Bioremediation of a mineral soil with high contents of clay and organic matter contaminated with herbicide 2,4-dichlorophenoxyacetic acid using slurry bioreactors: Effect of electron acceptor and supplementation with an organic carbon source

Niche-specification of aerobic 2,4-dichlorophenoxyacetic acid biodegradation by tfd-carrying bacteria in the rice paddy ecosystem

This study aimed for a better understanding of the niche specification of bacteria carrying the tfd-genes for aerobic 2,4-dichlorphenoxyacetic acid (2,4-D) degradation in the rice paddy ecosystem. To achieve this, a dedicated microcosm experiment was set up to mimic the rice paddy system, with and without 2,4-D addition, allowing spatial sampling of the different rice paddy compartments and niches, i.e., the main anaerobic bulk soil and the aerobic surface water, surface soil, root surface and rhizosphere compartments. No effect of 2,4-D on the growth and morphology of the rice plant was noted. 2,4-D removal was faster in the upper soil layers compared to the deeper layers and was more rapid after the second 2,4-D addition compared to the first. Moreover, higher relative abundances of the 2,4-D catabolic gene tfdA and of the mobile genetic elements IncP-1 and IS1071 reported to carry the tfd-genes, were observed in surface water and surface soil when 2,4-D was added. tfdA was also detected in the root surface and rhizosphere compartment but without response to 2,4-D addition. While analysis of the bacterial community composition using high-throughput 16S rRNA gene amplicon sequencing did not reveal expected tfd-carrying taxa, subtle community changes linked with 2,4-D treatment and the presence of the plant were observed. These findings suggest (i) that the surface soil and surface water are the primary and most favorable compartements/niches for tfd-mediated aerobic 2,4-D biodegradation and (ii) that the community structure in the 2,4-D treated rice paddy ecosystem is determined by a niche-dependent complex interplay between the effects of the plant and of 2,4-D.

Insights on biotic and abiotic 2,4-dichlorophenoxyacetic acid degradation by anaerobic iron-cycling bacteria

The use of the phenoxy herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been steadily increasing in recent years due to its selectivity against broad-leafed weeds and use on genetically modified crops resistant to 2,4-D. This increases the likelihood of 2,4-D persisting in agriculturally impacted soils, sediments, and aquatic systems. Aerobic microorganisms are capable of degrading 2,4-D enzymatically. Anaerobic degradation also occurs, though the enzymatic pathway is unclear. Iron-reducing bacteria (FeRB) have been hypothesized to augment anaerobic degradation through the production of a chemically reactive Fe(II) adsorbed to Fe(III) oxyhydroxides. To test whether this iron species can catalyze abiotic degradation of 2,4-D, an enrichment culture (BLA1) containing a photosynthetic Fe(II)-oxidizing bacterium (FeOB) "Candidatus Chlorobium masyuteum" and the FeRB "Candidatus Pseudopelobacter ferreus", both of which lacked known 2,4-D degradation genes was investigated. BLA1 produces Fe(II)-adsorbed to Fe(III) oxyhydroxides during alternating photoautotrophic iron oxidation and dark iron reduction (amended with acetate) cycles. No 2,4-D degradation occurred during iron oxidation by FeOB Ca. C. masyuteum or during iron reduction by FeRB Ca. P. ferreus under any incubation conditions tested (i.e., +/-Fe(II), +/-cells, and +/-light), or due to the presence of Fe(II) adsorbed to Fe(III) oxyhydroxides. Our results cast doubt on the hypothesis that the mineral-bound Fe(II) species augments the anaerobic degradation of 2,4-D in anoxic soils and waters by iron-cycling bacteria, and further justify the need to identify the genetic underpinnings of anaerobic 2,4-D degradation.

