A novel degradation pathway of chloroaniline in Diaphorobacter sp. PCA039 entails initial hydroxylation

lA multiple PAHs-degrading Shinella sp. strain and its potential bioremediation in wastewater

Polycyclic aromatic hydrocarbons (PAHs) and heterocyclic derivatives are organic pollutants which threaten ecosystems and human beings. In this study, a new strain, Shinella sp. FLN 14, was isolated and characterized. It can utilize fluorene as its sole carbon source and effectively co-metabolize multiple PAHs and heterocyclic derivatives, including phenanthrene, acenaphthene, and fluoranthene. Two possible metabolic pathways are proposed (i.e., salicylic acid pathway and phthalic acid pathway). Whole-genome sequencing revealed that strain FLN14 possesses a chromosome and four plasmids. However, when combined with ensemble genetic information, novel fluorene-degrading functional gene clusters were not located within the genome of FLN 14, except for some new dioxygenases and electron transport chains, which typically initiate the oxidation of aromatic compounds. In wastewater bioremediation, strain FLN14 removed nearly 95 % of PAHs within 5 days and maintained high degrading activity during the 18-day reaction compared to the control. Overall, our study provides a promising candidate to achieve bioremediation of PAHs-contaminated environments.

Reducing Phenanthrene Contamination in Trifolium repens L. With Root-Associated Phenanthrene-Degrading Bacterium Diaphorobacter sp. Phe15

Some root-associated bacteria could degrade polycyclic aromatic hydrocarbons (PAHs) in contaminated soil; however, their dynamic distribution and performance on root surface and in inner plant tissues are still unclear. In this study, greenhouse container experiments were conducted by inoculating the phenanthrene-degrading bacterium Diaphorobacter sp. Phe15, which was isolated from root surfaces of healthy plants contaminated with PAHs, with the white clover (Trifolium repens L.) via root irrigation or seed soaking. The dynamic colonization, distribution, and performance of Phe15 in white clover were investigated. Strain Phe15 could efficiently degrade phenanthrene in shaking flasks and produce IAA and siderophore. After cultivation for 30, 40, and 50 days, it could colonize the root surface of white clover by forming aggregates and enter its inner tissues via root irrigation or seed soaking. The number of strain Phe15 colonized on the white clover root surfaces was the highest, reaching 6.03 Log CFU⋅g^–1 FW, followed by that in the roots and the least in the shoots. Colonization of Phe15 significantly reduced the contents of phenanthrene in white clover; the contents of phenanthrene in Phe15-inoculated plants roots and shoots were reduced by 29.92–43.16 and 41.36–51.29%, respectively, compared with the Phe15-free treatment. The Phe15 colonization also significantly enhanced the phenanthrene removal from rhizosphere soil. The colonization and performance of strain Phe15 in white clove inoculated via root inoculation were better than seed soaking. This study provides the technical support and the resource of strains for reducing the plant PAH pollution in PAH-contaminated areas.

Microbial degradation of multiple PAHs by a microbial consortium and its application on contaminated wastewater

Polycyclic aromatic hydrocarbons (PAHs) are widely distributed in the environment and pose a serious threat to human health. Due to their unfavorable biological effects and persistent properties, it is extremely urgent to effectively degrade PAHs that are present in the environment, especially in wastewater. In this study, we obtained an efficient bacterial consortium (PDMC), consisting of the genera Sphingobium (58.57-72.40%) and Pseudomonas (25.93-39.75%), which is able to efficiently utilize phenanthrene or dibenzothiophene as the sole carbon source. The phenanthrene-cultivated consortium could also degrade naphthalene, acenaphthene, fluorene, anthracene, fluoranthene, benzo[a]anthracene, dibenzofuran, carbazole and indole, respectively. Furthermore, we identified the multiple key intermediates of aforementioned 11 substrates and discussed proposed pathways involved. Notably, a novel intermediate 1,2-dihydroxy-4a,9a-dihydroanthracene-9,10-dione of anthracene degradation was detected, which is extremely rare compared to previous reports. The PDMC consortium removed 100% of PAHs within 5 days in the small-scale wastewater bioremediation added with PAHs mixture, with a sludge settling velocity of 5% after 10 days of incubation. Experiments on the stability reveal the PDMC consortium always has excellent degrading ability for totaling 24 days. Combined with the microbial diversity analysis, the results suggest the PDMC consortium is a promising candidate to facilitate the bioremediation of PAHs-contaminated environments.

EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde

Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M. extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.

Aerobic degradation of 4-fluoroaniline and 2,4-difluoroaniline: performance and microbial community in response to the inocula

In this study, a distinct inoculum was investigated as an isolated variable within sequencing batch reactors via a comparison of the 4-fluoroaniline (4-FA) or 2,4-difluoroaniline (2,4-DFA) removal amounts. The inocula were derived from a treatment plant for treating pharmaceutical wastewater plus a small amount of municipal sewage (PMS), a treatment plant for treating fluoridated hydrocarbon wastewater (FHS), and a treatment plant for treating the comprehensive wastewater in an industrial park (CIS). There were slight differences among the degradation patterns of the 4-FA for the three inocula, whether during the enrichment period or the high concentration shock period. In contrast, it was observed that the degradation efficiency of 2,4-DFA initially varied with the inocula. The FHS-derived inoculum was determined to be optimal, exhibiting the earliest degradation reaction only after an acclimation of 7 days had the highest degradation rate constant of 0.519 h^-1, and had the fastest recovery time of three weeks after high concentration shock. Additionally, compared with the PMS-derived inoculum, the CIS-derived inoculum exhibited an earlier degradation reaction within three weeks, and a higher microbial diversity, but a lower shock resistance and degradation rate constant of 0.257 h^-1. High-throughput sequencing demonstrated that each final consortium was different in composition, and the microbial consortia developed well on the inoculum and substrate. In comparison of the similarity among the three 2,4-DFA enrichment cultures, the higher similarity (63.9-70.0%) among three final consortia enriching with 4-FA was observed. The results indicated that the inoculum played an important role in the degradation of FAs and the microbial bacterial communities of final consortia, and the effect extent might well depend on the fluorinated level of FAs.

Ecotoxicological effects of sulfonamide on and its removal by the submerged plant Vallisneria natans (Lour.) Hara

The extensive application of sulfonamides (SAs) raises concern regarding its negative environmental effects. In aquatic environments, macrophytes may not only be affected by various pollutants, they may also help to reduce the concentrations in the surrounding environment. We studied both the ecotoxicological effects of sulfonamide (SN) on and its removal by Vallisneria natans (Lour.) Hara, an important submerged macrophyte in Chinese lakes and rivers. The toxic effect and oxidative stress caused by SN resulted in a reduction of total chlorophyll (chl.a and b) and autofluorescence of chloroplast. Meanwhile, the levels of reactive oxygen species (ROS, including O₂^- and H₂O₂) and peroxidase (POD) increased with increasing SN concentration and duration of exposure. After 20 days' exposure, a reduction in the relative growth rate (RGR) and leaf length of V. natans was found under SN stress, but SN had only a weak effect on root length. Although high SN concentrations had toxic effects on the growth of V. natans, the plant was overall resistant to the SN doses that we used. We studied the effect of V. natans on sulfonamide removal in an additional 13-day exposure experiment with focus on the dynamics of dissolved oxygen (DO), the oxidation-reduction potential (ORP) and microbial communities in the water column, as well as in the periphyton on V. natans surfaces. The results show that presence of V. natans significantly improved the SN removal efficiency likely by increasing DO, ORP and bacterial diversity in the water column. The presence of V. natans led to higher relative abundances of Saccharimonadales and Rhizoniales. Lefse analysis showed that Saccharimonadales, Micrococcales, Sphingobacteriales, Bacteroidales, Obscuribacterales, Flavobacteriales, Pseudomonadaceae and Myxococcales, which are considered to be SN-resistant bacteria, increased significantly in the V + S+ (V. natans and SN) treatment compared with the V + S- (V. natans and no SN) treatment and V-S+ (no V. natans and SN) treatment. As far as we know, ours is the first study of the ecotoxicological effects of sulfonamide and its removal by submerged vascular plants (here V. natans). Thus, our results add to the understanding of the antibiotic removal mechanism of macrophytes in freshwater systems and help to clarify the linkages between antibiotics and macrophyte-microbe systems; thereby providing new insight into ecological-based removal of antibiotics in aquatic systems.

