Estimation of the yield coefficient of Pseudomonas sp. strain DP-4 with a low substrate (2,4-dichlorophenol [DCP]) concentration in a mineral medium from which uncharacterized organic compounds were eliminated by a non-DCP-degrading organism

Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium

2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.

The Growth Yield of Aminobacter niigataensis MSH1 on the Micropollutant 2,6-Dichlorobenzamide Decreases Substantially at Trace Substrate Concentrations

2,6-Dichlorobenzamide (BAM) is an omnipresent micropollutant in European groundwaters. Aminobacter niigataensis MSH1 is a prime candidate for biologically treating BAM-contaminated groundwater since this organism is capable of utilizing BAM as a carbon and energy source. However, detailed information on the BAM degradation kinetics by MSH1 at trace concentrations is lacking, while this knowledge is required for predicting and optimizing the degradation process. Contaminating assimilable organic carbon (AOC) in media makes the biodegradation experiment a mixed-substrate assay and hampers exploration of pollutant degradation at trace concentrations. In this study, we examined how the BAM concentration affects MSH1 growth and BAM substrate utilization kinetics in a AOC-restricted background to avoid mixed-substrate conditions. Conventional Monod kinetic models were unable to predict kinetic parameters at low concentrations from kinetics determined at high concentrations. Growth yields on BAM were concentration-dependent and decreased substantially at trace concentrations; i.e., growth of MSH1 diminished until undetectable levels at BAM concentrations below 217 μg-C/L. Nevertheless, BAM degradation continued. Decreasing growth yields at lower BAM concentrations might relate to physiological adaptations to low substrate availability or decreased expression of downstream steps of the BAM catabolic pathway beyond 2,6-dichlorobenzoic acid (2,6-DCBA) that ultimately leads to Krebs cycle intermediates for growth and energy conservation.

Assessing the substrate specificity of a micropollutant degrading strain: generalist or specialist?

Natural dissolved organic matter (DOM) can serve as an additional substrate for organic micropollutant (OMP) degrading bacteria, thus influencing OMP biodegradation in aquatic systems. DOM biodegradation depends on the OMP degrader's ability to grow on different DOM constituents, and on its capability to compete for DOM constituents against the rest of the resident aquatic microbial community. This study aimed to investigate the growth of a model OMP degrader strain, Novosphingobium sp. KN65.2 (assumed specialist), isolated for its ability to mineralize carbofuran, on thirteen DOM constituents; compare its metabolic capabilities to those of a common freshwater strain (Pseudomonas fluorescens sp. P17) (generalist); and to evaluate competition for specific compounds. Growth experiments were carried out in pure- and mixed culture batch experiments. The DOM constituents tested included aromatic amino acids and a range of phenolic acids (lignin derivatives). The OMP degrader could biodegrade approximately half of the tested compounds. It showed a high specialization for substrates containing a hydroxyl-group in the para-position of the primary aromatic ring substituent. However, its broad substrate range enabled the strain to grow on the same number of auxiliary substrates as the generalist. Moreover, the OMP degrader was able to successfully compete against the generalist for the biodegradation of one (4-hydroxybenzaldehyde) out of three substrates (4-hydroxybenzoic acid, 4-hydroxybenzaldehyde, L-tyrosine), which were biodegraded by both strains. The study results provide insight on the substrate specificity of a model OMP degrader, which can inform development of modeling frameworks investigating the influence of DOM on OMP biodegradation.

Pseudomonas in environmental bioremediation of hydrocarbons and phenolic compounds- key catabolic degradation enzymes and new analytical platforms for comprehensive investigation

