Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies

Mitigating risks from atrazine drift to soybeans through foliar pre-spraying with a degrading bacterium

Herbicides play a crucial role in managing weeds in agriculture, ensuring the productivity and quality of crops. However, herbicide drift poses a significant threat to sensitive plants, necessitating the consideration of ecosystem-based solutions to address this issue. In this study, foliar pre-spraying of atrazine-degrading Paenarthrobacter sp. AT5 was proposed as a new approach to mitigate the risks associated with atrazine drift on soybeans. Exposure to atrazine reduced chlorophyll levels and disturbed the antioxidant system and metabolic processes in soybean leaves, ultimately causing leaves to turn yellow. However, by pre-spraying, strain AT5 successfully colonized the surface of soybean leaves and mitigated the harmful effects of atrazine. This was achieved by slowing down atrazine absorption, expediting its reduction (half-life decreased from 2.22 d to 0.86 d), altering its degradation pathway (enhancing hydroxylation while weakening alkylation), and enhancing the interaction within phyllosphere bacteria communities. This study introduces a new approach that is both eco-friendly and user-friendly for reducing the risks of herbicide drift to sensitive crops, hence promoting the development of mixed cropping.

Engineering microbiomes for enhanced bioremediation

Bioremediation using synthetic microbiomes offers significant advantages over traditional single-strain-based approaches. In this Perspective, we outline 5 important considerations for the rational design of pollutant-degrading microbiomes for enhanced bioremediation.

Effects of biochar and compost on microbial community assembly and metabolic processes in glyphosate, imidacloprid and pyraclostrobin polluted soil under freezethaw cycles

Biochar and organic compost are widely used in agricultural soil remediation as soil immobilization agents. However, the effects of biochar and compost on microbial community assembly processes in polluted soil under freezingthawing need to be further clarified. Therefore, a freezethaw cycle experiment was conducted with glyphosate (herbicide), imidacloprid (insecticide) and pyraclostrobin (fungicide) polluted to understand the effect of biochar and compost on microbial community assembly and metabolic behavior. We found that biochar and compost could significantly promote the degradation of glyphosate, imidacloprid and pyraclostrobin in freezethaw soil decrease the half-life of the three pesticides. The addition of immobilization agents improved soil bacterial and fungal communities and promoted the transformation from homogeneous dispersal to homogeneous selection. For soil metabolism, the combined addition of biochar and compost alleviated the pollution of glyphosate, imidacloprid and imidacloprid to soil through up-regulation of metabolites (DEMs) in amino acid metabolism pathway and down-regulation of DEMs in fatty acid metabolism pathway. The structural equation modeling (SEM) results showed that soil pH and DOC were the main driving factors affecting microbial community assembly and metabolites. In summary, the combined addition of biochar and compost reduced the adverse effects of pesticides residues.

Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling

Engineering natural microbiomes for biotechnological applications remains challenging, as metabolic interactions within microbiomes are largely unknown, and practical principles and tools for microbiome engineering are still lacking. Here, we present a combinatory top-down and bottom-up framework to engineer natural microbiomes for the construction of function-enhanced synthetic microbiomes. We show that application of herbicide and herbicide-degrader inoculation drives a convergent succession of different natural microbiomes toward functional microbiomes (e.g., enhanced bioremediation of herbicide-contaminated soils). We develop a metabolic modeling pipeline, SuperCC, that can be used to document metabolic interactions within microbiomes and to simulate the performances of different microbiomes. Using SuperCC, we construct bioremediation-enhanced synthetic microbiomes based on 18 keystone species identified from natural microbiomes. Our results highlight the importance of metabolic interactions in shaping microbiome functions and provide practical guidance for engineering natural microbiomes.

Controllable and biocompatible 3D bioprinting technology for microorganisms: Fundamental, environmental applications and challenges

3D bioprinting is a new 3D manufacturing technology, that can be used to accurately distribute and load microorganisms to form microbial active materials with multiple complex functions. Based on the 3D printing of human cells in tissue engineering, 3D bioprinting technology has been developed. Although 3D bioprinting technology is still immature, it shows great potential in the environmental field. Due to the precise programming control and multi-printing pathway, 3D bioprinting technology provides a high-throughput method based on micron-level patterning for a wide range of environmental microbiological engineering applications, which makes it an on-demand, multi-functional manufacturing technology. To date, 3D bioprinting technology has been employed in microbial fuel cells, biofilm material preparation, microbial catalysts and 4D bioprinting with time dimension functions. Nevertheless, current 3D bioprinting technology faces technical challenges in improving the mechanical properties of materials, developing specific bioinks to adapt to different strains, and exploring 4D bioprinting for intelligent applications. Hence, this review systematically analyzes the basic technical principles of 3D bioprinting, bioinks materials and their applications in the environmental field, and proposes the challenges and future prospects of 3D bioprinting in the environmental field. Combined with the current development of microbial enhancement technology in the environmental field, 3D bioprinting will be developed into an enabling platform for multifunctional microorganisms and facilitate greater control of in situ directional reactions.

