Microbial degradation of 2,4-dichlorophenoxyacetic acid: Insight into the enzymes and catabolic genes involved, their regulation and biotechnological implications

Enhanced removal of 2,4-dichlorophenol by a novel biotic-abiotic hybrid system based on zeolitic imidazolate framework-8

Biotic-abiotic hybrid systems have recently emerged as a potential technique for stable and efficient removal of persistent contaminants due to coupling of microbial catabolic with abiotic adsorption/redox processes. In this study, Burkholderia vietnamensis C09V (B.V.C09V) was successfully integrated with a Zeolitic Imidazolate Framework-8 (ZIF-8) to construct a state-of-art biotic-abiotic system using polyvinyl alcohol/ sodium alginate (PVA/SA) as media. The biotic-abiotic system (PVA/SA-ZIF-8 @B.V.C09V) was able to remove 99.0 % of 2,4-DCP within 168 h, which was much higher than either PVA/SA, PVA/SA-ZIF-8 or PVA/SA@B.V.C09V (53.8 %, 72.6 % and 67.2 %, respectively). Electrochemical techniques demonstrated that the carrier effect of PVA/SA and the driving effect of ZIF-8 collectively accelerated electron transfer processes associated with enzymatic reactions. In addition, quantitative-PCR (Q-PCR) revealed that ZIF-8 stimulated B.V.C09V to up-regulate expression of tfdB, tfdC, catA, and catC genes (2.40-, 1.68-, 1.58-, and 1.23-fold, respectively), which encoded the metabolism of related enzymes. Furthermore, the effect of key physical, chemical, and biological properties of PVA/SA-ZIF-8 @B.V.C09V on 2,4-DCP removal were statistically investigated by Spearman correlation analysis to identify the key factors that promoted synergistic removal of 2,4-DCP. Overall, this study has created an innovative new strategy for the sustainable remediation of 2,4-DCP in aquatic environments.

Semi-rational design of nitroarene dioxygenase for catalytic ability toward 2,4-dichloronitrobenzene

Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems.IMPORTANCEAs a result of human activities, various nitroaromatic pollutants continue to enter the biosphere with poor degradability, and dioxygenation is an important kickoff step to remove toxic nitro-groups and convert them into degradable products. The biodegradation of many nitroarenes has been reported over the decades; however, many others still lack corresponding enzymes to initiate their degradation. Although rieske non-heme dioxygenase family enzymes play extraordinarily important roles in the aerobic biodegradation of various nitroaromatic pollutants, prediction of their substrate specificity is difficult. This work greatly improved the catalytic activity of dioxygenase against 2,4-dichloronitrobenzene by computer-aided semi-rational design, paving a new way for the evolution strategy of nitroarene dioxygenase. This study highlights the potential for using enzyme structure-function information with computational pre-screening methods to rapidly tailor the catalytic functions of enzymes toward poorly biodegradable contaminants.

Enhanced Bacterium-Phage Symbiosis in Attached Microbial Aggregates on a Membrane Surface Facing Elevated Hydraulic Stress

Phages are increasingly recognized for their importance in microbial aggregates, including their influence on microbial ecosystem services and biotechnology applications. However, the adaptive strategies and ecological functions of phages in different aggregates remain largely unexplored. Herein, we used membrane bioreactors to investigate bacterium-phage interactions and related microbial functions within suspended and attached microbial aggregates (SMA vs AMA). SMA and AMA represent distinct microbial habitats where bacterial communities display distinct patterns in terms of dominant species, keystone species, and bacterial networks. However, bacteria and phages in both aggregates exhibited high lysogenicity, with 60% lysogenic phages in the virome and 70% lysogenic metagenome-assembled genomes of bacteria. Moreover, substantial phages exhibited broad host ranges (34% in SMA and 42% in AMA) and closely interacted with habitat generalist species (43% in SMA and 49% in AMA) as adaptive strategies in stressful operation environments. Following a mutualistic pattern, phage-carried auxiliary metabolic genes (pAMGs; 238 types in total) presumably contributed to the bacterial survival and aggregate stability. The SMA-pAMGs were mainly associated with energy metabolism, while the AMA-pAMGs were mainly associated with antioxidant biosynthesis and the synthesis of extracellular polymeric substances, representing habitat-dependent patterns. Overall, this study advanced our understanding of phage adaptive strategies in microbial aggregate habitats and emphasized the importance of bacterium-phage symbiosis in the stability of microbial aggregates.

