Degradation of mixtures of phenolic compounds by Arthrobacter chlorophenolicus A6

Complete genome sequence of Arthrobacter sp. KFRI-F3372, a strain isolated from Korean soybean paste Doenjang

Arthrobacter sp. KFRI-F3372 is a Gram-positive bacterium with a high G + C content of 65.7%, which was isolated from Doenjang, a traditional Korean fermented soybean paste. In this report, we introduce the complete genome sequence of Arthrobacter sp. KFRI-F3372.

Phenol Degradation by Pseudarthrobacter phenanthrenivorans Sphe3

Phenol poses a threat as one of the most important industrial environmental pollutants that must be removed before disposal. Biodegradation is a cost-effective and environmentally friendly approach for phenol removal. This work aimed at studying phenol degradation by Pseudarthrobacter phenanthrenivorans Sphe3 cells and also, investigating the pathway used by the bacterium for phenol catabolism. Moreover, alginate-immobilized Sphe3 cells were studied in terms of phenol degradation efficiency compared to free cells. Sphe3 was found to be capable of growing in the presence of phenol as the sole source of carbon and energy, at concentrations up to 1500 mg/L. According to qPCR findings, both pathways of ortho- and meta-cleavage of catechol are active, however, enzymatic assays and intermediate products identification support the predominance of the ortho-metabolic pathway for phenol degradation. Alginate-entrapped Sphe3 cells completely degraded 1000 mg/L phenol after 192 h, even though phenol catabolism proceeds slower in the first 24 h compared to free cells. Immobilized Sphe3 cells retain phenol-degrading capacity even after 30 days of storage and also can be reused for at least five cycles retaining more than 75% of the original phenol-catabolizing capacity.

Transcriptional response of the xerotolerant Arthrobacter sp. Helios strain to PEG-induced drought stress

A new bacterial strain has been isolated from the microbiome of solar panels and classified as Arthrobacter sp. Helios according to its 16S rDNA, positioning it in the “Arthrobacter citreus group.” The isolated strain is highly tolerant to desiccation, UV radiation and to the presence of metals and metalloids, while it is motile and capable of growing in a variety of carbon sources. These characteristics, together with observation that Arthrobacter sp. Helios seems to be permanently prepared to handle the desiccation stress, make it very versatile and give it a great potential to use it as a biotechnological chassis. The new strain genome has been sequenced and its analysis revealed that it is extremely well poised to respond to environmental stresses. We have analyzed the transcriptional response of this strain to PEG6000-mediated arid stress to investigate the desiccation resistance mechanism. Most of the induced genes participate in cellular homeostasis such as ion and osmolyte transport and iron scavenging. Moreover, the greatest induction has been found in a gene cluster responsible for biogenic amine catabolism, suggesting their involvement in the desiccation resistance mechanism in this bacterium.

Co-metabolic biodegradation of 4-bromophenol in a mixture of pollutants system by Arthrobacter chlorophenolicus A6

Brominated phenols are listed as priority pollutants together with nitrophenol and chlorophenol are the key components of paper pulp wastewater. However, the biodegradation of bromophenol in a mixed substrate system is very scanty. In the present investigation, simultaneous biodegradation kinetics of three substituted phenols 4-bromophenol (4-BP), 4-nitrophenol (4-NP), and 4-chlorophenol (4-CP) were investigated using Arthrobacter chlorophenolicus A6. A 2³ full factorial design was applied with varying 4-BP and 4-CP from 75-125 mg/L and 4-NP from 50-100 mg/L. Almost complete degradation of this mixture of substituted phenols was achieved at initial concentration combinations of 125, 125, and 100 mg/L of 4-CP, 4-BP, and 4-NP, respectively, in 68 h. Statistical analysis of the results revealed that, among the three variables, 4-NP had the most prominent influence on the degradation of both 4-CP and 4-BP, while the concentration of 4-CP had a strong negative interaction effect on the biodegradation of 4-NP. Irrespective of the concentration levels of these three substrates, 4-NP was preferentially biodegraded over 4-CP and 4-BP. Furthermore, 4-BP biodegradation rates were found to be higher than those of 4-CP, followed by 4-NP. Besides, the variation of the biomass yield coefficient of the culture was investigated at different initial concentration combinations of these substituted phenols. Although the actinomycetes consumed 4-NP at a faster rate, the biomass yield was very poor. This revealed that the microbial cells were more stressed when grown on 4-NP compared to 4-BP and 4-CP. Overall, this study revealed the potential of A. chlorophenolicus A6 for the degradation of 4-BP in mixed substrate systems.