Cometabolic degradation of p-chloroaniline by the genus Brevibacillus bacteria with extra carbon sources

In this study, we discovered and isolated a new genus Brevibacillus strain from effluent of dyeing and finishing factory containing highly toxic p-chloroanilines (PCA). Based on the morphological, physiological and biochemical characteristics, as well as 16S rDNA sequence, the strain was identified and denominated as Brevibacillus S-618. Co-metabolism effect was found with extra carbon sources including sodium succinate, sodium citrate, ammonium chloride and glucose which can efficiently promote the biodegradation process of PCA. Under the optimal growth conditions at temperature of 30 °C, pH˜7 and air-water ratio of 0.3 m³/m³·min, the degradation rate of PCA in a 2 L pilot bioreactor with high concentration of 180 mg/L increased from 86.7% to 100% within 72 h after adding sodium succinate. The release of chloride ions during the growth process of the strain was equivalent to the degradation amount of PCA. Meanwhile, the cleavage pathway of PCA degradation by Brevibacillus S-618 was proposed by analysis of enzyme activities of microorganism and intermediate products in the reaction. Benefiting from excellent degradation ability and unique characters in high pollutant contents, high efficient bioreactor can easily be scale up for industrial application. Our study provides a facile route for cost-effectively and environmental-friendly degrading hazardous chemicals.

Bioaugmentation of triclocarban and its dechlorinated congeners contaminated soil with functional degraders and the bacterial community response

Partial removal of haloaromatic antimicrobial triclocarban (TCC) during wastewater treatment caused the final introduction of residual TCC into soils. Bioaugmentation has been proposed for the biodegradation of TCC and its dechlorinated congeners 4,4'-dichlorocarbanilide (DCC) and carbanilide (NCC) in soil. The isolated TCC-degrading strain Ochrobactrum sp. TCC-2 and chloroanilines-degrading strain Diaphorobacter sp. LD72 were used to study the removal efficiency of TCC, DCC and NCC mixture and their chloroanilines intermediates, respectively. The potential degradation competition between TCC and its dechlorinated congeners, and the response of bacterial community during the bioremediation were also investigated. The biodegradation of DCC and TCC was significantly enhanced for soil with inoculums compared with sterilized and natural soils. Chloroanilines products could also be effectively removed. For the degradation of combined substrates in the aqueous medium, NCC had negative effect on the degradation of TCC and DCC, while TCC and DCC negatively influenced each other. The bioaugmentation with two degraders obviously changed the phylogenetic composition and function of indigenous soil microbiome. Importantly, the inoculated degraders could be maintained, suggesting their adaptability and potential application in bioaugmentation for such recalcitrant contaminants. This study offers new insights into the enhanced bioremediation of TCC and its dechlorinated congeners contaminated soils by the bioaugmentation of functional degraders and the structure and function response of the indigenous soil microbiome to the bioremediation process.

Microbes affected the TYLCCNV transmission rate by the Q biotype whitefly under high O3

Ozone (O3) is a major air pollutant that has a profound effect on whole ecosystems. In this study we studied how hO3 affected the transmission of the Tomato yellow leaf curl China virus (TYLCCNV), a begomovirus, by the Q biotype Bemisia tabaci in a persistent, circulative manner. We found hO3 affected the transmission of TYLCCNV via the effect of it on the microbial community of the transmitting insect, such as Candidatus Hamiltonella, Ralstonia, Diaphorobacter, Caldilineaceae, Deinococcus, Rickettsia, Thysanophora penicillioides and Wallemia ichthyophaga. We concluded that hO3 decreased the resistance of acquiring virus tomatoes, and decreased the immune response and increased the endurance to extreme environments of viruliferous whiteflies by altering the composition and abundance of the microbial environments inside the body and on the surface of whitefly, as a result, it enhanced the TYLCV transmission rate by the Q biotype whitefly.