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

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

Greener Method for the Application of TiO2 Nanoparticles to Remove Herbicide in Water

TiO₂ nanoparticles have emerged as a great photocatalyst to degrade organic contaminants in water; however, the nanoparticles dispersed in water could be difficult to be recovered and potentially become contaminant. Herbicide like 2,4-dichlorophenoxyacetic acid (2,4-D) used in agriculture usually ends up with a large fraction remaining in water and sediment, which may cause potential risk to human health and the ecosystem. This study proposes a greener method to utilize TiO₂ as photocatalyst to remove 2,4-D from water. Accordingly, TiO₂ nanoparticles (10-45 nm) were synthesized and grafted on lightweight fired clay to generate a TiO₂-based floating photocatalyst. Experimental testing revealed that 60.2% of 2,4-D (0.1 mM) can be decomposed in 250 min under UV light with TiO₂-grafted lightweight fired clay floating on water. Degradation fits well into the pseudo-first-order kinetic model. The floating photocatalysts can degrade approximately 50% 2,4-D in 250 min under sunlight and the degradation efficiency is stable for cycles. The results revealed that the fabrication of floating photocatalyst could be a promising and greener way to remove herbicide contaminants in water using TiO₂.

Synthesizing Laboratory and Field Experiments to Quantify Dominant Transformation Mechanisms of 2,4-Dichlorophenoxyacetic Acid (2,4-D) in Aquatic Environments

Laboratory studies used to assess the environmental fate of organic chemicals such as pesticides fail to replicate environmental conditions, resulting in large errors in predicted transformation rates. We combine laboratory and field data to identify the dominant loss processes of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) in lakes for the first time. Microbial and photochemical degradation are individually assessed using laboratory-based microcosms and irradiation studies, respectively. Field campaigns are conducted in six lakes to quantify 2,4-D loss following large-scale herbicide treatments. Irradiation studies show that 2,4-D undergoes direct photodegradation, but modeling efforts demonstrated that this process is negligible under environmental conditions. Microcosms constructed using field inocula show that sediment microbial communities are responsible for degradation of 2,4-D in lakes. Attempts to quantify transformation products are unsuccessful in both laboratory and field studies, suggesting that their persistence is not a major concern. The synthesis of laboratory and field experiments is used to demonstrate best practices in designing laboratory persistence studies and in using those results to mechanistically predict contaminant fate in complex aquatic environments.

Managing gene expression in Pseudomonas simiae EGD-AQ6 for chloroaromatic compound degradation

Pseudomonas simiae EGD-AQ6 is capable of utilizing chloroaromatic compound i.e., 2-4-D efficiently in its biofilm phenotype. The differential accumulation of intermediate 4-chlorocatechol rates were significant in planktonic and biofilm phenotypes, as well as in the  increased biofilm adapted cell numbers. Interestingly, response surface analysis demonstrated the combined positive effects of 2-4-D degradation and 4-CCA accumulation rates and the gene expression profiles, with significant up-regulation of degradative and biofilm genes, and greater participation of pellicle genes in the biofilm phenotypes than their planktonic counterparts, thereby revealing a phenotype variation. It positively validated the physiological data. Furthermore, the sequence similarity of the 2-4-D catabolic and biofilm-forming proteins (pel ABCDEFG and pga ABCD), which are responsible for building carbohydrate rich extracellular matrix, were significant with the respective organisms. This is the first study, which endorses this strain to be unique in efficient chloro-aromatic degradation through phenotype variation, thereby proving a potential candidate in the improvement of bioremediation technologies.

