Functional genes and gene array analysis as tools for monitoring hydrocarbon biodegradation

Bioremediation, which is the exploitation of the intrinsic ability of environmental microbes to degrade and remove harmful compounds from nature, is considered to be an environmentally sustainable and cost-effective means for environmental clean-up. However, a comprehensive understanding of the biodegradation potential of microbial communities and their response to decontamination measures is required for the effective management of bioremediation processes. In this thesis, the potential to use hydrocarbon-degradative genes as indicators of aerobic hydrocarbon biodegradation was investigated. Small-scale functional gene macro- and microarrays targeting aliphatic, monoaromatic and low molecular weight polyaromatic hydrocarbon biodegradation were developed in order to simultaneously monitor the biodegradation of mixtures of hydrocarbons. The validity of the array analysis in monitoring hydrocarbon biodegradation was evaluated in microcosm studies and field-scale bioremediation processes by comparing the hybridization signal intensities to hydrocarbon mineralization, real-time polymerase chain reaction (PCR), dot blot hybridization and both chemical and microbiological monitoring data. The results obtained by real-time PCR, dot blot hybridization and gene array analysis were in good agreement with hydrocarbon biodegradation in laboratory-scale microcosms. Mineralization of several hydrocarbons could be monitored simultaneously using gene array analysis. In the field-scale bioremediation processes, the detection and enumeration of hydrocarbon-degradative genes provided important additional information for process optimization and design. In creosote-contaminated groundwater, gene array analysis demonstrated that the aerobic biodegradation potential that was present at the site, but restrained under the oxygen-limited conditions, could be successfully stimulated with aeration and nutrient infiltration. During ex situ bioremediation of diesel oil- and lubrication oil-contaminated soil, the functional gene array analysis revealed inefficient hydrocarbon biodegradation, caused by poor aeration during composting. The functional gene array specifically detected upper and lower biodegradation pathways required for complete mineralization of hydrocarbons. Bacteria representing 1 % of the microbial community could be detected without prior PCR amplification. Molecular biological monitoring methods based on functional genes provide powerful tools for the development of more efficient remediation processes. The parallel detection of several functional genes using functional gene array analysis is an especially promising tool for monitoring the biodegradation of mixtures of hydrocarbons.

Estudo em Escala Piloto de Parâmetros de Monitoramento e Operação de Biopilhas no Tratamento de Solos Contaminados por Hidrocarbonetos de Petróleo

O objetivo do trabalho foi identificar ferramentas e indicadores adequados ao monitoramento e à otimização de processos de biorremediação, incluindo parâmetros físicos, químicos e microbiológicos definidos em estudos de tratabilidade de solos contaminados por óleo cru em escala de laboratório e comparar estratégias de biorremediação, tais como bioestímulo e bioaumento conduzidas em simulações de biopilhas dinâmicas ou estáticas. Quando três métodos de extração de hidrocarbonetos de petróleo de solo arenoso e franco-argiloso para análise cromatográfica (Soxhlet-SOX, microondas-MARS e extração acelerada por solvente-ASE) foram comparados entre si, concluiu-se que a técnica que promove a melhor recuperação depende da fração de interesse (n-alcanos, HRP, MCNR, HPA), das características texturais do solo (teores de areia, silte e argila) e da idade da contaminação. Dentre os indicadores de densidade populacional microbiana (microrganismos heterotróficos totais-PHT, população de fungos-PF e população microbiana degradadora de óleo (PDO) passíveis de utilização para indicar a taxa de degradação de compostos orgânicos presentes no solo tais como os hidrocarbonetos de petróleo, o PDO mostrou-se o mais adequado em conjunto com a produção de CO2 aferida pelo método respirométrico. Quando a estratégia de biorremediação de solo franco-argiloso contaminado com óleo cru a 3% (m m-1) utilizando bioestímulo (ajuste de pH, umidade e taxa C:N:P) foi comparada ao bioaumento (bioestímulo e adição de inóculo de microrganismos extraídos, enriquecidos e aclimatizados ao óleo cru como fonte de carbono), em sistemas de bancada simulando biopilha dinâmica (microcosmo M) e biopilha estática com aeração forçada (reator B), o tratamento que apresentou melhor remoção (32%) de HTP após 121 dias foi o bioaumento em biopilha estática. Para HPA, o tratamento que alcançou a melhor remoção (33%) foi com bioestímulo também em biopilha estática. A avaliação da taxa de mortalidade (%) de Eisenia andrei exposta tanto a solos recém-contaminados por óleo cru e preparados para bioestímulo (BIOS) e bioaumento (BIOA) a serem tratados em biopilhas dinâmicas e estáticas em escala de laboratório mostrou que após 56 dias de exposição da E. andrei, todos os solos produziram letalidade de 100%, quer fossem os solos recém-contaminados e preparados para os diferentes tratamentos (BIOS M, BIOS B, BIOA M, BIOA B) ou após 121 dias de tratamento. Tal resultado confirma que a biorremediação foi incipiente também do ponto de vista de remoção da ecotoxicidade. Em linhas gerais, a biorremediação de solo franco-argiloso contaminado por óleo cru, contendo tanto contaminação antiga quanto recente, reúne os maiores desafios à biorremediação, tanto do ponto de vista da composição textural do solo quanto da natureza do contaminante. Os processos são aparentemente lentos e requerem ferramentas auxiliares para aceleração dos mesmos. Recomenda-se no futuro, condução de experimentos com o uso de diferentes surfactantes, com ênfase em biosurfactantes

