Petroleum contamination and bioaugmentation in bacterial rhizosphere communities from Avicennia schaueriana

ABSTRACT Anthropogenic activity, such as accidental oil spills, are typical sources of urban mangrove pollution that may affect mangrove bacterial communities as well as their mobile genetic elements. To evaluate remediation strategies, we followed over the time the effects of a petroleum hydrocarbon degrading consortium inoculated on mangrove tree Avicennia schaueriana against artificial petroleum contamination in a phytoremediation greenhouse experiment. Interestingly, despite plant protection due to the inoculation, denaturing gradient gel electrophoresis of the bacterial 16S rRNA gene fragments amplified from the total community DNA indicated that the different treatments did not significantly affect the bacterial community composition. However, while the bacterial community was rather stable, pronounced shifts were observed in the abundance of bacteria carrying plasmids. A PCR-Southern blot hybridization analysis indicated an increase in the abundance of IncP-9 catabolic plasmids. Denaturing gradient gel electrophoresis of naphthalene dioxygenase (ndo) genes amplified from cDNA (RNA) indicated the dominance of a specific ndo gene in the inoculated petroleum amendment treatment. The petroleum hydrocarbon degrading consortium characterization indicated the prevalence of bacteria assigned to Pseudomonas spp., Comamonas spp. and Ochrobactrum spp. IncP-9 plasmids were detected for the first time in Comamonas sp. and Ochrobactrum spp., which is a novelty of this study.

Temporal assessment of microbial communities in soils of two contrasting mangroves

ABSTRACT Variations in microbial communities promoted by alterations in environmental conditions are reflected in similarities/differences both at taxonomic and functional levels. Here we used a natural gradient within mangroves from seashore to upland, to contrast the natural variability in bacteria, cyanobacteria and diazotroph assemblages in a pristine area compared to an oil polluted area along a timespan of three years, based on ARISA (bacteria and cyanobacteria) and nifH T-RFLP (diazotrophs) fingerprinting. The data presented herein indicated that changes in all the communities evaluated were mainly driven by the temporal effect in the contaminated area, while local effects were dominant on the pristine mangrove. A positive correlation of community structure between diazotrophs and cyanobacteria was observed, suggesting the functional importance of this phylum as nitrogen fixers in mangroves soils. Different ecological patterns explained the microbial behavior in the pristine and polluted mangroves. Stochastic models in the pristine mangrove indicate that there is not a specific environmental factor that determines the bacterial distribution, while cyanobacteria and diazotrophs better fitted in deterministic model in the same area. For the contaminated mangrove site, deterministic models better represented the variations in the communities, suggesting that the presence of oil might change the microbial ecological structures over time. Mangroves represent a unique environment threatened by global change, and this study contributed to the knowledge of the microbial distribution in such areas and its response on persistent contamination historic events.

Characterization of dioxygenases and biosurfactants produced by crude oil degrading soil bacteria

ABSTRACT Role of microbes in bioremediation of oil spills has become inevitable owing to their eco friendly nature. This study focused on the isolation and characterization of bacterial strains with superior oil degrading potential from crude-oil contaminated soil. Three such bacterial strains were selected and subsequently identified by 16S rRNA gene sequence analysis as Corynebacterium aurimucosum, Acinetobacter baumannii and Microbacterium hydrocarbonoxydans respectively. The specific activity of catechol 1,2 dioxygenase (C12O) and catechol 2,3 dioxygenase (C23O) was determined in these three strains wherein the activity of C12O was more than that of C23O. Among the three strains, Microbacterium hydrocarbonoxydans exhibited superior crude oil degrading ability as evidenced by its superior growth rate in crude oil enriched medium and enhanced activity of dioxygenases. Also degradation of total petroleum hydrocarbon (TPH) in crude oil was higher with Microbacterium hydrocarbonoxydans. The three strains also produced biosurfactants of glycolipid nature as indicated d by biochemical, FTIR and GCMS analysis. These findings emphasize that such bacterial strains with superior oil degrading capacity may find their potential application in bioremediation of oil spills and conservation of marine and soil ecosystem.