Linking genomic and physiological characteristics of psychrophilic Arthrobacter to metagenomic data to explain global environmental distribution

BACKGROUND

Microorganisms drive critical global biogeochemical cycles and dominate the biomass in Earth's expansive cold biosphere. Determining the genomic traits that enable psychrophiles to grow in cold environments informs about their physiology and adaptive responses. However, defining important genomic traits of psychrophiles has proven difficult, with the ability to extrapolate genomic knowledge to environmental relevance proving even more difficult.

RESULTS

Here we examined the bacterial genus Arthrobacter and, assisted by genome sequences of new Tibetan Plateau isolates, defined a new clade, Group C, that represents isolates from polar and alpine environments. Group C had a superior ability to grow at -1°C and possessed genome G+C content, amino acid composition, predicted protein stability, and functional capacities (e.g., sulfur metabolism and mycothiol biosynthesis) that distinguished it from non-polar or alpine Group A Arthrobacter. Interrogation of nearly 1000 metagenomes identified an over-representation of Group C in Canadian permafrost communities from a simulated spring-thaw experiment, indicative of niche adaptation, and an under-representation of Group A in all polar and alpine samples, indicative of a general response to environmental temperature.

CONCLUSION

The findings illustrate a capacity to define genomic markers of specific taxa that potentially have value for environmental monitoring of cold environments, including environmental change arising from anthropogenic impact. More broadly, the study illustrates the challenges involved in extrapolating from genomic and physiological data to an environmental setting. Video Abstract.

Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation

BACKGROUND

The Arthrobacter group is a known set of bacteria from cold regions, the species of which are highly likely to play diverse roles at low temperatures. However, their survival mechanisms in cold regions such as Antarctica are not yet fully understood. In this study, we compared the genomes of 16 strains within the Arthrobacter group, including strain PAMC25564, to identify genomic features that help it to survive in the cold environment.

RESULTS

Using 16 S rRNA sequence analysis, we found and identified a species of Arthrobacter isolated from cryoconite. We designated it as strain PAMC25564 and elucidated its complete genome sequence. The genome of PAMC25564 is composed of a circular chromosome of 4,170,970 bp with a GC content of 66.74 % and is predicted to include 3,829 genes of which 3,613 are protein coding, 147 are pseudogenes, 15 are rRNA coding, and 51 are tRNA coding. In addition, we provide insight into the redundancy of the genes using comparative genomics and suggest that PAMC25564 has glycogen and trehalose metabolism pathways (biosynthesis and degradation) associated with carbohydrate active enzyme (CAZymes). We also explain how the PAMC26654 produces energy in an extreme environment, wherein it utilizes polysaccharide or carbohydrate degradation as a source of energy. The genetic pattern analysis of CAZymes in cold-adapted bacteria can help to determine how they adapt and survive in such environments.

CONCLUSIONS

We have characterized the complete Arthrobacter sp. PAMC25564 genome and used comparative analysis to provide insight into the redundancy of its CAZymes for potential cold adaptation. This provides a foundation to understanding how the Arthrobacter strain produces energy in an extreme environment, which is by way of CAZymes, consistent with reports on the use of these specialized enzymes in cold environments. Knowledge of glycogen metabolism and cold adaptation mechanisms in Arthrobacter species may promote in-depth research and subsequent application in low-temperature biotechnology.

The impact of calcium peroxide on groundwater bacterial diversity during naphthalene removal by permeable reactive barrier (PRB)

Oxygen-releasing compounds (ORCs) have recently gained much attention in contaminated groundwater remediation. We investigated the impact of calcium peroxide nanoparticles on the groundwater indigenous bacteria in a bioremediation process by permeable reactive barrier (PRB). Three sand-packed columns were applied, including (1) control column (fresh groundwater), (2) natural remediation column (contaminated groundwater), and (3) biostimulation column (contaminated groundwater amended with CaO₂). Actinobacteria and Proteobacteria constituted the main phyla among the identified isolates. According to the results of next-generation sequencing, Proteobacteria was the dominant phylum (81% relative abundance) in the natural remediation condition. But, it was declined to 38.1% in the biostimulation column. Meanwhile, the abundance of Actinobacteria and Bacteroidetes were increased to 25.9% and 15.4%, respectively, by exposing the groundwater microbial structure to CaO₂ nanoparticles. Furthermore, orders Chlamydiales, Nitrospirales, and Oceanospirillales existing in the control column were detected in the presence of naphthalene. Shannon index was 4.32 for the control column samples, while it was reduced to 2.73 and 2.00 in the natural and biostimulation columns, respectively. Therefore, the present study provides a considerable insight into the impact of ORCs on the groundwater microbial community during the bioremediation process.

