Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.This research was supported by the Technology Foundation, the Applied Science Division (STW) of the Netherlands Organization for Scientific Research (NWO), project number 08053, the graduate school WIMEK (Wageningen Institute for Environment and Climate Research, which is part of SENSE Research School for Socio-Economic and Natural Sciences of the Environment, www.wimek-new.wur.nl and www.sense.nl), SKB (Dutch Centre for Soil Quality Management and Knowledge Transfer, www.skbodem.nl) and the Consolider project CSD-2007-00055. The research was incorporated in the TRIAS (TRIpartite Approaches 469 toward Soil systems processes) program (http://www.nwo.nl/en/research-and-results/programmes/alw/trias-tripartite-approach-to-soil-system-processes/index. html). Flávia Talarico Saia was supported by a FAPESP (the State of São Paulo Research Foundation) scholarship (2006-01997/5). The work conducted by the DOE JGI is supported by the Office of Science of the United States Department of Energy under contract number DE-AC02-05CH11231. Alfons Stams acknowledges support by an ERC (European Research Counsil) advanced grant (project 323009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Contribution to technological research of the microbial studies done at program BIOTA FAPESP: evaluation of anaerobic Pentachlorophenol (PCP) biodegradation in a horizontal-flow anaerobic immobilized biomass (HAIB) reactor

