Biological agents for 2,4-dichlorophenoxyacetic acid herbicide degradation

Appreciating animal induced pluripotent stem cells to shape plant cell reprogramming strategies

Animals and plants have developed resilience mechanisms to effectively endure and overcome physical damage and environmental challenges throughout their life span. To sustain their vitality, both animals and plants employ mechanisms to replenish damaged cells, either directly, involving the activity of adult stem cells, or indirectly, via dedifferentiation of somatic cells that are induced to revert to a stem cell state and subsequently redifferentiate. Stem cell research has been a rapidly advancing field in animal studies for many years, driven by its promising potential in human therapeutics, including tissue regeneration and drug development. A major breakthrough was the discovery of induced pluripotent stem cells (iPSCs), which are reprogrammed from somatic cells by expressing a limited set of transcription factors. This discovery enabled the generation of an unlimited supply of cells that can be differentiated into specific cell types and tissues. Equally, a keen interest in the connection between plant stem cells and regeneration has been developed in the last decade, driven by the demand to enhance plant traits such as yield, resistance to pathogens, and the opportunities provided by CRISPR/Cas-mediated gene editing. Here we discuss how knowledge of stem cell biology benefits regeneration technology, and we speculate on the creation of a universal genotype-independent iPSC system for plants to overcome regenerative recalcitrance.

Penicillium chrysogenum: Beyond the penicillin

Almost one century after the Sir Alexander Fleming's fortuitous discovery of penicillin and the identification of the fungal producer as Penicillium notatum, later Penicillium chrysogenum (currently reidentified as Penicillium rubens), the molecular mechanisms behind the massive production of penicillin titers by industrial strains could be considered almost fully characterized. However, this filamentous fungus is not only circumscribed to penicillin, and instead, it seems to be full of surprises, thereby producing important metabolites and providing expanded biotechnological applications. This review, in addition to summarizing the classical role of P. chrysogenum as penicillin producer, highlights its ability to generate an array of additional bioactive secondary metabolites and enzymes, together with the use of this microorganism in relevant biotechnological processes, such as bioremediation, biocontrol, production of bioactive nanoparticles and compounds with pharmaceutical interest, revalorization of agricultural and food-derived wastes or the enhancement of food industrial processes and the agricultural production.

Synergistic toxicity of 2,4-dichlorophenoxyacetic acid and arsenic alters biomarkers in rats

2,4-dichlorophenoxyacetic acid (2,4-D) and arsenic cause severe and extensive biological toxicity in organisms. However, their interactions and toxic mechanisms in co-exposure remain to be fully elucidated. In this study, 28 four-week-old female rats were divided into four groups and exposed to 100 mg/L arsenic or/and 600 mg/L 2,4-D through drinking water for a period of 28 days. As a result, it was revealed that biochemical indicators (ALT, AST, ALP, blood urea nitrogen, and creatinine) were increased and decreased hormonal parameters (FSH, LH, PG, and E2) in arsenic and 2,4-D and arsenic combination-treated groups. Moreover, increased lipid peroxidation (malondialdehyde level) and decreased antioxidant status (superoxide dismutase and catalase activities) were found in the co-exposure groups compared with the individual-exposure groups. Meanwhile, severe DNA damage was observed in co-exposure groups. Additionally, the levels of apoptotic (Bax, Caspase-3, Caspase-8, Caspase-9, p53, and PARP) and inflammation (NFκB, Cox-2, TNF-α, and TGFβI) indexes in the co-exposure groups were markedly increased, whereas the levels of anti-apoptosis index (Bcl-2) were decreased. It was also observed that co-exposure with 2,4-D and arsenic caused more histopathological changes in tissues. Generally, these results show that co-exposure to 2,4-D and arsenic can seriously cause oxidative stress, DNA damage, apoptosis and inflammation while having toxicological risk for organisms.

