Efeito do petróleo sobre comunidades microbianas do solo

Crude oil is still the dominant energy source in Brazil where oil consumption keeps rising since 2013, reaching nowadays 2.2% of the world‟s energy consumption. A recent discovery of crude oil reservoirs at the Espirito Santo, Campos and Santos basins, can represent an excellent opportunity to meet the country‟s economic and energetic demands. However, offshore exploration offers risks to the microbiota and the whole sea life. Microbes are responsible for nutrient cycling can degrade recalcitrant organic compounds and several species have been reported as sensitive to petroleum hydrocarbons. This work aimed to evaluate microbial community shifts in soils under crude oil contamination and assess the effects of Biodiesel co-product (BCP) as a protecting agent of soil microbiota under crude oil addition. We used soils from the Trindade Island and from the Highfield research station at Rothamsted Research, UK. We assembled microcosms of 20 grams and contaminated the soils using weathered crude oil. Soils were incubated at 26° C with moisture correction to ca. 60% water holding capacity. We used CO2 evolution measurements to evaluate soil activity, during the incubation, and soil genomic DNA extraction, at the end of incubation period, to evaluate microbial community changes from treatments and controls. DNA was submitted to amplicon sequencing of 16S rDNA for Bacteria and Archaea and the ITS1 region for Fungi using Illumina MiSeq platform. We compared alpha and beta-diversity and taxonomic shifts. This thesis is divided in two chapters. The first describes the effects of crude oil on Trindade Island‟s soil microbial communities. In the second chapter we tested the protective effects of BCP on Trindade Island, Rothamsted‟s Bare Fallow and Grassland soils, against the amendment with crude oil. Crude oil had a major negative effect on microbial diversity for Trindade Island, but didn‟t change the diversity of Rothamsted agricultural soils. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.O petróleo é a principal fonte de energia no Brasil, onde o consumo de óleo continua subindo desde 2013, atingindo atualmente 2.2% do total de energia consumida no mundo. A descoberta recente de petróleo nas baias do Espirito Santo, Campos e Santos, pode representar uma excelente oportunidade para atender as demandas energéticas nacionais. Entretanto, a exploração de petróleo oferece riscos a microbiota e toda a vida marinha. Microrganismos são responsáveis pela ciclagem de nutrientes, podem degradar compostos orgânicos recalcitrantes e muitas espécies são reportadas como sensíveis à contaminação por hidrocarbonetos do petróleo. Esse trabalho teve o objetivo de avaliar as alterações na comunidade microbiana em solos sob a contaminação por petróleo e avaliar os efeitos do Co-produto de biodiesel (BCP) como um agente protetor da microbiota do solo perante a adição de petróleo. Foram utilizados solos da Ilha da Trindade, e da estação de pesquisa Highfield no Rothamsted Research, UK. Foram montados microcosmos com 20 gramas de solo e os tratamentos utilizaram petróleo intemperizado. Os solos foram incubados a 26° C com correção da umidade para cerca de 60% da capacidade de retenção de água dos solos. Foi utilizada a medição de evolução de CO2 para avaliar a atividade do solo, durante o período de incubação, e a extração de DNA genômico do solo, ao final do período de incubação, para avaliar as mudanças nas comunidades microbianas dos tratamentos e controles. O DNA foi submetido para o sequenciamento de amplicons de 16S rDNA para a avaliação de Bacteria e Archaea e de amplicons da região ITS1 para a avaliação de Fungos utilizando a plataforma Illumina HiSeq. Foi feita a comparação das diversidades alpha e beta e análise das alterações taxonômicas. Essa tese está dividida em dois capítulos. O primeiro descreve os efeitos do petróleo nas comunidades microbianas do solo da Ilha da Trindade. No segundo capítulo foi testado o efeito protetor do BCP sobre a microbiota dos solos da Ilha da Trindade, do campo Bare Fallow e do campo Grassland do Rothamsted Research contra a adição de óleo. O petróleo teve um grande efeito negativo sobre a diversidade microbiana da Ilha da Trindade, mas não mudou a diversidade microbiana dos solos agrícolas do Rothamsted. A comparação taxonômica mostrou aumento do filo Actinobacteria, mudanças em várias classes de Proteobacteria e redução da classe Nitrosphaerales do filo Archaea. Esse é o primeiro esforço para aquisição de conhecimento sobre o efeito da contaminação de solos de uma ilha oceânica brasileira com petróleo. Essa informação é importante para guiar qualquer futura estratégia de biorremediação que se faça necessária.Coordenação de Aperfeiçoamento de Pessoal de Nível Superio

