Characterization of S-triazine herbicide metabolism by a Nocardioides sp. isolated from agricultural soils

Nocardioides: "Specialists" for Hard-to-Degrade Pollutants in the Environment

Nocardioides, a genus belonging to Actinomycetes, can endure various low-nutrient conditions. It can degrade pollutants using multiple organic materials such as carbon and nitrogen sources. The characteristics and applications of Nocardioides are described in detail in this review, with emphasis on the degradation of several hard-to-degrade pollutants by using Nocardioides, including aromatic compounds, hydrocarbons, haloalkanes, nitrogen heterocycles, and polymeric polyesters. Nocardioides has unique advantages when it comes to hard-to-degrade pollutants. Compared to other strains, Nocardioides has a significantly higher degradation rate and requires less time to break down substances. This review can be a theoretical basis for developing Nocardioides as a microbial agent with significant commercial and application potential.

Characterization of endophytic bacteriome diversity and associated beneficial bacteria inhabiting a macrophyte Eichhornia crassipes

Introduction

The endosphere of a plant is an interface containing a thriving community of endobacteria that can affect plant growth and potential for bioremediation. Eichhornia crassipes is an aquatic macrophyte, adapted to estuarine and freshwater ecosystems, which harbors a diverse bacterial community. Despite this, we currently lack a predictive understanding of how E. crassipes taxonomically structure the endobacterial community assemblies across distinct habitats (root, stem, and leaf).

Methods

In the present study, we assessed the endophytic bacteriome from different compartments using 16S rRNA gene sequencing analysis and verified the in vitro plant beneficial potential of isolated bacterial endophytes of E. crassipes.

Results and discussion

Plant compartments displayed a significant impact on the endobacterial community structures. Stem and leaf tissues were more selective, and the community exhibited a lower richness and diversity than root tissue. The taxonomic analysis of operational taxonomic units (OTUs) showed that the major phyla belonged to Proteobacteria and Actinobacteriota (> 80% in total). The most abundant genera in the sampled endosphere was Delftia in both stem and leaf samples. Members of the family Rhizobiaceae, such as in both stem and leaf samples. Members of the family Rhizobiaceae, such as Allorhizobium- Neorhizobium-Pararhizobium-Rhizobium were mainly associated with leaf tissue, whereas the genera Nannocystis and Nitrospira from the families Nannocystaceae and Nitrospiraceae, respectively, were statistically significantly associated with root tissue. Piscinibacter and Steroidobacter were putative keystone taxa of stem tissue. Most of the endophytic bacteria isolated from E. crassipes showed in vitro plant beneficial effects known to stimulate plant growth and induce plant resistance to stresses. This study provides new insights into the distribution and interaction of endobacteria across different compartments of E. crassipes Future study of endobacterial communities, using both culture-dependent and -independent techniques, will explore the mechanisms underlying the wide-spread adaptability of E. crassipesto various ecosystems and contribute to the development of efficient bacterial consortia for bioremediation and plant growth promotion.

Characterization and catalytic mechanism of a direct demethylsulfide hydrolase for catabolism of the methylthiol-s-triazine prometryn

Demethylthio is one of the most important ways for microorganisms to metabolize triazine herbicides. Previous studies have found that the initial reaction of prometryn catabolism in Leucobacter triazinivorans JW-1 was the hydroxylation of its methylthio group, however, the corresponding functional enzyme was not yet clear. In this study, the gene proA was responsible for the initial step of prometryn catabolism from the strain JW-1 was cloned and expressed, and the purified amidohydrolases ProA have the ability to transform prometryn to 2-hydroxypropazine and methanethiol. The optimized reaction temperature and pH of ProA were 45 °C and 7.0, respectively, and the kinetic constants K_m and V_max of ProA for the catalysis of prometryn were 32.6 μM and 0.09 μmol/min/mg, respectively. Molecular docking analyses revealed that different catalysis efficiency of ProA and TrzN (Nocardioides sp. C190) for prometryn and atrazine was due to non-covalent changes in amino acid residues. Our findings provide new insights into the understanding of s-triazine catabolism at the molecular level.

Volatile compounds for biotechnological applications produced during competitive interactions between yeasts and fungi

Fungi, yeasts and bacteria produce volatile compounds during their metabolism. In this study, the volatile compounds produced by yeast strains (Saccharomyces cerevisiae and Rhodotorula mucilaginosa) and fungal strains (Aspergillus carbonarius and Aspergillus ochraceus) during competitive interactions were investigated by solid-phase microextraction coupled with gas chromatography-mass spectrometry. Fifty-six volatile compounds were identified representing alcohols, aldehydes, esters, ketones, aromatic compounds, acids, furans, phenols, and nitrogen compounds, being the largest amount in the class of esters and alcohols. Eight compounds were identified only in interactive culture conditions such as 2-amino-1-propanol, isopropylamine, dimethylamine, pentyl propanoate, ethyl-2-aminopropanoate, acetone, oxalic acid, and β-elemene and five of these were produced in cocultures including A. carbonarius. These will be developed for future biotechnological applications such as in the pharmaceutical and biological industry to produce drugs. Antimicrobial and antifungal activities; Solvent and herbicide; flavoring ingredient; solvent, plastic synthesis, nail polish remover and thinner, pesticide and herbicide; important in the complexation of minerals in the soil; and plant-environment interactions, defending predators, pathogens, and competitors.

Ultimate fate and possible ecological risks associated with atrazine and its principal metabolites (DIA and DEA) in soil and water environment

Atrazine (AT) is a triazine herbicide widely used to control weeds in several crops. De-isopropylatrazine (DIA) and de-ethylatrazine (DEA) are two of the eight primary metabolites produced by AT breakdown in soil and water. The physico-chemical properties of the soil determine their final fate. So, this study aimed to assess the function of clay loam and sandy loam soils in determining their ultimate fate and the potential ecological risks to non-target species during their persistence in soil and transportation to water bodies. The soil in pots was spiked with standard solutions of AT, DEA, and DIA at 0.3 and 0.6 mg/kg for the persistence study. The leaching potential was determined by placing soils in Plexi columns and spiking them with 50 and 100 µg standard solutions. Liquid-liquid extraction was used to prepare the samples, which were then analyzed using GC-MS/MS. The dynamics of dissipation were first-order. AT, DEA and DIA disappeared rapidly in sandy loam soil, with half-lives ranging from 6.2 to 8.4 days. AT and its metabolites had a significant amount of leaching potential. In sandy loam soil, leaching was more effective, resulting in maximal residue movement up to 30-40 cm soil depth. The presence of a notable collection of residues in leachate fractions suggests the potential for surface and groundwater contamination. In particular, DEA and DIA metabolites caused springtail Folsomia candida and earthworm Eisenia fetida to have longer and greater unacceptable risks. If the residues comparable to the amount acquired in leachate fractions reach water bodies, they could cause toxicity to a variety of freshwater fish, aquatic arthropods, amphibians, and aquatic invertebrates. Future studies should take a more comprehensive approach to evaluate ecological health and dangers to non-target species.