稠油污染土壤高级氧化-生物耦合修复研究

稠油中的胶质和沥青质是导致稠油污染土壤难以彻底降解的关键要素，而目前传统的生物修复方法很难满足其处理要求。针对这一难题，本文研究了高级氧化-生物耦合修复方法处理稠油污染土壤，达到了使稠油中胶质和沥青质高效去除的目的。 本文采用蛭石模拟土壤，研究稠油污染土壤的高级氧化（臭氧、芬顿）-生物耦合处理方法。分析了氧化时间、水土比、污染土壤陈化时间和污染浓度对臭氧氧化效率的影响，以及H2O2加入量和H2O2/Fe2+摩尔比对芬顿预处理效率的影响；同时优化了高级氧化与微生物混合菌之间的耦合条件；并根据稠油成分的变化，探讨了稠油降解机制。 实验结果表明，模拟稠油污染土壤的最佳臭氧-生物耦合条件为：臭氧氧化30min，生物段采用混合菌1降解14d，此时，土壤中总石油烃、饱和烃、芳烃、胶质和沥青质的降解率分别为60.78%、65.59%、82.74%、26.61％；芬顿-生物耦合处理的最佳条件为：H2O2 加入量为27ml，H2O2与Fe2+的摩尔比为10：1，此时，模拟土壤中稠油总石油烃、饱和烃、芳烃、胶质和沥青质的降解率分别为35.41%，9.33%，49.82%，45.19%。 高级氧化预处理不仅能够减小生物段负荷，而且能够提高胶质和沥青质的生物可利用性，微生物可将胶质和沥青质降解为饱和烃、芳烃或其他物质，降解效率取决于预处理的程度。高级氧化-生物耦合处理降解效率高于单独采用氧化预处理、生物处理效率，因而高级氧化-生物耦合修复方法是一种可行的稠油污染土壤修复方法。