Use of pilot-scale geomedia-amended biofiltration system for removal of polar trace organic and inorganic contaminants from stormwater runoff

Stormwater runoff capture and groundwater recharge can provide a sustainable means of augmenting the local water resources in water-stressed cities while simultaneously mitigating flood risk, provided that these processes do not compromise groundwater quality. We developed and tested for one year an innovative pilot-scale stormwater treatment train that employs cost-effective engineered geomedia in a continuous-flow unit-process system to remove contaminants from urban runoff during aquifer recharge. The system consisted of an iron-enhanced sand filter for phosphate removal, a woodchip bioreactor for nitrate removal coupled to an aeration step, and columns packed with different configurations of biochar- and manganese oxide-containing sand to remove trace metals and persistent, mobile, and toxic trace organic contaminants. During conditioning with authentic stormwater runoff over an extended period (8 months), the woodchip bioreactor removed 98% of the influent nitrate (9 g-N m^-3 d^-1), while phosphate broke through the iron-enhanced sand filter. During the challenge test (4 months), geomedia removed more than 80% of the mass of metals and trace organic compounds. Column hydraulic performance was stable during the entire study, and the weathered biochar and manganese oxide were effective at removing trace organic contaminants and metals, respectively. Under conditions likely encountered in the field, sustained nutrient removal is probable, but polar organic compounds such as 2,4-D could breakthrough after about a decade for conditions at the study site.

2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples

2,4-Dichlorophenoxyacetic acid (2,4-D) is the third most applied pesticide in Brazil to control broadleaf weeds in crop cultivation and pastures. Due to 2,4-D's high mobility and long half-life under anoxic conditions, this herbicide has high probability for groundwater contamination. Bioremediation is an attractive solution for 2,4-D contaminated anoxic environments, but there is limited understanding of anaerobic 2,4-D biodegradation. In this study, methanogenic enrichment cultures were obtained from Amazonian top soil (0-40 cm) and deep soil (50 -80 cm below ground) that biotransform 2,4-D (5 µM) to 4-chlorophenol and phenol. When these cultures were transferred (10% v/v) to fresh medium containing 40 µM or 160 µM 2,4-D, the rate of 2,4-D degradation decreased, and biotransformation did not proceed beyond 4-chlorophenol and 2,4-dichlorophenol in the top and deep soil cultures, respectively. 16S rRNA gene sequencing and qPCR of a selection of microbes revealed no significant enrichment of known organohalide-respiring bacteria. Furthermore, a member of the genus Cryptanaerobacter was identified as possibly responsible for phenol conversion to benzoate in the top soil inoculated culture. Overall, these results demonstrate the effect of 2,4-D concentration on biodegradation and microbial community composition, which are both important factors when developing pesticide bioremediation technologies.

Identificación de microorganismos aislados de suelos agrícolas con capacidad de tolerar 2.4-D y malatión

En el presente estudio, se analizó la diversidad microbiana de los suelos agrícolas de las localidades de Río Bravo y la Estación Cuauhtémoc en el estado de Tamaulipas y en los límites de Dolores Hidalgo en el estado de Guanajuato. Los plaguicidas utilizados fueron 2,4-D y malatión, con los que se establecieron pruebas preselectivas para el aislamiento de los microorganismos y su tolerancia. Para la identificación de las bacterias se amplificó el gen 16S y para los hongos la región ITS. El género bacteriano Pseudomonas, así como el género fúngico Penicillium fueron los de mayor abundancia en las muestras analizadas. Los resultados indicaron que las cepas tolerantes fueron Pseudomonas aeruginosa, Stenotrophomonas pavanii y Acinetobacter lactucae creciendo a una concentración > 2.0 g L-1 de 2,4-D y > 1.0 g L-1 de malatión. Así como Fusarium sp., a 2.0 g L-1 de malatión y 0.9 g L-1 de 2,4-D y el hongo Talaromyces variabilis con un crecimiento a 3.1 g L-1 de malatión. Para el caso de S. pavanii, A. Lactucae y T. variabilis no existen reportes de tolerancia a los plaguicidas mencionados, sin embargo, en este trabajo se demuestra por primera vez que pueden ser utilizados en técnicas de biorremediación de suelos.