Bacterial community structure and diversity in the rhizospheric soil of Robinia pseudoacacia and Juniperus sabina planted in iron tailings matrix

Iron tailings matrix is deficient in nutrients, and phytoremediation is one of the effective methods to improve tailings nutrients. The response of phytoremediation to tailings microorganisms remains to be studied. The present study analyzed rhizospheric soil of two kinds of plants bacterial diversity and community structure and their relationship with soil environmental factors. The results indicate that the rhizospheric soil bacteria species of Robinia pseudoacacia and Juniperus sabina were not significantly different from that of bare tailings, but rhizospheric soil bacterial community compositions and abundance were significantly different from that of bare tailings. Canonical correlation analysis (CCA) showed that soil alkali-hydrolyzable nitrogen (AN), soil total nitrogen (TN), and soil organic matter (SOM) were the main environmental factors affecting bacterial community diversity. Spearman's correlation analysis showed that AN, TN, and SOM were significantly positively correlated with the relative abundance of Gemmatimonadetes and Nitrospirae, and were significantly negatively correlated with that of Firmicutes, Fusobacteria, and Bacteroidetes. FAPROTAX function prediction showed that the functional microbial communities of rhizospheric soil of the two plants were significantly different from those of bare tailings. Overall, the findings support an increase of microbial diversity, SOM, and nitrogen in rhizospheric soil of revegetated tailings compared to bare tailings. These results provide theoretical support for the development and application of phytoremediation in abandoned mines.

Abiotic transformation of atrazine in aqueous phase by biogenic bixbyite-type Mn2O3 produced by a soil-derived Mn(II)-oxidizing bacterium of Providencia sp

Recently, biogenic Mn oxides (BioMnO_x) are considered as the promising degradation agents for environmental organic contaminants. However, little information is available for the degradation of atrazine by BioMnO_x. In this work, BioMnO_x, generated by a soil-derived Mn(II)-oxidizing bacterium, Providencia sp. LLDRA6, was explored to degrade atrazine. To begin with, collective results from mineral characterization analyses demonstrated that this BioMnO_x was biogenic bixbyite-type Mn₂O₃. After that, purified biogenic Mn₂O₃ was found to exhibit a much higher removal efficiency for atrazine in aqueous phase, as compared to unpurified biogenic Mn₂O₃ and LLDRA6 biomass. During the atrazine removal by biogenic Mn₂O₃, six intermediate degradation products were discovered, comprising deethylatrazine (DEA), hydroxylatrazine (HA), deethylhydroxyatrazine (DEHA), ammeline, cyanuric acid, and 5-methylhexahydro-1,3,5-triazine-2-thione (MTT). Particularly, the intermediate, MTT, was considered as a new degradation product of atrazine, which was not described previously. Meanwhile, Mn(II) ions were released from biogenic Mn₂O₃, and on the surface of biogenic Mn₂O₃, the content of hydroxyl O species increased at the expense of that of lattice and water O species, but the fundamental crystalline structure of this Mn oxide remained unchanged. Additionally, no dissociative Mn(III) was found to involve in atrazine degradation. In summary, these results demonstrated that both the non-oxidative and oxidative reactions underlay the degradation of atrazine by biogenic Mn₂O₃.

Comparison of bacterial diversity, root exudates and soil enzymatic activities in the rhizosphere of AVP1-transgenic and non-transgenic wheat (Triticum aestivum L.)

AIMS

Soil microbial communities are among the most diverse communities that might be affected due to transgenic crops. Therefore, risk assessment studies on transgenes are essentially required as any adverse effects may depend not only on the specific gene and crop involved but also on soil conditions.

METHODS AND RESULTS

The present study deals with the comparison of bacterial populations, root exudates, and activities of soil enzymes in non-transgenic and AVP1-transgenic wheat rhizosphere, overexpressing vacuolar H+pyrophosphatase for salinity and drought stress tolerance. Amounts of organic acids and sugars produced as root exudates and activities of dehydrogenase, phosphatase, and protease enzymes in soil solution showed no significant differences in AVP1-transgenic and non-transgenic wheat rhizosphere, except for urease and phenol oxidase activities. The higher copy number of nifH gene showed the abundance of nitrogen-fixing bacteria in the rhizosphere of AVP1-transgenic wheat compared with non-transgenic wheat. nifH gene sequence analysis indicated the common diazotrophic genera Azospirillum, Bradyrhizobium, Rhizobium, and Pseudomonas in AVP1-transgenic and non-transgenic wheat except for Zoogloea detected only in non-transgenic wheat. Using 454-pyrosequencing of 16S rRNA gene from soil DNA, a total of 156, 282 sequences of 18 phyla were obtained, which represented bacterial (128,006), Archeal (7,928), and unclassified (21,568) sequences. Proteobacteria, Crenarchaeota, and Firmicutes were the most abundant phyla in transgenic and non-transgenic wheat rhizosphere. Further comparison of different taxonomic units at the genus level showed similar distribution in transgenic and non-transgenic wheat rhizosphere.

CONCLUSION

We conclude that AVP1 gene in transgenic wheat has no apparent adverse effects on the soil environment and different bacterial communities. However, bacterial community depends on several other factors not only genetic composition of the host plants.

SIGNIFICANCE OF THE STUDY

The present research supports introduction and cultivation of transgenic plants in agricultural systems without any adverse effects on indigenous bacterial communities and soil ecosystem.

Disturbance by soil mixing decreases microbial richness and supports homogenizing community assembly processes

The spatial heterogeneity of soil’s microhabitats warrants the study of ecological patterns and community assembly processes in the context of physical disturbance that disrupts the inherent spatial isolation of soil microhabitats and microbial communities. By mixing soil at various frequencies in a 16-week lab incubation, we explored the effects of physical disturbance on soil bacterial richness, community composition, and community assembly processes. We hypothesized that well-mixed soil would harbor a less rich microbial community, with community assembly marked by homogenizing dispersal and homogeneous selection. Using 16S rRNA gene sequencing, we inferred community assembly processes, estimated richness and differential abundance, and calculated compositional dissimilarity. Findings supported our hypotheses, with > 20% decrease in soil bacterial richness in well-mixed soil. Soil mixing caused communities to diverge from unmixed controls (Bray–Curtis dissimilarity; 0.75 vs. 0.25), while reducing within-group heterogeneity. Our results imply that the vast diversity observed in soil may be supported by spatial heterogeneity and isolation of microbial communities, and also provide insight into the effects of physical disturbance and community coalescence events. By isolating and better understanding the effects of spatial heterogeneity and disconnectivity on soil microbial communities, we can better extrapolate how anthropogenic disturbances may affect broad soil functions.

