16S rRNA gene phylogeny and tfdA gene analysis of 2,4-D-degrading bacteria isolated in China

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

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

The Genome Sequence of Brucella intermedia DF13, a 2,4-Dichlorophenoxyacetic Acid-Degrading Soil Bacterium Isolated in Brazil

Brucella intermedia/Ochrobactrum intermedium strain DF13 was isolated from Brazilian soil and is able to degrade 2,4-dichlorophenoxyacetic acid (2,4-D). Here, we report on its genome sequence, with 4,570,268 bp and a 57.8% G+C content.

Novel pathway and acetate-facilitated complete atenolol degradation by Hydrogenophaga sp. YM1 isolated from activated sludge

Atenolol is a widely prescribed beta-blocker that has been detected in wastewater at concentrations up to 300 μg/L. The parent compound and its transformation products pose risks to aquatic organisms. Efficient atenolol degrading microorganism has yet to be identified, and its biodegradation pathway is unknown. In this study, Hydrogenophaga sp. YM1 isolated from activated sludge can degrade atenolol efficiently (286.1 ± 4.0 μg/g dry wt/h in actual wastewater), where atenolol acid, and four newly detected products (4-hydroxyphenylacetic acid, 3-(isopropylamino)-1,2-propanediol, 3-amino-1,2-propanediol and 4-(1-amino-2-hydroxy-3-propoxy) benzeneacetic acid) were the main intermediates. Key genes involved in atenolol degradation were proposed based on RNA-seq and validated by RT-qPCR. The ether bond cleavage of atenolol acid was the rate-limiting step likely catalyzed by the α-ketoglutarate dependent 2,4-dichlorophenoxyacetate dioxygenase. The further degradation of 4-hydroxyphenylacetic acid followed the homoprotocatechuate degradation pathway, enabling complete conversion to CO₂. Acetate addition (39-156 mg COD/L) under aerobic condition enhanced atenolol degradation by 29-37% and decreased the accumulation of atenolol acid, likely because acetate oxidation provided α-ketoglutarate and additional reducing power. Activated sludge core microorganisms have limited atenolol mineralization potentials. Enriching Hydrogenophaga-like populations and/or providing such as acetate can drive more complete conversion of atenolol in natural and engineered biosystems.

Identification of a phosphorus-solubilizing Tsukamurella tyrosinosolvens strain and its effect on the bacterial diversity of the rhizosphere soil of peanuts growth-promoting

Phosphate solubilizing microorganisms widely exist in plant rhizosphere soil, but report about the P solubilization and multiple growth-promoting properties of rare actinomycetes are scarce. In this paper, a phosphate solubilizing Tsukamurella tyrosinosolvens P9 strain was isolated from the rhizosphere soil of tea plants. Phosphorus-dissolving abilities of this strain were different under different carbon and nitrogen sources, the soluble phosphorus content was 442.41 mg/L with glucose and potassium nitrate as nutrient sources. The secretion of various organic acids, such as lactic acid, maleic acid, oxalic acid, etc., was the main mechanism for P solubilization and pH value in culture was very significant negative correlation with soluble P content. In addition, this strain had multiple growth-promoting characteristics with 37.26 μg/mL of IAA and 72.01% of siderophore relative content. Under pot experiments, P9 strain improved obviously the growth of peanut seedlings. The bacterial communities of peanut rhizoshpere soil were assessed after inoculated with P9 strain. It showed that there was no significant difference in alpha-diversity indices between the inoculation and control groups, but the P9 treatment group changed the composition of bacterial communities, which increased the relative abundance of beneficial and functional microbes, which relative abundances of Chitinophagaceae at the family level, and of Flavihumibacter, Ramlibacter and Microvirga at the genus level, were all siginificant increased. Specially, Tsukamurella tyrosinosolvens were only detected in the rhizosphere of the inoculated group. This study not only founded growth-promoting properties of T. tyrosinosolvens P9 strain and its possible phosphate solublizing mechanism, but also expected to afford an excellent strain resource in biological fertilizers.

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.