Phenanthrene s degradation in latosol: effect of contaminant s concentration and the addition of surfactin

Os hidrocarbonetos policíclicos aromáticos (HPAS) são constituídos exclusivamente por átomos de carbono e hidrogênio e organizados sob forma linear, angular ou agrupada. Diversos HPA ao sofrerem ativação enzimática, tendem a ligar-se ao DNA, c ausando erros de replicação e mutações. Muitas dessas moléculas são reconhecidas como tóxicas, mutagênicas e carcinogênicas. Os HPA são compostos recalcitrantes, em razão de sua baixa solubilidade em água e alta sorção ao solo. O uso de biossurfactantes é uma opção geralmente eficaz na remoção de contaminantes orgânicos hidrofóbicos de matrizes complexas, como o solo. A surfactina é um lipopeptídeo sintetizado por Bacillus subtilis e possui alta atividade de redução da tensão entre compostos hidrofóbicos e a água. Diferente de uma extração exaustiva, os biossurfactantes agem aumentando a biodisponibilidade do contaminante e facilitam a sua biodegradação. Neste trabalho, foi conduzido um experimento de biodegradação de fenantreno em latossolo argiloso, contaminado com 14C-fenantreno e com 4 concentrações de 12C-fenantreno (1, 10, 40 e 100 μg g-1). A biodegradação foi avaliada com a adição dos suplementos surfactina (0,825 mg g-1), extrato de levedura (1,0 mg g-1) e de um inóculo (30 mg g-1), obtido a partir da adição de óleo diesel a composto de resíduo sólido urbano, para enriquecimento de micro-organismos degradadores de hidrocarbonetos. Os frascos foram mantidos a 35 °C por 49 dias. O 14CO2 produzido foi capturado em tubos de cintilação, contendo 2 mL de KOH (1 mol L-1). Os frascos foram substituídos nos dias 8, 18, 25, 32, 37, 44 e 49. Após a troca do frasco no trigésimo segundo dia, foi feita uma segunda aplicação de surfactina (0,230 mg g-1), em todos os tratamentos. A maior atividade de degradação foi alcançada nos primeiros 8 dias de incubação, somente nos tratamentos que receberam o inóculo. Após o oitavo dia, até a nova suplementação com surfactina (32° dia), o aumento da atividade não foi significativo em nenhum dos tratamentos. A atividade voltou a aumentar após a adição suplementar de surfactina, porém, em uma taxa inferior à alcançada nos primeiros 8 dias. Esse resultado foi atribuído à menor concentração da surfactina e a efeitos de adsorção do fenantreno ao solo. Nas amostras com a maior concentração de fenantreno (100 μg g-1) a atividade de degradação não diferiu em função dos tratamentos com e sem surfactina. Esse resultado sugere que a concentração do fenantreno biodisponível, nessa dose, se manteve suficientemente alta para sustentar a atividade de degradação. A suplementação com extrato de levedura resultou em menor atividade de degradação, nos tratamentos com 10, 40 e 100 μg g-1 de fenantreno. Nos tratamentos com a menor dose de fenantreno (1 μg g-1), o extrato de levedura estimulou a degradação do contaminante. Conclui-se que a suplementação com extrato de levedura estimulou a degradação da surfactina, o que resultou em redução da degradação do fenantreno nas maiores concentrações do contaminante. Os resultados do trabalho indicam que a biorremediação de solos contaminados com HPA requer a manutenção de agentes solubilizadores, como a surfactina. Em razão da rápida degradação do biossurfactante no solo, sugere-se que a melhor estratégia seja a inoculação de micro-organismos produtores dessa classe de compostos e a manutenção de condições favoráveis a produção de biossurfactantes