Bacterial enzymatic degradation of recalcitrant organic pollutants: catabolic pathways and genetic regulations

Contamination of soil and natural water bodies driven by increased organic pollutants remains a universal concern. Naturally, organic pollutants contain carcinogenic and toxic properties threatening all known life forms. The conventional physical and chemical methods employed to remove these organic pollutants ironically produce toxic and non-ecofriendly end-products. Whereas microbial-based degradation of organic pollutants provides an edge, they are usually cost-effective and take an eco-friendly approach towards remediation. Bacterial species, including Pseudomonas, Comamonas, Burkholderia, and Xanthomonas, have the unique genetic makeup to metabolically degrade toxic pollutants, conferring their survival in toxic environments. Several catabolic genes, such as alkB, xylE, catA, and nahAc, that encode enzymes and allow bacteria to degrade organic pollutants have been identified, characterized, and even engineered for better efficacy. Aerobic and anaerobic processes are followed by bacteria to metabolize aliphatic saturated and unsaturated hydrocarbons such as alkanes, cycloalkanes, aldehydes, and ethers. Bacteria use a variety of degrading pathways, including catechol, protocatechuate, gentisate, benzoate, and biphenyl, to remove aromatic organic contaminants such as polychlorinated biphenyls, polycyclic aromatic hydrocarbons, and pesticides from the environment. A better understanding of the principle, mechanisms, and genetics would be beneficial for improving the metabolic efficacy of bacteria to such ends. With a focus on comprehending the mechanisms involved in various catabolic pathways and the genetics of the biotransformation of these xenobiotic compounds, the present review offers insight into the various sources and types of known organic pollutants and their toxic effects on health and the environment.

Improvements in Bioremediation Agents and Their Modified Strains in Mediating Environmental Pollution

Environmental pollution has been a significant concern around the globe as the release of toxic pollutants is associated with carcinogenic, mutagenic, and teratogenic impacts on living organisms. Since microorganisms have the natural potential to degrade toxic metabolites into nontoxic forms, an eco-friendly approach known as bioremediation has been used to tackle toxic-induced pollution. Bioremediation has three fundamental levels, i.e., natural attenuation, bio-augmentation, and biostimulation in which the synthetic biology approach has been lately utilized to enhance the conventional bioremediation techniques. Recently, a more advanced approach of programmable nucleases such as zinc finger nucleases, tale-like effector nucleases, and clustered regularly interspaced short palindromic repeats Cas is being employed to engineer several bacterial, fungal, and algal strains for targeted mutagenesis by knocking in and out specific genes which are involved in reconstructing the metabolic pathways of native microbes. These genetically engineered microorganisms possess heavy metal resistance, greater substrate range, enhanced enzymatic activity, and binding affinity which accelerate the biodegradation of toxic pollutants to environmentally safe levels. This review provides a comprehensive understanding of how we can correlate the novel genetics-based approaches employed to produce genetically engineered microorganisms to enhance the biodegradation of hazardous pollutants, hence, developing a clean and sustainable ecosystem.

Microbial degradation of organochlorine pesticide: 2,4-Dichlorophenoxyacetic acid by axenic and mixed consortium

The presence of 2,4-dichlorophenoxyacetic acid (2,4-D), an organochlorine herbicide, in the environment has raised public concern as it poses hazard to both humans and the ecosystem. Three potential strains having the capability to degrade 2,4-D were isolated from on site agricultural soil and identified as Arthrobacter sp. SVMIICT25, Sphingomonas sp. SVMIICT11 and Stenotrophomonas sp. SVMIICT13. Over 12 days of incubation, 81-90% of 100 mg/L of 2,4-D degradation was observed at 2% inoculum. A shorter lag phase with 80% of degradation efficiency was observed within 5 days when the inoculum size was increased to 10%. Six microbial consortia were prepared by combining the isolates along with in-house strains, Bacillus sp. and Pseudomonas sp. Consortia R3 (Arthrobacter sp. + Sphingomonas sp.), operated with 10% of inoculum, showed 85-90% degradation within 4 days and 98-100% in 9 days. Further, targeted exo-metabolite analysis confirmed the presence and catabolism of intermediate 2,4-dichlorophenol and 4-chlorophenol compounds.