Intra- and inter-field diversity of 2,4-dichlorophenoxyacetic acid-degradative plasmids and their tfd catabolic genes in rice fields of the Mekong delta in Vietnam

The tfd genes mediating degradation of the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) differ in composition and organization in bacterial isolates from different geographical origin and are carried by different types of mobile genetic elements (MGE). It is not known whether such global diversity of 2,4-D-catabolic MGE and their tfd gene cargo is reflected in the diversity at field scale. The genomic context of the 2,4-D catabolic genes of 2,4-D-degrading isolates from two rice fields with a 2,4-D application history, located in two distant provinces of the Vietnam Mekong delta, was compared. All isolates were β-proteobacteria, were unique for each rice field and carried the catabolic genes on MGE and especially plasmids. Most plasmids were IncP-1β plasmids and carried tfd clusters highly similar to those of the IncP-1β plasmid pJP4, typified by two chlorophenol catabolic gene modules (tfd-I and tfd-II). IncP-1β plasmids from the same field showed small deletions and/or insertions in accessory metabolic genes. One plasmid belonged to an unclassified plasmid group and carries a copy of both tfdA and tfd-II identical to those in the IncP-1β plasmids. Our results indicate intra-field evolution and inter-field exchange of 2,4-D-catabolic IncP-1β plasmids as well as the exchange of tfd genes between different plasmids within a confined local environment.

Potential impact of the herbicide 2,4-dichlorophenoxyacetic acid on human and ecosystems

The herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) is applied directly to aquatic and conventional farming systems to control weeds, and is among the most widely distributed pollutants in the environment. Non-target organisms are exposed to 2,4-D via several ways, which could produce toxic effects depending on the dose, frequency of exposure, and the host factors that influence susceptibility and sensitivity. An increasing number of experimental evidences have shown concerns about its presence/detection in the environment, because several investigations have pointed out its potential lethal effects on non-target organisms. In this review, we critically evaluated the environmental fate and behavior of 2,4-D along with its eco-toxicological effects on aquatic, plants and human life to provide concise assessment in the light of recently published reports. The findings demonstrate that 2,4-D is present in a low concentration in surface water of regions where its usage is high. The highest concentrations of 2,4-D were detected in soil, air and surface water surrounded by crop fields, which suggest that mitigation strategies must be implanted locally to prevent the entry of 2,4-D into the environment. A general public may have frequent exposure to 2,4-D due to its wide applications at home lawns and public parks, etc. Various in vivo and in vitro investigations suggest that several species (or their organs) at different trophic levels are extremely sensitive to the 2,4-D exposure, which may explain variation in outcomes of reported investigations. However, implications for the prenatal exposure to 2,4-D remain unknown because 2,4-D-induced toxicity thresholds in organism have only been derived from juveniles or adults. In near future, introduction of 2,4-D resistant crops will increase its use in agriculture, which may cause relatively high and potentially unsafe residue levels in the environment. The recent findings indicate the urgent need to further explore fate, accumulation and its continuous low level exposure impacts on the environment to generate reliable database which is key in drafting new regulation and policies to protect the population from further exposure.

Rapid Biodegradation of the Herbicide 2,4-Dichlorophenoxyacetic Acid by Cupriavidus gilardii T-1

Phytotoxicity and environmental pollution of residual herbicides have caused much public concern during the past several decades. An indigenous bacterial strain capable of degrading 2,4-dichlorophenoxyacetic acid (2,4-D), designated T-1, was isolated from soybean field soil and identified as Cupriavidus gilardii. Strain T-1 degraded 2,4-D 3.39 times more rapidly than the model strain Cupriavidus necator JMP134. T-1 could also efficiently degrade 2-methyl-4-chlorophenoxyacetic acid (MCPA), MCPA isooctyl ester, and 2-(2,4-dichlorophenoxy)propionic acid (2,4-DP). Suitable conditions for 2,4-D degradation were pH 7.0-9.0, 37-42 °C, and 4.0 mL of inoculums. Degradation of 2,4-D was concentration-dependent. 2,4-D was degraded to 2,4-dichlorophenol (2,4-DCP) by cleavage of the ether bond and then to 3,5-dichlorocatechol (3,5-DCC) via hydroxylation, followed by ortho-cleavage to cis-2-dichlorodiene lactone (CDL). The metabolites 2,4-DCP or 3,5-DCC at 10 mg L^-1 were completely degraded within 16 h. Fast degradation of 2,4-D and its analogues highlights the potential for use of C. gilardii T-1 in bioremediation of phenoxyalkanoic acid herbicides.

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

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

Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing (1)H and (13)C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3.

