The mechanism of different cyanobacterial responses to glyphosate.

Glyphosate, the most extensively used herbicide globally, has raised ecotoxicological concerns because it can be transported into the aquatic environment and cause adverse effects on the aquatic system. However, the functional mechanism of glyphosate on cyanobacteria are not completely disentangled. In this study, we selected six common cyanobacteria to evaluate glyphosate effects on cyanobacterial growth in monoculture experiment. Results showed that the growth of five tested cyanobacterial species were promoted under different degrees, and only Pseudanabaena was inhibited by glyphosate. In the phylogenetic tree based on gene sequences of 5-enol-pyruvylshikimate-3-phosphate synthase (EPSPS), a target for glyphosate, we found that the position of Pseudanabaena is the closest to plant, which was sensitive to glyphosate, thereby explaining the inhibitory effect of Pseudanabaena following glyphosate exposure. The primary degraded metabolites or analogs did not induce cyanobacterial growth, laterally demonstrating that glyphosate was used as a source of phosphorus to accelerate cyanobacterial growth because phosphorus levels increased in the medium of glyphosate treatment. Overall, this study provides a better understanding of the influence of glyphosate on the composition of aquatic microbiota and explains the mechanism of cyanobacterial response to glyphosate.

Development of a machine-learning model to identify the impacts of pesticides characteristics on soil microbial communities from high-throughput sequencing data.

High-throughput sequencing (HTS) of soil environmental DNA provides an advanced insight into the effects of pesticides on soil microbial systems. However, the association between the properties of the pesticide and its ecological impact remains methodically challenging. Risks associated with pesticide use can be minimized if pesticides with optimal structural traits were applied. For this purpose, we merged the 20 independent HTS studies, to reveal that pesticides significantly reduced beneficial bacteria associated with soil and plant immunity, enhanced the human pathogen and weaken the soil's ecological stability. Through the machine-learning approach, correlating these impacts with the physicochemical properties of the pesticides yielded a random forest model with good predictive capabilities. The models revealed that physical pesticide properties such as the dissociation constant (pKa), the molecular weight and water solubility, determined the ecological impact of pesticides to a large extent. Moreover, this study identified that eco-friendly pesticides should possess a value of pKa > 5 and a molecular weight in the range of 200-300 g/mol, which were found to be conducive to bacteria related to plant immunity promotion and exerted the lowest fluctuation of human opportunistic pathogen and keystone species. This guides the design of pesticides for which the impacts on soil biota are minimized.

Leaf metabolic influence of glyphosate and nanotubes on the Arabidopsis thaliana phyllosphere.

Chemical exposure can indirectly affect leaf microbiota communities, but the mechanism driving this phenomenon remains largely unknown. Results revealed that the co-exposure of glyphosate and multi-carbon nanotubes (CNTs) caused a synergistic inhibitory effect on the growth and metabolism of Arabidopsis thaliana shoots. However, only a slight inhibitory effect was induced by nanotubes or glyphosate alone at the tested concentrations. Several intermediate metabolites of nitrogen metabolism and fatty acid synthesis pathways were upregulated under the combined treatment, which increased the amount of energy required to alleviate the disruption caused by the combined treatment. Additionally, compared with the two individual treatments, the glyphosate/nanotube combination treatment induced greater fluctuations in the phyllosphere bacterial community members with low abundance (relative abundance (RA) <1%) at both the family and genus levels, and among these bacteria some plant growth promotion and nutrient supplement related bacteria were markable increased. Strikingly, strong correlations between phyllosphere bacterial diversity and metabolites suggested a potential role of leaf metabolism, particularly nitrogen and carbohydrate metabolism, in restricting the range of leaf microbial taxa. These correlations between phyllosphere bacterial diversity and leaf metabolism will improve our understanding of plant-microbe interactions and the extent of their drivers of variation and the underlying causes of variability in bacterial community composition.

Metabolomic modulations in a freshwater microbial community exposed to the fungicide azoxystrobin.

An effective broad-spectrum fungicide, azoxystrobin (AZ), has been widely detected in aquatic ecosystems, potentially affecting the growth of aquatic microorganisms. In the present study, the eukaryotic alga Monoraphidium sp. and the cyanobacterium Pseudanabaena sp. were exposed to AZ for 7 days. Our results showed that 0.2-0.5 mg/L concentrations of AZ slightly inhibited the growth of Monoraphidium sp. but stimulated Pseudanabaena sp. growth. Meanwhile, AZ treatment effectively increased the secretion of total organic carbon (TOC) in the culture media of the two species, and this phenomenon was also found in a freshwater microcosm experiment (containing the natural microbial community). We attempted to assess the effect of AZ on the function of aquatic microbial communities through metabolomic analysis and further explore the potential risks of this compound. The metabonomic profiles of the microcosm indicated that the most varied metabolites after AZ treatment were related to the citrate cycle (TCA), fatty acid biosynthesis and purine metabolism. We thereby inferred that the microbial community increased extracellular secretions by adjusting metabolic pathways, which might be a stress response to reduce AZ toxicity. Our results provide an important theoretical basis for further study of fungicide stress responses in aquatic microcosm microbial communities, as well as a good start for further explorations of AZ detoxification mechanisms, which will be valuable for the evaluation of AZ environmental risk.