The effect of the pesticide delivery method on the microbial community of field soil

The study deals with the effects of herbicides (metribuzin, tribenuron-methyl, fenoxaprop-P-ethyl) and fungicides (tebuconazole, epoxiconazole, azoxystrobin) applied to soil as free pesticides or as slow release formulations embedded in a biodegradable composite matrix on the structure of the soil microbial community. The matrix consisted of a natural biopolymer poly-3-hydroxybutyrate [P(3HB)] and a filler-one of the natural materials (peat, clay, and wood flour). The soil microbial community was characterized, including the major eco-trophic groups of bacteria, dominant taxa of bacteria and fungi, and primary P(3HB)-degrading microorganisms, such as Pseudomonas, Bacillus, Pseudarthrobacter, Streptomyces, Penicillium, and Talaromyces. The addition of free pesticides adversely affected the abundance of soil microorganisms; the decrease varied from 1.4 to 56.0 times for different types of pesticides. The slow release pesticide formulations, in contrast to the free pesticides, exerted a much weaker effect on soil microorganisms, no significant inhibition in the abundance of saprotrophic bacteria was observed, partly due to the positive effects of the composite matrix (polymer/natural material), which was a supplementary substrate for microorganisms. The slow release fungicide formulations, like the free fungicides, reduced the total abundance of fungi and inhibited the development of the phytopathogens Fusarium and Alternaria. Thus, slow release formulations of pesticides preserve the bioremediation potential of soil microorganisms, which are the main factor of removing xenobiotics from the biosphere.

Multiple Gene Clusters and Their Role in the Degradation of Chlorophenoxyacetic Acids in Bradyrhizobium sp. RD5-C2 Isolated from Non-Contaminated Soil

Bradyrhizobium sp. RD5-C2, isolated from soil that is not contaminated with 2,4-dichlorophenoxyacetic acid (2,4-D), degrades the herbicides 2,4-D and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). It possesses tfdAα and cadA (designated as cadA1), which encode 2,4-D dioxygenase and the oxygenase large subunit, respectively. In the present study, the genome of Bradyrhizobium sp. RD5-C2 was sequenced and a second cadA gene (designated as cadA2) was identified. The two cadA genes belonged to distinct clusters comprising the cadR1A1B1K1C1 and cadR2A2B2C2K2S genes. The proteins encoded by the cad1 cluster exhibited high amino acid sequence similarities to those of other 2,4-D degraders, while Cad2 proteins were more similar to those of non-2,4-D degraders. Both cad clusters were capable of degrading 2,4-D and 2,4,5-T when expressed in non-2,4-D-degrading Bradyrhizobium elkanii USDA94. To examine the contribution of each degradation gene cluster to the degradation activity of Bradyrhizobium sp. RD5-C2, cadA1, cadA2, and tfdAα deletion mutants were constructed. The cadA1 deletion resulted in a more significant decrease in the ability to degrade chlorophenoxy compounds than the cadA2 and tfdAα deletions, indicating that degradation activity was primarily governed by the cad1 cluster. The results of a quantitative reverse transcription-PCR analysis suggested that exposure to 2,4-D and 2,4,5-T markedly up-regulated cadA1 expression. Collectively, these results indicate that the cad1 cluster plays an important role in the degradation of Bradyrhizobium sp. RD5-C2 due to its high expression.