Bio-Augmentation of Cupriavidus sp. CY-1 into 2,4-D Contaminated Soil: Microbial Community Analysis by Culture Dependent and Independent Techniques

In the present study, a 2,4-dichlorophenoxyacetic acid (2,4-D) degrading bacterial strain CY-1 was isolated from the forest soil. Based on physiological, biochemical and 16S rRNA gene sequence analysis it was identified as Cupriavidus sp. CY-1. Further 2,4-D degradation experiments at different concentrations (200 to 800 mg l^-1) were carried out using CY-1. Effect of NaCl and KNO₃ on 2,4-D degradation was also evaluated. Degradation of 2,4-D and the metabolites produced during degradation process were analyzed using high pressure liquid chromatography (HPLC) and GC-MS respectively. The amount of chloride ions produced during the 2,4-D degradation were analyzed by Ion chromatography (IC) and it is stoichiometric with 2,4-D dechlorination. Furthermore two different types of soils collected from two different sources were used for 2,4-D degradation studies. The isolated strain CY-1 was bio-augmented into 2,4-D contaminated soils to analyze its degradation ability. Culture independent methods like denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP), and culture dependent methods like colony forming units (CFU) and most probable number (MPN) were used to analyze the survivability of strain CY-1 in contaminated soil. Results of T-RFLP were coincident with the DGGE analysis. From the DGGE, T-RFLP, MPN and HPLC results it was concluded that strain CY-1 effectively degraded 2,4-D without disturbing the ecosystem of soil indigenous microorganisms.

Isolation and 2,4-D-degrading characteristics of Cupriavidus campinensis BJ71

An indigenous bacterial strain capable of utilizing 2,4-dichlorophenoxyacetic acid as the sole carbon and energy source was isolated from a soil used for grown wheat with a long-term history of herbicide use in Beijing, China. The strain BJ71 was identified as Cupriavidus campinensis based on its 16S rRNA sequence analysis and morphological, physiological, and biochemical characteristics. The degradation characteristics of strain BJ71 were evaluated. The optimal conditions for 2,4-D degradation were as follows: pH 7.0, 30 °C, 3% (v/v) inoculum size, and an initial 2,4-D concentration of 350 mg L(-1). Up to 99.57% of the 2,4-D was degraded under optimal conditions after 6 days of incubation. Strain BJ71 was also able to degrade quizalofop and fluroxypyr. This is the first report of a 2,4-D-degrader containing tfdA gene that can utilize these two herbicides. In a biodegradation experiment, 87.13% and 42.53% of 2,4-D (initial concentration, 350 mg kg(-1)) was degraded in non-sterile and sterilized soil inoculated with BJ71, respectively, after 14 days. The 2,4-D degradation was more rapid in a soil microcosm including BJ71 than in a soil microcosm without BJ71. These results indicate that strain BJ71 is a potential candidate for the bioremediation of soil contaminated with the herbicide 2,4-D.

Cloning, expression, characterization and mutational analysis of the tfdA gene from Cupriavidus campinensis BJ71

2,4-Dichlorophenoxyacetic acid (2,4-D)/α-ketoglutarate (α-KG) dioxygenase (TfdA) is an Fe(II)-dependent enzyme that catalyzes the first step in degradation of the herbicide 2,4-D. Previous studies focused on the tfdA gene in Ralstonia eutropha JMP134 isolated in Australia. In this study, a new tfdA gene was cloned from Cupriavidus campinensis BJ71, an effective degrading bacteria from China, based on the iCOnsensus-DEgenerate Hybrid Oligonucleotide Primers (iCODEHOPs) protocol, combined with high-efficiency Thermal Asymmetric Interlaced PCR (hiTAIL-PCR). The open reading frame of 861 bp encoded a putative 287 amino acid protein with a theoretical molecular mass of 32.32 kDa. The gene was overexpressed in Escherichia coli BL21 (DE3) and the purified TfdA showed optimal activity at pH 6.75 and 30 °C. This enzyme was more thermostable and it could use 3-hydrocinnamic acid as substrate, with a similar enzyme activity compared with 2,4-D. TfdA and its variants were created as maltose-binding protein (MBP) tagged fusion proteins to examine the roles of putative substrate-binding residues. The MBP-N110A, MBP-V198A and MBP-R207K proteins showed decreased k cat and increased Km, and MBP-R278A was inactive, suggesting these residues may affect 2,4-D binding or catalysis.