Uso de Leersia hexandra (Poaceae) en la fitorremediación de suelos contaminados con petróleo fresco e intemperizado / Use of Leersia hexandra (Poaceae) for soil phytoremediation in soils contaminated with fresh and weathered oil

ResumenLa industria petrolera ha generado derrames crónicos de petróleo y su acumulación en Gleysoles en zonas anegadas en el estado de Tabasco, en el sureste de México. El anegamiento es un factor que limita el uso de tecnologías de remediación por el alto costo y los bajos niveles de degradación del petróleo, sin embargo, Leersia hexandra Sw. es un pasto que crece en estas zonas contaminadas con petróleo intemperizado. El objetivo del estudio fue evaluar la densidad de bacterias, producción de biomasa vegetal y fitorremediación de L.hexandra en suelo contaminado con petróleos fresco e intemperizado, bajo condiciones experimentales de anegamiento. Se realizaron dos experimentos (E1 y E2) en un túnel de plástico. El E1 se basó en ocho dosis: 6 000, 10 000, 30 000, 60 000, 90 000, 120 000, 150 000 y 180 000 mg kg-1 base seca (b.s.) de hidrocarburos totales de petróleo fresco (HTPF), y en el E2 se evaluaron cinco dosis: 14 173, 28 400, 50 598, 75 492 y 112 142 mg kg-1 b. s. de hidrocarburos totales de petróleo intemperizado (HTPI), con ocho repeticiones en cada experimento, además se utilizó un testigo con 2 607 mg kg-1 b. s. de HTP de origen biogénico. Las variables evaluadas a los tres y seis meses fueron 1) densidad microbiana de las bacterias fijadoras de nitrógeno de vida libre totales (BFN), del grupo Azospirillum (AZP) y Azotobacter (AZT), por cuenta viable en placa seriada; 2) producción de materia seca total (MS), se cuantificó por el peso seco por gravimetría, y 3) el porcentaje de descontaminación de los hidrocarburos (DSC) por extracción en equipo soxhlet. En suelos con HTPF, la población de BFN, AZP y AZT se estimuló hasta cinco veces más que el tratamiento testigo a los tres y seis meses; sin embargo, concentraciones de 150 000 y 180 000 mg kg-1 b. s. inhibieron entre un 70 y 89 % la densidad bacteriana. A su vez, en suelos con PI, la inhibición se registró hasta en un 90 %, a excepción del tratamiento con 14 173 mg kg-1 b. s., el cual estimuló las BNF y AZT en 2 y 0.10 veces más que testigo, respectivamente. La producción de MS fue continua en los experimentos hasta los seis meses, con valores de 63 y 89 g en PF y PI, respectivamente; sin diferencias significativas con el testigo (p ≤ 0.05). El DSC alcanzó valores del 66 % al 87 % en HTPF como HTPI a los seis meses, respectivamente. Estos resultados demuestran la habilidad del L. hexandra para desarrollar una rizósfera con alta densidad de BFN, producir biomasa vegetal y fitorremediar Gleysoles con petróleo fresco e intemperizado en ambientes tropicales inundados.