Biodegradation of persistent environmental pollutants by Arthrobacter sp

Persistent environmental pollutants are a growing problem around the world. The effective control of the pollutants is of great significance for human health. Some microbes, especially Arthrobacter, can degrade pollutants into nontoxic substances in various ways. Here, we review the biological properties of Arthrobacter adapting to a variety of environmental stresses, including starvation, hypertonic and hypotonic condition, oxidative stress, heavy metal stress, and low-temperature stress. Furthermore, we categorized the Arthrobacter species that can degrade triazines, organophosphorus, alkaloids, benzene, and its derivatives. Metabolic pathways behind the various biodegradation processes are further discussed. This review will be a helpful reference for comprehensive utilization of Arthrobacter species to tackle environmental pollutants.

4-Chlorophenol biodegradation facilitator composed of recombinant multi-biocatalysts immobilized onto montmorillonite

A biodegradation facilitator which catalyzes the initial steps of 4-chlorophenol (4-CP) oxidation was prepared by immobilizing multiple enzymes (monooxygenase, CphC-I and dioxygenase, CphA-I) onto a natural inorganic support. The enzymes were obtained via overexpression and purification after cloning the corresponding genes (cphC-I and cphA-I) from Arthrobacter chlorophenolicus A6. Then, the recombinant CphC-I was immobilized onto fulvic acid-activated montmorillonite. The immobilization yield was 60%, and the high enzyme activity (82.6%) was retained after immobilization. Kinetic analysis indicated that the Michaelis-Menten model parameters for the immobilized CphC-I were similar to those for the free enzyme. The enzyme stability was markedly enhanced after immobilization. The immobilized enzyme exhibited a high level of activity even after repetitive use (84.7%) and powdering (65.8%). 4-CP was sequentially oxidized by a multiple enzyme complex, comprising the immobilized CphC-I and CphA-I, via the hydroquinone pathway: oxidative transformation of 4-CP to hydroxyquinol followed by ring fission of hydroxyquinol.

Formulation and stabilization of an Arthrobacter strain with good storage stability and 4-chlorophenol-degradation activity for bioremediation

Chlorophenols are widespread and of environmental concern due to their toxic and carcinogenic properties. Development of less costly and less technically challenging remediation methods are needed; therefore, we developed a formulation based on micronized vermiculite that, when air-dried, resulted in a granular product containing the 4-chlorophenol (4-CP)-degrading Gram-positive bacterium Arthrobacter chlorophenolicus A6. This formulation and stabilization method yielded survival rates of about 60% that remained stable in storage for at least 3 months at 4 °C. The 4-CP degradation by the formulated and desiccated A. chlorophenolicus A6 cells was compared to that of freshly grown cells in controlled-environment soil microcosms. The stabilized cells degraded 4-CP equally efficient as freshly grown cells in two different set-ups using both hygienized and non-treated soils. The desiccated microbial product was successfully employed in an outdoor pot trial showing its effectiveness under more realistic environmental conditions. No significant phytoremediation effects on 4-CP degradation were observed in the outdoor pot experiment. The 4-CP degradation kinetics from both the microcosms and the outdoor pot trial were used to generate a predictive model of 4-CP biodegradation potentially useful for larger-scale operations, enabling better bioremediation set-ups and saving of resources. This study also opens up the possibility of formulating and stabilizing also other Arthrobacter strains possessing different desirable pollutant-degrading capabilities.

The response of soil Arthrobacter agilis lush13 to changing conditions: Transition between vegetative and dormant state

This work was aimed at studying the response of soil non-spore-forming actinobacterial strain Arthrobacter agilis Lush 13 to changing natural conditions, such as nutrient availability and the presence of degradable and recalcitrant aliphatic and aromatic substrates. The A. agilis strain Lush13 was able to degrade octane, nonane, hexadecane, benzoate, phenol, and 2,3-, 2,4-, 2,5-, 2,6-dichlorophenols, but not grew on 3,4-dichlorophenol, 2,3,4-, 2,4,5-, 2,4,6-trichlorophenol (TCP), pentachlorophenol (PCP), 2-chlorobenzoate, 3-chlorobenzoate, 3,5-dichlorobenzoate, 2,4-dichlorobenzoate. Under growth-arresting conditions due to nitrogen- or multiple starvation or recalcitrant (non-utilizable) carbon source, the studied strain preserved viability for prolonged periods (4-24 months) due to transition to dormancy in the form of conglomerated small and ultrasmall cyst-like dormant cells (CLC). Dormant cells were shown to germinate rapidly (30 min or later) after removal of starvation stress, and this process was followed by breakdown of conglomerates with the eliberation and further division of small multiple actively growing daughter cells. Results of this study shed some light to adaptive capabilities of soil arthrobacters in pure and polluted environments.