Pollution of the environment with petroleum hydrocarbons and phenolic compounds is one of the biggest problems in the age of industrialization and high technology. Species of the genus Pseudomonas, present in almost all hydrocarbon-contaminated areas, play a particular role in biodegradation of these xenobiotics, as the genus has the potential to decompose various hydrocarbons and phenolic compounds, using them as its only source of carbon. Plasticity of carbon metabolism is one of the adaptive strategies used by Pseudomonas to survive exposure to toxic organic compounds, so a good knowledge of its mechanisms of degradation enables the development of new strategies for the treatment of pollutants in the environment. The capacity of microorganisms to metabolize aromatic compounds has contributed to the evolutionally conserved oxygenases. Regardless of the differences in structure and complexity between mono- and polycyclic aromatic hydrocarbons, all these compounds are thermodynamically stable and chemically inert, so for their decomposition, ring activation by oxygenases is crucial. Genus Pseudomonas uses several upper and lower metabolic pathways to transform and degrade hydrocarbons, phenolic compounds, and petroleum hydrocarbons. Data obtained from newly developed omics analytical platforms have enormous potential not only to facilitate our understanding of processes at the molecular level but also enable us to instigate and monitor complex biodegradations by Pseudomonas. Biotechnological application of aromatic metabolic pathways in Pseudomonas to bioremediation of environments polluted with crude oil, biovalorization of lignin for production of bioplastics, biofuel, and bio-based chemicals, as well as Pseudomonas-assisted phytoremediation are also considered.

Challenges and opportunities for the biodegradation of chlorophenols: Aerobic, anaerobic and bioelectrochemical processes

Chlorophenols (CPs) are highly toxic and refractory contaminants which widely exist in various environments and cause serious harm to human and environment health and safety. This review provides comprehensive information on typical CPs biodegradation technologies, the most green and benign ones for CPs removal. The known aerobic and anaerobic degradative bacteria, functional enzymes, and metabolic pathways of CPs as well as several improving methods and critical parameters affecting the overall degradation efficiency are systematically summarized and clarified. The challenges for CPs mineralization are also discussed, mainly including the dechlorination of polychlorophenols (poly-CPs) under aerobic condition and the ring-cleavage of monochlorophenols (MCPs) under anaerobic condition. The coupling of functional materials and degraders as well as the operation of sequential anaerobic-aerobic bioreactors and bioelectrochemical system (BES) are promising strategies to overcome some current limitations. Future perspective and research gaps in this field are also proposed, including the further understanding of microbial information and the specific role of materials in CPs biodegradation, the potential application of innovative biotechnologies and new operating modes to optimize and maximize the function of the system, and the scale-up of bioreactors towards the efficient biodegradation of CPs.

Expression of an alcohol dehydrogenase gene in a heterotrophic bacterium induces carbon dioxide-dependent high-yield growth under oligotrophic conditions

Sphingobium japonicum strain UT26, whose γ-hexachlorocyclohexane-degrading ability has been studied in detail, is a typical aerobic and heterotrophic bacterium that needs organic carbon sources for its growth, and cannot grow on a minimal salt agar medium prepared without adding any organic carbon sources. Here, we isolated a mutant of UT26 with the ability to grow to visible state on such an oligotrophic medium from a transposon-induced mutant library. This high-yield growth under oligotrophic conditions (HYGO) phenotype was CO₂-dependent and accompanied with CO₂ incorporation. In the HYGO mutant, a transposon was inserted just upstream of the putative Zn-dependent alcohol dehydrogenase (ADH) gene (adhX) so that the adhX gene was constitutively expressed, probably by the transposon-derived promoter. The adhX-deletion mutant (UT26DAX) harbouring a plasmid carrying the adhX gene under the control of a constitutive promoter exhibited the HYGO phenotype. Moreover, the HYGO mutants spontaneously emerged among the UT26-derived hypermutator strain cells, and adhX was highly expressed in these HYGO mutants, while no HYGO mutant appeared among UT26DAX-derived hypermutator strain cells, indicating the necessity of adhX for the HYGO phenotype. His-tagged AdhX that was expressed in Escherichia coli and purified to homogeneity showed ADH activity towards methanol and other alcohols. Mutagenesis analysis of the adhX gene indicated a correlation between the ADH activity and the HYGO phenotype. These results demonstrated that the constitutive expression of an adhX-encoding protein with ADH activity in UT26 leads to the CO₂-dependent HYGO phenotype. Identical or nearly identical adhX orthologues were found in other sphingomonad strains, and most of them were located on plasmids, suggesting that the adhX-mediated HYGO phenotype may be an important adaptation strategy to oligotrophic environments among sphingomonads.