Core bacteria carrying the genes associated with the degradation of atrazine in different soils

Atrazine residues can pose serious threats to soil ecology and human health. Currently, the underlying relationship between soil microbial communities and the degradation genes associated with atrazine degradation remains unclear. In this study, the degradation characteristics of atrazine was investigated in ten different soil types. Further, diversity and abundance of degradation genes and succession of the bacterial community were also studied. The degradation of 10 mg/kg atrazine in different soil types exhibited an initial rapid trend followed by a gradual slowdown, adhering to the first-order kinetic equation. Atrazine significantly increased the absolute abundance of atz degradation genes. The increase in the absolute abundance of atzC gene was the largest, whereas that of atzA gene was the smallest, and the trzD gene was only detected in the Binzhou loam soil. Co-occurrence network analysis showed that the number of potential bacterial hosts of atzC was the highest compared with the other atz genes. Atrazine also altered the structural composition of the soil microbial community. The relative abundances of Ochrobactrum, Nocardiopsis, Lactobacillus, and Brevibacterium was increased in the atrazine-treated soils, while those of Conexibate, Solirubacter, and Micromonospora was decreased significantly compared with the control. Additionally, four atrazine-degrading bacterial strains Rhizobium AT1, Stenotrophomonas AT2, Brevibacterium AT3, and Bacillus AT4 were isolated from the atrazine-treated soils. After 14 d for inoculation, their degradation rate for 10 mg/L atrazine ranged from 17.56 % to 30.55 %. Moreover, the relative abundances of the bacterial genera, including these four isolates, in the atrazine-treated soil were significantly higher than those in the control, indicating that they were involved in the synergistic degradation of atrazine in the soil. This study revealed the degradation characteristics of atrazine, distribution of degradation genes, and succession of microbial communities, and explored the internal relationship between microbial community structure and atrazine degradation mechanisms in different soil types.

Degradation of iprodione by a novel strain Azospirillum sp. A1-3 isolated from Tibet

A bacterial strain A1-3 with iprodione-degrading capabilities was isolated from the soil for vegetable growing under greenhouses at Lhasa, Tibet. Based on phenotypic, phylogenetic, and genotypic data, strain A1-3 was considered to represent a novel species of genus Azospirillum. It was able to use iprodione as the sole source of carbon and energy for growth, 27.96 mg/L (50.80%) iprodione was reduced within 108 h at 25°C. During the degradation of iprodione by Azospirillum sp. A1-3, iprodione was firstly degraded to N-(3,5-dichlorophenyl)-2,4-dioxoimidazolidine, and then to (3,5-dichlorophenylurea) acetic acid. However, (3,5-dichlorophenylurea) acetic acid cannot be degraded to 3,5-dichloroaniline by Azospirillum sp. A1-3. A ipaH gene which has a highly similarity (98.72-99.92%) with other previously reported ipaH genes, was presented in Azospirillum sp. A1-3. Azospirillum novel strain with the ability of iprodione degradation associated with nitrogen fixation has never been reported to date, and Azospirillum sp. A1-3 might be a promising candidate for application in the bioremediation of iprodione-contaminated environments.

Aerobic Degradation Characteristics and Mechanism of Decabromodiphenyl Ether (BDE-209) Using Complex Bacteria Communities

Complex bacteria communities that comprised Brevibacillus sp. (M1) and Achromobacter sp. (M2) with effective abilities of degrading decabromodiphenyl ether (BDE-209) were investigated for their degradation characteristics and mechanisms under aerobic conditions. The experimental results indicated that 88.4% of 10 mg L^-1 BDE-209 could be degraded after incubation for 120 h under the optimum conditions of pH 7.0, 30 °C and 15% of the inoculation volume, and the addition ratio of two bacterial suspensions was 1:1. Based on the identification of BDE-209 degradation products via liquid chromatography-mass spectrometry (LC-MS) analysis, the biodegradation pathway of BDE-209 was proposed. The debromination, hydroxylation, deprotonation, breakage of ether bonds and ring-opening processes were included in the degradation process. Furthermore, intracellular enzymes had the greatest contribution to BDE-209 biodegradation, and the inhibition of piperyl butoxide (PB) for BDE-209 degradation revealed that the cytochrome P450 (CYP) enzyme was likely the key enzyme during BDE-209 degradation by bacteria M (1+2). Our study provided alternative ideas for the microbial degradation of BDE-209 by aerobic complex bacteria communities in a water system.