Effects of Soil Pre-Treatment with Basamid® Granules, Brassica juncea, Raphanus sativus, and Tagetes patula on Bacterial and Fungal Communities at Two Apple Replant Disease Sites

Nurseries producing apple and rose rootstock plants, apple orchards as well as rose production often experience replanting problems after several cultivations at the same site when a chemical soil disinfectant is not applied. The etiology of apple and rose replanting problems is most likely caused by soil-borne pathogen complex, defined as "replant disease (RD)". Symptoms typical of RD are reduced shoot and root growth, a smaller leaf area, a significant decrease in plant biomass, yield and fruit quality and a shorter life span. In our previous study, we showed that RD symptoms were reduced when apple rootstock M106 were grown in RD soils treated either with the soil fumigant Basamid or after biofumigation by incorporating Brassica juncea or Raphanus sativus or by growing Tagetes under field conditions compared to untreated control soil. The present study aimed at identifying potential bacterial and fungal taxa that were affected by different soil treatments and linking bacterial and fungal responders to plant performance. Miseq® Illumina® sequencing of 16S rRNA gene fragments (bacteria) and ITS regions (fungi) amplified from total community DNA extracted from soil samples taken 4 weeks after treatments were performed. Soil properties and culture history of the two RD sites greatly influenced soil microbiomes. Several bacterial genera were identified that significantly increased in treated soils such as Arthrobacter (R. sativus, both sites), Curtobacterium (Basamid, both sites), Terrimonas (Basamid and R. sativus, site A) and Ferruginibacter (B. juncea, site K and R. sativus, site A) that were also significantly and positively correlated with growth of apple M106 plants. Only few fungal genera, such as Podospora, Monographella and Mucor, were significantly promoted in soils treated with B. juncea and R. sativus (both sites). The least pronounced changes were recorded for bacterial as well as fungal communities in the RD soils planted with Tagetes. The detection of bacterial and fungal genera that were significantly increased in relative abundance in response to the treatments and that were positively correlated with plant growth suggests that management of the soil microbial community could contribute to overcome the apple RD encountered at affected sites.

Bioaugmentation: an effective commercial technology for the removal of phenols from wastewater

Phenol represents a huge problem in industrial wastewater effluents and needs to be removed due to its toxic and carcinogenic nature. The removal of phenol from the wastewater is often both expensive and time consuming; there is therefore a requirement for a more effective, sustainable solution for the removal of phenol from wastewaters. Bioaugmentation or the addition of phenol degrading microorganisms to contaminated effluents is one such sustainable approach being considered. Here, we describe how bioaugmentation has been applied for the biological treatment of phenol in industrial wastewaters.

Complete genome sequence of a psychotrophic Pseudarthrobacter sulfonivorans strain Ar51 (CGMCC 4.7316), a novel crude oil and multi benzene compounds degradation strain

Pseudarthrobacter sulfonivorans strain Ar51, a psychotrophic bacterium isolated from the Tibet permafrost of China, can degrade crude oil and multi benzene compounds efficiently in low temperature. Here we report the complete genome sequence of this bacterium. The complete genome sequence of Pseudarthrobacter sulfonivorans strain Ar51, consisting of a cycle chromosome with a size of 5.04Mbp and a cycle plasmid with a size of 12.39kbp. The availability of this genome sequence allows us to investigate the genetic basis of crude oil degradation and adaptation to growth in a nutrient-poor permafrost environment.

Optimization study of 2-hydroxyquinoxaline (2-HQ) biodegradation by Ochrobactrum sp. HQ1

A novel aerobic gram-negative bacterial strain capable of utilizing 2-hydroxyquinoxaline (2-HQ) as sole source of carbon and energy was isolated from Indian agricultural soil and named as HQ1. Strain HQ1 was identified as Ochrobactrum sp. on the basis of morphology, physico-biochemical characteristics and 16S rRNA sequence analysis. The generation time of Ochrobactrum sp. HQ1 on 2-HQ at log phase is 0.71 h or 42.6 min. The degradation of 2-HQ by HQ1 under various physico-chemical parameters was analysed by HPLC and observed to be optimum with a high inoculum density (1.0 OD) at pH 7–8, temperatures 37–40°C and a high concentration of 2-HQ (500 ppm). Degradation of 2-HQ was also improved when additional nitrogen sources were used and this was attributed to the enhanced growth of the bacterium on the readily available nitrogen sources. Analysis of 2-HQ degradation by GC–MS resulted in elucidation of the degradation pathway for HQ1, a novel observation for aerobic Gram-negative bacteria. These findings are a possible indication of the application of HQ1 in the bioremediation of pesticide/metabolite contamination.