Abstract:The oil industry has generated chronic oil spills and their accumulation in wetlands of the state of Tabasco, in Southeastern Mexico. Waterlogging is a factor that limits the use of remediation technologies because of its high cost and low levels of oil degradation. However, Leersia hexandra is a grass that grows in these contaminated areas with weathered oil. The aim of the study was to evaluate the bacteria density, plant biomass production and phytoremediation of L. hexandra in contaminated soil. For this, two experiments in plastic tunnel were performed with fresh (E1) and weathered petroleum (E2) under waterlogging experimental conditions. The E1 was based on eight doses: 6 000, 10 000, 30 000, 60 000, 90 000, 120 000, 150 000 and 180 000 mg.kg-1 dry basis (d. b.) of total petroleum hydrocarbons fresh (TPH-F), and the E2, that evaluated five doses: 14 173, 28 400, 50 598, 75 492 and 112 142 mg. kg-1 d. b. of total petroleum hydrocarbons weathered (TPH-W); a control treatment with 2 607 mg.kg-1 d. b. was used. Each experiment, with eight replicates per treatment, evaluated after three and six months: a) microbial density of total free-living nitrogen-fixing bacteria (NFB) of Azospirillum (AZP) and Azotobacter group (AZT), for viable count in serial plate; b) dry matter production (DMP), quantified gravimetrically as dry weight of L. hexandra; and c) the decontamination percentage of hydrocarbons (PDH) by Soxhlet extraction. In soil with TPH-F, the NFB, AZP y AZT populations were stimulated five times more than the control both at the three and six months; however, concentrations of 150 000 and 180 000 mg.kg-1 d. b. inhibited the bacterial density between 70 and 89 %. Likewise, in soil with TPH-W, the FNB, AZP and AZT inhibitions were 90 %, with the exception of the 14 173 mg.kg-1 d. b. treatment, which stimulated the NFB and AZT in 2 and 0.10 times more than the control, respectively. The DMP was continued at the six months in the experiments, with values of 63 and 89 g in fresh and weathered petroleum, respectively; had no significant differences with the control (p≤0.05). The PDH reached values of 66 to 87 % both TPH-F and TPH-W at six months, respectively. These results demonstrated the ability the L. hexandra rhizosphere to stimulate the high NFB density, vegetal biomass production and phytoremediation of contaminated soils (with fresh and weathered petroleum), in a tropical waterlogging environment. Rev. Biol. Trop. 65 (1): 21-30. Epub 2017 March 01.

Sphingomonas from petroleum-contaminated soils in Shenfu, China and their PAHs degradation abilities

Abstract Members of the Sphingomonas genus are often isolated from petroleum-contaminated soils due to their unique abilities to degrade polycyclic aromatic hydrocarbons (PAHs), which are important for in situ bioremediation. In this study, a combined phenotypic and genotypic approach using streptomycin-containing medium and Sphingomonas -specific PCR was developed to isolate and identify culturable Sphingomonas strains present in petroleum-contaminated soils in the Shenfu wastewater irrigation zone. Of the 15 soil samples examined, 12 soils yielded yellow streptomycin-resistant colonies. The largest number of yellow colony-forming units (CFUs) could reach 105 CFUs g-1 soil. The number of yellow CFUs had a significant positive correlation (p < 0.05) with the ratio of PAHs to total petroleum hydrocarbons (TPH), indicating that Sphingomonas may play a key role in degrading the PAH fraction of the petroleum contaminants at this site. Sixty yellow colonies were selected randomly and analyzed by colony PCR using Sphingomonas -specific primers, out of which 48 isolates had PCR-positive signals. The 48 positive amplicons generated 8 distinct restriction fragment length polymorphism (RFLP) patterns, and 7 out of 8 phylotypes were identified as Sphingomonas by 16S rRNA gene sequencing of the representative strains. Within these 7 Sphingomonas strains, 6 strains were capable of using fluorene as the sole carbon source, while 2 strains were phenanthrene-degrading Sphingomonas. To the best of our knowledge, this is the first report to evaluate the relationship between PAHs contamination levels and culturable Sphingomonas in environmental samples.

Biodegradation of petroleum hydrocarbons in hypersaline environments

Literature on hydrocarbon degradation in extreme hypersaline media presents studies that point to a negative effect of salinity increase on hydrocarbonoclastic activity, while several others report an opposite tendency. Based on information available in the literature, we present a discussion on the reasons that justify these contrary results. Despite the fact that microbial ability to metabolize hydrocarbons is found in extreme hypersaline media, indeed some factors are critical for the occurrence of hydrocarbon degradation in such environments. How these factors affect hydrocarbon degradation and their implications for the assessment of hydrocarbon biodegradation in hypersaline environments are presented in this review.