Land use and roles of soil bacterial community in the dissipation of atrazine

Atrazine (ATZ) is one of the most widely used herbicides in the world even though it is classified as a carcinogenic endocrine disruptor. This study focused on how land use (grazing versus cultivation in parallel soils, the latter under no-till with a seven-year history of ATZ application) and bacterial community diversity affected ATZ dissipation. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, and Gemmatimonadetes were the dominant phyla in both soils. The mineralization of ATZ was much higher in soils under cultivation up to the onset of moderate diversity depletion (dilution =10^-3), corresponding to 44-52% of the amount applied (< 5% in the grazed soil). This was attributed to the higher diversity and complexity of the soils´ bacterial communities which consist of microbial groups that were more adapted as a result of previous exposure to ATZ. In these cases, ATZ dissipation was attributed mainly to mineralization (DT₅₀ = 4-11 d). However, formation of non-extractable ATZ residues was exceptionally important in the other cases (DT₅₀ = 17-44 d). The cultivated soils also presented a higher number of bacterial genera correlated with ATZ dissipation, in which Acidothermus, Aquicela, Arenimonas, Candidatus_Koribacter, Hirschia, MND1, Nitrospira, Occallatibacter, OM27_clade, and Ralstonia are suggested as potential ATZ-degraders. Finally, ATZ dissipation was mostly associated with an abundance of microbial functions related to energy supply and N-metabolism, suggesting co-metabolism is its first biodegradation step.

Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste

Strain NGK65T, a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. Strain NGK65T hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 °C, in 0–1% NaCl and at pH 7.5–8.0. Glycerol, d-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate, sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. The predominant membrane fatty acids were iso-C16:0 followed by iso-C17:0 and C18:1 ω9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. The cell-wall peptidoglycan type was A3γ, with ll-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65T belongs to the genus Nocardioides (phylum Actinobacteria ), appearing most closely related to Nocardioides daejeonensis MJ31T (98.6%) and Nocardioides dubius KSL-104T (98.3%). The genomic DNA G+C content of strain NGK65T was 68.2%. Strain NGK65T and the type strains of species involved in the analysis had average nucleotide identity values of 78.3–71.9% as well as digital DNA–DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides . Based on phenotypic and molecular characterization, strain NGK65T can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. The type strain is NGK65T (=DSM 113112T=NCCB 100846T).

Soil bacterial community dynamics following bioaugmentation with Paenarthrobacter sp. W11 in atrazine-contaminated soil

Atrazine is one of the most widely used herbicides, however it and its metabolites cause widespread contamination in soil and ground water. Bioaugmentation is an effective method for remediation of environmental organic pollutants. High-throughput sequencing provides an important tool for understanding the changes of microbial community and function in response to pollutants degradation based on bioaugmentation. In this study, the effect of biodegradation with Paenarthrobacter sp. W11 and the change of microbial community during atrazine degradation were investigated. The results showed that bioaugmentation significantly accelerated the degradation rate of atrazine in soil and reduced the toxic effect of atrazine residues on wheat growth. The extra available NH₄⁺ through atrazine mineralization could serve as a nitrogen source to increase microbial numbers. High-throughput sequencing further revealed that the microbial community restored a new balance. The function of microbial community predicted by PICRUSt2 suggested that the biodegradation process of atrazine affected not only the atrazine degradation pathway, but also the nitrogen metabolism pathway. Methylobacillus and Pseudomonas were considered as the most important indigenous atrazine-degrading microorganisms, because their relative abundances were positively correlated with the relative abundance of Paenarthrobacter and atrazine degradation pathway. This study provides insight into the cooperation between indigenous microorganisms and external inoculums on atrazine degradation process.

Repeated sampling of individuals reveals impact of tropical and temperate habitats on microbiota of a migratory bird

Migratory animals experiencing substantial change in diet and habitat across the annual cycle may have corresponding shifts in host-associated microbial diversity. Using automated telemetry and radio tags to recapture birds, we examined gut microbiota structure in the same population and often same individual of Kirtland's Warblers (Setophaga kirtlandii) initially sampled on their wintering grounds in The Bahamas and subsequently resampled within their breeding territories in Michigan, USA. Initial sampling occurred in March and April and resampling occurred in May, June and early July. The composition of the most abundant phyla and classes of the warblers' microbiota is similar to that of other migratory birds. However, we detected notable variation in abundance and diversity of numerous bacterial taxa, including a decrease in microbial richness and significant differences in microbial communities when comparing the microbiota of birds first captured in The Bahamas to that of birds recaptured in Michigan. This is observed at the individual and population level. Furthermore, we found that 22 bacterial genera exhibit heightened abundance within specific sampling periods and are probably associated with diet and environmental change. Finally, we described a small, species-specific shared microbial profile that spans multiple time periods and environments within the migratory cycle. Our research highlights that the avian gut microbiota is dynamic over time, most significantly impacted by changing environments associated with migration. These results support the need for full annual cycle monitoring of migratory bird microbiota to improve understanding of seasonal host movement ecologies and response to recurrent physiological stressors.

Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1

The genus Pseudomonas is widely recognized for its potential for environmental remediation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmental stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrading various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger monooxygenase (BVMO) encoded by a gene in the chromosome of strain DY-1. The result of gene knock-out suggested that the sulfate starvation-induced (SSI) genes in this strain might also involve in the process of prometryne degradation. These results would provide the molecular basis for the application of strain DY-1 in various fields and would contribute to the study of prometryne biodegradation mechanism as well.

Network-directed isolation of the cooperator Pseudomonas aeruginosa ZM03 enhanced the dibutyl phthalate degradation capacity of Arthrobacter nicotianae ZM05 under pH stress

Dibutyl phthalate (DBP), widely used as plasticizer, is a typical soil contaminant. A new isolate, Arthrobacter nicotianae ZM05, is efficient at degrading DBP but lacks stress resistance to adverse environments. In this study, to isolate effective cooperators of strain ZM05 under pH stress and explore the effects of DBP on the bacterial community structure and interaction between bacteria, a microcosm experiment was conducted by supplying the exogenous DBP-degrading bacteria ZM05. 16S rRNA gene sequencing analysis showed that DBP contamination decreased microbial community diversity and weakened potential interactions between microorganisms, evidenced by fewer links, lower average degree, and lower average clustering coefficients in the cooccurrence network. Furthermore, the subnetworks showed that DBP shifted the interactions between strain ZM05 and other microbes. Based on the prediction of the network, the nondegrading bacterium Pseudomonas aeruginosa ZM03 was isolated and proven through coculture experiments to have a positive interaction with strain ZM05 during DBP degradation under pH stress. Strain ZM03 could utilize downstream acidic metabolites to alleviate acid inhibition and accelerate degradation. This study provides solid evidence that bacterial communities adjust their interactions to adapt to DBP stress and provides new insight into the prediction of microbes that are cooperative with degrading bacteria.