Efficient biodegradation of 1,4-dioxane commingled with additional organic compound: Role of interspecies interactions within consortia

Microbial consortia-mediated biodegradation of 1,4-dioxane (1,4-D), an emerging water contaminant, is always a superior choice over axenic cultures. Thus, better understanding of the functions of coexisting microbes and their interspecies interactions within the consortia is crucial for predicting biodegradation efficiency and designing efficient 1,4-D-degrading microbial consortia. This study evaluated how microbial community compositions and interspecies interactions govern the microbial consortia-mediated 1,4-D biodegradation by investigating the biodegradability and microbial community dynamics of both enriched (N112) and synthetic (SCDs and SCDNs) microbial consortia in the absence or presence of additional organic compound (AOC). In the absence of AOC, N112 exhibited 100% 1,4-D biodegradation efficiency at a rate of 12.5 mg/L/d, whereas the co-occurrence of AOC resulted in substrate-dependent biodegradation inhibition and thereby reduced the biodegradation efficiency and activity (2.0-10.0 mg/L/d). The coexistence and negative influence of certain low-abundant non-degraders on both 1,4-D-degraders and key non-degraders in N112 was identified as the prime cause behind such biodegradation inhibition. Comparing with N112, SCDN-1 composed of 1,4-D-degraders and key non-degraders significantly improved the 1,4-D biodegradation efficiency in the presence of AOC, confirming the absence of negative influence of low-abundant non-degraders and cooperative interactions between 1,4-D-degraders and key non-degraders in SCDN-1. On the contrary, both two-species and three-species SCDs comprised of only 1,4-D-degraders resulted in lower 1,4-D biodegradation efficiency as compared to SCDN-1 under all treatment conditions, while max. 91% 1,4-D biodegradation occurred by SCDs in the absence of AOC. These results were attributed to the negative interaction among 1,4-D-degraders and the absence of complementary roles of key non-degraders in SCDs. The findings improve our understanding of how interspecies interactions can regulate the intrinsic abilities and functions of coexisting microbes during biodegradation in complex environments and provide valuable guidelines for designing highly efficient and robust microbial consortia for practical bioremediation of 1,4-D like emerging organic contaminants.

Pollution pressure and soil depth drive prokaryotic microbial assemblage and co-occurrence patterns in an organic polluted site

Organic polluted sites have become a global concern of soil contamination, yet little is known about microbial vertical distribution and community assembly in organic polluted sites. Here, high-throughput sequencing technology was employed to investigate prokaryotic microbial diversity and community assembly along soil profile in an abandoned chemical organic contaminated site. Results showed that there was no significant difference (P > 0.05) observed in microbial alpha diversity among different soil layers, whereas the structure of microbial communities presented significantly different (P < 0.05) in the superficial layer (0-0.5 m) compared with intermediate (1-1.5 m) and bottom (2.5-3 m) layers. Soil prokaryotic microbial community evolved to possess the potential of degrading organic pollutants under long-term organic pollution stress. A relatively homogeneous environment created by the organic polluted site mainly induced the ecological process of homogeneous selection driving community assembly, while dispersal limitation gained importance with the increase of soil depth. Organic contaminants were identified as the key driver of destabilizing co-occurrence networks, while the frequent cooperative behaviors among species could combat organic pollution stress and sustain prokaryotic community stability. Collectively, pollution pressure and soil depth jointly affected prokaryotic microbial assemblage and co-occurrence that underpinned the spatial scaling patterns of organic contaminated sites microbiota.

Correlating biodegradation kinetics of 2,3,7,8-tetrachlorodibenzo-p-dioxin to the dynamics of microbial communities originating from soil in Vietnam contaminated with herbicides and dioxins