O estudo que ora se apresenta integrou o conjunto de pesquisas do sub-projeto - Diversidade de Bactérias Associadas à Degradação de Compostos Recalcitrantes, do projeto temático BIOTA FAPESP - Ecologia Molecular e Taxonomia Polifásica de Bactérias de Interesse Ambiental e Agro-Industrial. Apresenta caráter inovador, na medida em que procurou avaliar o potencial de aplicação biotecnológica de microrganismos anaeróbios de uma área severamente contaminada no Brasil, o estuário de Santos-São Vicente, em degradar o pentaclorofenol (PCP). A pergunta fundamental a ser respondida pelos resultados experimentais realizados foi: são os microrganismos autóctones do estuário capazes de servirem de inóculo para degradar o pentaclorofenol em biorreatores sob condições metanogênicas? Dois grupos de amostras foram avaliados, o primeiro, uma parcela composta por vários sedimentos coletados no estuário e, o segundo, sedimentos coletados na região do Largo de Canéus e na frente da Companhia Siderúrgica Paulista (COSIPA). O estabelecimento da determinação cromatográfica do PCP e congêneres menos clorados para o monitoramento experimental mostrou que na análise da presença dos clorofenóis nos sedimentos, o método de extração por ultrassom com posterior metilação dos analitos foi adequado para concentração mínima de 200 'mü'g clorofenóis/Kg sedimento para 2,3; 2,6 diclorofenóis; 2,4,6 e 2,3,6 triclorofenóis. Contudo, não foi adequado para a determinação do PCP e 2,3,4 triclorofenol. Para o meio de cultivo, o método de extração do PCP por agitação em vórtex e acetilação dos analitos mostrou-se adequado para todos os clorofenóis e com limite de quantificação de 0,1 mg/L. A avaliação do potencial metanogênico foi realizada com as amostras compostas do estuário enriquecidas sob condições halofílicas. O valor estável de metano no biogás de 50% foi obtido nos primeiros 20 dias de incubação. O sedimento nessas condições foi utilizado como inóculo para fins de isolamento de culturas metanogênicas, redutoras do íon sulfato e degradadoras de PCP. Não foram obtidas culturas desalogenadoras; porém foram isoladas arquéias metanogênicas, cultivadas em metanol, acetato e formiato de sódio, bem como bactérias cultivadas em lactato de sódio na presença e ausência de sulfato de sódio. Ensaios fisiológicos aliados aos métodos moleculares FISH e DGGE permitiram identificar arquéias metanogênicas do gênero Methanosarcina sp. e microrganismos do domínio Bacteria. Os sedimentos individualmente estudados foram coletados com maior controle de anaerobiose empregando-se amostrador do tipo corer. O enriquecimento destes sedimentos, inicialmente sob concentração de 2,5 mg PCP/g STV e com adições periódicas de 50% da concentração inicial do clorofenol e 1,25 a 2,5 g/L de glicose por 13 meses a 30 graus Celsius, resultou na obtenção de culturas degradadoras do PCP sob anaerobiose estrita. Nos reatores controles sem PCP, já primeiros 20 dias de incubação 70% de metano foi determinado no biogás. Nos reatores com PCP, a produção do metano (20%) iniciou após 100 dias. A adsorção foi o principal mecanismo de remoção de 50% do PCP nas primeiras 12 horas de incubação dos enriquecimentos. Posteriormente, a redução do PCP no meio de 77% para a amostra de Canéus e 70% para a da COSIPA foi relacionada a mecanismos de biodegradação anaeróbia, como a desalogenação redutiva. Exames microscópicos mostraram a seleção de microrganismos na presença de PCP, com predomínio de bacilos formadores de esporos semelhantes ao gênero Clostridium sp., filamentos diversos e filamentos semelhantes as arquéias metanogênicas acetoclásticas relacionadas ao gênero Methanosaeta sp. O enriquecimento foi realizado sob condições halofílicas, segunda a salinidade de cada amostra estudada no estuário. Não houve perda do clorofenol por volatilização. Os resultados obtidos no enriquecimento anterior viabilizaram o estudo seguro do potencial anaeróbio dos microrganismos oriundos do sedimento da COSIPA em metabolizar o PCP em reator contínuo do tipo RAHLF. Assim, sedimento enriquecido sob condições metanogênicas e halofílicas foi inoculado no RAHLF, controlando-se rigorosamente a anaerobiose. O reator preenchido com cubos de espuma de poliuretana foi operado por 126 dias e tempo de detenção hidráulica de 18 horas, com meio de cultura salino contendo glicose (1 g/L) como principal fonte de carbono e PCP-Na nas concentrações de 5, 13, 15 e 21 mg/L. O desempenho do RAHLF foi estável com boa eficiência durante toda a operação. A redução dos níveis de matéria orgânica medida em DQO variou de 70 a 100% e a de PCP foi de 99%, com detecção de intermediários menos clorados e sob teores de metano no biogás de 20%. Da massa de 1111,73 mg de PCP aplicada no reator, 286,9 mg ficou retida no sistema pelo processo de adsorção nas biopartículas e 824,83 mg foi biodegradada. As análises morfológicas dos tipos celulares, em conjunto com as técnicas moleculares DGGE e FISH, revelaram a presença de grupos microbianos do domínio Archaea pertencente à família Methanosarcinacea e grupos do domínio Bacteria. A participação de grupos de domínio Bacteria, cuja estrutura dos tipos microbianos na comunidade variou ao longo do RAHLF e das concentrações de PCP, e dos organismos metanogênicos da família Methanosarcinacea, possibilitou responder a questão inicialmente formulada, uma vez que se pode afirmar que os microrganismos autóctones foram capazes de degradar o PCP sob condições metanogênicas e halofílicas, com eficiência adequada. A prática para a seleção dos microrganismos retirados do ambiente estuarino, de interesse para biotecnologia anaeróbia aplicada ao saneamento ambiental, que empregou o reator do tipo RAHLF, parece promissora para avanços da engenharia na remediação biológica de uma área cuja relevância é indiscutível para o estado de São PauloThis study has an innovative character, once aimed to evaluate the biotechnological application of anaerobic microorganisms degrading pentachlorophenol (PCP) at a severely polluted area in Brazil, estuary of Santos-São Vicente, São Paulo state. This study integrated a group of researches of the sub-project - Diversity of Bacteria Associated to the Degradation of Recalcitrant Compounds, supported by major project BIOTA FAPESP which theme is Molecular Ecology and Polyphasic Taxonomy of Bacteria of Environmental and Agriculture-Industrial Interest. The fundamental question to be answered by the accomplished experimental results was: are the autochthonus microorganisms of the estuary capable of serving as inoculum to degrade the PCP in bioreactors under methanogenic conditions? In order to evaluate this hypothesis, two groups of samples were collected: sediments taken from several sites of the estuary and sediments taken from two sites, one severely contaminated with organochlorine compounds, in front of the São Paulo Metallurgical Company (COSIPA) and other, less contaminated, in the area of Canéus. The establishment of protocol for the PCP and less chlorinated compounds chromatographic determination showed that the extraction method by ultrosonication followed by metilation of the chlorinated compounds was appropriated to evaluate concentrations of 200 ug chlorophenol/Kg of sediment, 2,3; 2,6 dichlorophenols; 2,4,6 and 2,3,6 trichlorophenols. However, it was not appropriated for evaluation of PCP and 2,3,4 trichlorophenol. For the culture medium, the extraction method by vortex agitation followed by acetilation was appropriated for all of the chlorophenols compounds. The quantification limit was 0,1 mg/L. The evaluation of the methanogenic potential and PCP biodegradation was accomplished with the samples of the estuary enriched under halophylic conditions. In the experiments without PCP was possible to obtain cultures of Methanosarcina sp, identified by FISH technique and cells of domain Bacteria, identified by DGGE. In the experiment with PCP dehalogenated cultures were not obtained. To evaluate PCP anaerobic biodegradation by sediments of COSIPA and Caneus sites, sediments collected under anaerobic conditions by a corer device were enriched in a halophylic brine medium with glucose and PCP at concentration of 2.5 mg PCP/g VTS. Periodic additions of 50% of the initial concentration of PCP and 1.25 to 2.5 g/L of glucose were done. With this strategy was possible to obtain PCP dehalogenated cultures. The adsorption was the main mechanism of 50% of PCP removal in the first 12 hours of incubation. The PCP reduction of 77% for Caneus reactor and 70% for COSIPA reactor was related to anaerobic biodegradation. Microscopic exams showed selection of microorganisms, with predominance of cells related to Clostridium sp., and filaments related to methanogenic acetoclastic archaea Methanosaeta sp. chlorophenols volatilization was not observed. The biotechnological application of HAIB reactor in PCP biodegradation was evaluated using sediment of COSIPA site previously enriched with glucose. The reactor was operated by 126 days and hydraulic detention time of 18 hours, with saline brine medium containing glucose (1 g/L) and NaPCP in concentrations of 5, 13, 15 and 21 mg/L. PCP amendments did not affect the overall performance and functional stability of the process. COD and PCP reduction was close to 80% and 100%, respectively with detection of trichlorophenols and dichlorophenols. Percentage of methane in the biogas closed to 30%. Adsorption analyses demonstrated that 287 mg of PCP was removed by adsorption in the biofilm and 825 mg was removed by biodegradation. Biofilm DGGE-profiling showed the presence of specific bands of Bacteria and Archaea domains when PCP was amended. The appearance of new bands of Bacteria showed that this organisms had a direct influence at PCP dehalogentation. Archaea organisms of Methanosarcinaceae family had an indirect influence in this metabolism. This thesis demonstrated that HAIB reactors, using autochthonous microorganisms under halophylic and methanogenic conditions, are a potential alternative for organochlorines bioremediatio