Isolation and Identification of Pseudomonas sp. Strain DY-1 from Agricultural Soil and Its Degradation Effect on Prometryne

Prometryne is a widely used herbicide in China to control annual grasses and broadleaf weeds. However, the stability of prometryne makes it difficult to be degraded, which poses a threat to human health. This study presents a bacterial strain isolated from soil samples with a prometryne application history, designated strain DY-1. Strain DY-1, identified as Pseudomonas sp., is capable of utilizing prometryne as a sole carbon source for growth and degrading 100% of prometryne within 48 h from an initial concentration of 50 mg L^-1. To further optimize the degradation of prometryne, the prometryne concentration, temperature, pH, and salt concentration were examined. The optimal conditions for degradation of prometryne by strain DY-1 were an initial prometryne concentration of 50 mg L^-1, 30 °C, pH 7-8, and NaCl concentration of 200 mg L^-1. The same strain also degraded other s-triazine herbicides, including simetryne, ametryne, desmetryne, and metribuzin, under the same conditions. The biodegradation pathway of prometryne was established by isolating sulfoxide prometryne as the first metabolite and by the identification of sulfone prometryne and 2-hydroxy prometryne by liquid chromatography-mass spectrometry (LC-MS/MS). The results illustrated that strain DY-1 achieved the removal of prometryne by gradually oxidizing and hydrolyzing the methylthio groups. A bioremediation trial with contaminated soil and pot experiments showed that after treating the prometryne-contaminated soil with strain DY-1, the content of prometryne was significantly reduced (P < 0.05). This study provides an efficient bacterial strain and approach that could be potentially useful for detoxification and bioremediation of prometryne analogs.

Purification, characterization, and catalytic mechanism of N-Isopropylammelide isopropylaminohydrolase (AtzC) involved in the degradation of s-triazine herbicides

Deamination is ubiquitous in nature and has important biological significance. Leucobacter triazinivorans JW-1, recently isolated from sludge, can rapidly degrade s-triazine herbicides. The responsible enzymes, however, have not been purified and characterized. Herein, we purified an amidohydrolase, i.e., N-isopropylammelide isopropylaminohydrolase (AtzC) from JW-1 cells by ammonium sulfate precipitation and three chromatography steps. The purified AtzC catalyzed amidohydrolysis of N-isopropylammelide to cyanuric acid. The optimal catalytic conditions of the purified AtzC were 42 °C and pH 7.0, and the K_m and V_max of AtzC was 0.811 mM and 28.19 mmol/min·mg. AtzC could catalyze amidohydrolysis of an N-alkyl substituent from dihydroxy s-triazines to cyanuric acid. Molecular docking and structural alignments were used to infer AtzC catalytic mechanism. The structural architecture of AtzC resembled that of cytosine deaminase in class III amidohydrolase, with a single Zn²⁺ coordinated by His and Asp. Interestingly, the AtzC lacks an acidic residue putatively to activate water for hydrolysis as compared to the other amidohydrolases. His253 in AtzC probably functions as a single general acid-base catalyst. These findings further enhance our understanding how aminohydrolases catalyze the metabolism of s-triazine herbicides.

AQP2 as a target of lycopene protects against atrazine-induced renal ionic homeostasis disturbance

Atrazine (ATR), a ubiquitous environmental contaminant in water and soil, causes environmental nephrosis. To reveal the toxic effect of ATR on the kidney and the potential chemical nephroprotective effect of lycopene (LYC), Kun-Ming mice of specific pathogen-free (SPF) grade were treated with LYC (5 mg kg-1) and/or ATR (50 mg kg-1 or 200 mg kg-1) for 21 days. The degree of renal injury was evaluated by measuring the ion concentration, ATPase activities and the mRNA expressions/levels of associated ATPase subunits. In addition, the expression of renal aquaporins (AQPs) was analyzed. The results showed that the renal tubular epithelial cells of ATR-exposed mice were swollen, the glomeruli were significantly atrophied, and the ion concentrations were obviously changed. The activity of Na+-K+-ATPase and the transcription of its subunits were downregulated. The activity of Ca2+-Mg2+-ATPase and the transcription of its subunits were upregulated. The expression of AQPs, especially the critical AQP2, was affected. Notably, ATR-induced nephrotoxicity was significantly improved by LYC supplementation. Therefore, LYC could protect the kidney against ATR-induced nephrotoxicity via maintaining ionic homeostasis, reversing the changes in ATPase activity and controlling the expression of AQPs on the cell membrane. These results suggested that AQP2 was a target of LYC and protected against ATR-induced renal ionic homeostasis disturbance.

Atrazine Removal from Municipal Wastewater Using a Membrane Bioreactor

As the demand for potable water increases, direct potable reuse of wastewater is an attractive alternative method to produce potable water. However, implementation of such a process will require the removal of emerging contaminants which could accumulate in the drinking water supply. Here, the removal of atrazine, a commonly used herbicide, has been investigated. Using real and synthetic wastewater, as well as sludge from two wastewater treatment facilities in the United States in Norman, Oklahoma and Fayetteville, Arkansas, atrazine removal has been investigated. Our results indicate that about 20% of the atrazine is removed by adsorption onto the particulate matter present. Significant biodegradation of atrazine was only observed under aerobic conditions for sludge from Norman, Oklahoma. Next-generation sequencing of the activated sludge revealed the abundance of Noncardiac with known atrazine degradation pathways in the Norman aerobic sludge, which is believed to be responsible for atrazine biodegradation in our study. The detection of these bacteria could also be used to determine the likelihood of biodegradation of atrazine for a given wastewater treatment facility.

Soil bacterial diversity correlates with precipitation and soil pH in long-term maize cropping systems

Unraveling the key drivers of bacterial community assembly in agricultural soils is pivotal for soil nutrient management and crop productivity. Presently, the drivers of microbial community structure remain unexplored in maize cropping systems under complex and variable environmental scenarios across large spatial scales. In this study, we conducted high-throughput 16S rRNA gene sequencing and network analysis to identify the major environmental factors driving bacterial community diversity and co-occurrence patterns in 21 maize field soils across China. The results show that mean annual precipitation and soil pH are the major environmental factors that shape soil bacterial communities in maize soils. The similarities of bacterial communities significantly decreased with increasing geographic distance between different sites. The differences in spatial turnover rates across bacterial phyla indicate the distinct dispersal capabilities of bacterial groups, and some abundant phyla exhibited high dispersal capabilities. Aeromicrobium, Friedmanniella, Saccharothrix, Lamia, Rhodococcus, Skermanella, and Pedobacter were identified as keystone taxa. Based on the node-level and network-level topological features, members of the core microbiome were more frequently found in the center of the ecosystem network compared with other taxa. This study highlights the major environmental factors driving bacterial community assembly in agro-ecosystems and the central ecological role of the core microbiome in maintaining the web of complex bacterial interactions.