Characterization of pyrene utilizing Bacillus spp. from crude oil contaminated soil

Pyrene, a high molecular weight polycyclic aromatic hydrocarbon (PAH), is a priority pollutant present in soil contaminated with crude oil, coal-tar and complex PAHs. Bacterial consortium CON-3 developed from crude oil contaminated soil of Patiala, Punjab (India) cometabolized 50 µg ml-1 pyrene in the presence of glucose (0.5 %; w/v) at 30 °C, as determined by reverse-phase high performance liquid chromatography (HPLC). Bacillus sp. PK-12, Bacillus sp. PK-13 and Bacillus sp. PK-14 from CON-3, identified by 16S rRNA gene sequence analysis, were able to cometabolize 64 %, 55 % and 53 % of pyrene in 35 days, respectively. With the increase in glucose concentration to 1.0 % (w/v) in growth medium isolates PK-12, PK-13 and PK-14 showed 19 - 46 % uptake of 50 µg ml-1 pyrene in 4 days, respectively. Uptake of pyrene was correlated with growth and biosurfactant activity, which is suggestive of the potential role of members of Bacillus genera in pyrene mobilization and its uptake.

Bioconversion of petroleum hydrocarbons in soil using apple filter cake / Bioconversão de hidrocarbonetos de petróleo no solo pelo uso de bagaço de maçã

The aim of this study was to investigate the feasibility of using apple filter cake, a fruit-processing waste to enhance the bioremediation of petroleum contaminated soil. A rotating barrel system was used to study the bioconversion of the xenobiotic compound by natural occurring microbial population. The soil had been accidentally polluted with a total petroleum hydrocarbon concentration of 41,000 ppm. Although this global value was maintained during the process, microbial intervention was evidenced through transformation of the petroleum fractions. Thus, fractions that represent a risk for the environment (GRO, Gasoline Range Organics i.e., C6 to C10-12; DRO, Diesel Range Organics i.e., C8-12 to C24-26 and RRO, Residual Range Organics i.e., C25 to C35) were significantly reduced, from 2.95 percent to 1.39 percent. On the contrary, heavier weight fraction from C35 plus other organics increased in value from 1.15 percent to 3.00 percent. The noticeable diminution of low molecular weight hydrocarbons content and hence environmental risk by the process plus the improvement of the physical characteristics of the soil, are promising results with regard to future application at large scale.

O objetivo deste estudo foi investigara viabilidade de aplicação de bagaço de maçã, um resíduo do processamento de frutas, para melhorar a biorremediação de solo contaminado com petróleo. Para estudar a bioconversão de compostos xenobióticos pela população microbiana naturalmente presente empregou-se um sistema de barril rotativo. O solo havia sido acidentalmente contaminado com um total de hidrocarbonetos de petróleo na concentração de 41.000 ppm. Embora esse valor tenha se mantido durante o processo, a intervenção microbiana ficou evidenciada através da transformação de frações do petróleo. Assim, as frações de risco para o meio ambiente (GRO, Gasoline Range Organics, i.e., C6 a C10-12; DRO, Diesel Ramge Organics, i.e. C8-12 a C24-26 e RRO, Residual Range Organics, i.e. C25 a C35) foram significativamente reduzidas de 2,95 por cento para 1,39 por cento. Por outro lado, frações mais pesadas, acima de C35, e outros compostos orgânicos aumentaram de 1,15 por cento para 3,00 por cento. A diminuição notável do conteúdo de hidrocarbonetos de baixo peso molecular e conseqüentemente do risco ambiental por esse processo, além da melhoria das características físicas do solo, são resultados promissores para uma futura aplicação em grande escala.