Biodegradation of sulfonamide antibiotics in sludge

Sulfonamide antibiotics are widely used in human and veterinary medicine. This study assessed the degradation of three sulfonamides (100 mg kg(-1) each of sulfamethoxazole, sulfadimethoxine and sulfamethazine) and changes in the microbial communities of sewage sludge. Sulfamethoxazole degradation was enhanced by spent mushroom compost (SMC), SMC extract, and extract-containing microcapsules in the sludge. The degradation of sulfonamides in sludge and SMC mixtures occurred in the order of sulfamethoxazole > sulfadimethoxine > sulfamethazine. Bioreactor experiments revealed that the sulfonamides removal rates in sludge with SMC were greater than those in sludge alone. The sulfonamides removal rates were enhanced by the addition of SMC for six time additions. The sulfonamides concentrations were 200 and 500 mg kg(-1) for the first to third additions and the fourth to sixth additions, respectively. With the high correlations between TOC and the proportions of sulfonamides remaining in sludge, sulfonamides may be mineralized to a greater extent with SMC in sludge than in sludge alone. Four bacterial genera were identified from the different settings and stages of the bioreactor experiments. Acinetobacter and Pseudomonas were major bacterial communities that were responsible for sulfonamide degradation in sludge.

Stimulation of oxygen to bioanode for energy recovery from recalcitrant organic matter aniline in microbial fuel cells (MFCs)

The challenge of energy generation from biodegradation of recalcitrant organics in microbial fuel cells (MFCs) is mainly attributed to their persistence to degradation under anaerobic condition in anode chamber of MFCs. In this work, we demonstrated that electricity generation from aniline, a typical recalcitrant organic matter under anaerobic condition was remarkably facilitated by employing oxygen into bioanode of MFCs. By exposing bioanode to air, electrons of 47.2 ± 6.9 C were recovered with aniline removal efficiency of 91.2 ± 2.2% in 144 h. Limited oxygen supply (the anodic headspace was initially filled with air and then closed) resulted in the decrease of electrons recovery and aniline removal efficiency by 52.5 ± 9.4% and 74.2 ± 2.1%, respectively, and further decline by respective 64.3 ± 4.5% and 82.7 ± 1.0% occurred under anaerobic condition. Community analysis showed that anode biofilm was predominated by several aerobic aniline degrading bacteria (AADB) and anode-respiration bacteria (ARB), which likely cooperated with each other and finally featured the energy recovery from aniline. Cyclic voltammetry indicated that anodic bacteria transferred electrons to anode mainly through electron shuttle. This study provided a new sight to acquaint us with the positive role of oxygen in biodegradation of recalcitrant organics on anode as well as electricity generation.

Bacterial degradation of monocyclic aromatic amines

Aromatic amines are an important group of industrial chemicals, which are widely used for manufacturing of dyes, pesticides, drugs, pigments, and other industrial products. These compounds have been considered highly toxic to human beings due to their carcinogenic nature. Three groups of aromatic amines have been recognized: monocyclic, polycyclic, and heterocyclic aromatic amines. Bacterial degradation of several monocyclic aromatic amines has been studied in a variety of bacteria, which utilizes monocyclic aromatic amines as their sole source of carbon and energy. Several degradation pathways have been proposed and the related enzymes and genes have also been characterized. Many reviews have been reviewed toxicity of monocyclic aromatic amines; however, there is lack of review on biodegradation of monocyclic aromatic amines. The aim of this review is to summarize bacterial degradation of monocyclic aromatic amines. This review will increase our current understanding of biochemical and molecular basis of bacterial degradation of monocyclic aromatic amines.

Degradation of p-chloroaniline by FeO3−xH3−2x/Fe0 in the presence of persulfate in aqueous solution

Sulfate radical based advanced oxidation processes are promising techniques for the removal of organic compounds in aqueous solutions.