芘降解菌在石油污染土壤修复过程中的代谢调控

沈抚灌区是我国面积最大、污灌历史最长的石油类污水灌溉区，土壤中大分子量多环芳烃污染严重，对当地粮食生产与生态安全造成严重危害。对此类污染土壤进行生物修复，对保证农产品的安全，实现当地人与自然的可持续发展具有重大的意义。 本研究以沈抚灌区污染土壤中大分子多环芳烃芘为主要研究对象，采用稳定同位素比率分析技术（IRMS），以磷脂脂肪酸（PLFA）为生物标记物，分析污染土壤参与芘降解的优势微生物类群；并以此为指导，采用分子生物学手段和传统微生物学分析方法，筛选土壤中的高效降解菌，并追踪其释放到土壤中后的动态变化与调控。 从沈抚灌区土壤富集培养芘的降解菌，经过双层平板法初筛和芘降解菌液体摇瓶复筛，获得5株以芘为唯一碳源生长的具有较高降解活性菌株。 将筛选的降解菌投加到污染土壤中，以13C标记的芘为代谢底物，以土壤微生物的磷脂脂肪酸为生物标记物，采用稳定同位素比率分析方法(GC-C-IRMs)，分析投加的降解菌在原位土壤中的降解作用。结果显示，与不加菌的对照土壤相比，富含13C的磷脂脂肪酸指纹图谱相似度较高的为投加了菌株B05和菌株B15的土壤，芘的降解效率也最高，表明这两株菌在原位土壤芘降解中发挥了重要作用。根据形态学观察、16项生理生化鉴定和16S rDNA序列分析结果，将菌株B05鉴定为 Aminobacter ciceronei，将菌株B15鉴定为 Microbacterium arabinogalactanolyticum。菌株B05初步确定为一株新的芘降解菌，并对菌株培养条件进行了优化。 采用PCR-DGGE方法，研究了筛选的5株降解菌在不同的营养条件下释放到土壤中后的数量和代谢活性的变化。PCR-DGGE图谱分析表明：投加初期外加菌在竞争中占据优势，但是随时间推移，营养物质的消耗，优势逐渐消失，PCR-DGGE的条带趋向于一致。菌株B05的稳定期相对较长，在DGGE图谱中的条带相对密度大，而且对芘的降解率最高，是一株具有潜在应用价值的高效降解菌。混合菌比单一菌降解率高，添加碳氮源有利于外加菌群更快更好的适应在污染土壤中生存，而且有助于对多环芳烃的降解。

稠油污染土壤生物修复的微生物筛选及工艺调控

稠油组分非常复杂，胶质沥青质含量较高，使稠油污染土壤的生物修复难度很大。对稠油中胶质沥青质分的降解是彻底修复稠油污染土壤的关键。试验中利用辽河油田污染土壤中筛选并纯化出来的几株细菌、真菌和放线菌，以胶质沥青质作为碳源，考察不同菌株处理的去除率变化。发现0d-14d期间是微生物去除胶质沥青质的活跃期，42d之后土壤中胶质沥青质的减少趋缓，是生物修复的转折点。筛选出优势降解菌株：细菌22B；真菌中F2006、F2008、F9902，放线菌A2013、A2016混合菌F2006+22B、F6＋22B。同时考查了表面活性剂吐温-80对菌株去除胶质沥青质能力的影响，发现吐温-80对不同菌株有促进或抑制作用。利用上述优势菌株处理5ryn稠油污染土壤，并在42d时，通过采取补加菌液、添加N、P营养物质和添加碳源处理来提高微生物对土壤中稠油的去除能力。经过56天的处理，细菌22B对稠油的去除率最高，达27．420＆；混合菌的去除率在23.64％-26.24％。比较三种处理措施对微生物降解稠油能力的影响时，发现不同菌株对这三种措施的反应并不相同。同时土壤中残留石油烃的族分析证实了土壤中的重质成分是可以被微生物降解的；而稠油污染土壤中的烷烃和芳香烃的含量则呈现动态变化。稠油污染土壤的生物修复后的毒性检验表明，不同菌株处理土壤的毒性因选择的菌株及采取的措施不同而异，其中土壤毒性最小的是22B添加碳源处理；毒性最强的是F2008加菌处理。补加菌液、添加营养和碳源措施会使微生物对稠油降解能力有所加强，但是也加速了某些微生物产生毒性较稠油更大的中间产物的生成，使土壤更加不适合植物的生长。本研究从辽河油田污染土壤中筛选出石油烃降解菌株，对稠油中最难降解的胶质沥青质进行处理，从中选择优势的降解菌株对稠油污染土壤进行生物修复，为稠油污染土壤的生物修复打下理论基础。

Novel photocatalytic reactor development for removal of hydrocarbons from water

Hydrocarbons contamination of the marine environment generated by the offshore oil and gas industry is generated from a number of sources including oil contaminated drill cuttings and produced waters. The removal of hydrocarbons from both these sources is one of the most significant challenges facing this sector as it moves towards zero emissions. The application of a number of techniques which have been used to successfully destroy hydrocarbons in produced water and waste water effluents has previously been reported. This paper reports the application of semiconductor photocatalysis as a final polishing step for the removal of hydrocarbons from two waste effluent sources. Two reactor concepts were considered: a simple flat plate immobilised film unit, and a new rotating drum photocatalytic reactor. Both units proved to be effective in removing residual hydrocarbons from the effluent with the drum reactor reducing the hydrocarbon content by 90% under 10 minutes. 

