Integrating Shotgun Metagenomics, 16s Rrna Gene Metabarcoding and Culture Approaches: A Better Outlook for Functional Profiling of a Pah-Contaminated Soil

Understanding bacterial diversity and function is critical for designing bioremediation strategies. This research aimed to assess chronically hydrocarbon contaminated soil bacterial diversity and their aromatic compound degradation (ACD) potential by integrating shotgun metagenomic, 16S rRNA gene metabarcoding and culture approaches. While soil metabarcoding showed dominance of Proteobacteria, metagenomics indicated that 99,5% of the sequences were taxonomically assigned to Streptomycetales order and that almost all genes related to ACD were assigned to the latter. To inspect other phyla contribution to ACD, a functional prediction was delved, and two culture approaches were used. PICRUSt2 revealed that ACD pathways were mostly found in Alphaproteobacteria, Actinobacteria and Gammaproteobacteria classes. An enrichment culture (r-EFP) was obtained with pyrene as sole carbon and energy source and a bacterial strain (S19P6), identified as a member of Mycolicibacterium genus, was isolated. Both cultures demonstrated the ability to degrade more than 90% of the supplemented pyrene after 21 days of incubation. 16S rRNA gene metabarcoding and shotgun metagenomics approaches in r-EFP indicated predominance of Proteobacteria Phylum and the presence of genes responsible for the degradation of ACD mostly assigned to the predominant phyla. Complementing different methodologies enable the recognition of the metabolic potential of soil Proteobacteria related to ACD.Fil: 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: Granada, 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: Irazoqui, José Matías. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; ArgentinaFil: Cuadros Orellana, Sara. Universidad Catolica de Maule; ChileFil: Quevedo, Claudio. Universidad Catolica de Maule; ChileFil: 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: 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; Argentina. Provincia de Buenos Aires. Gobernación. Comisión de Investigaciones Científicas; Argentin

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.Peer reviewe

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Isolation and characterization of haloarqueas grown in aromatics and construction of molecular tools to study the protein secretion in the Domain Archaea

Orientador: Lucia Regina DurrantTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de AlimentosResumo: O metabolismo de compostos aromáticos depende de fatores físico-químicos como temperatura, pH e salinidade, e é bem conhecido e caracterizado em microrganismos mesófilos e em condições ambientais moderadas. No entanto, pouco se conhece sobre o metabolismo desses compostos em ambientes hipersalinos. este trabalho, cinco ambientes hipersalinos foram analisados quanto à presença de arqueas halofílicas capazes de metabolizar compostos aromáticos: Salar de Uyuni (Bolívia), salinas de Cahuil (Chile), salinas de Cabo Rojo (Porto Rico), sabkhas da região do Golfo Pérsico (Arábia Saudita) e Mar Morto (Israel e Jordânia). A estratégia empregada para o enriquecimento e isolamento de arqueas halofílicas capazes de crescer em presença de compostos aromáticos foi bem sucedida. Foram isoladas 12 linhagens capazes de crescer em presença de 1 ,2--benzoantraceno (2 mM) e 44 linhagens capazes de crescer em presença de ácido p-hidroxibenzóico (10 mM) como única fonte de carbono e energia. O isolado MM 17, proveniente de uma amostra de água do Mar Morto, apresentou o melhor resultado de crescimento e foi capaz de degradar completamente os ácidos benzóico (10 mM) e p-hidroxibenzóico (10 mM) após 200 h de cultivo. As análises bioquímica e genética dos isolados, juntamente com a análise dos perfis de lipídeos polares, indicaram que as linhagens estudadas pertencem a pelo menos dois gêneros: Haloferax e Halobacterium. Foi determinada a secreção de uma proteína de alto peso molecular por Haloferax volcanii em resposta à presença de 2 mM 1 ,2-benzoantraceno no meio de cultivo. Com o objetivo de estudar o mecanismo de secreção protéica em haloarqueas, o qual não é completamente entendido_ foram realizadas a clonagem molecular dos genes secD e secY de Haloferax volcanii, a expressão heteróloga em Escherichia coli e a purificação dos produtos gênicos, além de uma tentativa preliminar de obtenção de anticorpos policlonais através da imunização de coelhosAbstract: The metabolism of aromatic compounds depends on physical-chemical factors such as temperature, pH and salinity, and is well known and characterized in mesophilic microorganisms under mild environmental conditions. Little is known, however, about the metabolism of these compounds in highly saline environments. Here, five hypersaline sites were tested for the presence of halophilic archaea able to metabolize aromatic compounds: the Uyuni Salt Marsh (Bolivia), the crystallizer ponds in Cahuil (Chile), the crystallizer ponds in Cabo Rojo (Puerto Rico), the sabkhas in the Persian Gulf (Saudi Arabia) and the Dead Sea (Israel and Jordan). The strategy used for the enrichment and isolation of halophilic archaea able to grow in aromatic compounds was successful. Twelve strains able to grow in 1,2-benzoantracene (2 mM) and 44 strains able to grow in p-hydroxybenzoic acid (10 mM) as the sole carbon and energy source were isolated. Strain MM17, isolated from a Dead Sea water sample, showed the best growth and was able to degrade benzoic (10 mM) and p-hydroxybenzoic (10 mM) acids afier 200 h of cultivation. Biochemical and genetic analyses of the isolates, together with the analysis of polar lipid profiles, indicate that the strains belong to at least two different genera: Haloferax and Halobacterium. The secretion of a high molecular weight protein by Haloferax volcanii following cultivation in 2 mM 1,2-benzoantracene was observed. To study the mechanism of protein secretion in halophilic archaea, a process that is not completely understood, preliminary studies were conducted, which included cloning of secO and secY genes of Haloferax volcanii, their heterologous expression in Escherichia coli and the purification of the gene products. In addition, a preliminary attempt to obtain polyclonal antibodies through rabbit immunization was madeDoutoradoDoutor em Ciência de Alimento