Spatial heterogeneity in degradation characteristics and microbial community composition of pesticide biopurification systems

AIMS

To investigate spatial and temporal differences in degradation characteristics and microbial community composition of pesticide biopurification systems.

METHODS AND RESULTS

Pilot-scale biofilters were supplemented with the potato-sprouting suppressant chloropropham. Two biofilters were inoculated with a chloropropham-degrading mixed culture, while the other two were not inoculated. Biodegradation rate, size and composition of the microbial community were monitored during 72 days at different biofilter depths. First of all, results showed that inoculation was not necessary to obtain efficient degradation although it shortens the biofilter's start-up period. Secondly, a higher biodegradation rate and chloropropham- and 3-chloroaniline-degrading microbial community size could be seen in the top part of the inoculated as well as the noninoculated biofilters. Finally, analysis of the microbial community composition shows that no clear spatial stratification of the microbial community could be found in any biofilter. However, the microbial diversity increases over time in all biofilters and on all biofilter depths, suggesting that during the time of the experiment, the biofilters develop a broad carrying capacity in which a genetically very diverse range of chloropropham- and 3-chloroaniline-degrading species can thrive.

CONCLUSIONS

In this study, a vertical gradient of the chloropropham- and 3-chloroaniline-degrading community composition, in terms of density and temporal and spatial diversity, was clearly established and was directly connected to a vertical gradient of chloropropham biodegradation activity.

SIGNIFICANCE AND IMPACT OF THE STUDY

The major part of degradation activity takes place in the top part of the biofilter, suggesting that it could be possible to use shorter biofilter reactors or higher loading rates to treat chloropropham waste streams, making this type of bioremediation technique economically more feasible.

Aerobic degradation study of three fluoroanilines and microbial community analysis: the effects of increased fluorine substitution

The fate of fluorinated compounds in the environment, especially polyfluorinated aromatics, is a matter of great concern. In this work, 4-Fluoroaniline (4-FA), 2,4-Difluoroanilines (2,4-DFA), and 2,3,4-Trifluoroanilines (2,3,4-TFA), were chosen as the target pollutants to study their biodegradability under aerobic conditions. The required enriched time of the mixed bacterial culture for degrading 4-FA, 2,4-DFA, and 2,3,4-TFA was 26, 51, and 165 days, respectively, which suggested that the longer enrichment time was required with the increase of fluorine substitution. At the initial concentrations of 100-200 mg L(-1), the 4-FA, 2,4-DFA, and 2,3,4-TFA could be degraded completely by the mixed bacterial culture. The maximum specific degradation rates of 4-FA, 2,4-DFA, and 2,3,4-TFA were 22.48 ± 0.55, 15.27 ± 2.04, and 8.84 ± 0.93 mg FA (g VSS h)(-1), respectively. Also, the three FAs enriched cultures showed certain potential of degrading other two FAs. The results from enzyme assay suggested the expression of meta-cleavage pathways during three FAs degradation. The denaturing gradient gel electrophoresis analysis revealed that unique bacterial communities were formed after FAs enrichment and these were principally composed of β-Proteobacteria, Oscillatoriophycideae, δ-Proteobacteria, α-Proteobacteria, Thermales, Xanthomonadales, Deinococci, Flavobacteriia, and Actinobacteridae. The Shannon-Wiener indexes in three FAs enriched culture decreased with the increase of fluorine substitution, indicating the significant effect of fluorine substitution on the microbial diversity. These findings supply important information on the fate of three FAs under aerobic environment, and the bacterial communities in their degradation systems.