INVESTIGATIONS ON THE STRESS EFFECTS OF PETROLEUM HYDROCARBONS ON METAPENAEUS DOBSON (MIERS)

The present investigation has addressed the effects of PHC contaminated culture medium on the morphology, physiology and behaviour of shrimps. The shrimp Metapenaeus dobsoni is an important member of the crustacean animal community abounding the oil contaminated benthic regions of Cochin backwater system. Since it is known that true pollutants can disrupt the sustainability of ecosystems by its effect on species, populations and communities,a representative species was used for the study. The results discussed in this work is bound to help in understanding the ecotoxicant resistance that the animal may display under toxic conditions compared to dynamic steady-state systems in nature.

Investigations on the stress effects of petroleum hydrocarbons on Metapenaeus dobsoni (Miers)

The present investigation has addressed the eflects of PHC contaminated culture medium on the morphology, physiology and behaviour of shrimps] The shrimp Metapenaeus dobsoni is an important member of the crustacean animal community abounding the oil contaminated benthic regions of Cochin backwater system. Since it is known that true pollutants can disrupt the sustainability of ecosystems by its eflect on species, populations and communities, a representative species was used for the study. The results discussed in this work is bound to help in understanding the ecotoxicant resistance that the animal may display under toxic conditions compared to aynamic steaay-state systems in nature

Microbial Biosurfactants – Review

Biosurfactants are surface active compounds released by microorganisms. They are biodegradable non-toxic and eco-friendly materials. In this review we have updated the information about different microbial surfactants. The biosurfactant production depends on the fermentation conditions, environmental factors and nutrient availability. The extraction of the biosurfactants from the cell-free supernatant using the solvent extraction procedure and the qualitative and quantitative analysis has been discussed with appropriate equipment details. The application of the biosurfactant includes biomedical, cosmetic and bioremediation. The type of microbial biosurfactants include trehalose lipids, rhamnolipids, sophorolipids, glycolipids, cellobiose lipids, polyol lipids, diglycosyl diglycerides, lipoloysaccharides, arthrofactin, lichensyn A and B, surfactin, viscosin, phospholipids, sulphonyl lipids and fatty acids. Rhamnolipid biosurfactants produced by Pseudomonas aeruginosa DS10-129 showed significant applications in the bioremediation of hydrocarbons in gasoline spilled soil and petroleum oily sludge. Rhamnolipid biosurfactant enhanced the bioremediation process by releasing the weathered oil from the soil matrices and enhanced the bioavailability of hydrocarbons for microbial degradation. It is having potential applications in the remediation of hydrocarbon contaminated sites. Biosurfactants from marine microorganisms also offer great potential in bioremediation of oil contaminated oceanic environments

Studies on the effect of Polycyclic Aromatic Hydrocarbons in the life and activity of Perna spp

In the present study an endeavour has been made to analyse the acute toxicity of WAFs of Bombay High crude and Light Diesel oil on commercially important bivalve species Perna viridis and Perna indica by static bioassay methods. The toxic effects of chemicals in the WAF on the organisms ; their tissues and eventually on rate functions have been elucidated. Marine oil pollution not only affects productivity and quality of marine organisms but also eventually affects the health of human population due to a possible health risk by way of consumption of oil contaminated seafood

Applied models to biodegradation kinetics of lubricant and vegetable oils in wastewater

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Imageamento Elétrico 3D em área contaminada por hidrocarbonetono polo industrial de Cubatão - SP

Este trabalho mostra os resultados obtidos com ensaios geofísicos realizados em uma área contaminada por hidrocarboneto no Polo Industrial de Cubatão - São Paulo, com objetivo de caracterizar as anomalias geoelétricas associadas à presença dos hidrocarbonetos, bem como delimitar e cubar tais anomalias. Para tanto, utilizou-se o método da eletrorresistividade, por meio das técnicas de Sondagem Elétrica Vertical (SEV) e Imageamento Elétrico 3D. Os resultados obtidos permitem indicar que a presença de hidrocarboneto está associada a anomalias condutivas devido aos produtos da biodegradação. As anomalias condutivas ocorrem de forma disseminada na área, totalizando um volume de 1365,3 m³; entretanto, este volume corresponde somente à presença de contaminante em fase residual.