Hydrogen production in reactors: The influence of organic loading rate, inoculum and support material

Hydrogen production was evaluated in two thermophilic structured bed (USBR) reactors. USBR1was inoculated with auto-fermented sugarcane vinasse and low-density polyethylene cubes were used as support material. USBR2 was inoculated with anaerobic sludge from an up-flow anaerobic sludge blanket (UASB) reactor treating sugarcane vinasse, and polyurethane foam matrices was used as support material. The reactors were operated in parallel with sugar cane molasses at organic loading rate (OLR) from 30 to 120 g COD L−1d−1 during 45 days. Hydrogen production was detected during the whole operational period, with maximum values of 1123 mL H2 d−1L−1 and 2041 mL H2 d−1L−1 for USBR1 and USBR2, respectively. The number of gene copies encoding for Fe-hydrogenase was higher in USBR2 for all OLR applied. DNA sequences related to Thermoanaerobacterium and Clostridium sensu stricto were predominant in USBR1. In USBR2, in addition to these microorganisms, Lactobacillus, Pseudomonas and Thermotuga, and sequences with low frequency of abundance (<5%) involved directly and indirectly in hydrogen production were also present. The taxonomical and functional more diverse inoculum of USBR2 was associated with a higher hydrogen production. Besides fermentation, an unknown metabolism was relevant in USBR2, revealing the importance of physiological characterization of the microbial community present.</p

Development of a simple method to quantify fipronil and its intermediates in soil