Biodegradation of 2,4-dichlorophenoxyacetic acid by bacteria with highly antibiotic-resistant pattern isolated from wheat field soils in Kurdistan, Iran

Recently, there has been increasing interest to clean up the soils contaminated with herbicide. Our aim was to determine the bioremediation of 2,4-dichlorophenoxyacetic acid (2,4-D) from wheat fields which have a long history of herbicide in Sanandaj. Based on our literature survey, this study is the first report to isolate and identify antimicrobial resistant bacteria from polluted wheat field soils in Sanandaj which has the capacity to degrade 2,4-D. From 150 2,4-D-exposed soil samples, five different bacteria were isolated and identified based on biochemical tests and 16S ribosomal RNA (rRNA). Pseudomonas has been the most frequently isolated genus. By sequencing the 16S rRNA gene of the isolated bacteria, the strains were detected and identified as a member of the genus Pseudomonas sp, Entrobacter sp, Bacillus sp, Seratia sp, and Staphylococcus sp. The sequence of Sanandaj 1 isolate displayed 87% similarity with the 16S rRNA gene of a Pseudomonas sp (HE995788). Similarly, all the isolates were compared to standard strains based on 16S rRNA. Small amounts of 2,4-D could be transmitted to a depth of 10-20 cm; however, in the depth of 20-40 cm, we could not detect the 2,4-D. The isolates were resistant to various antibiotics particularly, penicillin, ampicillin, and amoxicillin.

Surface Colonization and Activity of the 2,6-Dichlorobenzamide (BAM) Degrading Aminobacter sp. Strain MSH1 at Macro- and Micropollutant BAM Concentrations

Aminobacter sp. MSH1 uses the groundwater micropollutant 2,6-dichlorobenzamide (BAM) as a C and N source and is a potential catalyst for biotreatment of BAM-contaminated groundwater in filtration units of drinking water treatment plants (DWTPs). The oligotrophic environment of DWTPs including trace pollutant concentrations, and the high flow rates impose challenges for micropollutant biodegradation in DWTPs. To understand how trace BAM concentrations affect MSH1 surface colonization and BAM degrading activity, MSH1 was cultivated in flow channels fed continuously with BAM macro- and microconcentrations in a N- and C-limiting medium. At all BAM concentrations, MSH1 colonized the flow channel. BAM degradation efficiencies were concentration-dependent, ranging between 70 and 95%. Similarly, BAM concentration affected surface colonization, but at 100 μg/L BAM and lower, colonization was similar to that in systems without BAM, suggesting that assimilable organic carbon and nitrogen other than those supplied by BAM sustained colonization at BAM microconcentrations. Comparison of specific BAM degradation rates in flow channels and in cultures of suspended freshly grown cells indicated that starvation conditions in flow channels receiving BAM microconcentrations resulted into MSH1 biomasses with 10-100-times reduced BAM degrading activity and provided a kinetic model for predicting BAM degradation under continuous C and N starvation.

The potential of using low cost naturally available biogenic substrates for biological removal of chlorophenol

This study details the application of naturally available biogenic substrates (NABS) in microbial degradation of 2-chlorophenol (CP). Jatropha deoiled cakes (JDC) and Karanja deoiled cakes (KDC) are used as NABS. The potential of NABS is compared with standard biogenic substrate, glucose. The study was carried out with both acclimatized mixed culture and pure culture, Pseudomonas putida. Microbial activity of the culture was monitored by measuring reduction in chlorophenol concentration, COD, toxicity and Cl(-) ions evolution. The study was carried out for a total of 42days. It was observed that culture having NABS has shown similar chlorophenol reduction but higher COD and toxicity reduction. Amongst NABS, Jatropha deoiled cake (JDC) has shown superior results of 71% COD reduction compared to glucose and KDC. This study is one of the first kind illustrating the potential of these substrates in removing toxic chemicals from wastewaters.