In-situ synthesis of novel dual S-scheme AgI/Ag6Mo7O24/g-C3N4 heterojunctions with tandem structure for photocatalytic degradation of organic pollutants

The controllable design of multivariate heterojunction with sequential structures is of significant relevance for breaking the performance limit of binary composite photocatalysts. In this work, the novel dual S-scheme ternary-component AgI/Ag₆Mo₇O₂₄/exfoliated g-C₃N₄ (ECN) composite was prepared by a two-step in-situ synthetic strategy. The energy band bending at the heterointerface and the formation of dual built-in electric field could be observed due to distinct work functions of different components in the ternary composite. Benefiting from the sequential heterojunction structure, the AgI/Ag₆Mo₇O₂₄/ECN composite achieved 98.7% removal efficiency of 2-nitrophenol (2-NP) within 70 min under visible light irradiation, and AgI/Ag₆Mo₇O₂₄/ECN also showed higher degradation efficiency for a variety of organic pollutants such as methylene blue (MB), rhodamine B (RhB), methyl orange (MO), 4-nitrophenol (4-NP), 2-sec-butyl-4,6-dinitrophenol (DNBP) and tetracycline (TC). Notably, •OH and •O₂^- played dominant roles in the AgI/Ag₆Mo₇O₂₄/ECN set up, which was consistent with the dual S-scheme charge transfer mechanism. In-depth insights for the photodegradation of 2-NP were presented based on a combined DFT study and GC-MS analysis. Additionally, the photoreduction of Ag⁺ in AgI/Ag₆Mo₇O₂₄/ECN was also evaded by the fast transfer of photogenerated electrons through the dual S-scheme pathway, achieving the effect of killing two birds with one stone.

Fungal biodegradation of chlorinated herbicides: an overview with an emphasis on 2,4-D in Argentina

Chlorinated herbicides are one of the main types of pesticide used in agriculture. In Argentina, 2,4-dichlorophenoxyacetic acid (2,4-D) is the most applied herbicide for the control of broadleaf weeds, but the risks it poses for the environment and human health are cause for great concern. A promising technology to remove this kind of pollutants, or neutralize them in such a way that they become less or non-toxic, is the use of degrading or detoxifying microorganisms from contaminated sites. Filamentous fungi can bioremediate xenobiotics thanks to their efficient enzymatic machinery. However, most studies on the degradation of 2,4-D have been carried out with bacteria, and little is known about whether it can be efficiently biodegraded by fungi. In the environment, fungal strains and native microbiota may detoxify contaminants through mechanisms like biosorption, bioabsortion, biotransformation, and/or degradation. Whether these processes occur separately or simultaneously depends on the metabolic ability of the strains that conform the microbial community. Another important concern when attempting to introduce detoxifying microorganisms into a contaminated environment is the GRAS ("Generally Recognized As Safe") assessment or status. These are studies that help predict a biodegrading microorganism's pathogenicity, toxicity, and infectivity before in situ application. This application, moreover, is regulated by different legal frameworks. The present review aims to outline the main aspects of 2,4-D degradation by fungi, and to summarize the current state of research on the topic in Argentina.