Isolation, identification and characterization of a novel Ralstonia sp. FD-1, capable of degrading 4-fluoroaniline

A gram-negative strain, designated as FD-1, isolated from aerobic activated sludge was capable of metabolizing 4-fluoroaniline (4-FA) as its sole carbon and nitrogen source and energy supply. According to the Biolog GNIII detection method 17 of 71 carbon substrates were easily utilized, while 12 of 23 substrates did not inhibit strain FD-1. The 16S rDNA sequence from strain FD-1 was 99 % similar to Ralstonia sp., suggesting that it belonged to the genus Ralstonia. The optimal conditions for growth and 4-FA degradation were pH 7 and 30 °C. The tolerance to 4-FA were 1,250 mg/L, while the tolerance to salinity was 15 g/L. Catechol 2,3-dioxygenase activity was detected and degradation intermediates were analyzed by liquid chromatography mass spectrometry leading to a proposed degradation pathway and suggesting that extradiol cleavage was involved in 4-FA degradation. This is the first report on the degradation of 4-FA by a bacterium from the Ralstonia genus.

Bacterial pyridine hydroxylation is ubiquitous in environment

Ten phenol-degrading bacterial strains were isolated from three geographically distant environments. Five of them, identified as Diaphorobacter, Acidovorax, Acinetobacter (two strains), and Corynebacterium, could additionally transform pyridine, through the transcription of phenol hydroxylase genes induced both by phenol and pyridine. HPLC-UV and LC-MS analyses indicated that one metabolite (m/e = 96.07) with the same molecular weight as monohydroxylated pyridine was produced from the five phenol-degrading strains, when pyridine was the sole carbon source. Phenol (50 mg l(-1)) could initially inhibit and later stimulate the pyridine transformation. In addition, heterologous expression of the phenol hydroxylase gene (pheKLMNOP) resulted in the detection of monohydroxylated pyridine, which confirmed the phenol hydroxylase could catalyze pyridine hydroxylation. Phylogeny of the phenol hydroxylase genes revealed that the genes from the five pyridine-hydroxylating strains form a clade with each other and with those catalyzing the hydroxylation of phenol, BTEX (acronym of benzene, toluene, ethylbenzene, and xylene), and trichloroethylene. These results suggest that pyridine transformation via hydroxylation by phenol hydroxylase may be prevalent in environments than expected.

Simultaneous degradation of phenol and n-hexadecane by Acinetobacter strains

Three phenol- and alkanes-degrading bacterial strains were isolated from a freshwater sample. Upon the 16S rRNA gene analysis, phenotype and physiological features, the three strains were designated as Acinetobacter sp. with both phenol hydroxylase gene (phe) and alkane monooxygenase gene (alkM) detected. They could simultaneously degrade phenol and n-hexadecane for growth, but prefer phenol than n-hexadecane. Between phenol (400mgl(-1)) and n-hexadecane (400mgl(-1)), n-hexadecane enhanced phenol degradation in mineral salt medium (MSM), while phenol affects negatively the n-hexadecane degradation. However, combination of phenol (400mgl(-1)) and n-hexadecane (400mgl(-1)) in MSM led to higher growth of the strains than the phenol and n-hexadecane separately. The transcription levels of phe and alkM genes supported the physiological properties of the strains.

Planktonic versus biofilm catabolic communities: importance of the biofilm for species selection and pesticide degradation

Chloropropham-degrading cultures were obtained from sludge and soil samples by using two different enrichment techniques: (i) planktonic enrichments in shaken liquid medium and (ii) biofilm enrichments on two types of solid matrixes (plastic chips and gravel). Denaturing gradient gel electrophoresis fingerprinting showed that planktonic and biofilm cultures had a different community composition depending on the presence and type of added solid matrix during enrichment. This was reflected in the unique chloropropham-degrading species that could be isolated from the different cultures. Planktonic and biofilm cultures also differed in chloropropham-degrading activity. With biofilm cultures, slower chloropropham removal was observed, but with less build-up of the toxic intermediate 3-chloroaniline. Disruption of the biofilm architecture resulted in degradation characteristics shifting toward those of the free suspensions, indicating the importance of a well-established biofilm structure for good performance. These results show that biofilm-mediated enrichment techniques can be used to select for pollutant-degrading microorganisms that like to proliferate in a biofilm and that cannot be isolated using conventional shaken-liquid procedures. Furthermore, the influence of the biofilm architecture on the pesticide degradation characteristics suggests that for bioaugmentation the use of biofilm catabolic communities might be a proficient alternative to using planktonic freely suspended cultures.