Bioremediation of pesticide-contaminated water resources: the challenge of low concentrations

The use of pesticides in agricultural and urban environments has improved quality of life around the world. However, the resulting accumulation of pesticide residues in fresh water resources has negative effects on aquatic ecosystem and human health. Bioremediation has been proposed as an environmentally sound alternative for the remediation of pesticide-contaminated water resources, though full-scale implementation has thus far been limited. One major challenge that has impeded progress is the occurrence of pesticides at low concentrations. Recent research has improved our fundamental understanding of pesticide biodegradation processes occurring at low concentrations under a variety of environmental scenarios and is expected to contribute to the development of applied bioremediation strategies for pesticide-contaminated water resources.

Insights into the catalytic mechanism of chlorophenol 4-monooxygenase: a quantum mechanics/molecular mechanics study

The degradation mechanism of chlorophenol 4-monooxygenase toward pollutants 2,4,5-trichlorophenol, 2,4,6-trichlorophenol, and 2,5-dichloro-p-hydroquinone was studied by QM/MM investigations.

A model framework to describe growth-linked biodegradation of trace-level pollutants in the presence of coincidental carbon substrates and microbes

Pollutants such as pesticides and their degradation products occur ubiquitously in natural aquatic environments at trace concentrations (μg L(-1) and lower). Microbial biodegradation processes have long been known to contribute to the attenuation of pesticides in contaminated environments. However, challenges remain in developing engineered remediation strategies for pesticide-contaminated environments because the fundamental processes that regulate growth-linked biodegradation of pesticides in natural environments remain poorly understood. In this research, we developed a model framework to describe growth-linked biodegradation of pesticides at trace concentrations. We used experimental data reported in the literature or novel simulations to explore three fundamental kinetic processes in isolation. We then combine these kinetic processes into a unified model framework. The three kinetic processes described were: the growth-linked biodegradation of micropollutant at environmentally relevant concentrations; the effect of coincidental assimilable organic carbon substrates; and the effect of coincidental microbes that compete for assimilable organic carbon substrates. We used Monod kinetic models to describe substrate utilization and microbial growth rates for specific pesticide and degrader pairs. We then extended the model to include terms for utilization of assimilable organic carbon substrates by the specific degrader and coincidental microbes, growth on assimilable organic carbon substrates by the specific degrader and coincidental microbes, and endogenous metabolism. The proposed model framework enables interpretation and description of a range of experimental observations on micropollutant biodegradation. The model provides a useful tool to identify environmental conditions with respect to the occurrence of assimilable organic carbon and coincidental microbes that may result in enhanced or reduced micropollutant biodegradation.

Bacterial degradation of chlorophenols and their derivatives

Chlorophenols (CPs) and their derivatives are persistent environmental pollutants which are used in the manufacture of dyes, drugs, pesticides and other industrial products. CPs, which include monochlorophenols, polychlorophenols, chloronitrophenols, chloroaminophenols and chloromethylphenols, are highly toxic to living beings due to their carcinogenic, mutagenic and cytotoxic properties. Several physico-chemical and biological methods have been used for removal of CPs from the environment. Bacterial degradation has been considered a cost-effective and eco-friendly method of removing CPs from the environment. Several bacteria that use CPs as their sole carbon and energy sources have been isolated and characterized. Additionally, the metabolic pathways for degradation of CPs have been studied in bacteria and the genes and enzymes involved in the degradation of various CPs have been identified and characterized. This review describes the biochemical and genetic basis of the degradation of CPs and their derivatives.

Kinetics and yields of pesticide biodegradation at low substrate concentrations and under conditions restricting assimilable organic carbon