Complete genome sequence of a psychotrophic Arthrobacter strain A3 (CGMCC 1.8987), a novel long-chain hydrocarbons producer

Arthrobacter strain A3, a psychotrophic bacterium isolated from the Tian Shan Mountain of China, can degrade the cellulose and synthesis the long-chain hydrocarbons efficiently in low temperature. Here we report the complete genome sequence of this bacterium. The complete genome sequence of Arthrobacter strain A3, consisting of a cycle chromosome with a size of 4.26 Mbp and a cycle plasmid with a size of 194kbp. In this genome, a hydrocarbon biosynthesis gene cluster (oleA, oleB/oleC and oleD) was identified. To resistant the extreme environment, this strain contains a unique mycothiol-biosynthetic pathway (mshA-D), which has not been found in other Arthrobacter species before. The availability of this genome sequence allows us to investigate the genetic basis of adaptation to growth in a nutrient-poor permafrost environment and to evaluate of the biofuel-synthetic potential of this species.

Complete Genome Sequence of Arthrobacter sp. Strain LS16, Isolated from Agricultural Soils with Potential for Applications in Bioremediation and Bioproducts

Here we report the complete genomic sequence of the bacterium Arthrobacter sp. strain LS16, consisting of a single circular chromosome of 3.85 Mb with no identified plasmid. Data contained within will facilitate future genetic modification and engineering of the Arthrobacter sp. LS16 metabolic network to enhance traits relevant to bioremediation and bioproducts.

Biodegradation of 2-hydroxyquinoxaline (2-HQ) by Bacillus sp

An aerobic Gram +ve bacterial strain capable of utilizing 2-Hydroxyquinoxaline (2-HQ) as sole source of carbon and energy was isolated from Chrysanthemum indicum Indian agricultural soil and named as HQ2. On the basis of morphology, physico-biochemical characteristics and 16S rRNA sequence analysis, strain HQ2 was identified as Bacillus sp. The generation time of Bacillus sp. in log phase during growth on 2-HQ is 0.79 h or 47.4 min. The optimal conditions for 2-HQ degradation by Bacillus sp. were inoculum density of 1.0 OD, pH of 6-8, temperature of 37-45 °C and 2-HQ concentration of 500 ppm. Among the additional carbon and nitrogen sources, carbon sources did not influence the degradation rate of 2-HQ, but nitrogen sources-yeast extract marginally enhanced the rate of degradation of 2-HQ. GC-MS analysis of the culture Bacillus sp. grown on 2-HQ indicated the formation of dimers from 2 molecules of 2-hydroxyquinoxaline. The formation of dimer for degradation of 2-HQ by the culture appears to be the first report to our scientific knowledge.

Bacterial degradation of nitrophenols and their derivatives

This review intends to provide an overview of bacterial degradation of nitrophenols (NPs) and their derivatives. The main scientific focus is on biochemical and genetic characterization of bacterial degradation of NPs. Other aspects such as bioremediation and chemotaxis correlated with biodegradation of NPs are also discussed. This review will increase our current understanding of bacterial degradation of NPs and their derivatives.

Bioaugmentation of biological contact oxidation reactor (BCOR) with phenol-degrading bacteria for coal gasification wastewater (CGW) treatment

This study was conducted to evaluate the performance of the biological contact oxidation reactor (BCOR) treating coal gasification wastewater (CGW) after augmented with phenol degrading bacteria (PDB). The PDB were isolated with phenol, 4-methyl phenol, 3,5-dimethyl phenol and resorcinol as carbon resources. Much of the refractory phenolic compounds were converted into easily-biodegradable compounds in spite of low TOC removal. The bioaugmentation with PDB significantly enhanced the removal of COD, total phenols (TP) and NH3-N, with efficiencies from 58% to 78%, 66% to 80%, and 5% to 25%, respectively. In addition, the augmented BCOR exhibited strong recovery capability in TP and COD removal while recovery of NH3-N removal needed longer time. Microbial community analysis revealed that the PDB presented as dominant populations in the bacteria consortia, which in turn determined the overall performance of the system.

Biodegradation of 4-bromophenol by Arthrobacter chlorophenolicus A6 in batch shake flasks and in a continuously operated packed bed reactor

The present study investigated growth and biodegradation of 4-bromophenol (4-BP) by Arthrobacter chlorophenolicus A6 in batch shake flasks as well as in a continuously operated packed bed reactor (PBR). Batch growth kinetics of A. chlorophenolicus A6 in presence of 4-BP followed substrate inhibition kinetics with the estimated biokinetic parameters value of μ max = 0.246 h(-1), K i = 111 mg L(-1), K s  = 30.77 mg L(-1) and K = 100 mg L(-1). In addition, variations in the observed and theoretical biomass yield coefficient and maintenance energy of the culture were investigated at different initial 4-BP concentration. Results indicates that the toxicity tolerance and the biomass yield of A. chlorophenolicus A6 towards 4-BP was found to be poor as the organism utilized the substrate mainly for its metabolic maintenance energy. Further, 4-BP biodegradation performance by the microorganism was evaluated in a continuously operated PBR by varying the influent concentration and hydraulic retention time in the ranges 400-1,200 mg L(-1) and 24-7.5 h, respectively. Complete removal of 4-BP was achieved in the PBR up to a loading rate of 2,276 mg L(-1) day(-1).