We studied the succession of bacterial communities during the biodegradation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (2,3,7,8-TCDD). The communities originated from a mesocosm with soil from Bien Hoa airbase in Vietnam heavily contaminated with herbicides and dioxins. They were grown in defined media with different carbon and Gibbs energy sources and 2,3,7,8-TCDD. Cultures with dimethyl sulfoxide (DMSO) as the sole carbon and energy source degraded about 95% of 2,3,7,8-TCDD within 60 days of cultivation. Those with an additional 1 mM of vanillin did that in roughly 90 days. Further 16S rRNA gene amplicon sequencing showed that the increase in relative abundance of members belonging to the genera Bordetella, Sphingomonas, Proteiniphilum, and Rhizobium correlated to increased biodegradation of 2,3,7,8-TCDD in these cultures. A higher concentration of vanillin slowed down the biodegradation rate. Addition of alternative carbon and Gibbs energy sources, such as amino acids, sodium lactate and sodium acetate, even stopped the degradation of 2,3,7,8-TCDD completely. Bacteria from the genera Bordetella, Achromobacter, Sphingomonas and Pseudomonas dominated most of the cultures, but the microbial profiles also significantly differed between cultures as judged by non-metric multidimensional scaling (NMDS) analyses. Our study indicates that 2,3,7,8-TCDD degradation may be stimulated by bacterial communities preadapted to a certain degree of starvation with respect to the carbon and energy source. It also reveals the succession and abundance of defined bacterial genera in the degradation process.

Impact of Paenarthrobacter ureafaciens ZF1 on the soil enzyme activity and microbial community during the bioremediation of atrazine-contaminated soils

Bioremediation of atrazine-contaminated soil is considered a safe and effective approach in removing contaminates from the soil. However, the effects of adding foreign organisms to assist bioremediation on soil environmental quality and ecosystem are unclear. Here, the ecological remediation potential of strain Paenarthrobacter ureafaciens ZF1 on atrazine-contaminated soil was investigated through miniature experiments using variations in soil enzymes and bacterial communities as indicators. The results showed that strain ZF1 accelerated atrazine degradation, which could completely degrade atrazine at concentrations of 100 mg·L^− 1 atrazine within 2 h in liquid medium and could remove up to 99.3% of atrazine (100 mg·kg^− 1 in soil) within 6 days. During soil bioremediation, atrazine promoted the activities of urease and cellulase, and inhibited the activities of sucrase and catalase, while the strain ZF1 significantly promoted the activities of these four enzymes. High-throughput sequencing of 16S rRNA genes showed that ZF1 affected the relative abundance and bacterial community structure, and promoted bacterial diversity and evenness. Furthermore, redundancy analysis revealed a certain correlation among the strain ZF1, atrazine residue, soil enzyme activity, and soil bacterial community. The strain ZF1 in this work demonstrated remarkable potential for ecological restoration, and can be an effective and environmentally friendly alternative in remediating atrazine-contaminated soil.

Bioaugmentation of Atrazine-Contaminated Soil With Paenarthrobacter sp. Strain AT-5 and Its Effect on the Soil Microbiome

Atrazine, a triazine herbicide, is widely used around the world. The residue of atrazine due to its application in the fore-rotating crop maize has caused phytotoxicity to the following crop sweet potato in China. Bioaugmentation of atrazine-contaminated soil with atrazine-degrading strains is considered as the most potential method to remove atrazine from soil. Nevertheless, the feasibility of bioaugmentation and its effect on soil microbiome still need investigation. In this study, Paenarthrobacter sp. AT-5, an atrazine-degrading strain, was inoculated into agricultural soils contaminated with atrazine to investigate the bioaugmentation process and the reassembly of the soil microbiome. It was found that 95.9% of 5 mg kg⁻¹ atrazine was removed from the soils when inoculated with strain AT-5 with 7 days, and the phytotoxicity of sweet potato caused by atrazine was significantly alleviated. qRT-PCR analysis revealed that the inoculated strain AT-5 survived well in the soils and maintained a relatively high abundance. The inoculation of strain AT-5 significantly affected the community structure of the soil microbiome, and the abundances of bacteria associated with atrazine degradation were improved.

A Synergistic Consortium Involved in rac-Dichlorprop Degradation as Revealed by DNA Stable Isotope Probing and Metagenomic Analysis

