Shifts in structure and dynamics of the soil microbiome in biofuel/fuel blend-affected areas triggered by different bioremediation treatments.

The use of biofuels has grown in the last decades as a consequence of the direct environmental impacts of fossil fuel use. Elucidating structure, diversity, species interactions, and assembly mechanisms of microbiomes is crucial for understanding the influence of environmental disturbances. However, little is known about how contamination with biofuel/petrofuel blends alters the soil microbiome. Here, we studied the dynamics in the soil microbiome structure and composition of four field areas under long-term contamination with biofuel/fossil fuel blends (ethanol 10% and gasoline 90%-E10; ethanol 25% and gasoline 75%-E25; soybean biodiesel 20% and diesel 80%-B20) submitted to different bioremediation treatments along a temporal gradient. Soil microbiomes from biodiesel-polluted areas exhibited higher richness and diversity index values and more complex microbial communities than ethanol-polluted areas. Additionally, monitored natural attenuation B20-polluted areas were less affected by perturbations caused by bioremediation treatments. As a consequence, once biostimulation was applied, the degradation was slower compared with areas previously actively treated. In soils with low diversity and richness, the impact of bioremediation treatments on the microbiomes was greater, and as a result, the hydrocarbon degradation extent was higher. The network analysis showed that all abundant keystone taxa corresponded to well-known degraders, suggesting that the abundant species are core targets for biostimulation in soil remediation processes. Altogether, these findings showed that the knowledge gained through the study of microbiomes in contaminated areas may help design and conduct optimized bioremediation approaches, paving the way for future rationalized and efficient pollutant mitigation strategies.

Metaproteomic and gene expression analysis of interspecies interactions in a PAH-degrading synthetic microbial consortium constructed with the key microbes of a natural consortium.

Polycyclic Aromatic Hydrocarbons (PAHs) impose adverse effects on the environment and human life. The use of synthetic microbial consortia is promising in bioremediation of contaminated sites with these pollutants. However, the design of consortia taking advantage of natural interactions has been poorly explored. In this study, a dual synthetic bacterial consortium (DSC_AB) was constructed with two key members (Sphingobium sp. AM and Burkholderia sp. Bk), of a natural PAH degrading consortium. DSC_AB showed significantly enhanced degradation of PAHs and toxic intermediary metabolites relative to the axenic cultures, indicating the existence of synergistic relationships. Metaproteomic and gene-expression analyses were applied to obtain a view of bacterial performance during phenanthrene removal. Overexpression of the Bk genes, naph, biph, tol and sal and the AM gene, ahdB, in DSC_AB relative to axenic cultures, demonstrated that both strains are actively participating in degradation, which gave evidence of cross-feeding. Several proteins related to stress response were under-expressed in DSC_AB relative to axenic cultures, indicating that the division of labour reduces cellular stress, increasing the efficiency of degradation. This is the one of the first works revealing bacterial relationships during PAH removal in a synthetic consortium applying an omics approach. Our findings could be used to develop criteria for evaluating the potential effectiveness of synthetic bacterial consortia in bioremediation.

Biotechnological Aspects and Mathematical Modeling of the Biodegradation of Plastics under Controlled Conditions.

The strong environmental impact caused by plastic pollution has led research to address studies from different perspectives. The mathematical modeling of the biodegradation kinetics of solid materials is a major challenge since there are many influential variables in the process and there is interdependence of microorganisms with internal and external factors. In addition, as solid substrates that are highly hydrophobic, mass transfer limitations condition degradation rates. Some mathematical models have been postulated in order to understand the biodegradation of plastics in natural environments such as oceans. However, if tangible and optimizable solutions are to be found, it is necessary to study the biodegradation process under controlled conditions, such as using bioreactors and composting systems. This review summarizes the biochemical fundamentals of the main plastics (both petrochemical and biological origins) involved in biodegradation processes and combines them with the main mathematical equations and models proposed to date. The different biodegradation studies of plastics under controlled conditions are addressed, analyzing the influencing factors, assumptions, model developments, and correlations with laboratory-scale results. It is hoped that this review will provide a comprehensive overview of the process and will serve as a reference for future studies, combining practical experimental work and bioprocess modeling systems.