2,4-Dichlorophenoxyacetic acid (2,4-D) adsorptive removal by algal magnetic activated carbon nanocomposite

In the present study, ferric oxide nanoparticles impregnated with activated carbon from Ulva prolifera biomass (UPAC-Fe₂O₃) were prepared and employed to remove 2,4-Dichlorophenoxyacetic acid (2,4-D) by adsorption. The UPAC-Fe₂O₃ nanocomposite was characterized for its structural and functional properties by a variety of techniques. The nanocomposite had a jagged, irregular surface with pores due to uneven scattering of Fe₂O₃ nanoparticles, whereas elemental analysis portrayed the incidence of carbon, oxygen, and iron. XRD analysis established the crystalline and amorphous planes corresponding to the iron oxide and carbon phase respectively. FT-IR analyzed the functional groups that confirmed the integration of Fe₂O₃ nanoparticles onto nanocomposite surfaces. VSM and XPS studies uncovered the superparamagnetic nature and presence of carbon and Fe₂O_3, respectively, in the UPAC-Fe₂O₃ nanocomposite. While the surface area was 292.51 m²/g, the size and volume of the pores were at 2.61 nm and 0.1906 cm³/g, respectively, indicating the mesoporous nature and suitability of the nanocomposites that could be used as adsorbents. Adsorptive removal of 2,4-D by nanocomposite for variations in process parameters like pH, dosage, agitation speed, adsorption time, and 2,4-D concentration was studied. The adsorption of 2,4-D by UPAC-Fe₂O₃ nanocomposite was monolayer chemisorption owing to Langmuir isotherm behavior along with a pseudo-second-order kinetic model. The maximum adsorption capacity and second order rate constant values were 60.61 mg/g and 0.0405 g/mg min respectively. Thermodynamic analysis revealed the spontaneous and feasible endothermic adsorption process. These findings confirm the suitability of the synthesized UPAC-Fe₂O₃ nanocomposite to be used as an adsorbent for toxic herbicide waste streams.

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.

Degradation of 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) by fungi originating from Vietnam

Three different fungi were tested for their ability to degrade 2,4-dichlorophenoxyacetic acid and 2,4,5-trichlorophenoxyacetic acid and for the role of laccases and cytochromes P450-type in this process. We studied a white-rot fungus Rigidoporus sp. FMD21, which has a high laccase activity, for its efficiency to degrade these herbicides. A positive correlation was found between its laccase activity and the corresponding herbicide degradation rate. Even more, the doubling of the enzyme activity in this phase corresponded with a doubling of the herbicide degradation rate. It is, therefore, tempting to speculate that laccase is the most dominant enzyme in the degradation of 2,4-D and 2,4,5-T under these conditions. In addition, it was shown that Rigidoporus sp. FMD21 partly relies on cytochromes P450-type for the breakdown of the herbicides as well. Two filamentous fungi were isolated from soil contaminated with herbicides and dioxins located at Bien Hoa airbase. They belong to genera Fusarium and Verticillium of the phylum Ascomycota as judged by their 18S rRNA gene sequences. Both isolated fungi were able to degrade the herbicides but with different rates. Their laccase activity, however, was very low and did not correlate with the rate of breakdown of the herbicides. These data indicate that the white-rot fungus most likely synthesizes laccase and cytochromes P450-type for the breakdown of the herbicides, while the types of enzyme used for the breakdown of the herbicides by the two Ascomycota remain unclear.

Fungal and bacterial assisted bioremediation of environmental toxicant (N-[2-[3-chloro-5-(trifluoromethyl)-2-pyridinyl] ethyl]-2-(trifluoromethyl) benzamide) holding benzamidic genesis elucidating the eco-friendly strategy

Fluopyram (FLP) containing benzamidic genesis utilized for seed detoxification and as a foliar application is associated with low profound toxicity in mammals but long-term toxicology investigations have revealed that FLP can stimulate tumor growth. FLP attenuation has been the first time scrutinized employing microorganisms originally identified from soils. Biodegrative assays of four fungal strains; Aspergillus fumigatus (AFu), Aspergillus terreus (AT), Aspergillus flavus (AF), Aspergillus niger (AN), and three bacterial strains: Streptococcus pneumoniae (SP) Streptococcus pyogenes (SPy), and Escherichia coli (EC), were employed. Ten milligrams per liter FLP concentration was made employing separately microbe and analyzed for 35 days. The analytical technique was inclusive of ultraviolet-visible spectrophotometric and high-performance liquid chromatography procedure endeavored to test FLP biodegradation. SP and AT exhibited maximal potentiality to metabolize FLP. HPLC is indicative of several metabolites formations. FLP degradation by AFu, EC, SPy, AN, AF, AT, SP was observed to be 24.2%, 82.7%, 89.8%, 90.7%, 91.3%, 95.4%, and 99.3%, explicating the efficacy of all strains employed in FLP degradation. Current investigations are indicative of significant bioremediation strategies for xenobiotic mitigation. Furthermore, the current examinations are inclusive of the augmentation of biodegradative assays to be utilized on a large scale for efficient environmental management cost-effectively and sustainably.