The fundamentals of growth-linked biodegradation occurring at low substrate concentrations are poorly understood. Substrate utilization kinetics and microbial growth yields are two critically important process parameters that can be influenced by low substrate concentrations. Standard biodegradation tests aimed at measuring these parameters generally ignore the ubiquitous occurrence of assimilable organic carbon (AOC) in experimental systems which can be present at concentrations exceeding the concentration of the target substrate. The occurrence of AOC effectively makes biodegradation assays conducted at low substrate concentrations mixed-substrate assays, which can have profound effects on observed substrate utilization kinetics and microbial growth yields. In this work, we introduce a novel methodology for investigating biodegradation at low concentrations by restricting AOC in our experiments. We modified an existing method designed to measure trace concentrations of AOC in water samples and applied it to systems in which pure bacterial strains were growing on pesticide substrates between 0.01 and 50 mg liter(-1). We simultaneously measured substrate concentrations by means of high-performance liquid chromatography with UV detection (HPLC-UV) or mass spectrometry (MS) and cell densities by means of flow cytometry. Our data demonstrate that substrate utilization kinetic parameters estimated from high-concentration experiments can be used to predict substrate utilization at low concentrations under AOC-restricted conditions. Further, restricting AOC in our experiments enabled accurate and direct measurement of microbial growth yields at environmentally relevant concentrations for the first time. These are critical measurements for evaluating the degradation potential of natural or engineered remediation systems. Our work provides novel insights into the kinetics of biodegradation processes and growth yields at low substrate concentrations.

Acclimated biomass that degrades Sulfonated Naphthalene Formaldehyde Condensate

A number of aerobic species were isolated from textile industry activated sludge wastewater. The bacterial consortium was acclimated during seven days before testing its capacity of Sulfonated Naphthalene-Formaldehyde Condensate (SNFC) recalcitrant compound degradation. SNFC's degradation was evaluated by using different techniques including: vapour pressure osmometry, spectroscopy UV-Visible and Chemical Oxygen Demand (COD). The degradation of SNFC by acclimated bacterial consortium was determined by monitoring the decrease of absorbance and of COD at wavelength 288 nm. We were able to deduce that biodegradation of SNFC involves two steps: cleavage of CH2 bridges and the degradation of the aromatic nuclei. The bacteria species community that was able to degrade SNFC consisted of aerobic Gram-negative rods belonging to the Pseudomonadaceae family. The strains were identified as Bukholderia cepacia, Brevundimonas vesicularis, Pseudomonas stutzeri, Ralostonia picketti, Shewanella putrefaciens, Sphingomonas paucimobilis and Agrobacterium radiobacter.

Bioremediation of crystal violet using air bubble bioreactor packed with Pseudomonas aeruginosa

Seven water and sediment samples were collected and tested for decolorizing crystal violet. Pseudomonas aeruginosa was the most effective isolate for dye decolorization. The LC50 of the crystal violet (115 mg/l) was measured using Artemia salina as a biomarker. The effect of different heavy metals on crystal violet decolorization was investigated. Cd2+ and Fe3+ ions showed marginal enhancement of the decolorization process, the rate was 1.35 mg/l/h compared to (1.25 mg/l/h) for the control. Phenol and m-cresol showed no effect on crystal violet decolorization, meanwhile p-cresol and p-nitrophenol reduced the decolorization rate to 1.07 and 0.01 mg/l/h, respectively. P. aeruginosa cells were immobilized by entrapment in agar-alginate beads. The beads were cultivated and reused in Erlenmeyer flask and in an air bubble column bioreactor and they enhanced the crystal violet decolorization rate to 3.33 and 7.5 mg/l/h, respectively.

Bioremediation of crystal violet using air bubble bioreactor packed with Pseudomonas aeruginosa

Seven water and sediment samples were collected and tested for decolorizing crystal violet. Pseudomonas aeruginosa was the most effective isolate for dye decolorization. The LC(50) of the crystal violet (115 mg/l) was measured using Artemia salina as a biomarker. The effect of different heavy metals on crystal violet decolorization was investigated. Cd(2+) and Fe(3+) ions showed marginal enhancement of the decolorization process, the rate was 1.35 mg/l/h compared to 1.25 mg/l/h for the control. Phenol and m-cresol showed no effect on crystal violet decolorization, meanwhile p-cresol and p-nitrophenol reduced the decolorization rate to 1.07 and 0.01 mg/l/h, respectively. P. aeruginosa cells were immobilized by entrapment in agar-alginate beads. The beads were cultivated and reused in Erlenmeyer flask and in an air bubble column bioreactor and they enhanced the crystal violet decolorization rate to 3.33 and 7.5 mg/l/h, respectively.