Assessment of contamination by anthropogenic dissolved organic matter in the aquifer that underlies the agricultural area.

The use of wastewater for agricultural irrigation is a common practice worldwide; long-term use of wastewater can have adverse effects, such as the migration of the anthropogenic dissolved organic matter into the aquifer. Three-dimensional fluorescence spectroscopy (EEM) was used to investigate the characteristics of dissolved organic matter (DOM) in groundwater and irrigation wastewater, to establish the effect of intensive irrigation on the water quality from the aquifer that underlies the area. The fluorescence spectra showed the presence of humic and fulvic acids and anthropogenic organic compounds similar to aromatic proteins and soluble microbial products in wastewater resources. The significant fraction of DOM in groundwater samples are aromatic proteins and soluble microbial products, identical to wastewater. Chlorides and nitrate ion concentrations suggest a local flow system. High levels of TDS are associated with intensive irrigation with residual water and the return irrigation associated with a gradual increase in salts of CO32-, NO3-, HCO3-, Cl-, and SO42-. The anthropogenic DOM is a useful indicator of water quality management in groundwater based on origin tracking of DOM and changes in organic pollutants. Fluorescence spectroscopy can be used to investigate groundwater pollution characteristics and monitor DOM dynamics in groundwater.

Cloning and characterisation of four catA genes located on the chromosome and large plasmid of Pseudomonas putida ND6

Background: Although the functional redundancy of catechol 1,2-dioxygenase (C12O) genes has been reported in several microorganisms, limited enzymes were characterised, let alone the advantage of the coexistence of the multiple copies of C12O genes. Results: In this study, four novel C12O genes, designated catA, catAI, catAII and catAIII, in the naphthalene-degrading strain Pseudomonas putida ND6, were cloned and characterised. Phylogenetic analysis of their deduced amino acid sequences revealed that the four C12O isozymes each formed independent subtrees, together with homologues from other organisms. All four enzymes exhibited maximum activity at pH 7.4 and higher activity in alkaline than in acidic conditions. Furthermore, CatA, CatAI and CatAIII were maximally active at a temperature of 45°C, whereas a higher optimum temperature was observed for CatAII at a temperature of 50°C. CatAI exhibited superior temperature stability compared with the other three C12O isozymes, and kinetic analysis indicated similar enzyme activities for CatA, CatAI and CatAII, whereas that of CatAIII was lower. Significantly, among metal ions tested, only Cu2+ substantially inhibited the activity of these C12O isozymes, thus indicating that they have potential to facilitate bioremediation in environments polluted with aromatics in the presence of metals. Moreover, gene expression analysis at the mRNA level and determination of enzyme activity clearly indicated that the redundancy of the catA genes has increased the levels of C12O. Conclusion: The results clearly imply that the redundancy of catA genes increases the available amount of C12O in P. putida ND6, which would be beneficial for survival in challenging environments.

Macondo oil in northern Gulf of Mexico waters - Part 2: Dispersant-accelerated PAH dissolution in the Deepwater Horizon plume.

During the Deepwater Horizon blowout, unprecedented volumes of dispersant were applied both on the surface and at depth. Application at depth was intended to disperse the oil into smaller microdroplets that would increase biodegradation and also reduce the volumes buoyantly rising to the surface, thereby reducing surface exposures, recovery efforts, and potential stranding. In forensically examining 5300 offshore water samples for the Natural Resource Damage Assessment (NRDA) effort, profiles of deep-plume oil droplets (from filtered water samples) were compared with those also containing dispersant indicators to reveal a previously hypothesized but undocumented, accelerated dissolution of the polycyclic aromatic hydrocarbons (PAH) in the plume samples. We interpret these data in a fate-and-transport context and conclude that dispersant applications were functionally effective at depth.