Biodegradation of herbicides by a plant nonheme iron dioxygenase: mechanism and selectivity of substrate analogues

Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogs by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C 2 -hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R - and S -methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R -isomer give high rebound barriers.

Immobilisation of phosphonium-based ionic liquid in polysulfone capsules for the removal of phenolic compounds, with an emphasis on 2,4-dichlorophenol, in aqueous solution

Phosphonium-based ionic liquid immobilised in polysulfone capsules were prepared by the phase inversion technique for the adsorption of different phenolic compounds from aqueous solution. Some techniques, including Scanning Electron Microscopy (SEM), surface analysis by Brunauer-Emmett-Teller (BET), Fourier Transform Infrared Spectroscopy (FT-IR) and Thermogravimetric Analysis (TGA), were used to characterize the capsule and indicated that trihexyltetradecylphosphonium decanoate (ionic liquid) was successfully immobilised in polysulfone, the immobilisation was determined to be 63.29%. Adsorption tests showed that the developed capsules have the potential to remove varied phenolic compounds. For compounds 2,4-dichlorophenol (2,4-DCP) the best removal was achieved between pH 3.0 and 9.0. Temperature variation (25-70 °C) and sodium chloride concentration (0-1000 mg⋅L^-1) had no significant changes in adsorption, demonstrating the scope for using this adsorbent with real effluents. Adsorption kinetics demonstrated the mechanism occurs in second order, the Weber-Morris model delimited the intraparticle diffusion as the adsorption limiter. The Redlich-Peterson model was the isothermal analysis that best suited the experimental data, with a β value equal to 0.821 approaching the Langmuir model, which obtained a q_max of 404.50 mg⋅g^-1. Consequently, these results demonstrate that these capsules have potential application in the treatment of environmental pollution caused by phenolic compounds.

Mechanistic insights into 2,4-D photoelectrocatalytic removal from water with TiO2 nanotubes under dark and solar light irradiation

Removal of recalcitrant pollutants from water is a major challenge, to which the photoelectrocatalytic processes may be a solution. Applied potential plays a key role in the photocatalytic activity of the semiconductor. This paper investigated the effect of applied potential on the photoelectrocatalytic oxidation of 2,4-Dichlorophenoxyacetic acid (2,4-D) with TiO₂ nanotubular anodes under solar light irradiation. The process was investigated at constant potentials in different regions of the polarization curve: the ohmic region, the saturation region and in the region of the Schottky barrier breakdown. PEC tests were performed in aqueous solutions of 2,4-D, and in the presence of methanol or formic acid, as scavengers of OH^• radicals and holes. Results showed the main mechanism is oxidation by OH^• radicals from water oxidation, while runs with hole scavenger revealed a second mechanism of direct oxidation by holes photogenerated at the electrode surface, with high removal rates due to current doubling effect.