A Comparison of the Microbial Community and Functional Genes Present in Free-Living and Soil Particle-Attached Bacteria from an Aerobic Bioslurry Reactor Treating High-Molecular-Weight PAHs

High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) contaminate a wide range of ecosystems, including soils, groundwater, rivers and harbor sediments. The effective removal of HMW PAHs is a difficult challenge if a rapid remediation time and low economic cost are required. Bioremediation provides a cheap and eco-friendly cleanup strategy for the removal of HMW PAHs. Previous studies have focused on removal efficiency during PAHs bioremediation. In such studies, only limited research has targeted the bacterial communities and functional genes present in such bioremediation systems, specifically those of free-living (aqueous) bacteria and soil particle-attached bacteria present. In this study, a high-level of HMW PAH (1992 mg/kg pyrene) was bioremediated in an aerobic bioslurry reactor (ABR) for 42 days. The results showed a pseudo first order constant rate for pyrene biodegradation of 0.0696 day−1. The microbial communities forming free-living bacteria and soil-attached bacteria in the ABR were found to be different. An analysis of the aqueous samples identified free-living Mycobacterium spp., Pseudomonas putida, Rhodanobacter spp. and Burkholderia spp.; these organisms would seem to be involved in pyrene biodegradation. Various biointermediates, including phenanthrene, catechol, dibenzothiophene, 4,4′-bipyrimidine and cyclopentaphenanthrene, were identified and measured in the aqueous samples. When a similar approach was taken with the soil particle samples, most of the attached bacterial species did not seem to be involved in pyrene biodegradation. Furthermore, community level physiological profiling resulted in significantly different results for the aqueous and soil particle samples. Nevertheless, these two bacterial populations both showed positive signals for the presence of various dioxygenases, including PAHs-RHDα dioxygenases, riesk iron-sulfur motif dioxygenases and catechol 2,3-dioxygenases. The present findings provide a foundation that should help environmental engineers when designing future HMW PAH bioremediation systems that use the ABR approach.

Anaerobic degradation of 2,4-dichlorophenoxyacetic acid by Thauera sp. DKT

Thauera sp. strain DKT isolated from sediment utilized 2,4-dichlorophenoxyacetic acid (2,4D) and its relative compounds as sole carbon and energy sources under anaerobic conditions and used nitrate as an electron acceptor. The determination of 2,4D utilization at different concentrations showed that the utilization curve fitted well with the Edward model with the maximum degradation rate as 0.017 ± 0.002 mM/day. The supplementation of cosubstrates (glucose, acetate, sucrose, humate and succinate) increased the degradation rates of all tested chemical substrates in both liquid and sediment slurry media. Thauera sp. strain DKT transformed 2,4D to 2,4-dichlorophenol (2,4DCP) through reductive side-chain removal then dechlorinated 2,4DCP to 2-chlorophenol (2CP), 4-chlorophenol (4CP) and phenol before complete degradation. The relative degradation rates by the isolate in liquid media were: phenol > 2,4DCP > 2CP > 4CP > 2,4D ≈ 3CP. DKT augmentation in sediment slurry enhanced the degradation rates of 2,4D and chlorophenols. The anaerobic degradation rates in the slurry were significantly slower compared to the rates in liquid media.

Combination of bioaugmentation and biostimulation for remediation of paddy soil contaminated with 2,4-dichlorophenoxyacetic acid

The batch and fed-batch tests were performed to evaluate the efficiency of bioaugmentation in combination with biostimulation for remediation of paddy soil contaminated with 2,4-dichlorophenoxyacetic acid (2,4-D). 2,4-D degrading enrichments were used for bioaugmentation, and effluents prepared through biological hydrogen production process were used as substrate for biostimulation. The batch tests indicated that 2,4-D degradation depended on the enrichment/substrate ratio (E/S), where E/S of 0.03 showed an excellent performance. The fed-batch tests showed that biostimulation only led to an improvement in 2,4-D degradation, while the pattern of repeated augmentation of enrichments (FRA) together with biostimulation obviously improved degradation of 2,4-D, 2-chlorophenol (2-CP) and phenol. DNA-sequencing approach showed that the FRA pattern altered the bacterial community composition, and high removal of 2,4-D, 2-CP and phenol may be attributed to the acclimation and persistence of Thauera. The findings demonstrated the importance of the FRA pattern on remediation of paddy soil contaminated with 2,4-D.