Biodegradation of ritalinic acid by Nocardioides sp. - Novel imidazole-based alkaloid metabolite as a potential marker in sewage epidemiology

The consumption of methylphenidate, a nootropic drug used to improve mental performance, is becoming increasingly serious. Methylphenidate is metabolized in human liver to ritalinic acid, which has been commonly detected in sewage and surface waters. Additionally, ritalinic acid serves as a biomarker in sewage epidemiology studies. Thus knowledge of the stability and microbial degradation pathways of ritalinic acid is essential for proper estimation of methylphenidate consumption. In the study reported here, we describe the fast formation of a previously unknown, dead-end metabolite of ritalinic acid by Nocardioides sp. strain MW5. HRMS and 2D NMR analyses allowed precisely identification of the compound as an imidazole-based alkaloid cation with chemical formula 11-[3-(formylamino)propyl]-1,2,3,4,6,7,8,9-octahydrodipyrido[1,2-a:1',2'-c]imidazole-5-ium. In experiments, Nocardioides sp. strain MW5 transformed 34% of ritalinic acid into this metabolite, while 52% was mineralized into CO₂. Alkaloid was not biodegraded during the OECD 301 F test. This study provides new insight into the environmental fate of methylphenidate and its metabolites. The data collected are essential for assessing nootropic drug consumption by sewage epidemiology and should lead to a better understanding of microbial degradation of ritalinic acid.

Influence of terminal electron-accepting conditions on the soil microbial community and degradation of organic contaminants of emerging concern

Better understanding of the fate and persistence of trace organic contaminants of emerging concern (CEC) in agricultural soils is critical for assessing the risks associated with using treated wastewater effluent to irrigate crops and land application of wastewater biosolids. This study reports on the influence of prevailing terminal electron-accepting processes (TEAPs, i.e., aerobic, nitrate-reducing, iron(III)-reducing, and sulfate-reducing conditions) and exposure to a mixture of nine trace CEC (90 ng/g each) on both the microbial community structure and CEC degradation in agricultural soil. DNA analysis revealed significant differences in microbial community composition following establishment of different TEAPs, but no significant change upon exposure to the mixture of CEC. The largest community shift was observed after establishing nitrate-reducing conditions and the smallest shift for sulfate-reducing conditions. Two of the CEC (atrazine and sulfamethoxazole) showed significant degradation in both bioactive and abiotic (i.e., sterilized) conditions, with half-lives ranging from 1 to 64 days for different TEAPs, while six of the CEC (amitriptyline, atenolol, trimethoprim, and three organophosphate flame retardants) only degraded in bioactive samples, with half-lives ranging from 27 to 90 days; carbamazepine did not degrade appreciably within 90 days in any of the incubations. Amplicon sequence variants (ASVs) from Firmicutes Hydrogenispora, Gemmatimonadetes Gemmatimonadaceae, and Verrucomicrobia OPB34 soil group were identified as potentially responsible for the biodegradation of organophosphate flame retardants, and ASVs from other taxa groups were suspected to be involved in biodegrading the other target CEC. These results demonstrate that CEC fate and persistence in agricultural soils is influenced by the prevailing TEAPs and their influence on the microbial community, suggesting the need to incorporate these factors into contaminant fate models to improve risk assessment predictions.

Bacterial catabolism of s-triazine herbicides: biochemistry, evolution and application

The synthetic s-triazines are abundant, nitrogen-rich, heteroaromatic compounds used in a multitude of applications including, herbicides, plastics and polymers, and explosives. Their presence in the environment has led to the evolution of bacterial catabolic pathways in bacteria that allow use of these anthropogenic chemicals as a nitrogen source that supports growth. Herbicidal s-triazines have been used since the mid-twentieth century and are among the most heavily used herbicides in the world, despite being withdrawn from use in some areas due to concern about their safety and environmental impact. Bacterial catabolism of the herbicidal s-triazines has been studied extensively. Pseudomonas sp. strain ADP, which was isolated more than thirty years after the introduction of the s-triazine herbicides, has been the model system for most of these studies; however, several alternative catabolic pathways have also been identified. Over the last five years, considerable detail about the molecular mode of action of the s-triazine catabolic enzymes has been uncovered through acquisition of their atomic structures. These structural studies have also revealed insights into the evolutionary origins of this newly acquired metabolic capability. In addition, s-triazine-catabolizing bacteria and enzymes have been used in a range of applications, including bioremediation of herbicides and cyanuric acid, introducing metabolic resistance to plants, and as a novel selectable marker in fermentation organisms. In this review, we cover the discovery and characterization of bacterial strains, metabolic pathways and enzymes that catabolize the s-triazines. We also consider the evolution of these new enzymes and pathways and discuss the practical applications that have been considered for these bacteria and enzymes. One Sentence Summary: A detailed understanding of bacterial herbicide catabolic enzymes and pathways offer new evolutionary insights and novel applied tools.

Toxicity comparison of three imidazolium bromide ionic liquids to soil microorganisms

Ionic liquids (ILs) are extensively used in several chemistry fields. And research about the effects of ILs on soil microbes is needed. In this study, brown soil was exposed to 1-butyl-3-methylimidazolium bromide ([C₄mim]Br), 1-hexyl-3-methylimidazolium bromide ([C₆mim]Br) and 1-decyl-3-methylimidazolium bromide ([C₁₀mim]Br). The toxicities of the three ILs are evaluated by measuring the soil culturable microbial number, enzyme activity, microbial diversity and, abundance of the ammonia monooxygenase (amoA) genes of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Results showed that all tested ILs caused a decrease in culturable microbial abundance. Tested ILs exposure inhibit urease activity and promote acid phosphatase and β-glucosidase activities. Tested ILs reduced soil microbial diversity and the abundances of AOB-amoA and AOA-amoA genes significantly. After a comparison of the integrated biomarker response (IBR) index, the toxicities of tested ILs to soil microorganisms were as follows: [C₁₀mim]Br > [C₆mim]Br > [C₄mim]Br. Among all collected biomarkers, the abundance of the AOA-amoA gene was the most sensitive one and was easily affected after ILs exposure.