Caracterização do processo de reciclagem do óleo lubrificante usado em postos de combustíveis e identificação de desafios frente à política nacional de resíduos sólidos

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Análise do enxofre corrosivo em óleo mineral isolante e remoção do dibenzil dissulfeto com nanotubos de carbono baseados em matriz metálica

Falhas inesperadas em transformadores levaram a identificação da formação de sulfeto de cobre, depositado sobre os condutores, avaliando-se da presença qualitativa de enxofre corrosivo resultando na alteração da norma brasileira ABNT NBR 10505, que avalia a presença de enxofre corrosivo em óleo mineral, alterando-se o tempo e a temperatura de ensaio para 150 °C por 48 horas. Realizando-se a especiação química de compostos organosulfurados via cromatografia gasosa acoplada a espectrometria de massas, onde foram encontrados 13 compostos sulfurados no óleo Nynas e 9 compostos no óleo da Petrobras, sendo o dibenzil dissulfeto (DBDS) o de maior concentração, encontrado apenas no óleo Nynas. Para realizar a determinação da presença do DBDS em óleo mineral isolante foi desenvolvido um método através de cromatografia gasosa acoplada a espectrometria de massas, e por este método foi possível quantificar o teor de DBDS em amostras de OMI oriundas de transformadores de potência. Foi avaliado o processo de passivação do cobre por benzotriazol e tolutriazol, utilizados como aditivos anticorrosivos no núcleo dos equipamentos elétricos, verificando-se que o efeito da adição agente de passivação torna-se ineficaz com o passar do tempo. A solução para a remoção de DBDS em óleo mineral foi a utilização de nanotubo de carbono baseado em matriz metálica (NTC/Al) como agente de remoção do DBDS. Verificou-se que o agente de adsorção foi capaz de efetuar a remoção total do DBDS do OMI até um volume de 4000 mL de óleo contaminado com DBDS.

Expressão heteróloga de biossurfactantes identificados em bibliotecas metagenômicas

The microorganisms have a vast genetic diversity and they are present throughout the biosphere, however, only about 1% of the species can be cultivated by traditional cultivation techniques. Within this diversity there is a huge pool genetic and biological being explored. The metagenomics has enabled direct access to microbial genome derived from environmental samples using independent methods of cultivation. The methodology enables to obtain functional information about the proteins, as well as identify potential products with biotechnological interest and new industrially exploitable biological resources, such as new solutions to environmental impacts. Oil-contaminated areas are characterized by a large accumulation of hydrocarbons and surfactants may be used for bioremediation. Thus, the metagenomic approach was used in this study in order to select genes involved in the degradation and hydrocarbon emulsification. In a previous work, the environmental DNA (eDNA) was extracted from soil samples collected from two different areas (Caatinga and Saline River) of Rio Grande do Norte (Brazil), the metagenomic libraries were constructed and functionally analyzed. The clone able to degrade the oil was evaluated for the ability to synthesize biosurfactants. The sequence analysis revealed an ORF with 897 bp, 298 amino acids and a protein with around 34 kDa. The search for homology in GenBank revealed sequence similarity with a hypothetical protein of representatives Halobacteriaceae family, who were recently shown as strains producing biosurfactants. The presence of the inserted coding sequence and the acquired phenotype was confirmed. Primers were designed and the ORF amplified by PCR. The ORF was subcloned into pETDuet-1 expression vector for subsequent purification of the protein of interest containing a histidine tail. The tests performed to confirm the biosurfactant activity and the ability of hydrocarbon degradation showed positive results. The immunodetection test (western blot) using the monoclonal AntiHis® confirmed the presence of the environmental protein. This study was the first to report a possible protein with biosurfactant activity obtained from a metagenomic approach