Enantioselective effects of imazethapyr residues on Arabidopsis thaliana metabolic profile and phyllosphere microbial communities.

Imazethapyr (IM) is a widely used acetolactate synthase-inhibiting chiral herbicide. It has long-term residuals that may be absorbed by the human body through the edible parts of plants, such as vegetable leaves or fruits. Here, we selected a model plant, Arabidopsis thaliana, to determine the effects of R-IM and S-IM on its leaf structure, photosynthetic efficiency, and metabolites, as well as the structures of microorganisms in the phyllosphere, after 7 days of exposure. Our results indicated enantiomeric differences in plant growth between R-IM and S-IM; 133 µg/kg R-IM showed heavier inhibition of photosynthetic efficiency and greater changes to subcellular structure than S-IM. R-IM and S-IM also had different effects on metabolism and leaf microorganisms. S-IM mainly increased lipid compounds and decreased amino acids, while R-IM increased sugar accumulation. The relative abundance of Moraxellaceae human pathogenic bacteria was increased by R-IM treatment, indicating that R-IM treatment may increase leaf surface pathogenic bacteria. Our research provides a new perspective for evaluating the harmfulness of pesticide residues in soil, phyllosphere microbiome changes via the regulation of plant metabolism, and induced pathogenic bacterial accumulation risks.

Enantioselective Oxidative Stress Induced by S- and Rac-metolachlor in Wheat (Triticum aestivum L.) Seedlings.

The unfounded use of chiral pesticides has caused widespread concern. In this study, the enantioselective effects of S- and racemic (Rac)-metolachlor on the oxidative stress of wheat seedlings was determined based on physiological and gene transcription differences. Growth inhibition increased with increasing concentrations of tested metolachlor, and S-metolachlor had a stronger inhibitory effect than did Rac-metolachlor. Root growth was also significantly inhibited, but no enantioselective effects from the tested concentrations of the metolachlor enantiomers were observed. At a concentration of 5 mg L-1, the maximal fresh weight inhibition reached 63.7% and 53.8% for S-metolachlor and Rac-metolachlor, respectively. In response to the S-metolachlor treatment, the maximum level of superoxide anions and malondialdehyde (MDA) increased to 1.73 and 2.55 times that in response to the control treatment, both of which were greater than those in response to the Rac-metolachlor treatment. The activity of superoxide dismutase (SOD) also increased in response to the S-metolachlor treatment, but the activity of peroxidase (POD) decreased. Real-time polymerase chain reaction (PCR) revealed that, compared with the Rac-metolachlor treatment, the S-metolachlor treatment attenuated the expression of several antioxidant genes. Together, these results demonstrate that S-metolachlor has a greater effect than does Rac-metolachlor on wheat seedlings.

Effects of imazethapyr spraying on plant growth and leaf surface microbial communities in Arabidopsis thaliana.

Imazethapyr (IM) is an acetolactate synthase (ALS)-inhibiting herbicide that has been widely used in recent years. However, IM spraying can lead to the accumulation of herbicide residues in leaves. Here, we determined the effects of IM spraying on the plant growth and leaf surface microbial communities of Arabidopsis thaliana after 7 and 14 days of exposure. The results suggested that IM spraying inhibited plant growth. Fresh weight decreased to 48% and 26% of the control value after 7 and 14 days, respectively, of 0.035 kg/ha IM exposure. In addition, anthocyanin content increased 9.2-fold and 37.2-fold relative to the control content after 7 and 14 days of treatment, respectively. Furthermore, IM spraying destroyed the cell structures of the leaves, as evidenced by increases in the number of starch granules and the stomatal closure rate. Reductions in photosynthetic efficiency and antioxidant enzyme activity were observed after IM spraying, especially after 14 days of exposure. The diversity and evenness of the leaf microbiota were not affected by IM treatment, but the composition of community structure at the genus level was altered by IM spraying. Imazethapyr application increased the abundance of Pseudomonas, a genus that includes species pathogenic to plants and humans, indicating that IM potentially increased the abundance of pathogenic bacteria on leaves. Our findings increase our understanding of the relationships between herbicide application and the microbial community structures on plant leaves, and they provide a new perspective for studying the ecological safety of herbicide usage.

Changes in bacterial community structure and antibiotic resistance genes in soil in the vicinity of a pharmaceutical factory.