Novel insights into the metabolic pathway of iprodione by soil bacteria.

Microbial degradation constitutes the key soil dissipation process for iprodione. We recently isolated a consortium, composed of an Arthrobacter sp. strain C1 and an Achromobacter sp. strain C2, that was able to convert iprodione to 3,5-dichloroaniline (3,5-DCA). However, the formation of metabolic intermediates and the role of the strains on iprodione metabolism remain unknown. We examined the degradation of iprodione and its suspected metabolic intermediates, 3,5-dichlorophenyl-carboxamide (metabolite I) and 3,5-dichlorophenylurea-acetate (metabolite II), by strains C1 and C2 and their combination under selective (MSM) and nutrient-rich conditions (LB). Bacterial growth during degradation of the tested compounds was determined by qPCR. Strain C1 rapidly degraded iprodione (DT50 = 2.3 h) and metabolite II (DT50 = 2.9 h) in MSM suggesting utilization of isopropylamine, transiently formed by hydrolysis of iprodione, and glycine liberated during hydrolysis of metabolite II, as C and N sources. In contrast, strain C1 degraded metabolite I only in LB and growth kinetics suggested the involvement of a detoxification process. Strain C2 was able to transform iprodione and its metabolites only in LB. Strain C1 degraded vinclozolin, a structural analog of iprodione, and partially propanil, but not procymidone and phenylureas indicating a structure-dependent specificity related to the substituents of the carboxamide moiety.

Isolation of an aryloxyphenoxy propanoate (AOPP) herbicide-degrading strain Rhodococcus ruber JPL-2 and the cloning of a novel carboxylesterase gene (feh).

The strain JPL-2, capable of degrading fenoxaprop-P-ethyl (FE), was isolated from the soil of a wheat field and identified as Rhodococcus ruber. This strain could utilize FE as its sole carbon source and degrade 94.6% of 100 mg L(-1) FE in 54 h. Strain JPL-2 could also degrade other aryloxyphenoxy propanoate (AOPP) herbicides. The initial step of the degradation pathway is to hydrolyze the carboxylic acid ester bond. A novel esterase gene feh, encoding the FE-hydrolyzing carboxylesterase (FeH) responsible for this initial step, was cloned from strain JPL-2. Its molecular mass was approximately 39 kDa, and the catalytic efficiency of FeH followed the order of FE > quizalofop-P-ethyl > clodinafop-propargyl > cyhalofop-butyl > fluazifop-P-butyl > haloxyfop-P-methyl > diclofop-methy, which indicated that the chain length of the alcohol moiety strongly affected the hydrolysis activity of the FeH toward AOPP herbicides.

Isolation of an aryloxyphenoxy propanoate (AOPP) herbicide-degrading strain Rhodococcus ruber JPL-2 and the cloning of a novel carboxylesterase gene (feh)

The strain JPL-2, capable of degrading fenoxaprop-P-ethyl (FE), was isolated from the soil of a wheat field and identified as Rhodococcus ruber. This strain could utilize FE as its sole carbon source and degrade 94.6% of 100 mg L−1 FE in 54 h. Strain JPL-2 could also degrade other aryloxyphenoxy propanoate (AOPP) herbicides. The initial step of the degradation pathway is to hydrolyze the carboxylic acid ester bond. A novel esterase gene feh, encoding the FE-hydrolyzing carboxylesterase (FeH) responsible for this initial step, was cloned from strain JPL-2. Its molecular mass was approximately 39 kDa, and the catalytic efficiency of FeH followed the order of FE > quizalofop-P-ethyl > clodinafop-propargyl > cyhalofop-butyl > fluazifop-P-butyl > haloxyfop-P-methyl > diclofop-methy, which indicated that the chain length of the alcohol moiety strongly affected the hydrolysis activity of the FeH toward AOPP herbicides.(AU)

