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.

Draft genome analysis of Dietzia sp. 111N12-1, isolated from the South China Sea with bioremediation activity

Abstract Dietzia sp. 111N12-1, isolated from the seawater of South China Sea, shows strong petroleum hydrocarbons degradation activity. Here, we report the draft sequence of approximately 3.7-Mbp genome of this strain. To the best of our knowledge, this is the first genome sequence of Dietzia strain isolated from the sea. The genome sequence may provide fundamental molecular information on elucidating the metabolic pathway of hydrocarbons degradation in this strain.

Biodegradation of crude oil by individual bacterial strains and a mixed bacterial consortium

Three bacterial isolates identified as Alcanivorax borkumensis SK2, Rhodococcus erythropolis HS4 and Pseudomonas stutzeri SDM, based on 16S rRNA gene sequences, were isolated from crude oil enrichments of natural seawater. Single strains and four bacterial consortia designed by mixing the single bacterial cultures respectively in the following ratios: (Alcanivorax: Pseudomonas, 1:1), (Alcanivorax: Rhodococcus, 1:1), (Pseudomonas: Rhodococcus, 1:1), and (Alcanivorax: Pseudomonas: Rhodococcus, 1:1:1), were analyzed in order to evaluate their oil degrading capability. All experiments were carried out in microcosms systems containing seawater (with and without addition of inorganic nutrients) and crude oil (unique carbon source). Measures of total and live bacterial abundance, Card-FISH and quali-, quantitative analysis of hydrocarbons (GC-FID) were carried out in order to elucidate the co-operative action of mixed microbial populations in the process of biodegradation of crude oil. All data obtained confirmed the fundamental role of bacteria belonging to Alcanivorax genus in the degradation of linear hydrocarbons in oil polluted environments.

Crecimiento de Casuarina equisetifolia (Casuarinaceae) en suelo con diésel, y aplicación de bioestimulación y bioaumentación / Casuarina equisetifolia (Casuarinaceae) growth in soil with diesel and application of biostimulation and bioaugmentation

Phytoremediation is an ecologically sound biotechnology directed to cleaning up contaminated soils. The study of tree species to treat petroleum contaminated soils is scarce; moreover, the combination of phytoremediation with bioaugmentation and biostimulation processes is also limited. Thus, this work evaluated the effects of the inoculation of Glomus intraradices, a bacterial consortium (M2BOS1-R2 and M2BOSI-F4) and Trichoderma viride, on the growth of Casuarina equisetifolia, fertilized with Floranid® or Triple 17, when sown in a diesel-contaminated soil (7 500mg/kg). The factorial experiment 2x5x3 included 30 treatments with 10 replicates in a completely randomized design under greenhouse conditions for 120 days. Diesel significantly diminished plant height, total biomass, and plant index quality (PIQ). Glomus or bacterial consortium significantly increased plant height, total biomass and PIQ when compared to the inoculation of the three microorganisms or to the control. Floranid had negative effects on plant growth and PIQ at diesel contamination. Fertilization with Triple 17 combined with the three microorganisms stimulated plant growth in the absence of diesel, whereas in the presence of this contaminant the treatments combining Triple 17 with the bacterial consortium or with Trichoderma had better plant growth and PIQ. Mycorrhizal colonization was inhibited due to diesel contamination, and especially when Floranid was applied. The fertilizer Triple 17 (biostimulation) combined with the beneficial microorganisms (bioaugmentation) improved growth responses of C. equisetifolia in diesel-contaminated soil.