Dominant role of abundant rather than rare bacterial taxa in maintaining agro-soil microbiomes under environmental disturbances

Elucidating the mechanisms underpinning the responses of abundant and rare microbial taxa to environmental disturbances is essential for understanding the biodiversity-stability relationship and maintaining microbial diversity. Here, we explored the response patterns of abundant and rare bacterial taxa to disturbances by invasive plant growth and oil contamination in agricultural soils across a large spatial scale (latitude gradient = 18.62°-46.51°). Our meta-analysis based on existing Illumina sequencing datasets showed that abundant taxa persisted under the disturbances whereas rare taxa were more easily affected, indicating the higher resilience or resistance of abundant taxa to disturbances. The responses of abundant taxa were associated with mean annual temperature at the sampling sites, while rare taxa instead showed stochastic responses. There were significantly negative linear regressions between bacterial α-diversity and community dissimilarities (disturbed vs. undisturbed soils), suggesting stronger resilience or resistance in those bacterial communities with higher α-diversity. This resilience or resistance was mainly associated with the α-diversity of abundant taxa. Our network analysis showed that the disturbances substantially decreased the strength of the connections, loosened the co-occurrence relationships, and reshaped the complex bacterial interactions. In the undisturbed soils, abundant taxa were located in central positions within the network more often than were rare taxa, while these trends were reversed in the disturbed soils. Our results suggest that abundant taxa play a dominant role in the stability and maintenance of agro-soil bacterial communities, while rare taxa could greatly influence local bacterial interactions under environmental disturbances.

Dissipation, dehalogenation, and denitration of chloroaromatic compounds by Nocardioides sp. strain PD653: Characterization of the substrate specificity

The substrate range of Nocardioides sp. strain PD653, capable of mineralizing hexachlorobenzene, was investigated based on the dissipation of substrates and the liberation of halogen ions. Strain PD653 dehalogenated 10 out of 18 halophenol congeners; however, it could dehalogenate only hexachlorobenzene out of seven halobenzene congeners tested. Moreover, dehalogenation activities were shown for chloronitrobenzenes, along with an increase in the number of substituted chlorine atoms except for 2,3,4,5-tetrachloro-1-nitrobenzene. These results suggested that this strain might be applicable to remediate soil contaminated with these persistent chloroaromatic compounds.

Pesticide detection by a miniature microbial fuel cell under controlled operational disturbances

Microbial fuel cell (MFC) technology holds enormous potential for inexpensive real-time and onsite testing of water sources. With the intent of defining optimal operational conditions, we investigated the effect of environmental factors (changes in temperature, pH and ionic strength), on the performance of a single chamber miniature MFC sensor. The pH of the influent had the greatest effect on the MFC performance, with a 0.531 ± 0.064 μA cm^-2 current variation per unit change of pH. Within the range tested, temperature and ionic strength had only a minor impact (0.010 ± 0.001 μA °C^-1 cm^-2 and of 0.027 ± 0.003 μA mS^-1 cm cm^-2 respectively). Under controlled operational conditions, for the first time, we demonstrated the ability of this biosensor to detect one of the most commonly applied pesticides worldwide, atrazine. The sensitivity to atrazine was 1.39 ± 0.26 ppm^-1 cm^-2, with a detection range of 0.05-0.3 ppm. Guidelines for systematic studies of MFC biosensors for practical applications through a factorial design approach are also provided. Consequently, our work not only enforces the promise of miniature MFC biosensors for organic pollutants detection in waters, but it also provides important directions towards future investigations for infield applications.

Non-synchronous Structural and Functional Dynamics During the Coalescence of Two Distinct Soil Bacterial Communities

Soil is a unique environment in which the microbiota is frequently subjected to community coalescence. Additions of organic fertilizer and precipitation of dust induce coalescent events in soil. However, the fates of these communities after coalescence remain uncharted. Thus, to explore the effects of microbiota coalescence, we performed reciprocal inoculation and incubation experiments in microcosms using two distinct soils. The soils were, respectively, collected from a cropland and an industrial site, and the reciprocal inoculation was performed as models for the incursion of highly exotic microbiota into the soil. After incubation under either aerobic or anaerobic conditions for two months, the soils were assayed for their bacterial community structure and denitrification function. According to the 16S rRNA gene sequencing results, the inoculated soil showed a significant shift in bacterial community structure after incubation-particularly in the industrial soil. The structures of the bacterial communities changed following the coalescence but were predicted to have the same functional potential, e.g., nitrogen metabolism, as determined by the quantification of denitrifying genes and nitrogen gas production in the inoculated soil samples, which showed values equivalent those in the original recipient soil samples regardless of inoculum used. The functional prediction based on the known genomes of the taxa that shifted in the incubated sample communities indicates that the high functional overlap and redundancy across bacteria acted as a mechanism that preserved all the metabolic functions in the soil. These findings hint at the mechanisms underlying soil biodiversity maintenance and ecosystem function.

Defining lower limits of biodegradation: atrazine degradation regulated by mass transfer and maintenance demand in Arthrobacter aurescens TC1

Exploring adaptive strategies by which microorganisms function and survive in low-energy natural environments remains a grand goal of microbiology, and may help address a prime challenge of the 21st century: degradation of man-made chemicals at low concentrations (“micropollutants”). Here we explore physiological adaptation and maintenance energy requirements of a herbicide (atrazine)-degrading microorganism (Arthrobacter aurescens TC1) while concomitantly observing mass transfer limitations directly by compound-specific isotope fractionation analysis. Chemostat-based growth triggered the onset of mass transfer limitation at residual concentrations of 30 μg L⁻¹ of atrazine with a bacterial population doubling time (t_d) of 14 days, whereas exacerbated energy limitation was induced by retentostat-based near-zero growth (t_d = 265 days) at 12 ± 3 μg L⁻¹ residual concentration. Retentostat cultivation resulted in (i) complete mass transfer limitation evidenced by the disappearance of isotope fractionation (ε¹³C = −0.45‰ ± 0.36‰) and (ii) a twofold decrease in maintenance energy requirement compared with chemostat cultivation. Proteomics revealed that retentostat and chemostat cultivation under mass transfer limitation share low protein turnover and expression of stress-related proteins. Mass transfer limitation effectuated slow-down of metabolism in retentostats and a transition from growth phase to maintenance phase indicating a limit of ≈10 μg L⁻¹ for long-term atrazine degradation. Further studies on other ecosystem-relevant microorganisms will substantiate the general applicability of our finding that mass transfer limitation serves as a trigger for physiological adaptation, which subsequently defines a lower limit of biodegradation.