Promoting degradation of 2,4-dichlorophenoxyacetic acid with fermentative effluents from hydrogen-producing reactor

This research aims to identifying the potential effect of using a hydrogen-producing reactor's effluent as an enrichment amendment for enhancing the degradation rates of 2,4-dichlorophenoxyacetic acid (2,4-D) during the bioremediation of contaminated paddy soils. The results showed that addition of the effluents to 2,4-D- degrading enrichment culture enhanced (up to 1.3-fold) the degradation rate constant of 2,4-D. The enhancement effect most probably resulted from the co-metabolic degradation of 2,4-D facilitated by volatile fatty acids (e.g., acetate, propionate, and butyrate) in the effluents which served as the beneficial substrates. Results from DNA sequencing analysis showed that the effluent additions shifted the bacterial community composition in the enrichment culture. Dechloromonas and Clostridium were two dominant bacterial genera involved in 2,4-D degradation. The findings will make a substantial contribution to remediation of soils contaminated with 2,4-D.

Removal mechanisms in aerobic slurry bioreactors for remediation of soils and sediments polluted with hydrophobic organic compounds: An overview

Hydrophobic organic compound (HOC)-contaminated soils are a great environmental and public health concern nowadays. Further research is necessary to develop environmental friendly biotechnologies that allows public and private sectors to implement efficient and adaptable treatment approaches. Aerobic soil-slurry bioreactor technology has emerged as an effective and feasible technique with a high remediation potential, especially for silt and clay soil fractions, which often contain the highest pollutant concentration levels and are usually difficult to remove by implementing conventional methods. However, the mechanisms involved in the HOC removal in bioslurry reactor are still not completely understood. Gas-liquid and solid-liquid mass transfer, mass transport and biodegradation phenomena are the main known processes taking place in slurry bioreactors. This review compiles the most up-to-date information available about these phenomena and tries to link them, enlightening the possible interactions between parameters. It gathers the basic information needed to understand the complex bioremediation technology and raises awareness of some considerations that should be made.

Rapid degradation of 2,4-dichlorophenoxyacetic acid facilitated by acetate under methanogenic condition

Acetate can be used as an electron donor to stimulate 2,4-dichlorophenoxyacetic acid (2,4-D), which has not been determined under methanogenic condition. This study applied high-throughput sequencing and methanogenic inhibition approaches to investigate the 2,4-D degradation process using the enrichments obtained from paddy soil. Acetate addition significantly promoted 2,4-D degradation, which was 5-fold higher than in the acetate-unsupplemented enrichments in terms of the 2,4-D degradation rate constant. Dechloromonas and Pseudomonas were the dominant 2,4-D degraders. Methanogenic inhibition experiments indicated that the 2,4-D degradation was independent of methanogenesis. It was proposed that the accelerated 2,4-D degradation in the acetate-supplemented enrichment involved an unusual interaction, where members of the acetate oxidizers primarily oxidized acetate and produced H₂. H₂ was utilized by the 2,4-D degraders to degrade 2,4-D, but also partially consumed by the hydrogenotrophic methanogens to produce methane. The findings presented here provide a new strategy for the remediation of 2,4-D-polluted soils.

Ex-Situ Remediation Technologies for Environmental Pollutants: A Critical Perspective

Pollution and the global health impacts from toxic environmental pollutants are presently of great concern. At present, more than 100 million people are at risk from exposure to a plethora of toxic organic and inorganic pollutants. This review is an exploration of the ex-situ technologies for cleaning-up the contaminated soil, groundwater and air emissions, highlighting their principles, advantages, deficiencies and the knowledge gaps. Challenges and strategies for removing different types of contaminants, mainly heavy metals and priority organic pollutants, are also described.