Comparação entre duas técnicas utilizadas no teste de sensibilidade antibacteriana do extrato hidroalcoólico de própolis vermelha

Submitted by Nuzia Santos ([email protected]) on 2014-10-23T11:17:10Z No. of bitstreams: 1 Comparação entre duas técnicas utilizadas no teste de sensibilidade antibacteriana do extrato hidroalcoólico de própolis vermelha..pdf: 76266 bytes, checksum: 0f21c8edac4a408e5b590b879ef771dc (MD5)Approved for entry into archive by Nuzia Santos ([email protected]) on 2014-10-23T11:20:20Z (GMT) No. of bitstreams: 1 Comparação entre duas técnicas utilizadas no teste de sensibilidade antibacteriana do extrato hidroalcoólico de própolis vermelha..pdf: 76266 bytes, checksum: 0f21c8edac4a408e5b590b879ef771dc (MD5)Made available in DSpace on 2014-10-23T11:20:20Z (GMT). No. of bitstreams: 1 Comparação entre duas técnicas utilizadas no teste de sensibilidade antibacteriana do extrato hidroalcoólico de própolis vermelha..pdf: 76266 bytes, checksum: 0f21c8edac4a408e5b590b879ef771dc (MD5) Previous issue date: 2011Universidade Federal de Sergipe. Laboratório de Cromatografia e Flavor. São Cristóvão,SE, BrasilUniversidade Tiradentes. Aracaju, SE, BrasilFundação Oswaldo Cruz. Centro de Pesquisas René Rachou. Belo Horizonte, MG, BrasilUniversidade Federal de Sergipe. Laboratório de Genética e Conservação de Recursos Naturais. São Cristóvão, SE, BrasilA própolis é uma resina natural extraída de vegetais e modificada pelas abelhas melíferas. Esta resina possui ação antimicrobiana e serve para vedar caixas e manter a assepsia da colmeia. O objetivo deste estudo foi comparar os métodos de difusão em agar (técnicas do poço e do disco de papel) avaliando a atividade antibacteriana do extrato de própolis vermelha obtidas na região da foz do rio São Francisco em três diluições frente à Staphylococcus aureus. O extrato hidroalcoólico de própolis vermelha possui atividade antibacteriana frente a S. aureus, sendo a quantidade de 15 μL a que melhor inibiu o microrganismo, caracterizando dose-dependência. Não houve diferença estatística significativa entre as duas técnicas avaliadas, porem, pode sugerir que a técnica de difusão em poço apresenta maior confiabilidade nos resultados apresentados neste estudo

Long-term rock phosphate fertilization impacts the microbial communities of maize rhizosphere.

Phosphate fertilization is a common practice in agriculture worldwide, and several commercial products are widely used. Triple superphosphate (TSP) is an excellent soluble phosphorus (P) source. However, its high cost of production makes the longterm use of crude rock phosphate (RP) a more attractive alternative in developing countries, albeit its influence on plant-associated microbiota remains unclear. Here, we compared long-term effects of TSP and RP fertilization on the structure of maize rhizosphere microbial community using next generation sequencing. Proteobacteria were dominant in all conditions, whereas Oxalobacteraceae (mainly Massilia and Herbaspirillum) was enriched in the RP-amended soil. Klebsiella was the second most abundant taxon in the RP-treated soil. Burkholderia sp. and Bacillus sp. were enriched in the RP-amended soil when compared to the TSP-treated soil. Regarding fungi, Glomeromycota showed highest abundance in RP-amended soils, and the main genera were Scutellospora and Racocetra. These taxa are already described as important for P solubilization/acquisition in RP-fertilized soil. Maize grown on TSP and RP-treated soil presented similar productivity, and a positive correlation was detected for P content and the microbial community of the soils. The results suggest changes of the microbial community composition associated to the type of phosphate fertilization. Whilst it is not possible to establish causality relations, our data highlights a few candidate taxa that could be involved in RP solubilization and plant growth promotion. Moreover, this can represent a shorter path for further studies aiming the isolation and validation of the taxa described here concerning P release on the soil plant system and their use as bioinoculants.Made available in DSpace on 2017-10-04T10:32:20Z (GMT). No. of bitstreams: 1 Longterm.pdf: 2180247 bytes, checksum: 542626c4a904bb640d2448275b260ac1 (MD5) Previous issue date: 2017-10-03bitstream/item/164606/1/Long-term.pdfArticle 1266

Antimicrobial Properties of Chilean Native Plants: Future Aspects in Their Application in the Food Industry

Food contamination with microorganisms is responsible for food spoilage, deterioration and change of organoleptic properties of foods. Besides, the growth of pathogenic microorganisms can provoke serious health problems if food is consumed. Innovative packaging, such as active packaging, is increasing rapidly in the food industry, especially in applying antimicrobials into delivery systems, such as sachets. Chile is a relevant hotspot for biodiversity conservation and a source of unique bio-resources with antimicrobial potential. In this review, fifteen native plants with antimicrobial properties are described. Their antimicrobial effects include an effect against human pathogens. Considering the emergence of antimicrobial resistance, searching for new antimicrobials to design new strategies for food pathogen control is necessary. Chilean flora is a promising source of antimicrobials to be used in active packaging. However, further studies are required to advance from laboratory tests of their antimicrobial effects to their possible effects and uses in active films