La fitorremediación es una biotecnología ecológicamente racional que está dirigida a la limpieza de suelos contaminados; sin embargo, el estudio de especies arbóreas para la fitorremediación de suelos con hidrocarburos del petróleo es limitado. Más aún, la combinación de la fitorremediación con procesos de bioaumentación y bioestimulación es también limitada. Por lo anterior, este estudio evaluó el efecto de la inoculación de Glomus intraradices, un consorcio bacteriano (M2BOS1-R2 y M2BOSI-F4) y Trichoderma viride en el crecimiento de plantas de Casuarina equisetifolia L. fertilizadas con Floranid® o Triple 17, en suelo contaminado con diésel (7 500mg/kg). El experimento factorial 2x5x3 incluyó 30 tratamientos y 10 repeticiones, distribuidos completamente al azar en invernadero, durante 120 días. El diésel disminuyó significativamente la altura, la biomasa total y el índice de calidad (ICP) de planta. Glomus o las bacterias aumentaron significativamente la altura, la biomasa seca total y el ICP con respecto al tratamiento sin inocular o con la triple inoculación. El Floranid redujo el crecimiento vegetal y el ICP, en presencia de diésel. El Triple 17 combinado con los tres microorganismos produjo mayor crecimiento vegetal en ausencia de contaminación, pero en presencia de diésel, el Triple 17 combinado con bacterias o con Trichoderma, estimuló la biomasa seca total y el ICP. La colonización micorrízica fue inhibida por el diesel, especialmente con la fertilización del Floranid. El Triple 17 (bioestimulación) combinado con los microorganismos (bioaumentación), favoreció el crecimiento de Casuarina en suelo contaminado con diésel.

In situ biosurfactant production and hydrocarbon removal by Pseudomonas putida CB-100 in bioaugmented and biostimulated oil-contaminated soil

In situ biosurfactant (rhamnolipid) production by Pseudomonas putida CB-100 was achieved during a bioaugmented and biostimulated treatment to remove hydrocarbons from aged contaminated soil from oil well drilling operations. Rhamnolipid production and contaminant removal were determined for several treatments of irradiated and non-irradiated soils: nutrient addition (nitrogen and phosphorus), P. putida addition, and addition of both (P. putida and nutrients). The results were compared against a control treatment that consisted of adding only sterilized water to the soils. In treatment with native microorganisms (non-irradiated soils) supplemented with P. putida, the removal of total petroleum hydrocarbons (TPH) was 40.6%, the rhamnolipid production was 1.54 mg/kg, and a surface tension of 64 mN/m was observed as well as a negative correlation (R = -0.54; p < 0.019) between TPH concentration (mg/kg) and surface tension (mN/m), When both bacteria and nutrients were involved, TPH levels were lowered to 33.7%, and biosurfactant production and surface tension were 2.03 mg/kg and 67.3 mN/m, respectively. In irradiated soil treated with P. putida, TPH removal was 24.5% with rhamnolipid generation of 1.79 mg/kg and 65.6 mN/m of surface tension, and a correlation between bacterial growth and biosurfactant production (R = -0.64; p < 0.009) was observed. When the nutrients and P. putida were added, TPH removal was 61.1%, 1.85 mg/kg of biosurfactants were produced, and the surface tension was 55.6 mN/m. In summary, in irradiated and non-irradiated soils, in situ rhamnolipid production by P. putida enhanced TPH decontamination of the soil.

Growth and biosurfactant synthesis by Nigerian hydrocarbon-degrading estuarine bacteria

The ability of microorganisms to degrade petroleum hydrocarbons is important for finding an environmentally-friendly method to restoring contaminated environmental matrices. Screening of hydrocarbon-utilizing and biosurfactant-producing abilities of organisms from an estuarine ecosystem in Nigeria, Africa, resulted in the isolation of five microbial strains identified as Corynebacterium sp. DDv1, Flavobacterium sp. DDv2, Micrococcus roseus DDv3, Pseudomonas aeruginosa DDv4 and Saccharomyces cerevisae DDv5. These isolates grew readily on several hydrocarbons including hexadecane, dodecane, crude oil and petroleum fractions. Axenic cultures of the organisms utilized diesel oil (1.0 % v/v) with generation times that ranged significantly (t-test, P < 0.05) between 3.25 and 3.88 day, with concomitant production of biosurfactants. Kinetics of growth indicates that biosurfactant synthesis occurred predominantly during exponential growth phase, suggesting that the bioactive molecules are primary metabolites. Strains DDv1 and DDv4 were evidently the most metabolically active in terms of substrate utilization and biosurfactant synthesis compared to other strains with respective emulsification index of 63 and 78 %. Preliminary biochemical characterization indicates that the biosurfactants are heteropolymers consisting of lipid, protein and carbohydrate moieties. The hydrocarbon catabolic properties coupled with biosurfactant-producing capabilities is an asset that could be exploited for cleanup of oil-contaminated matrices and also in food and cosmetic industries. Rev. Biol. Trop. 56 (4): 16031611. Epub 2008 December 30.