Molecular structure and vibrational assignments of 2,4-dichlorophenoxyacetic acid herbicide

The structural stability of 2,4-dichlorophenoxyacetic acid was investigated by the DFT-B3LYP and the ab initio MP2 calculations with the 6-311G** basis set. From the calculations at both levels of theory the Cgcpp structure was predicted to be the lowest energy minimum for the acid. The DFT and the MP2 levels disagreed about the nature of the second stable structure of 2,4-dichlorophenoxyacetic acid. At the DFT-B3LYP level of calculation the planar Tttp (transoid O=C-O-H) and the non-planar Tgcpp (cisoid O=C-O-H) forms were predicted to be 0.7 and 1.5 kcal/mol, respectively higher in energy than the Cgcpp conformation. At the MP2 level the two high energy Tttp and Tgcpp forms were predicted to be 2.7 and 1.4 kcal/mol, respectively higher in energy than the ground state Cgcpp structure. The Tgcpp form was adopted as the second possible structure of 2,4-dichlorophenoxyacetic acid on the basis of the fact that the Møller-Plesset calculations account better than the DFT ones for the non-bonding Ocdots, three dots, centeredH interactions. The vibrational frequencies of the lowest energy Cgcpp conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis and experimental infrared and Raman data.

A review on slurry bioreactors for bioremediation of soils and sediments

The aim of this work is to present a critical review on slurry bioreactors (SB) and their application to bioremediation of soils and sediments polluted with recalcitrant and toxic compounds. The scope of the review encompasses the following subjects: (i) process fundamentals of SB and analysis of advantages and disadvantages; (ii) the most recent applications of SB to laboratory scale and commercial scale soil bioremediation, with a focus on pesticides, explosives, polynuclear aromatic hydrocarbons, and chlorinated organic pollutants; (iii) trends on the use of surfactants to improve availability of contaminants and supplementation with degradable carbon sources to enhance cometabolism of pollutants; (iv) recent findings on the utilization of electron acceptors other than oxygen; (v) bioaugmentation and advances made on characterization of microbial communities of SB; (vi) developments on ecotoxicity assays aimed at evaluating bioremediation efficiency of the process.From this review it can be concluded that SB is an effective ad situ and ex situ technology that can be used for bioremediation of problematic sites, such as those characterized by soils with high contents of clay and organic matter, by pollutants that are recalcitrant, toxic, and display hysteretic behavior, or when bioremediation should be accomplished in short times under the pressure and monitoring of environmental agencies and regulators. SB technology allows for the convenient manipulation and control of several environmental parameters that could lead to enhanced and faster treatment of polluted soils: nutrient N, P and organic carbon source (biostimulation), inocula (bioaugmentation), increased availability of pollutants by use of surfactants or inducing biosurfactant production inside the SB, etc. An interesting emerging area is the use of SB with simultaneous electron acceptors, which has demonstrated its usefulness for the bioremediation of soils polluted with hydrocarbons and some organochlorinated compounds. Characterization studies of microbial communities of SB are still in the early stages, in spite of their significance for improving reactor operation and design optimization.We have identified the following niches of research needs for SB in the near and mid term future, inter alia: (i) application of SB with sequential and simultaneous electron acceptors to soils polluted with contaminants other than hydrocarbons (i.e., pesticides, explosives, etc.), (ii) evaluation of the technical feasibility of triphasic SB that use innocuous solvents to help desorbing pollutants strongly attached to soils, and in turn, to enhance their biodegradation, (iii) gaining deeper insight of microbial communities present in SB with the intensified application of molecular biology tools such as PCR-DGGE, PCR-TGGE, ARDRA, etc., (iv) development of more representative ecotoxicological assays to better assess the effectiveness of a given bioremediation process.