Herbicide bioremediation: from strains to bacterial communities

There is high demand for herbicides based on the necessity to increase crop production to satisfy world-wide demands. Nevertheless, there are negative impacts of herbicide use, manifesting as selection for resistant weeds, production of toxic metabolites from partial degradation of herbicides, changes in soil microbial communities and biogeochemical cycles, alterations in plant nutrition and soil fertility, and persistent environmental contamination. Some herbicides damage non-target microorganisms via directed interference with host metabolism and via oxidative stress mechanisms. For these reasons, it is necessary to identify sustainable, efficient methods to mitigate these environmental liabilities. Before the degradation process can be initiated by microbial enzymes and metabolic pathways, microorganisms need to tolerate the oxidative stresses caused by the herbicides themselves. This can be achieved via a complex system of enzymatic and non-enzymatic antioxidative stress systems. Many of these response systems are not herbicide specific, but rather triggered by a variety of substances. Collectively, these nonspecific response systems enhance the survival and fitness potential of microorganisms. Biodegradation studies and remediation approaches have relied on individually selected strains to effectively remediate herbicides in the environment. Nevertheless, it has been shown that microbial communication systems that modulate social relationships and metabolic pathways inside biofilm structures among microorganisms are complex; therefore, use of isolated strains for xenobiotic degradation needs to be enhanced using a community-based approach with biodegradation pathway integration. Bioremediation efforts can use omics-based technologies to gain a deeper understanding of the molecular complexes of bacterial communities to achieve to more efficient elimination of xenobiotics. With this knowledge, the possibility of altering microbial communities is increased to improve the potential for bioremediation without causing other environmental impacts not anticipated by simpler approaches. The understanding of microbial community dynamics in free-living microbiota and those present in complex communities and in biofilms is paramount to achieving these objectives. It is also essential that non-developed countries, which are major food producers and consumers of pesticides, have access to these techniques to achieve sustainable production, without causing impacts through unknown side effects.

Herbicides based on 2,4-D: its behavior in agricultural environments and microbial biodegradation aspects. A review

One of the main herbicides used in the agricultural environments is 2,4-dichlorophenoxyacetic acid (2,4-D). It is a synthetic plant hormone auxin employed in many crops including rice, wheat, sorghum, sugar cane, and corn to control wide leaf weeds. The indiscriminate use of pesticides can produce numerous damages to the environment. Therefore, this review has the objective to provide an overview on the main characteristics of the herbicides based on 2,4-D, mostly on the role of microorganisms in its degradation and its main degradation metabolite, 2,4- dichlorophenol (2,4-DCP). The remediation processes carried out by microorganisms are advantageous to avoid the pollution of the environment as well as to safeguard the population health.

Azotobacter: A potential bio-fertilizer for soil and plant health management

Stressor (biotic as well as abiotic) generally hijack the plant growth and yield characters in hostile environment leading to poor germination of the plants and yield. Among the plant growth promoting rhizobacteria, Azotobacter spp. (Gram-negative prokaryote) are considered to improve the plant health. Various mechanisms are implicated behind improved plant health in Azotobacter spp. inoculated plants. For example, acceleration of phytohormone like Indole-3-Acetic Acid production, obviation of various stressors, nitrogen fixation, pesticides and oil globules degradation, heavy metals metabolization, etc. are the key characteristics of Azotobacter spp. action. In addition, application of this bacteria has also become helpful in the reclamation of soil suggesting to be a putative agent which can be used in the transformation of virgin land to fertile one. Application of pesticides of chemical origin are being put on suspension mode as the related awareness program is still on. As far as the limitations of this microbe is concerned, commercial level formulations availability is still a great menace. Present review has been aimed to appraise the researchers pertaining to utility of Azotobacter spp. in the amelioration of plant health in sustainable agroecosystem. The article has been written with the target to gather maximum information into single pot so that it could reach to the dedicated researchers.

Efficient Degradation of Phenoxyalkanoic Acid Herbicides by the Alkali-Tolerant Cupriavidus oxalaticus Strain X32