La capacidad de los microorganismos para degradar hidrocarburos del petróleo es de gran importancia para hallar un método aceptable y ambientalmente amigable para la restauración de terrenos ambientalmente contaminados. Al investigar las capacidades de los organismos de un ecosistema de estuario que utilizan hidrocarburos y producen biosurfactantes, se produjo como resultado el aislamiento de cinco cepas microbianas identificadas como Corynebacterium sp. DDv1, Flavobacterium sp. DDv2, Micrococcus roseus DDv3, Pseudomonas aeruginosa y DDv4 Saccharomyces cerevisiae DDv5. Estas cepas crecieron fácilmente en varios hidrocarburos incluyendo hexadecanos, dodecanos, petróleo crudo y fracciones de petróleo. Los cultivos axénicos de organismos utilizaron diesel (1.0% v/v) con períodos por generación con ámbitos significativos (t-test, P <0.05) de entre 3.25 y 3.88 días, con la consiguiente producción de bio-surfactantes. La cinética del crecimiento indica que la síntesis de bio-surfactante se produjo principalmente durante la fase de crecimiento exponencial, lo que sugiere que las moléculas bioactivas son metabolitos primarios. Las cepas DDv1 y DDv4 fueron evidentemente las más metabólicamente activas en términos de utilización del sustrato y la síntesis de bio-surfactantes en comparación con otras cepas con índices respectivos de emulsificación de 63 y 78%. La caracterización bioquímica preliminar indica que los bio-surfactantes son heteropolímeros constituidos de fracciones de lípidos, proteínas y carbohidratos. Las propiedades catabólicas de los hidrocarburos, junto con las capacidades de producción de bio-surfactantes, es una ventaja que puede ser aprovechada para la limpieza de terrenos contaminados con petróleo y también en la industria alimentaria y cosmética.

Enhanced crude oil biodegradation and rhamnolipid production by Pseudomonas stutzeri strain G11 in the presence of Tween-80 and Triton X-100.

In this study, the growth of sixty-one bacterial strains in crude oil were determined spectrophotometrically at 620 nm. Pseudomonas aeruginosa G1, Pseudomonas fluorescens G6, Pseudomonas stutzeri G11 and Pseudomonas putida G15 were chosen for the study based on the efficiency of crude oil utilisation. At 1% (v/v) crude oil concentration, P. stutzeri G11 strain degraded a maximum of 69%. The percentage of degradation by the P. stutzeri G11 strain decreased from 69% to 59% as the concentration of crude oil was increased from 1% (v/v) to 2.5% (v/v). Strain G11 was selected to determine the effects of surfactants (Tween-80 and TritonX-100) on the biodegradation of crude oil. While strain G11 showed 76% degradation at mineral salts medium (MSM) containing 1% (v/v) crude oil + 1% (v/v) TritonX-100, it showed 61% degradation at MSM containing 2.5% (v/v) crude oil + 2.5% (v/v) TritonX-100. Also, degradation rate of this strain was 96% in the presence of 1% (v/v) crude oil + 1% (v/v) Tween-80, while degradation rate was 48% in the presence of 25% (v/v) crude oil+ 2.5% (v/v) Tween-80. Additionally, we investigated the rhamnolipid production of P. stutzeri G11 strain both in crude oil and in crude oil + two different surfactants (TritonX-100 and Tween-80, separately). These results suggest that surfactants have improved both crude oil degradation and rhamnolipid production and the degradation rates have depended very much on the chemical structure of surfactants.

Biodegradation of crude petroleum and petroleum products by fungi isolated from two oil seeds (melon and soybean).