Bacterial diversity characterization in petroleum samples from Brazilian reservoirs / Caracterização da diversidade bacteriana em amostras de petróleo provenientes de reservatórios brasileiros

This study aimed at evaluating potential differences among the bacterial communities from formation water and oil samples originated from biodegraded and non-biodegraded Brazilian petroleum reservoirs by using a PCR-DGGE based approach. Environmental DNA was isolated and used in PCR reactions with bacterial primers, followed by separation of 16S rDNA fragments in the DGGE. PCR products were also cloned and sequenced, aiming at the taxonomic affiliation of the community members. The fingerprints obtained allowed the direct comparison among the bacterial communities from oil samples presenting distinct degrees of biodegradation, as well as between the communities of formation water and oil sample from the non-biodegraded reservoir. Very similar DGGE band profiles were observed for all samples, and the diversity of the predominant bacterial phylotypes was shown to be low. Cloning and sequencing results revealed major differences between formation water and oil samples from the non-biodegraded reservoir. Bacillus sp. and Halanaerobium sp. were shown to be the predominant components of the bacterial community from the formation water sample, whereas the oil sample also included Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. and Acidithiobacillus ferrooxidans. The PCR-DGGE technique, combined with cloning and sequencing of PCR products, revealed the presence of taxonomic groups not found previously in these samples when using cultivation-based methods and 16S rRNA gene library assembly, confirming the need of a polyphasic study in order to improve the knowledge of the extent of microbial diversity in such extreme environments.

Este estudo teve como objetivo comparar as comunidades bacterianas de amostras de água de formação e de óleo de reservatórios de petróleo brasileiros com diferentes graus de biodegradação usando a técnica de PCR-DGGE. O DNA ambiental foi isolado e empregado em reações de PCR com primers bacterianos, com subseqüente separação dos fragmentos de DNAr 16S em DGGE. Os produtos de PCR foram também clonados e seqüenciados, visando à afiliação taxonômica dos membros da comunidade. Os fingerprints obtidos permitiram a comparação direta entre as comunidades bacterianas das amostras de óleo com diferentes graus de biodegradação, assim como entre as comunidades da água de formação e do óleo do reservatório não biodegradado. Perfis de DGGE muito similares foram observados para todas as amostras, e a diversidade dos filotipos bacterianos predominantes mostrou-se baixa. Os resultados de clonagem e seqüenciamento revelaram diferenças mais significativas entre as amostras de água de formação e de óleo do reservatório não biodegradado. Bacillus sp. e Halanaerobium sp. mostraram-se os componentes predominantes da comunidade bacteriana da presente na amostra de água de formação, ao passo que a amostra de óleo incluiu também Alicyclobacillus acidoterrestris, Rhodococcus sp., Streptomyces sp. e Acidithiobacillus ferrooxidans. A técnica de PCR-DGGE, combinada com clonagem e seqüenciamento dos produtos de PCR, revelou a presença de grupos taxonômicos não encontrados anteriormente nestas amostras quando métodos baseados em cultivo e na construção de bibliotecas de genes RNAr 16S foram utilizados, evidenciando a necessidade de um estudo polifásico a fim de contribuir para o conhecimento da diversidade microbiana em ambientes extremos como reservatórios de petróleo.

Cytochrome P450 1A activity in liver and fixed wavelength fluorescence detection of polycyclic aromatic hydrocarbons in the bile of tongue-fish (Cynoglossus acrolepidotus, Bleeker) in relation to petroleum hydrocarbons in the eastern Gulf of Thailand.

This investigation was conducted in an area of oil spill along the east coast of Thailand to examine the relations among cytochrome P450 1A activity in liver and PAHs in the bile of the tonguefish and petroleum hydrocarbons in the sediments. PAH sediment concentrations in the reference and oil spill areas were 5.03 +/- 0.42 and 0.21 +/- 0.043 microg(-1) dry weight respectively Cytochrome activity in fish liver from oil spill area was 45.40 +/- 3.50 pmoles/ min/mg protein, almost threefold higher than that from the reference sites. Flourescense detection in bile metabolites at the oil spill area, 69.8 +/- 9.9 flourescense unit was significantly higher than that at the reference sites, 22.9 +/- 5.5 and 22.2 +/- 3.5 fluorescence unit. A strong correlation was found among cytochrome P450 1A activity in liver, PAH of bile metabolites and petroleum hydrocarbons. Both cytochrome and bile metabolites activity decreased seaward varying to the distance from the oil polluted area. We concluded that both detections in tonguefish can be regarded as a complementary biomarkers for the exposure of PAHs in tropical marine environments.