Isolation of an aryloxyphenoxy propanoate (AOPP) herbicide-degrading strain Rhodococcus ruber JPL-2 and the cloning of a novel carboxylesterase gene (feh)

The strain JPL-2, capable of degrading fenoxaprop-P-ethyl (FE), was isolated from the soil of a wheat field and identified as Rhodococcus ruber. This strain could utilize FE as its sole carbon source and degrade 94.6% of 100 mg L−1 FE in 54 h. Strain JPL-2 could also degrade other aryloxyphenoxy propanoate (AOPP) herbicides. The initial step of the degradation pathway is to hydrolyze the carboxylic acid ester bond. A novel esterase gene feh, encoding the FE-hydrolyzing carboxylesterase (FeH) responsible for this initial step, was cloned from strain JPL-2. Its molecular mass was approximately 39 kDa, and the catalytic efficiency of FeH followed the order of FE > quizalofop-P-ethyl > clodinafop-propargyl > cyhalofop-butyl > fluazifop-P-butyl > haloxyfop-P-methyl > diclofop-methy, which indicated that the chain length of the alcohol moiety strongly affected the hydrolysis activity of the FeH toward AOPP herbicides.

Diversity and effectiveness of tropical mangrove soil microflora on the degradation of polythene carry bags

The diversity and load of heterotrophic bacteria and fungi associated with the mangrove soil from Suva, Fiji Islands, was determined by using the plate count method. The ability of the bacterial isolates to produce various hydrolytic enzymes such as amylase, gelatinase and lipase were determined using the plate assay. The heterotrophic bacterial load was considerably higher than the fungal load. There was a predominance of the gram positive genus, Bacillus. Other genera encountered included Staphylococcus, Micrococcus, Listeria and Vibrio. Their effectiveness on the degradation of commercial polythene carry bags made of high density polyethylene (HDPE) and low density polyethylene (LDPE) was studied over a period of eight weeks in the laboratory. Biodegradation was measured in terms of mean weight loss, which was nearly 5 % after a period of eight weeks. There was a significant increase in the bacterial load of the soil attached to class 2 (HDPE) polythene. After eight weeks of submergence in mangrove soil, soil attached to class 1 and class 3 polythene mostly had Bacillus (Staphylococcus predominated in class 2 polythene). While most of the isolates were capable of producing hydrolytic enzymes such as amylase and gelatinase, lipolytic activity was low. Class 2 HDPE suffered the greatest biodegradation. Rev. Biol. Trop. 55 (3-4): 777-786. Epub 2007 December, 28.

Se determinó la diversidad y la carga de bacterias heterotróficas, así como los hongos asociados al suelo del manglar de Suva, Islas Fiji, utilizando el método de conteo de placas, usado también para medir la capacidad de bacterias aisladas para producir enzimas hidrolíticas como amilasa, gelatinasa y lipasa. La carga bacteriana heterotrófica resultó ser considerablemente más alta que la carga funguicida. Hubo predominancia de bacterias "Gram-positivas" del género de Bacillus. Otros géneros encontrados fueron Staphylococcus, Micrococcus, Listeria y Vibrio. La eficacia de esta microflora en la degradación del polietileno comercial de bolsas hechas de polietileno de alta densidad (HDPE) y de baja densidad (LDPE) fue estudiada en el laboratorio por un periodo de ocho semanas. La biodegradación fue medida en términos de pérdida de peso, la cual indicó una disminución del 5 %. Después de ocho semanas en el suelo de un manglar, el polietileno clase 1 y clase 3 contenía fundamentalmente Bacillus, pero en el polietileno clase 2 predominó el género Staphylococcus. Mientras que la mayoría de bacterias aisladas fueron capaces de producir enzimas hidrolíticas como la amilasa y la gelatinasa, la actividad lipolítica fue muy baja. La clase 2 (HDPE) experimentó la mayor biodegradación.