Phenoxyalkanoic acid (PAA) herbicides are mainly metabolized by microorganisms in soils, but the degraders that perform well under alkaline environments are rarely considered. Herein, we report Cupriavidus oxalaticus strain X32, which showed encouraging PAA-degradation abilities, PAA tolerance, and alkali tolerance. In liquid media, without the addition of exogenous carbon sources, X32 could completely remove 500 mg/L 2,4-dichlorophenoxyacetic acid (2,4-D) or 4-chloro-2-methylphenoxyacetic acid within 3 days, faster than that with the model degrader Cupriavidus necator JMP134. Particularly, X32 still functioned at pH 10.5. Of note, with X32 inoculation, we observed 2,4-D degradation in soils and diminished phytotoxicity to maize (Zea mays). Furthermore, potential mechanisms underlying PAA biodegradation and alkali tolerance were then analyzed by whole-genome sequencing. Three modules of tfd gene clusters involved in 2,4-D catabolism and genes encoding monovalent cation/proton antiporters involved in alkali tolerance were putatively identified. Thus, X32 could be a promising candidate for the bioremediation of PAA-contaminated sites, especially in alkaline surroundings.

Expression and cloning of catA encoding a catechol 1,2-dioxygenase from the 2,4-D-degrading strain Cupriavidus campinensis BJ71

Catechol 1,2-dioxygenases catalyze catechol ring-opening, a critical step in the degradation of aromatic compounds. Cupriavidus campinensis BJ71, an efficient 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacterial strain, was previously isolated from an environment contaminated with 2,4-D. In this study, catA encoding a catechol 1,2-dioxygenase was cloned from the BJ71 strain. The gene was 939 bp long and encoded a polypeptide of 312 amino acids with a molecular weight of 34 kDa. To investigate its enzymatic characteristics, CatA was heterologously expressed in Escherichia coli. Optimal reaction conditions for the pure enzyme were 35 °C and pH 8.0. The enzyme remained stable within a range of 25 °C-45 °C and pH 6.0-9.0, thus indicating that CatA has wide temperature and pH adaptability. After incubation at 45 °C, the enzyme activity of CatA decreased to 37.12%, but its activity was not affected by incubation at pH 9.0. The pure enzyme was able to use catechol, 4-methyl-catechol and 4-chlorocatechol as substrates. Enzyme kinetic parameters K_m and V_max were 39.97 µM and 10.68 U/mg, respectively. This is the first report of the cloning of a gene encoding a catechol 1,2-dioxygenase from a 2,4-D-degrading bacterial strain.

Microbial degradation of halogenated aromatics: molecular mechanisms and enzymatic reactions

Halogenated aromatics are used widely in various industrial, agricultural and household applications. However, due to their stability, most of these compounds persist for a long time, leading to accumulation in the environment. Biological degradation of halogenated aromatics provides sustainable, low-cost and environmentally friendly technologies for removing these toxicants from the environment. This minireview discusses the molecular mechanisms of the enzymatic reactions for degrading halogenated aromatics which naturally occur in various microorganisms. In general, the biodegradation process (especially for aerobic degradation) can be divided into three main steps: upper, middle and lower metabolic pathways which successively convert the toxic halogenated aromatics to common metabolites in cells. The most difficult step in the degradation of halogenated aromatics is the dehalogenation step in the middle pathway. Although a variety of enzymes are involved in the degradation of halogenated aromatics, these various pathways all share the common feature of eventually generating metabolites for utilizing in the energy-producing metabolic pathways in cells. An in-depth understanding of how microbes employ various enzymes in biodegradation can lead to the development of new biotechnologies via enzyme/cell/metabolic engineering or synthetic biology for sustainable biodegradation processes.

Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants

The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and α-ketoglutarate (Fe/αKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from Bradyrhizobium diazoefficiens USDA 110 as a catalyst to degrade (S)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (R)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (S)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.