Microbial demetallization of crude oil using Aspergilus sp.: vanadium oxide octaethyl porphyrin [VOOEP] as a model of metallic petroporphyrins

An isolate from polluted soil identified as Aspergillus sp. MS-100 was able to consume vanadium oxide octaethyl porphyrin as a model for protoporphyrins in crude oil. The isolate degrades about 55% of vanadium oxide octaethyl porphyrin [VOOEP] under optimum conditions during 7 days. The release of more than 0.96 mgL-1 of free vanadium into the aqueous phase was confirmed using atomic absorption. By using the Taguchi experimental design method, the optimum values of pH, temperature and initial concentration of VOOEP were determined as 5.5, 30C, and 20 mg/l, respectively. The reduction of VOOEP in the culture medium was accelerated by Ag+ and inhibited by Zn2+ and EDTA. The Sn2+ and Pb2+ ions showed a stimulatory effect at 0.1 mM and an inhibitory effect at 1 mM

Effect of organic loading on the performance of aerated submerged fixed-film reactor [ASFFR] for crude oil-containing wastewater treatment

An aerated submerged fixed-film [ASFF] bioreactor was developed to treat an artificial wastewater based on crude oil. Bee-Cell 2000 was used as support media having porosity of 87% and a specific surface area of 650 m[2]/m[3]. The system was able to achieve 83.14-97.05 percentage removal efficiencies of soluble chemical oxygen demand [SCOD] in the organic loading rate range of 0.84 to 9.41 g SCOD/m[2]day showed that the effluent SCOD concentration ranged between 18.93 and 100.93 mg/L at organic loadings experienced. Therefore, an ASFF process showed that it was feasible to treat high oily wastewater in order to meet the discharge standards

Evaluation of paraffins biodegradation and biosurfactant production by Bacillus subtilis in the presence of crude oil

Os experimentos com Bacillus subtilis para avaliacão da tensão superficial foram realizados com meio de cultivo contendo como nutrientes básicos 0,4 por cento de ions nitrato e 4 por cento de glicose, na presenca de petróleo. A producão de surfactina foi observada pela reducão da tensão superficial do meio de cultura fermentado. Surfactina foi isolada a partir do meio de cultura fermentado por B. subtilis, por precipitacão ácida seguida de extracão com clorofórmio-metanol. A avaliacão da composicão dos alcanos lineares (parafinas) foi realizada por cromatografia gasosa. Observamos uma significativa reducão da tensão superficial do meio de cultura indicando que a producão de biosurfactante não foi inibida pela presenca de parafina, e que as parafinas leves podem ter sido consumidas.

Deteccíon bacteriológica de contaminacíon por petróleo en el estuario de Bahía Blanca / Bacteriological detection of crude oil contamination in the Bahía Blanca estuary

Para conocer la deriva y determinar el área afectada por las pérdidas de petróleo producidas durante las tareas de transvasamiento mediante Boyas Suecas, se cuantificaron bacterias degradadoras de petróleo por el método del Número Más Probable en sedimentos superficiales del estuario de Bahía Blanca. Se establecieron diez estaciones intermareales de nuestreo, localizadas entre las boyas 21 y 16. Se realizó el recuento de bacterias heterótrofas aerobias marinas sobre Agar Marine 2216, y la determinación de materia orgánica. De acuerdo a la abundancia de bacterias degradadoras, el análisis estadístico diferenció dos zonas con distinto grado de contaminación. Una comprendida por las estaciones ubicadas en el Canal Principal de navegación, con recuentos medios, expresados en log10, de 2,98 a 3,65 bactérias/g de sedimento seco, y la otra con valores de 4,16 a 4,37, que se interna en canales y arroyos del veril sur. Estos resultados indican una deriva del contaminante en sentido perpendicular al Canal Principal, debido a la influencia de los vientos predominantes con dirección N y NNO. Mediante el análisis de regresión lineal simple se estableció una relación altamente significativa de la materia orgánica con los dos grupos bacterianos. Este estudio señala que el petróleo proveniente de los volcados está afectando zonas productivas del estuario