Eficácia do herbicida acetochlor na semeadura direta e convencional com ou sem palha e os efeitos sobre o rendimento do milho

An experiment was carried out at Federal University at Rio Grande do Sul, with the objective of avaluating herbicide acetochlor efficacy on conventional tillage and no-till soils. The soil is classified as at Paleudult. The following treatments were tested: acetochlor at 0, 1680, 3360 and 5040g ha-1, applied on tillage and no-tillage systems on oat straw mulch presence (4,5t ha-1) and absence. Assessements included crop injury, weed control at 15, 30 and 45 days after herbicide application, and corn crop yeld. The weed control with acetochlor herbicide was more efficient on tillage than on no-tillage system. Straw mulch reduced acetochlor herbicide weed control. Corn plant height was higher on no-tillage than on tillage systems, indicating lower herbicide activity on the first. Corn yield was higher on tillage system and straw mulch presence, due to better weed control.

O experimento foi conduzido na Faculdade de Agronomia da Universidade Federal do Rio Grande do Sul, ano agrícola de 2000/2001, com o objetivo de avaliar a eficácia de controle das plantas daninhas com o herbicida acetochlor em Argissolo Vermelho, conduzido sob semeadura direta e preparo convencional, na presença ou ausência de palha. O delineamento experimental utilizado foi blocos casualizados com quatro repetições. Os tratamentos constaram de acetochlor nas doses de 0, 1680, 3360 e 5040g ha-1, aplicado em solo sob semeadura direta e preparo convencional, na presença (4,5t ha-1) ou ausência de palha de aveia. Foram avaliados o controle das plantas daninhas, além da altura de plantas e rendimento de grãos de milho. O acetochlor foi mais eficiente para o controle das plantas daninhas no preparo convencional, comparado à semeadura direta. A palha reduziu a eficácia de controle pelo acetochlor. A altura das plantas de milho foi maior na semeadura direta. O rendimento de grãos de milho foi maior no preparo convencional e na presença da palha devido ao melhor controle das plantas daninhas.

Eficácia do herbicida acetochlor na semeadura direta e convencional com ou sem palha e os efeitos sobre o rendimento do milho

An experiment was carried out at Federal University at Rio Grande do Sul, with the objective of avaluating herbicide acetochlor efficacy on conventional tillage and no-till soils. The soil is classified as at Paleudult. The following treatments were tested: acetochlor at 0, 1680, 3360 and 5040g ha-1, applied on tillage and no-tillage systems on oat straw mulch presence (4,5t ha-1) and absence. Assessements included crop injury, weed control at 15, 30 and 45 days after herbicide application, and corn crop yeld. The weed control with acetochlor herbicide was more efficient on tillage than on no-tillage system. Straw mulch reduced acetochlor herbicide weed control. Corn plant height was higher on no-tillage than on tillage systems, indicating lower herbicide activity on the first. Corn yield was higher on tillage system and straw mulch presence, due to better weed control.

O experimento foi conduzido na Faculdade de Agronomia da Universidade Federal do Rio Grande do Sul, ano agrícola de 2000/2001, com o objetivo de avaliar a eficácia de controle das plantas daninhas com o herbicida acetochlor em Argissolo Vermelho, conduzido sob semeadura direta e preparo convencional, na presença ou ausência de palha. O delineamento experimental utilizado foi blocos casualizados com quatro repetições. Os tratamentos constaram de acetochlor nas doses de 0, 1680, 3360 e 5040g ha-1, aplicado em solo sob semeadura direta e preparo convencional, na presença (4,5t ha-1) ou ausência de palha de aveia. Foram avaliados o controle das plantas daninhas, além da altura de plantas e rendimento de grãos de milho. O acetochlor foi mais eficiente para o controle das plantas daninhas no preparo convencional, comparado à semeadura direta. A palha reduziu a eficácia de controle pelo acetochlor. A altura das plantas de milho foi maior na semeadura direta. O rendimento de grãos de milho foi maior no preparo convencional e na presença da palha devido ao melhor controle das plantas daninhas.