Crude petroleum oil degrading fungi were isolated from two oil seeds, Cucumeropsis mannii (melon) and Glycine max (soybean) seeds in the presence and absence of petroleum fumes. An assessment of the relative ability of each fungus to degrade crude petroleum, diesel and kerosene on minimum salt solution was done using change in optical density read on spectrophotometer. Twenty-one fungal species (14 genera) were isolated altogether during this experiment. These include eight species of Aspergillus; one species each of Botryodiplodia, Bipolaris, Cladosporium, Cunnighamella, Dreschlera, Fusarium, Helminthosporium, Macrophomina, Mucor, Paeciliomyces, Penicillium, Rhizopus and Talariomyces. It was evident that most of the fungi tested were able to biodegrade the crude petroleum oil, though at different rates. Bipolaris had a low rate of biodegradation of the petroleum oil of all the fungal species isolated Botryodiplodia theobromae had the highest degrading ability on the crude oil, while Aspergillus flavus had the least after 40 days of incubation. Aspergillus flavus had the highest ability to biodegrade diesel while A. niger had the least ability. In kerosene, Macrophomina phaseolina had the highest ability while A. niger had the least ability to biodegrade it. There was fluctuation in the growth pattern of the fungi in the petroleum oil medium. The implication of these are discussed.

Biomanagement of petrochemical sludge using an exotic earthworm Eudrilus eugineae.

Petrochemical industry have severe problem in disposing effluent and semisolid sludge despite repeated recycling. It requires further treatment prior to disposal of sludge. In recent years biological treatment methods received much attention and considered as an efficient low-cost treatment. One such method is vermiculture treatment The end product of vermicompost is rich in essential micro and macronutrients along with microorganisms in a very simple form. Adding cast, not only improves the soil structure and fertility but also leads to improvement in overall plant growth and thus increase their yield. The present study was carried out to dispose the petrochemical sludge biologically using an exotic earthworm Eudrilus eugineae. The petrochemical sludge at various concentrations 25, 50 and 75% were subjected to vermicomposting treatment for a period of 60 days. During the period of study, data were collected on life form of earthworm and chemical analysis of the sludge before and after treatment. The microbial analysis was carried out fortnightly. The results indicate that 25 and 50% concentration of sludge was ideal for the vermicomposting, whereas the higher concentration inhibits the vermicomposting.

Microbiologically influenced corrosion in petroleum product pipelines--a review.

Microbiologically influenced corrosion is responsible for most of the internal corrosion problems in oil transportation pipelines and storage tanks. One problematic area in treating gas lines is the occurrence of the stratification of water in the line. Under these conditions, corrosion inhibitors do not come into contact properly and oil and inhibitors undergo degradation. The role of bacteria on oil degradation, the consequences of oil degradation in fuel systems and its influence on corrosion have been explained in detail. Besides, factors influencing on degradation of oil and corrosion inhibitors have also been discussed. Mechanism of microbiologically influenced corrosion in oil pipeline has been explained. Many of the misapplication of biocides/inhibitors occur mainly because the characteristics of biocides/inhibitors are not considered before use in pipeline industry. List of biocides and monitoring programme have been collected from literature and presented.

Inorganic nutrient utilisation by "adapted" Pseudomonas putida strain used in the bioremediation of agricultural soil polluted with crude petroleum.

Garden soil samples polluted with crude petroleum were bioremediated by inorganic nutrient monitoring with appropriate adjustment and inoculation with crude oil-adapted strain of Pseudomonasputida (PP) isolated from oil-impacted soils. Soil samples without PP inoculation served as the control samples to compare the abilities of the native soil microflora with the adapted PP strain in biodegrading crude oil pollutant. In the experimental samples, oil concentration and all the inorganic nutrient sources tested decreased more rapidly with a proportional increase in the population densities of both PP and the native soil microflora than were observed in the control samples. This trend was particularly strong for PO4(3-) and NO3- which eventually became limiting both in all the experimental samples and in some control samples. Inoculation of crude oil-impacted agricultural soils by oil -adapted PP strain with nutrient monitoring and adjustment can be effective as bioremediation methods of agricultural land upon pollution with petroleum or petroleum products.