rac-Dichlorprop, a commonly used phenoxyalkanoic acid herbicide, is frequently detected in environments and poses threats to environmental safety and human health. Microbial consortia are thought to play key roles in rac-dichlorprop degradation. However, the compositions of the microbial consortia involved in rac-dichlorprop degradation remain largely unknown. In this study, DNA stable isotope probing (SIP) and metagenomic analysis were integrated to reveal the key microbial consortium responsible for rac-dichlorprop degradation in a rac-dichlorprop-degrading enrichment. OTU340 (Sphingobium sp.) and OTU348 (Sphingopyxis sp.) were significantly enriched in the rac-[¹³C]dichlorprop-labeled heavy DNA fractions. A rac-dichlorprop degrader, Sphingobium sp. strain L3, was isolated from the enrichment by a traditional enrichment method but with additional supplementation of the antibiotic ciprofloxacin, which was instructed by metagenomic analysis of the associations between rac-dichlorprop degraders and antibiotic resistance genes. As revealed by functional profiling of the metagenomes of the heavy DNA, the genes rdpA and sdpA, involved in the initial degradation of the (R)- and (S)-enantiomers of dichlorprop, respectively, were mostly taxonomically assigned to Sphingobium species, indicating that Sphingopyxis species might harbor novel dichlorprop-degrading genes. In addition, taxonomically diverse bacterial genera such as Dyella, Sphingomonas, Pseudomonas, and Achromobacter were presumed to synergistically cooperate with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. IMPORTANCE Understanding of the key microbial consortium involved in the degradation of the phenoxyalkanoic acid herbicide rac-dichlorprop is pivotal for design of synergistic consortia used for enhanced bioremediation of herbicide-contaminated sites. However, the composition of the microbial consortium and the interactions between community members during the biodegradation of rac-dichlorprop are unclear. In this study, DNA-SIP and metagenomic analysis were integrated to reveal that the metabolite 2,4-dichlorophenol degraders Dyella, Sphingomonas, Pseudomonas, and Achromobacter synergistically cooperated with the key degraders Sphingobium/Sphingopyxis for enhanced degradation of rac-dichlorprop. Our study provides new insights into the synergistic degradation of rac-dichlorprop at the community level and implies the existence of novel degrading genes for rac-dichlorprop in nature.

Biochar decreased enantioselective uptake of chiral pesticide metalaxyl by lettuce and shifted bacterial community in agricultural soil

A 35-day microcosmic experiment was conducted with lettuce (Lactuca sativa L.) and two metalaxyl (MET) enantiomers (R-MET and S-MET) to understand the roles of biochar in the enantioselective fate of chiral pesticides in soil-plant ecosystems. Wood waste-derived biochar (WBC) amendment effectively decreased the shoot concentrations of R-MET/S-MET and their metabolites R-MET/S-MET acid by 57.7-86.3% and 13.3-32.5%, respectively. The reduced uptake was mainly attributed to the decreased bioavailability of R-MET and S-MET. A lower fraction of R-MET was accumulated by the lettuce in the WBC-amended soils relative to the control, suggesting a decrease in the enantioselective uptake of the chiral pesticide MET in the presence of biochar. Regardless of the WBC amendment, no enantiomerization of MET or MET acid occurred. The application of WBC stimulated soil bacterial diversity, shifted the bacterial community, and enhanced the abundance of pesticide degrading bacteria (e.g., Luteimonas, Methylophilus, and Hydrogenophaga), which were responsible for the enantioselective degradation of MET in the soil. This work expands our understanding of the enantioselective fate of chiral pesticides in the biochar-amended soil ecosystems. These findings can be used to develop biochar-based technologies to remediate soils contaminated with these chiral pesticides to ensure food safety.

Mineralization of the herbicide swep by a two-strain consortium and characterization of a new amidase for hydrolyzing swep

BACKGROUND

Swep is an excellent carbamate herbicide that kills weeds by interfering with metabolic processes and inhibiting cell division at the growth point. Due to the large amount of use, swep residues in soil and water not only cause environmental pollution but also accumulate through the food chain, ultimately pose a threat to human health. This herbicide is degraded in soil mainly by microbial activity, but no studies on the biotransformation of swep have been reported.

RESULTS

In this study, a consortium consisting of two bacterial strains, Comamonas sp. SWP-3 and Alicycliphilus sp. PH-34, was enriched from a contaminated soil sample and shown to be capable of mineralizing swep. Swep was first transformed by Comamonas sp. SWP-3 to the intermediate 3,4-dichloroaniline (3,4-DCA), after which 3,4-DCA was mineralized by Alicycliphilus sp. PH-34. An amidase gene, designated as ppa, responsible for the transformation of swep into 3,4-DCA was cloned from strain SWP-3. The expressed Ppa protein efficiently hydrolyzed swep and a number of other structural analogues, such as propanil, chlorpropham and propham. Ppa shared less than 50% identity with previously reported arylamidases and displayed maximal activity at 30 °C and pH 8.6. Gly449 and Val266 were confirmed by sequential error prone PCR to be the key catalytic sites for Ppa in the conversion of swep.

CONCLUSIONS

These results provide additional microbial resources for the potential remediation of swep-contaminated sites and add new insights into the catalytic mechanism of amidase in the hydrolysis of swep.