in situ, ao longo do processo de biorremediação.Polycyclic aromatic hydrocarbons (PAH) consist exclusively of carbon and hydrogen atoms arranged in a linear, angular or clustered. Several PAH suffer enzymatic activation and tend to bind to DNA, causing mutations and replication errors. Many of these molecules are known to be toxic, mutagenic and carcinogenic. The PAH are recalcitrant compounds due to its low water solubility and high sorption to soil. The use of biosurfactants has been an option usually effective for removing hydrophobic organic contaminants in complex matrices such as soil. The surfactin is a lipopeptide synthesized by Bacillus subtilis and highly effective in reduction of tension between water and hydrophobiccompounds.Unlike of an exhaustive extraction, the biosurfactants act by increasing the bioavailability of the contaminant and facilitates its degradation.In this work the experiment of phenanthrene biodegradation was conducted in clayed soils contaminated with 14C-phenanthrene and 4 12C-phenanthrene concentrations (1, 10, 40 and 100 mg g-1). Biodegradation was evaluated with the addition of supplements: surfactin (0.825 mg g-1), yeast extract (1.0 mg g-1) and an inoculum (30 mg g-1) obtained from the addition of diesel to a compost made of the municipal solid waste, for enrichment of microorganisms degraders of hydrocarbons. The flasks were kept at 35 °C for 49 days. The 14CO2 produced was captured in scintillation vials containing 2 ml of KOH (1 mol L-1). The bottles were changed on days 8, 18, 25, 32, 37, 44 and 49. After replacing the vials on the thirtieth-second day, was made a second application of surfactin (0.230 mg g-1) in all treatments. The highest degradation activity was achieved in the first 8 days of incubation, only treatments that received the inoculum. After the eighth day until the new surfactin supplementation (32 days), increased activity was not significant in any of the treatments. The activity increased again after the addition of surfactin further, but at a lower rate than achieved in the first 8 days. This result was attributed to the lower concentration of surfactin and the effects of adsorption of phenanthrene to the soil. The degradation activity in samples with the highest concentration of phenanthrene (100 mg g-1) did not differ in the treatments with and without surfactin. This result suggests that the concentration of bioavailable phenanthrene on this dose remained high enough to sustain the activity of degradation. Supplementation with yeast extract resulted in a lower degradation activity in treatments with 10, 40 and 100 mg g-1 of phenanthrene. In the treatments with the lowest dose of phenanthrene (1 mg g-1), yeast extract stimulated the degradation of the contaminant. It is concluded that supplementation with yeast extract stimulated the degradation of surfactin, which resulted in reducing the degradation of phenanthrene in higher concentrations of the contaminant. The results of the work indicate that the bioremediation of soils contaminated with PAH requires the maintenance of solubilizing agents such as surfactin. Due to the rapid degradation of biosurfactant on the ground, it is suggested that the best strategy is to inoculate microorganisms producers of this class of compounds and the maintenance of favorable conditions to ensure the production of biosurfactants in situ, during the process of bioremediation.Conselho Nacional de Desenvolvimento Científico e Tecnológic

Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects

We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1 C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario

Explorative Meta-Analysis of 417 Extant Archaeal Genomes to Predict Their Contribution to the Total Microbiome Functionality

Revealing the relationship between taxonomy and function in microbiomes is critical to discover their contribution to ecosystem functioning. However, while the relationship between taxonomic and functional diversity in bacteria and fungi is known, this is not the case for archaea. Here, we used a meta-analysis of 417 completely annotated extant and taxonomically unique archaeal genomes to predict the extent of microbiome functionality on Earth contained within archaeal genomes using accumulation curves of all known level 3 functions of KEGG Orthology. We found that intergenome redundancy as functions present in multiple genomes was inversely related to intragenome redundancy as multiple copies of a gene in one genome, implying the tradeoff between additional copies of functionally important genes or a higher number of different genes. A logarithmic model described the relationship between functional diversity and species richness better than both the unsaturated and the saturated model, which suggests a limited total number of archaeal functions in contrast to the sheer unlimited potential of bacteria and fungi. Using the global archaeal species richness estimate of 13,159, the logarithmic model predicted 4164.1 ± 2.9 KEGG level 3 functions. The non-parametric bootstrap estimate yielded a lower bound of 2994 ± 57 KEGG level 3 functions. Our approach not only highlighted similarities in functional redundancy but also the difference in functional potential of archaea compared to other domains of life

Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation

Submitted by Nuzia Santos ([email protected]) on 2019-10-04T19:06:31Z No. of bitstreams: 1 Metataxonomic analyses reveal .pdf: 1940255 bytes, checksum: 61c6985af211c1dd5f4a04c4ac1b6e92 (MD5)Approved for entry into archive by Nuzia Santos ([email protected]) on 2019-10-04T19:26:32Z (GMT) No. of bitstreams: 1 Metataxonomic analyses reveal .pdf: 1940255 bytes, checksum: 61c6985af211c1dd5f4a04c4ac1b6e92 (MD5)Made available in DSpace on 2019-10-04T19:26:32Z (GMT). No. of bitstreams: 1 Metataxonomic analyses reveal .pdf: 1940255 bytes, checksum: 61c6985af211c1dd5f4a04c4ac1b6e92 (MD5) Previous issue date: 2019Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Microbiologia. Laboratório de Microbiologia Aplicada. Belo Horizonte, MG, Brasil.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Microbiologia. Laboratório de Microbiologia Aplicada. Belo Horizonte, MG, Brasil.Fundação Oswaldo Cruz. Instituto René Rachou. Grupo de Informática e Genômica de Biossistemas. Belo Horizonte, MG, Brasil.Laboratory of Environmental Microbiology. Institute of Microbiology of the Czech Academy of Sciences – CAS. Prague, Czech Republic.Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Microbiologia. Laboratório de Microbiologia Aplicada. Belo Horizonte, MG, Brasil.Metataxonomic approach was used to describe the bacterial community from a creosote-contaminated aquifer and to access the potential for in situ bioremediation of the polycyclic aromatic hydrocarbons (PAHs) by biostimulation. In general, the wells with higher PAH contamination had lower richness and diversity than others, using the Shannon and Simpson indices. By the principal coordinate analysis (PCoA) it was possible to observe the clustering of the bacterial community of most wells in response of the presence of PAH contamination. The significance analysis using edgeR package of the R program showed variation in the abundance of some Operational Taxonomic Units (OTUs) of contaminated wells compared to uncontaminated ones. Taxons enriched in the contaminated wells were correlated positively (p < 0.05) with the hydrocarbons, according to redundancy analysis (RDA). All these enriched taxa have been characterized as PAH degrading agents, such as the genus Comamonas, Geobacter, Hydrocarboniphaga, Anaerolinea and Desulfomonile. Additionally, it was possible to predict, with the PICRUSt program, a greater proportion of pathways and genes related to the degradation of PAHs in the wells with higher contamination levels. We conclude that the contaminants promoted the enrichment of several groups of degrading bacteria in the area, which strengthens the feasibility of applying biostimulation as an aquifer remediation strategy

Draft genome of Nocardia farcinica TRH1, a linear and polycyclic aromatic hydrocarbon-degrading bacterium isolated from the coast of Trindade Island, Brazil