Restructured fungal community diversity and biological interactions promote metolachlor biodegradation in soil microbial fuel cells

Soil microbial fuel cells (MFCs) provide an inexhaustible electron acceptor for the removal of metolachlor and in situ biocurrent stimulation for fungal activity was investigated. The metolachlor degradation rates enhanced by 33%-36% upon the introduction of electrodes after 23 d. In closed MFCs, the abundance of Mortierella as the most dominant genus increased to 43%-54% from 17% in the original soil, whereas those of Aphanoascus and Penicillium decreased to 0.24%-0.39% and 0.38-0.72% from 14% to 11%, respectively. Additionally, a 10-fold amplification of unique OTUs was observed, mainly from increase on the electrode surface. The different treatments were clustered, especially samples near the cathode. The linear discriminant analysis showed that Aphanoascus fulvescens acted as a biomarker between the original and treated soils. The co-occurrence networks demonstrated that Mortierella universally competed for growth with coexisting species while Cladosporium exhibited the most affiliations with species from the 36 other genera present. The correlation analysis indicated that the species associated with degradation belonged to Mortierella, Kernia, Chaetomium and Trichosporon, while the species associated with electrogenesis were Debaryomyces hansenii and Mortierella polycephala. Importantly, this study is the first to reveal fungal community structure in soil MFCs with degrading pollutants and producing electricity.

Core Microbiota in Agricultural Soils and Their Potential Associations with Nutrient Cycling

Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services.

IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

Whole Cell Actinobacteria as Biocatalysts

Production of fuels, therapeutic drugs, chemicals, and biomaterials using sustainable biological processes have received renewed attention due to increasing environmental concerns. Despite having high industrial output, most of the current chemical processes are associated with environmentally undesirable by-products which escalate the cost of downstream processing. Compared to chemical processes, whole cell biocatalysts offer several advantages including high selectivity, catalytic efficiency, milder operational conditions and low impact on the environment, making this approach the current choice for synthesis and manufacturing of different industrial products. In this review, we present the application of whole cell actinobacteria for the synthesis of biologically active compounds, biofuel production and conversion of harmful compounds to less toxic by-products. Actinobacteria alone are responsible for the production of nearly half of the documented biologically active metabolites and many enzymes; with the involvement of various species of whole cell actinobacteria such as Rhodococcus, Streptomyces, Nocardia and Corynebacterium for the production of useful industrial commodities.

Augmentation of Atrazine biodegradation by two Bacilli immobilized on α-Fe2O3 magnetic nanoparticles

In this study, a novel immobilizing carrier with α-Fe₂O₃ magnetic nanoparticles was developed and used for immobilization of atrazine-degrading bacterial isolates of Bacillus spp. Since the free cells of microorganisms generally not succeed to degrade pollutants; thus, extra treatments are alluring to make strides biodegradation. Scanning electron microscope (SEM) images appeared that after immobilization the bacterial cells were totally retained and entirely distributed on the surface of α-Fe₂O₃ magnetic nanoparticles_. The performance of α-Fe₂O₃ immobilized cells in atrazine (ATZ) degradation was compared with the free cells, which was about 90.56% in 20 days. Experimental results exhibited that ATZ could be degraded at a broad range of physicochemical parameters viz. pH (4.0 to 9.0), temperature (20 to 45 °C), ATZ concentration (50 to 300 mg L⁻¹) and agitation speed (50 to 300 rpm), which underlines that α-Fe₂O₃ immobilized cells could tolerate a higher range of ATZ concentration as compared to free cells. This research demonstrated that α-Fe₂O₃ could be applied as a potential carrier in cell immobilization and biodegradation of ATZ herbicide with greater efficiency.

Reduced phytotoxicity of propazine on wheat, maize and rapeseed by salicylic acid

Propazine belongs to the triazine herbicide family and widely used in the farmland for crop production. Recent studies have shown that the residue of propazine in environment is accumulative. This inevitably results in accumulation of propazine in crops. Therefore, reduction of propazine toxicity and accumulation in crops is critically important. In this study, the growth of wheat, maize and rapeseed was significantly inhibited by 2, 8 and 0.4 mg kg^-1 propazine in soils. The chlorophyll content of the three crops also showed significant decrease, while the electrolyte permeability, a biomarker of cellular damage, increased in the plant cells. However, when plants were sprayed with 5 mg L^-1 of salicylic acid (SA), the propazine phytotoxicity of the crops was relieved, with increased chlorophyll content and reduced electrolyte permeability of all crops. Meanwhile, the activities of peroxidase (POD) and glutathione transferase (GST) remained lower. The propazine accumulation in the crops and the residues in the soil were determined by high performance liquid chromatography. The concentration of propazine in plants and soils treated by SA was less than that of the untreated control. Six propazine degraded products (derivatives) in rhizosphere of wheat were characterized using ultraperformance liquid chromatography with a quadrupole-time-of-flight tandem mass spectrometer. Our work indicates that the improved growth of crops was possibly due to the acceleration of propazine degradation by salicylic acid.

Biodegradation of atrazine by the novel Citricoccus sp. strain TT3

A previously undescribed atrazine-degrading bacterial strain TT3 capable of growing with atrazine as its sole nitrogen source was isolated from soil at the wastewater outfall of a pesticide factory in China. Phenotypic characterization and 16S rRNA gene sequencing indicated that the isolate belonged to the genus Citricoccus. Polymerase chain reaction (PCR) analysis revealed that TT3 contained the atrazine-degrading genes trzN, atzB, and atzC. The range for growth and atrazine degradation of TT3 was found to be pH 6.0-11.0, with a preference for alkaline conditions. At 30°C and pH 7.0, the strain removed 50mg/L atrazine in 66h with 1% inoculum. These results demonstrate that Citricoccus sp. TT3 has great potential for bioremediation of atrazine-contaminated sites, particularly in alkaline environments. To the best of our knowledge, there are no previous reports of Citricoccus strains that degrade atrazine, and therefore this work provides a novel candidate for atrazine bioremediation.

Activity, biomass and composition of microbial communities and their degradation pathways in exposed propazine soil

Propazine is a s-triazine herbicide widely used for controlling weeds for crop production. Its persistence and contamination in environment nagatively affect crop growth and food safety. Elimination of propazine residues in the environment is critical for safe crop production. This study identified a microbial community able to degrade propazine in a farmland soil. About 94% of the applied propazine was degraded within 11 days of incubation when soil was treated with 10mgkg^-1 propazine as the initial concentration. The process was accompanied by increased microbial biomass and activities of soil enzymes. Denaturing gradient gel electrophoresis (DGGE) revealed multiple bacterial strains in the community as well as dynamic change of the composition of microbial community with a reduced microbial diversity (H' from 3.325 to 2.78). Tracking the transcript level of degradative genes AtzB, AtzC and TrzN showed that these genes were induced by propazine and played important roles in the degradation process. The activities of catalase, dehydrogenase and phenol oxidase were stimulated by propazine exposure. Five degradation products (hydroxyl-, methylated-, dimeric-propazine, ammeline and ammelide) were characterized by UPLC-MS², revealing a biodegradation of propazine in soil. Several novel methylated and dimeric products of propazine were characterized in thepropazine-exposed soil. These data help understand the pathway, detailed mechanism and efficiency of propazine biodegradation in soil under realistic field condition.

Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T

Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71.38% of the genes were assigned putative functions. Through the sequence analysis, dozens of genes involved in steroid metabolism, especially its degradation, were detected. Most of the identified genes were located in large gene clusters, which showed high similarities with the gene clusters in Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated with steroid catabolism indicate that it could be used for research and application of steroids in science and industry.

Ecotoxicological assessment of pesticides and their combination on rhizospheric microbial community structure and function of Vigna radiata

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata. Effect on culturable fraction was assessed by enumeration on selective media, while PCR-denaturing gradient gel electrophoresis (DGGE) was employed to capture total bacterial community diversity. This was followed by a metabolic sketch using community-level physiological profiling (CLPP), to obtain a broader picture of the non-target effects on rhizospheric microbial community. Although plant parameters were not significantly affected by pesticide application, the microbial community structure experienced an undesirable impact as compared to control devoid of pesticide treatment. Examination of DGGE banding patterns through cluster analysis revealed that microbial community structure of pesticide-treated soils had only 70% resemblance to control rhizospheric soil even at 45 days post application. Drastic changes in the metabolic profiles of pesticide-treated soils were also detected in terms of substrate utilization, rhizospheric diversity, and evenness. It is noteworthy that the effects exacerbated by biopesticide were comparable to that of synthetic pesticides, thus emphasizing the significance of ecotoxicological assessments before tagging biopesticides as "safe alternatives."

Bioelectroventing: an electrochemical-assisted bioremediation strategy for cleaning-up atrazine-polluted soils

The absence of suitable terminal electron acceptors (TEA) in soil might limit the oxidative metabolism of environmental microbial populations. Bioelectroventing is a bioelectrochemical strategy that aims to enhance the biodegradation of a pollutant in the environment by overcoming the electron acceptor limitation and maximizing metabolic oxidation. Microbial electroremediating cells (MERCs) are devices that can perform such a bioelectroventing. We also report an overall profile of the ¹⁴ C-ATR metabolites and ¹⁴ C mass balance in response to the different treatments. The objective of this work was to use MERC principles, under different configurations, to stimulate soil bacteria to achieve the complete biodegradation of the herbicide ¹⁴ C-atrazine (ATR) to ¹⁴ CO₂ in soils. Our study concludes that using electrodes at a positive potential [+600 mV (versus Ag/AgCl)] ATR mineralization was enhanced by 20-fold when compared to natural attenuation in electrode-free controls. Furthermore, ecotoxicological analysis of the soil after the bioelectroventing treatment revealed an effective clean-up in < 20 days. The impact of electrodes on soil bioremediation suggests a promising future for this emerging environmental technology.

Microbial changes linked to the accelerated degradation of the herbicide atrazine in a range of temperate soils

Accelerated degradation is the increased breakdown of a pesticide upon its repeated application, which has consequences for the environmental fate of pesticides. The herbicide atrazine was repeatedly applied to soils previously untreated with s-triazines for >5 years. A single application of atrazine, at an agriculturally relevant concentration, was sufficient to induce its rapid dissipation. Soils, with a range of physico-chemical properties and agricultural histories, showed similar degradation kinetics, with the half-life of atrazine decreasing from an average of 25 days after the first application to <2 days after the second. A mathematical model was developed to fit the atrazine-degrading kinetics, which incorporated the exponential growth of atrazine-degrading organisms. Despite the similar rates of degradation, the repertoire of atrazine-degrading genes varied between soils. Only a small portion of the bacterial community had the capacity for atrazine degradation. Overall, the microbial community was not significantly affected by atrazine treatment. One soil, characterised by low pH, did not exhibit accelerated degradation, and atrazine-degrading genes were not detected. Neutralisation of this soil restored accelerated degradation and the atrazine-degrading genes became detectable. This illustrates the potential for accelerated degradation to manifest when conditions become favourable. Additionally, the occurrence of accelerated degradation under agriculturally relevant concentrations supports the consideration of the phenomena in environmental risk assessments.

Nitrogen-containing organic compounds: Origins, toxicity and conditions of their photocatalytic mineralization over TiO2

Sustainable water management remains a global concern to meet the food needs of industrial and agricultural activities. Therefore, pollution abatement techniques, cheap and environmentally, are highly desired and recommended. The present review is devoted to the origin and the toxicity of nitrogen-containing organic compounds in water. The progress made in removing these pollutants, in recent years, is addressed. However, a prominent place is given to the photocatalytic degradation process using the TiO₂ as a semiconductor, the conditions for good mineralization and especially the factors influencing it. The parameters that impact the performance of this method are the pH, the temperature, the reactor used, the light, the concentration of the pollutant, the amount of catalyst, etc. Up to now, the importance of one parameter relative to another has not been established because in the context of the photocatalytic degradation, certain parameters are often tightly coupled. Consequently, the mineralization is dependent on the initial degree of oxidation of nitrogen atom contained in the pollutant to be degraded. The hydroxyl nitrogen is primarily converted into nitrate ions (NO₃^-), while the amides and the primary amines are converted into ammonium ions (NH₄⁺).

Novel hydrolytic de-methylthiolation of the s-triazine herbicide prometryn by Leucobacter sp. JW-1

s-Triazine herbicides have been widely used in recent decades and caused serious concern over contamination of groundwater, surface water and soil. A novel bacterial strain JW-1 was isolated from activated sludge and identified as Leucobacter sp. based on comparative morphology, physiological characteristics and comparison of the 16S rDNA gene sequence. JW-1 was capable of using methylthio-s-triazine prometryn as a sole source of carbon and energy in pure culture. Favorable conditions for prometryn degradation were found at pH7.0-9.0 and temperature of 37-42°C. The degradation half-life of prometryn at 50mgL^-1 was remarkably as short as 1.1h, and increased to 6.0h when the initial concentration increased to 400mgL^-1. The strain JW-1 could degrade 100% of ametryn, 99% of simetryn, 41% of propazine, 43% of atrazine, 28% of simazine, 12% of terbutylhylazine, 10% of prometon and 13% of atraton at 50mgL^-1 of each herbicide in 2days. Prometryn was converted to 2-hydroxypropazine and methanthiol via a novel hydrolysis pathway. 2-Hydroxypropazine was then transformed to N-isopropylammelide and the final product cyanuric acid via two sequential deamination reactions. In addition to biodegradation by Leucobacter sp. JW-1, the hydrolytic de-methylthiolation would be valuable in biocatalysis.

Constrained evolution of a bispecific enzyme: lessons for biocatalyst design

Analysis of the natural evolution of bispecificity in triazine hydrolase highlights the importance of epistasis in protein engineering and evolution.