Phenotypic characteristics and transcriptome profile of Cryptococcus gattii biofilm

In this study, we characterized Cryptococcus gattii biofilm formation in vitro. There was an increase in the density of metabolically active sessile cells up to 72 h of biofilm formation on polystyrene and glass surfaces. Scanning electron microscopy and confocal laser scanning microscopy analysis revealed that in the early stage of biofilm formation, yeast cells adhered to the abiotic surface as a monolayer. After 12 h, extracellular fibrils were observed projecting from C. gattii cells, connecting the yeast cells to each other and to the abiotic surface; mature biofilm consisted of a dense network of cells deeply encased in an extracellular polymeric matrix. These features were also observed in biofilms formed on polyvinyl chloride and silicone catheter surfaces. We used RNA-Seq-based transcriptome analysis to identify changes in gene expression associated with C. gattii biofilm at 48 h compared to the free-floating planktonic cells. Differential expression analysis showed that 97 and 224 transcripts were up-regulated and down-regulated in biofilm, respectively. Among the biological processes, the highest enriched term showed that the transcripts were associated with cellular metabolic processes, macromolecule biosynthetic processes and translation.

Microbial Synthesis and Transformation of Inorganic and Organic Chlorine Compounds

Organic and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.

Microbial Degradation of Pesticide Residues and an Emphasis on the Degradation of Cypermethrin and 3-phenoxy Benzoic Acid: A Review

Nowadays, pesticides are widely used in preventing and controlling the diseases and pests of crop, but at the same time pesticide residues have brought serious harm to human's health and the environment. It is an important subject to study microbial degradation of pesticides in soil environment in the field of internationally environmental restoration science and technology. This paper summarized the microbial species in the environment, the study of herbicide and pesticides degrading bacteria and the mechanism and application of pesticide microbial degrading bacteria. Cypermethrin and other pyrethroid pesticides were used widely currently, while they were difficult to be degraded in the natural conditions, and an intermediate metabolite, 3-phenoxy benzoic acid would be produced in the degradation process, causing the secondary pollution of agricultural products and a series of problems. Taking it above as an example, the paper paid attention to the degradation process of microorganism under natural conditions and factors affecting the microbial degradation of pesticide. In addition, the developed trend of the research on microbial degradation of pesticide and some obvious problems that need further solution were put forward.

Diversity and Niche of Archaea in Bioremediation

Bioremediation is the use of microorganisms for the degradation or removal of contaminants. Most bioremediation research has focused on processes performed by the domain Bacteria; however, Archaea are known to play important roles in many situations. In extreme conditions, such as halophilic or acidophilic environments, Archaea are well suited for bioremediation. In other conditions, Archaea collaboratively work alongside Bacteria during biodegradation. In this review, the various roles that Archaea have in bioremediation is covered, including halophilic hydrocarbon degradation, acidophilic hydrocarbon degradation, hydrocarbon degradation in nonextreme environments such as soils and oceans, metal remediation, acid mine drainage, and dehalogenation. Research needs are addressed in these areas. Beyond bioremediation, these processes are important for wastewater treatment (particularly industrial wastewater treatment) and help in the understanding of the natural microbial ecology of several Archaea genera.

Biodegradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid by a New Isolated Strain of Achromobacter sp. LZ35

In this study, a bacterial strain of Achromobacter sp. LZ35, which was capable of utilizing 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxy acetic acid (MCPA) as the sole sources of carbon and energy for growth, was isolated from the soil in a disused pesticide factory in Suzhou, China. The optimal 2,4-D degradation by strain LZ35 occurred at 30 °C and pH 8.0 when the initial 2,4-D concentration was 200 mg L^-1. Strain LZ35 harbored the conserved 2,4-D/alpha-ketoglutarate dioxygenase (96%) and 2,4-dichlorophenol hydroxylase (99%), and catabolized 2,4-D via the intermediate 2,4-dichlorophenol. The inoculation of 7.8 × 10⁶ CFU g^-1 soil of strain LZ35 cells to 2,4-D-contaminated soil could efficiently remove over 75 and 90% of 100 and 50 mg L^-1 2,4-D in 12 days and significantly released the phytotoxicity of maize caused by the 2,4-D residue. This is the first report of an Achromobacter sp. strain that was capable of mineralizing both 2,4-D and MCPA. This study provides us a promising candidate for its application in the bioremediation of 2,4-D- or MCPA-contaminated sites.

Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments

The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.