Submitted by Nuzia Santos ([email protected]) on 2018-06-27T15:02:05Z No. of bitstreams: 1 Draft genome of Nocardia farcinica.pdf: 246979 bytes, checksum: 8fe0c178ce3ea38e1e3a837402da730d (MD5)Approved for entry into archive by Nuzia Santos ([email protected]) on 2018-06-27T15:05:59Z (GMT) No. of bitstreams: 1 Draft genome of Nocardia farcinica.pdf: 246979 bytes, checksum: 8fe0c178ce3ea38e1e3a837402da730d (MD5)Made available in DSpace on 2018-06-27T15:05:59Z (GMT). No. of bitstreams: 1 Draft genome of Nocardia farcinica.pdf: 246979 bytes, checksum: 8fe0c178ce3ea38e1e3a837402da730d (MD5) Previous issue date: 2017Universidade Federal de Viçosa. Departamento de Microbiologia. Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente. Viçosa, MG, Brazil.Universidade Federal de Viçosa. Centro de Ciências Biológicas. Núcleo de Análise de Biomoléculas. Viçosa, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Grupo de Biologia Computacional e Genônica. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Grupo de Biologia Computacional e Genônica. Belo Horizonte, MG, Brazil.Fundação Oswaldo Cruz. Instituto René Rachou. Grupo de Biologia Computacional e Genônica. Belo Horizonte, MG, Brazil.Universidade Federal do Pampa. São Gabriel, RS, Brazil.Universidade Federal de Viçosa. Departamento de Microbiologia. Laboratório de Biotecnologia e Biodiversidade para o Meio Ambiente. Viçosa, MG, Brazil.Here, we report the draft genome sequence and annotation of Nocardia farcinica TRH1, a petroleum hydrocarbons degrading Actinobacteria isolated from the coastal water of Trindade Island, Brazil

Aliphatic hydrocarbon enhances phenanthrene degradation by autochthonous prokaryotic communities from a pristine seawater

The microbial diversity and functioning around oceanic islands is poorly described, despite its importance for ecosystem homeostasis. Here, we aimed to verify the occurrence of microbe-driven phenanthrene co-oxidation in the seawater surrounding the Trindade Island (Brazil). We also used Next-Generation Sequencing to evaluate the effects of aliphatic and polycyclic aromatic hydrocarbons (PAHs) on these microbial community assemblies. Microcosms containing seawater from the island enriched with either labelled (9^-14C) or non-labelled phenanthrene together with hexadecane, weathered oil, fluoranthene or pyrene, and combinations of these compounds were incubated. Biodegradation of phenanthrene-9^-14C was negatively affected in the presence of weathered oil and PAHs but increased in the presence of hexadecane. PAH contamination caused shifts in the seawater microbial community—from a highly diverse one dominated by Alphaproteobacteria to less diverse communities dominated by Gammaproteobacteria. Furthermore, the combination of PAHs exerted a compounded negative influence on the microbial community, reducing its diversity and thus functional capacity of the ecosystem. These results advance our understanding of bacterial community dynamics in response to contrasting qualities of hydrocarbon contamination. This understanding is fundamental in the application and monitoring of bioremediation strategies if accidents involving oil spillages occur near Trindade Island and similar ecosystems

ZIKV – CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms

Background: In early 2015, a ZIKA Virus (ZIKV) infection outbreak was recognized in northeast Brazil, where concerns over its possible links with infant microcephaly have been discussed. Providing a causal link between ZIKV infection and birth defects is still a challenge. MicroRNAs (miRNAs) are small noncoding RNAs (sncRNAs) that regulate post-transcriptional gene expression by translational repression, and play important roles in viral pathogenesis and brain development. The potential for flavivirus-mediated miRNA signalling dysfunction in brain-tissue development provides a compelling hypothesis to test the perceived link between ZIKV and microcephaly. Methodology/Principal Findings: Here, we applied in silico analyses to provide novel insights to understand how Congenital ZIKA Syndrome symptoms may be related to an imbalance in miRNAs function. Moreover, following World Health Organization (WHO) recommendations, we have assembled a database to help target investigations of the possible relationship between ZIKV symptoms and miRNA-mediated human gene expression. Conclusions/Significance: We have computationally predicted both miRNAs encoded by ZIKV able to target genes in the human genome and cellular (human) miRNAs capable of interacting with ZIKV genomes. Our results represent a step forward in the ZIKV studies, providing new insights to support research in this field and identify potential targets for therapy.</p