Draft Genome Sequence of the 2-Chloro-4-Nitrophenol-Degrading Bacterium Arthrobacter sp. Strain SJCon

We report the 4.39-Mb draft genome sequence of the 2-chloro-4-nitrophenol-degrading bacterium Arthrobacter sp. strain SJCon, isolated from a pesticide-contaminated site. The draft genome sequence of strain SJCon will be helpful in studying the genetic pathways involved in the degradation of several aromatic compounds.

Layer of organic pine forest soil on top of chlorophenol-contaminated mineral soil enhances contaminant degradation

Chlorophenols, like many other synthetic compounds, are persistent problem in industrial areas. These compounds are easily degraded in certain natural environments where the top soil is organic. Some studies suggest that mineral soil contaminated with organic compounds is rapidly remediated if it is mixed with organic soil. We hypothesized that organic soil with a high degradation capacity even on top of the contaminated mineral soil enhances degradation of recalcitrant chlorophenols in the mineral soil below. We first compared chlorophenol degradation in different soils by spiking pristine and pentachlorophenol-contaminated soils with 2,4,6-trichlorophenol in 10-L buckets. In other experiments, we covered contaminated mineral soil with organic pine forest soil. We also monitored in situ degradation on an old sawmill site where mineral soil was either left intact or covered with organic pine forest soil. 2,4,6-Trichlorophenol was rapidly degraded in organic pine forest soil, but the degradation was slower in other soils. If a thin layer of the pine forest humus was added on top of mineral sawmill soil, the original chlorophenol concentrations (high, ca. 70 μg g(-1), or moderate, ca. 20 μg g(-1)) in sawmill soil decreased by >40 % in 24 days. No degradation was noticed if the mineral soil was kept bare or if the covering humus soil layer was sterilized beforehand. Our results suggest that covering mineral soil with an organic soil layer is an efficient way to remediate recalcitrant chlorophenol contamination in mineral soils. The results of the field experiment are promising.

Influence of nutrient mixtures on p-nitrophenol degradation by Stenotrophomonas sp. isolated from groundwater

We isolated strain CERAR5, a Stenotrophomonas sp., from an aquifer contaminated with chlorinated hydrocarbons that utilizes up to 1.0 mM PNP within 62 h in M9 medium as a source of carbon and nitrogen. To assess the potential of this strain for use in bioremediation, we investigated the influence of external sources of carbon and nitrogen on bacterial degradation of PNP following a full factorial design analysis. Glucose, sodium acetate, phenol, sodium nitrate and ammonium chloride were the factors chosen, while per cent removal of PNP, growth of the bacterial strain, and change in pH of the medium were the responses measured. Glucose and acetate had significant positive influence on the removal PNP. In particular, acetate exhibited a significant positive effect on all the three responses measured, clearly suggesting that the addition of acetate greatly contributes to an efficient bioremediation of habitats contaminated with PNP by Stenotrophomonas sp. CERAR5.

Pollutant interactions during the biodegradation of phenolic mixtures with either 2- or 3-mononitrophenol in a continuously operated packed bed reactor

Pollutant interactions during the aerobic biodegradation of phenolic mixtures with either 2-nitrophenol (2-NP) or 3-nitrophenol (3-NP) by a NP-adapted microbial consortium in simulated wastewater were studied in a packed-bed bench scale bioreactor continuously operated in a flow mode. Phenol/2-NP and phenol/3-NP mixtures with varied phenol/nitrophenol ratios were shown to exhibit different biodegradability patterns. The presence of 2-NP led to a much lower overall elimination capacity and lower process stability in comparison to mixtures with 3-NP. In contrast to the expected greater degradation of a more biodegradable substrate in mixtures, phenol was degraded with a lower efficiency at higher phenol concentrations than NPs, although this difference became less pronounced with the gradual biofilm adaptation to phenol. This unusual substrate interaction, which appears to be common in the biotreatment of substituted phenol mixtures, was explained by prior biofilm adaptation to less degradable substrates, NPs. The biofilm composition was significantly altered during the long-term reactor operation. Although eukaryotes were not present in the inoculum, four fungal species were isolated from the biofilm after 1.5 years of operation. Of the initially present strains, only Chryseobacterium sp. and several Pseudomonas species persisted till the end of operation.