Ultrasonic coupling with electrical current to effective activation of Persulfate for 2, 4 Dichlorophenoxyacetic acid herbicide degradation: modeling, synergistic effect, and a by-product study

In this research work, we investigated the ability of the oxidative degradation of 2, 4-Dichlorophenoxy acetic acid herbicide via ultrasonic-assisted in electro-activation of the persulfate system in the presence of nano-zero valent iron. The effect of experimental parameters such as pH value [4-8], electrical current (0.5-1 A), persulfate concentration (0.25-0.5 mg.l-1), nano zero-valent iron dose (0.05-0.1 mg.l-1), and initial organic pollutant concentration (50-100 mg.l-1) on the ultrasonic-electropersulfate process performance was assessed via central composite design. The combination of ultrasonic waves with the electrochemical process to activation of persulfate showed better efficiency into 2, 4-Dichlorophenoxy acetic acid herbicide degradation compared to their implementation in individual and binary systems. Following optimal conditions (pH = 5.62, 0.80 A applied electrical current, 0.39 mg/L persulfate concentration, 0.07 mg/L nano-zero valent iron, and 50 mg/L 2,4-Dichlorophenoxy acetic acid concentration in 40 min reaction), nearly 91% removal was done. Moreover, the complete removal of 2, 4-Dichlorophenoxy acetic acid, 92% COD, and 88% TOC removal was achieved by this process near 140 min reaction. The scavenging experiment confirmed the role of free oxidizing species in the degradation of 2, 4-Dichlorophenoxy acetic acid during the process. Approximately 50% improved 2, 4-Dichlorophenoxy acetic acid removal in the process against the inclusive efficiency of single mechanisms. The obtained results were fitted to the pseudo-first-order kinetic model with a high correlation coefficient (R2 = 0.96). Five important intermediate products of 2, 4-D oxidation were 2, 4-dichlorophenol (2, 4-DCP), 2, 6-dichlorophenol (2, 6-DCP), 4, 6 dichlororesorcinol (4, 6-DCR), 2-chlorohydroquinone (2-CHQ), and 2-chloro-1, 4-benzoquinone (2-CBQ). In the end, can be employed as a satisfactory advanced oxidation process in high mineralization of 2, 4-D and refractory organic pollutants.

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.

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides

Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.

Current Perspectives on the Auxin-Mediated Genetic Network that Controls the Induction of Somatic Embryogenesis in Plants

Auxin contributes to almost every aspect of plant development and metabolism as well as the transport and signalling of auxin-shaped plant growth and morphogenesis in response to endo- and exogenous signals including stress conditions. Consistently with the common belief that auxin is a central trigger of developmental changes in plants, the auxin treatment of explants was reported to be an indispensable inducer of somatic embryogenesis (SE) in a large number of plant species. Treating in vitro-cultured tissue with auxins (primarily 2,4-dichlorophenoxyacetic acid, which is a synthetic auxin-like plant growth regulator) results in the extensive reprogramming of the somatic cell transcriptome, which involves the modulation of numerous SE-associated transcription factor genes (TFs). A number of SE-modulated TFs that control auxin metabolism and signalling have been identified, and conversely, the regulators of the auxin-signalling pathway seem to control the SE-involved TFs. In turn, the different expression of the genes encoding the core components of the auxin-signalling pathway, the AUXIN/INDOLE-3-ACETIC ACIDs (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs), was demonstrated to accompany SE induction. Thus, the extensive crosstalk between the hormones, in particular, auxin and the TFs, was revealed to play a central role in the SE-regulatory network. Accordingly, LEAFY COTYLEDON (LEC1 and LEC2), BABY BOOM (BBM), AGAMOUS-LIKE15 (AGL15) and WUSCHEL (WUS) were found to constitute the central part of the complex regulatory network that directs the somatic plant cell towards embryogenic development in response to auxin. The revealing picture shows a high degree of complexity of the regulatory relationships between the TFs of the SE-regulatory network, which involve direct and indirect interactions and regulatory feedback loops. This review examines the recent advances in studies on the auxin-controlled genetic network, which is involved in the mechanism of SE induction and focuses on the complex regulatory relationships between the down- and up-stream targets of the SE-regulatory TFs. In particular, the outcomes from investigations on Arabidopsis, which became a model plant in research on genetic control of SE, are presented.