpredictable results. The molecular techniques based on DNA studies have allowed the identification of numerous catabolic genes opening new opportunities in the development of bioremediation processes. In this new post-genomic era, emerging metatranscriptomics, metaproteomics and metabolomics are remarkable promises as tools to study the mechanisms involved in the regulation of degradation pathways, which in the future will allow us to develop predictive models of degrading activity of the soil microbial community according to the various biotic and abiotic parameters, establishing specific and clear criteria for the selection and evaluation of bioremediation strategies.Centro de Investigación y Desarrollo en Fermentaciones IndustrialesConsejo Nacional de Investigaciones Científicas y TécnicasComisión de Investigaciones Científicas de la provincia de Buenos Aire

La biorremediación en la era post-genómica

La biorremediación tiene hoy en día gran aceptación como una estrategia efectiva para la recuperación de suelos contaminados, sin embargo la falta de información sobre los factores que rigen el funcionamiento metabólico de las comunidades microbianas en los ambientes contaminados hace que, aún en la actualidad, los procesos de biorremediación tengan resultados impredecibles. Las técnicas moleculares basadas en el estudio del DNA, han permitido la identificación de numerosos genes catabólicos abriendo nuevas oportunidades en el desarrollo de los procesos de biorremediación. En esta nueva era post-genómica, las emergentes metatranscriptómica, metaproteómica y metabolómica resultan promesas notables como herramientas para estudiar los mecanismos implicados en la regulación de las vías de degradación, lo que en un futuro nos permitirá desarrollar modelos predictivos sobre la actividad degradadora de la comunidad microbiana del suelo en función de los distintos parámetros bióticos y abióticos, y establecer criterios específicos y claros sobre la elección y evaluación de las estrategias de biorremediación.Bioremediation is nowadays widely accepted as an effective strategy for the recovery of contaminated soils; however the lack of information about the factors that govern the metabolic functioning of microbial communities in contaminated environments means that, still at present, the bioremediation processes have unpredictable results. The molecular techniques based on DNA studies have allowed the identification of numerous catabolic genes opening new opportunities in the development of bioremediation processes. In this new post-genomic era, emerging metatranscriptomics, metaproteomics and metabolomics are remarkable promises as tools to study the mechanisms involved in the regulation of degradation pathways, which in the future will allow us to develop predictive models of degrading activity of the soil microbial community according to the various biotic and abiotic parameters, establishing specific and clear criteria for the selection and evaluation of bioremediation strategies.Centro de Investigación y Desarrollo en Fermentaciones IndustrialesConsejo Nacional de Investigaciones Científicas y TécnicasComisión de Investigaciones Científicas de la provincia de Buenos Aire

Configuraciones urbanas y arquitectónicas del hábitat social en el territorio : El caso “Fábrica Vieja”, de la localidad de Gorina, La Plata-Pcia de Buenos Aires-Argentina

El predio de “la Fábrica” de Gorina, se encuentra ocupado desde hace años por numerosas familias, que han desarrollado fuertes vínculos con el hábitat. Edificios y galpones construidos en el marco de las actividades industriales que tuvieron lugar allí previamente, constituyen hoy, huellas de una historia vinculada al crecimiento y desarrollo de la localidad. Se trata de un asentamiento inmerso en un territorio suburbano con características de alternancia con el espacio rural que se ha transformado en un “área de oportunidad” en la integración-preservación urbana y ambiental de Gorina. Sobre la base de un acuerdo entre la Comisión Nacional de Tierras para el Hábitat Social y la FAU UNLP, se avanza en un proyecto para la regularización dominial y la construcción de viviendas a partir de un trazado urbano que integre al barrio en el conjunto de la localidad. Esta iniciativa involucra directamente a las familias, participando como actores centrales junto a las instituciones, tanto en la configuración de la identidad y la fisonomía del nuevo barrio, como en las diferentes instancias de regularización de la tierra. El reordenamiento e inclusión en la estructura urbana y territorial, propone el desafío de articular actuaciones que integren otras disciplinas, decisiones políticas e institucionales y acciones de autogestión, en términos físicos, ambientales y sociales con características particulares.Facultad de Arquitectura y Urbanism

A historical legacy of antibiotic utilization on bacterial seed banks in sediments

The introduction of antibiotics for both medical and non-medical purposes has had a positive effect on human welfare and agricultural output in the past century. However, there is also an important ecological legacy regarding the use of antibiotics and the consequences of increased levels of these compounds in the environment as a consequence of their use and disposal. This legacy was investigated by quantifying two antibiotic resistance genes (ARG) conferring resistance to tetracycline (tet(W)) and sulfonamide (sul1) in bacterial seed bank DNA in sediments. The industrial introduction of antibiotics caused an abrupt increase in the total abundance of tet(W) and a steady increase in sul1. The abrupt change in tet(W) corresponded to an increase in relative abundance from ca. 1960 that peaked around 1976. This pattern of accumulation was highly correlated with the abundance of specific members of the seed bank community belonging to the phylum Firmicutes. In contrast, the relative abundance of sul1 increased after 1976. This correlated with a taxonomically broad spectrum of bacteria, reflecting sul1 dissemination through horizontal gene transfer. The accumulation patterns of both ARGs correspond broadly to the temporal scale of medical antibiotic use. Our results show that the bacterial seed bank can be used to look back at the historical usage of antibiotics and resistance prevalence.Departamento de Ciencias Biológica