Branching of the p-nitrophenol (PNP) degradation pathway in burkholderia sp. Strain SJ98: Evidences from genetic characterization of PNP gene cluster

Aerobic microbial degradation of p-nitrophenol (PNP) has been classically shown to proceed via ‘Hydroquinone (HQ) pathway’ in Gram-negative bacteria, whereas in Gram-positive PNP degraders it proceed via ‘Benzenetriol (BT) pathway’. These pathways are characterized by the ring cleavage of HQ and BT as terminal aromatic intermediates respectively. Earlier reports on PNP degradation have indicated these pathways to be mutually exclusive. We report involvement of both ‘HQ’ and ‘BT’ ring cleavage pathways in PNP degradation by Burkholderia sp. strain SJ98. Genetic characterization of an ~41 Kb DNA fragment harboring PNP degradation gene cluster cloned and sequenced from strain SJ98 showed presence of multiple orfs including pnpC and pnpD which corresponded to previously characterized ‘benzenetriol-dioxygenase (BtD)’ and ‘maleylacetate reductase (MaR)’ respectively. This gene cluster also showed presence of pnpE1 and pnpE2, which shared strong sequence identity to cognate sub-units of ‘hydroquinone dioxygenase’ (HqD). Heterologous expression and biochemical characterization ascertained the identity of PnpE1 and PnpE2. In in vitro assay reconstituted heterotetrameric complex of PnpE1 and PnpE2 catalyzed transformation of hydroquinone (HQ) into corresponding hydroxymuconic semialdehyde (HMS) in a substrate specific manner. Together, these results clearly establish branching of PNP degradation in strain SJ98. We propose that strain SJ98 presents a useful model system for future studies on evolution of microbial degradation of PNP.

Treatment of substituted phenol mixtures in single phase and two-phase solid-liquid partitioning bioreactors

The biological treatment of phenolics is constrained by the inherent cytotoxicity of these compounds. One method to alleviate such toxicity is to add a sequestering phase to absorb, and subsequently release, the substrate(s) to the micro-organisms; such a system is termed a Two Phase Partitioning Bioreactor. Here we have compared the performance of a TPPB, relative to single phase operation, in which a small volume (5%, v/v) of beads of the polymer Hytrel 8206 was used to treat aqueous mixtures of 2,4-dimethylphenol and 4-nitrophenol. Hytrel 8206 was selected from a range of polymers that were tested for their partition coefficients (PCs) for the target molecules, with the more hydrophobic compound (2,4-dimethylphenol) having a higher PC value (201) than 4-nitrophenol (143). Significantly increased removal rates for both substrates were demonstrated in TPPB mode relative to single phase operation. Additionally, the differential release of the compounds to the aqueous phase and their distinct PC values changed the kinetic pattern of the biotreatment system, smoothing out the cellular oxygen demand. Release of the substrates by the polymer over 60 operating cycles was virtually complete (>97%) demonstrating the reusability and robustness of the use of polymers in overcoming cytotoxicity of phenolic substrates.

Biodegradation kinetics of 4-fluorocinnamic acid by a consortium of Arthrobacter and Ralstonia strains

Arthrobacter sp. strain G1 is able to grow on 4-fluorocinnamic acid (4-FCA) as sole carbon source. The organism converts 4-FCA into 4-fluorobenzoic acid (4-FBA) and utilizes the two-carbon side-chain for growth with some formation of 4-fluoroacetophenone as a dead-end side product. We also have isolated Ralstonia sp. strain H1, an organism that degrades 4-FBA. A consortium of strains G1 and H1 degraded 4-FCA with Monod kinetics during growth in batch and continuous cultures. Specific growth rates of strain G1 and specific degradation rates of 4-FCA were observed to follow substrate inhibition kinetics, which could be modeled using the kinetic models of Haldane–Andrew and Luong–Levenspiel. The mixed culture showed complete mineralization of 4-FCA with quantitative release of fluoride, both in batch and continuous cultures. Steady-state chemostat cultures that were exposed to shock loadings of substrate responded with rapid degradation and returned to steady-state in 10–15 h, indicating that the mixed culture provided a robust system for continuous 4-FCA degradation.

Modelling the pH dependence of the kinetics of aerobic p-nitrophenol biodegradation

There are a number of publications in the literature that might indicate a connection between pH and the kinetics of the aerobic p-nitrophenol (PNP) biodegradation. In this study two hypotheses were postulated to elucidate the kinetics dependence on pH: (i) the substrate inhibition does not depend on the pH value, therefore the half-saturation coefficient and the substrate inhibition constant will be the same at any pH and (ii) the substrate inhibition depends on the pH value, therefore the half-saturation coefficient and the substrate inhibition constant will have a different value depending on the pH. A PNP-degrading activated sludge was used to carry out three batch respirometric experiments at different pH values: 6.5±0.1, 7.0±0.1, 8.0±0.1. The ability to describe the experimental results with the kinetic models derived from both postulated hypotheses was quantitatively evaluated through the norm of the prediction error array. The time course of specific oxygen uptake rate and PNP concentration was satisfactorily described by a Haldane kinetics that includes the pH effect, based on the PNP acid-base equilibrium, on the kinetic parameters. The results suggest that the nonionised form of PNP is the real substrate and also the inhibitor of the aerobic PNP biodegradation.