A simple and reproducible method was developed and validated for simultaneous quantification of the pesticide fipronil and its intermediates fipronil desulfinyl, fipronil sulfone and fipronil sulfide, in soil. The analytes were extracted by ultrasonic bath and the ratio of solvents (hexane/acetone), number and time of cycles were optimized by Box-Behnken design with a triplicate central point. The optimal extraction conditions were achieved through a response surface analysis. The clean-up step was conducted by cartridges of solid phase extraction (SPE) containing silica (Florisil®) and aluminum oxide. Gas chromatography with electron capture detection (GC-ECD) was employed for separating fipronil and its intermediates with a suitable resolution and runtime of 20 minutes. The best quantification was achieved with 1 : 1 (v/v) acetone/hexane and 2 ultrasound cycles of 15 minutes each. The recovery values were between 81 to 108%, with relative standard deviation (RSD) lower than 6%, with no effect of the used matrix. Analytical curves presented regression coefficients values above 0.9908 for a concentration range from 0.005 to 0.6 μg g-1. Limits of detection (LOD) from 0.002 to 0.006 μg g-1 and limits of quantification (LOQ) from 0.006 to 0.020 μg g-1 were reached for all analytes. This method can be used to monitor and quantify fipronil and its intermediates in soil.</p

A strictly anaerobic Betaproteobacterium Georgfuchsia toluolica gen.nov., sp.nov. degrades aromatic compounds with Fe(III), Mn(IV) or nitrate as electron acceptor.

A bacterium (strain G5G6) that grows anaerobically with toluene was isolated from a polluted aquifer (Banisveld, the Netherlands). The bacterium uses Fe(III), Mn(IV) and nitrate as terminal electron acceptors for growth on aromatic compounds. The bacterium does not grow on sugars, lactate or acetate. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain G5G6 belonged to the Betaproteobacteria. Its closest, but only distantly related, cultured relative is Sterolibacterium denitrificans Chol-1ST (94.6% similarity of the 16S rRNA genes), a cholesterol-oxidizing, denitrifying bacterium. Strain G5G6 possesses the benzylsuccinate synthase A (bssA) gene encoding the a-subunit of Bss, which catalyzes the first step in anaerobic toluene degradation. The deduced BssA amino acid sequence is closely related to those of Azoarcus and Thauera species, which also belong to the Betaproteobacteria. Strain G5G6 is the first toluene-degrading, iron-reducing bacterium that does not belong to the Geobacteraceae within the Deltaproteobacteria. Based on phylogenetic and physiological comparison, strain G5G6 could not be assigned to a described species. Therefore, strain G5G6 (DSMZ 19032T=JCM 14632T) is a novel taxon of the Betaproteobacteria. We propose the name Georgfuchsia toluolica gen. nov., sp. no

Main metabolic pathways of <i>A. denitrificans</i>.

<p>Pathways are indicated using arrows. Black arrows indicate pathways of both strain BC and K601^T, red arrows indicate pathways of strain BC, and blue arrows pathways of strain K601^T. Red gene numbers indicate genes of strain BC (geneID is Alide_red gene number) and blue gene numbers genes of strain K601^T (geneID is Alide2_blue gene number).</p

Degradation of benzene (1), toluene (2) and acetate (3) with chlorate (a), nitrate (b) or oxygen (c) as electron acceptor by <i>A. denitrificans</i> strain BC.

<p>Benzene, toluene and acetate degradation is indicated with diamonds. Benzene and toluene concentrations are outlined on a secondary y-axis while acetate and electron acceptor concentrations are indicated on the primary y-axis. Chlorate, nitrate and oxygen consumption is depicted with squares. Chloride production when chlorate is used as electron acceptor is indicated with triangles and no electron acceptor consumption is shown when no significant difference could be observed because of presence of the electron acceptor in abundance.</p

Gene cluster for chlorate reduction in <i>A. denitrificans</i> strain BC (<i>Aden</i>) compared to <i>I. dechloratans</i> (<i>Idec</i>).

<p>The gene cluster for chlorate reduction comprises of chlorite dismutase (<i>cld</i>), chlorate reductase subunit A, B, C and D (<i>clrA, clrB, clrC, clrD</i>), and in <i>I. dechloratans</i> it also includes an insertion sequence (<i>ISIde1</i>). The numbers represent the location of nucleotide differences (in red) of strain BC compared to <i>I. dechloratans</i> counted from the first nucleotide of each gene. The scale bar represents 500 bp. Sequences for the chlorate reduction gene cluster of <i>I. dechloratans</i> were obtained from the EMBL nucleotide sequence database (accession numbers AJ296077 and AJ566363).</p

Overview of substrate range of <i>A. denitrificans</i> strains BC and K601^T.

<p>+: growth, −: no growth, n.d.: not determined,</p>a<p>previous data <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066971#pone.0066971-Mechichi1" target="_blank">[6]</a>.</p