Potential roles for microbial endophytes in herbicide tolerance in plants

Herbicide tolerance in crops and weeds is considered to be monotrophic, i.e. determined by the relative susceptibility of the physiological process targeted and the plant's ability to metabolise and detoxify the agrochemical. A growing body of evidence now suggests that endophytes, microbes that inhabit plant tissues and provide a range of growth, health and defence enhancements, can contribute to other types of abiotic and biotic stress tolerance. The current evidence for herbicide tolerance being bitrophic, with both free-living and plant-associated endophytes contributing to tolerance in the host plant, has been reviewed. We propose that endophytes can directly contribute to herbicide detoxification through their ability to metabolise xenobiotics. In addition, we explore the paradigm that microbes can 'prime' resistance mechanisms in plants such that they enhance herbicide tolerance by inducing the host's stress responses to withstand the downstream toxicity caused by herbicides. This latter mechanism has the potential to contribute to the growth of non-target-site-based herbicide resistance in weeds. Microbial endophytes already contribute to herbicide detoxification in planta, and there is now significant scope to extend these interactions using synthetic biology approaches to engineer new chemical tolerance traits into crops via microbial engineering.

Detoxification of Indole by an Indole-Induced Flavoprotein Oxygenase from Acinetobacter baumannii

Indole, a derivative of the amino acid tryptophan, is a toxic signaling molecule, which can inhibit bacterial growth. To overcome indole-induced toxicity, many bacteria have developed enzymatic defense systems to convert indole to non-toxic, water-insoluble indigo. We previously demonstrated that, like other aromatic compound-degrading bacteria, Acinetobacter baumannii can also convert indole to indigo. However, no work has been published investigating this mechanism. Here, we have shown that the growth of wild-type A. baumannii is severely inhibited in the presence of 3.5 mM indole. However, at lower concentrations, growth is stable, implying that the bacteria may be utilizing a survival mechanism to oxidize indole. To this end, we have identified a flavoprotein oxygenase encoded by the iifC gene of A. baumannii. Further, our results suggest that expressing this recombinant oxygenase protein in Escherichia coli can drive indole oxidation to indigo in vitro. Genome analysis shows that the iif operon is exclusively present in the genomes of A. baumannii and Pseudomonas syringae pv. actinidiae. Quantitative PCR and Western blot analysis also indicate that the iif operon is activated by indole through the AraC-like transcriptional regulator IifR. Taken together, these data suggest that this species of bacteria utilizes a novel indole-detoxification mechanism that is modulated by IifC, a protein that appears to be, at least to some extent, regulated by IifR.

2,4-Dichlorophenol hydroxylase for chlorophenol removal: Substrate specificity and catalytic activity

Chlorophenols (CPs) are common environmental pollutants. As such, different treatments have been assessed to facilitate their removal. In this study, 2,4-dichlorophenol (2,4-DCP) hydroxylase was used to systematically investigate the activity and removal ability of 19CP congeners at 25 and 0 °C. Results demonstrated that 2,4-DCP hydroxylase exhibited a broad substrate specificity to CPs. The activities of 2,4-DCP hydroxylase against specific CP congeners, including 3-CP, 2,3,6-trichlorophenol, 2-CP, and 2,3-DCP, were higher than those against 2,4-DCP, which is the preferred substrate of previously reported 2,4-DCP hydroxylase. To verify whether cofactors are necessary to promote hydroxylase activity against CP congeners, we added FAD and found that the added FAD induced a 1.33-fold to 5.13-fold significant increase in hydroxylase activity against different CP congeners. The metabolic pathways of the CP degradation in the enzymatic hydroxylation step were preliminarily proposed on the basis of the analyses of the enzymatic activities against 19CP congeners. We found that the high activity and removal rate of 2,4-DCP hydroxylase against CPs at 0 °C enhance the low-temperature-adaptability of this enzyme to the CP congeners; as such, the proposed removal process may be applied to biochemical, bioremediation, and industrial processes, particularly in cold environments.