Genomic heterogeneity within conservedmetabolic pathways of Arthrobacter species - a bioinformatic approach

A comparative genomic analysis of three species of the soil bacterium Arthrobacter was undertaken with specific emphasis on genes involved in important and core energy metabolism pathways like glycolysis and amino acid metabolism. During the course of this study, it was revealed that codon bias of a particular species, namely Arthrobacter aurescens TC1, is significantly lower than that of the other two species A. chlorophenolicus A6 and Arthrobacter sp. FB24. The codon bias was also found to be negatively correlated with gene expression level which is determined by computing codon adaptation index of the genes. Uniformity in codon usage pattern among three species is evident in terms of genes which has high codon bias and multifunctional nature. Further, it was observed that this trend is present amongst the genes of important metabolic pathways, such as glycolysis and amino acid metabolism. The evolutionary divergence of the pathway gene sequences was calculated and was found to be equivalent in nature in the case of Arthrobacter sp. FB24 and Arthrobacter chlorophenolicus A6, but turned out to be dissimilar in the case of Arthrobacter aurescens TC1. A strong correlation between synonymous substitution rate and effective codon number or Nc was also observed. These observations clearly point out that the genes having low bias, in Arthrobacter aurescens TC1, and even of those that are part of highly conserved metabolic pathways like glycolysis and amino acid ensemble pathways have undergone a different type of evolution and might be subjected to positive selection pressure in comparison with Arthrobacter sp. FB24 and Arthrobacter chlorophenolicus A6.

Isolation and characterization of Arthrobacter sp. HY2 capable of degrading a high concentration of p-nitrophenol

A soil bacterium strain, capable of using p-nitrophenol (PNP) as its sole source of carbon and energy, was isolated by enrichment on minimal salt medium (MSM). On the basis of a phylogenetic analysis of 16S rRNA gene sequences the bacterium is a species of Arthrobacter, closely related to Arthrobacter ureafaciens DSM 20126. This strain has an unusually high substrate tolerance for PNP degradation in MSM. Greatest degradation of PNP was observed at 30 degrees C and under slightly alkaline pH (pH 7-9) conditions. Effective degradation rates slowed as the concentration of PNP was increased. Addition of glucose from 0.1% to 0.5% generally enhanced the degradation of PNP at high concentration (400 mg/l) although acidification as a result of glucose metabolism had a negative effect on PNP depletion. Biodegradation of PNP at high concentration was greatly accelerated by beta-cyclodextrin at a concentration of 0.5%, indicating that beta-cyclodextrin could be a promising addictive for effective PNP bioremediation.

Impact of phenolic substrate and growth temperature on the Arthrobacter chlorophenolicus proteome

We compared the Arthrobacter chlorophenolicus proteome during growth on 4-chlorophenol, 4-nitrophenol, or phenol at 5 and 28 degrees C, both for the wild-type and a mutant strain with mass spectrometry based proteomics. A label-free workflow employing spectral counting identified 3749 proteins across all growth conditions, representing over 70% of the predicted genome and 739 of these proteins form the core proteome. Statistically significant differences were found in the proteomes of cells grown under different conditions including differentiation of hundreds of unknown proteins. The 4-chlorophenol-degradation pathway was confirmed, but not that for phenol.

Biodegradation of mixed phenolic compounds under high salt conditions and salinity fluctuations by Arthrobacter sp. W1

High salt concentration and salinity fluctuations in wastewater challenge the efficiency of microbial strains used for cleanup of pollutants. In this study, it was investigated that the new isolated Arthrobacter sp. W1 degraded mixed phenolic compounds under complex salt conditions. The results showed that Arthrobacter sp. W1 was able to utilize various phenolic compounds as carbon source under high salt conditions. It can degrade phenol and p-cresol mixture at 10% NaCl, although rates of degradation and cell growth were lower compared to 5% NaCl. The presence of trace p-cresol significantly inhibited phenol biodegradation. When salinity fluctuations were between 1% and 10% NaCl, strain W1 was able to degrade substrates and survived. It was also suggested that the presence of salts (i.e., NaCl, KCl, Na(2)SO(4), and K(2)SO(4)) had almost no effects on the microbial growth and biodegradation process. Therefore, Arthrobacter sp. W1 would be a promising candidate for bioremediation of phenolic compounds under complex salt conditions.