China is the largest global producer of antibiotics. With the demand for antibiotics increasing every year, it is necessary to assess potential environmental risks and the spread of antibiotic resistance genes (ARGs) associated with antibiotic production. Here, we investigated the occurrence and distribution of ARGs in soil in the vicinity of a pharmaceutical factory. The results showed that antibiotic concentrations were under the detection limit; however, ARGs were present in soil and tended to be enriched near the factory. A significant correlation between the relative abundance of intI-1 and tetracycline ARGs implied that horizontal gene transfer might play an important role in the spread of ARGs. The occurrence of these ARGs could be the results of previous antibiotic contamination. However, the soil bacterial community structure seemed to be more affected by nutrients or other factors than by antibiotics. Overall, this study supports the viewpoint that long-term pharmaceutical activity might have a negative effect on environmental health, thus, underscoring the need to regulate antibiotic production and management.

Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification.

A better knowledge of the intertwined effects of herbicides on plant physiology and microbiome as well as nutrient biogeochemical cycles are needed for environmental management. Here we studied the influence of herbicide diclofop-methyl (DM) on the rice root microbiome and its relationship with N cycle. To do so, we exposed rice seedlings to 100 µg/L DM and studied rhizosphere microbiota using MiSeq-pyrosequencing, root exudation by GC-MS, and denitrification activity by 15N isotope-tracing and qRT-PCR. The richness and diversity of rhizosphere microorganisms, significantly increased after DM exposure combined with an increase in root exudation of amino acids, sugars, and fatty acids. Transcription of denitrification-related gene and denitrification rate increased significantly in the rice rhizosphere. Our results suggest that DM strongly influenced the root exudation of bacteria nutrients, which affected root microbiome community and potentially influenced N cycle in rice rhizosphere.

Ecological Effects of Single-Walled Carbon Nanotubes on Soil Microbial Communities and Soil Fertility.

The manufacturers of single-walled carbon nanotubes (SWCNTs) are continuously expanding their manufacturing and commercial markets, indicating that the environmental release and accumulation of SWCNTs in soil is inevitable. However, little is known about the effects of SWCNTs on soil physicochemical properties and soil microbial communities. Our results showed that treatment with SWCNTs resulted in an enhancement of microorganism metabolism related to soil organic compound degradation and a change in the structure of soil microbial communities, but the diversity of soil microorganisms was not significantly affected. The decrease in soil urease activity and the increase in the relative abundance of Nitrospirae after SWCNTs exposure might be relevant to the induction of soil nitrification. The relative abundances of phosphate-solubilizing microorganisms increased after exposure to SWCNTs, which was beneficial for phosphorus bioavailability in the soil. Our current study highlights that exposure to SWCNTs at concentrations of 3 and 10 µg/g can change the composition of soil microorganism communities, promote soil organic degradation and improve soil fertility by enhancing N and P availability in a short time.

Physiological and Molecular Response of Arabidopsis thaliana to CuO Nanoparticle (nCuO) Exposure.

The widespread application of copper oxide nanoparticles (nCuO) results in ecological risk when nanoparticles enter the environment. This study clarifies the mechanism of nCuO toxicity in Arabidopsis thaliana seedlings via comparison with copper (Cu) ion bioeffects. Under the same culture conditions, Cu2+ ion exposure exerted a stronger inhibitory effect on plant fresh weight and growth and caused stronger oxidative disruption (measured by malondialdehyde, MDA) than nCuO exposure. The Cu2+ ions also showed a stronger induction effect than did nCuO on the activity of antioxidant enzymes and the transcription of antioxidant-related genes. Dissolved Cu2+ ions contributed a minority of the toxicity of nCuO, implying that nCuO itself showed relative strong phytotoxicity. The work presented here will help increase our understanding of the toxicity of metal nanoparticles in plants.

Multigenerational Adaptation Can Enhance the Pathogen Resistance of Plants via Changes in Rhizosphere Microbial Community Assembly.

Plants withstand pathogen attacks by recruiting beneficial bacteria to the rhizosphere and passing their legacy on to the next generation. However, the underlying mechanisms involved in this process remain unclear. In our study, we combined microbiomic and transcriptomic analyses to reveal how the rhizosphere microbiome assembled through multiple generations and defense-related genes expressed in Arabidopsis thaliana under pathogen attack stress. Our results showed that continuous exposure to the pathogen Pseudomonas syringae pv tomato DC3000 led to improved growth and increased disease resistance in a third generation of rps2 mutant Arabidopsis thaliana. It could be attributed to the enrichment of specific rhizosphere bacteria, such as Bacillus and Bacteroides. Pathways associated with plant immunity and growth in A. thaliana, such as MAPK signaling pathways, phytohormone signal transduction, ABC transporter proteins, and flavonoid biosynthesis, were activated under the influence of rhizosphere bacterial communities. Our findings provide a scientific basis for explaining the relationship between beneficial microbes and defense-related gene expression. Understanding microbial communities and the mechanisms involved in plant responses to disease can contribute to better plant management and reduction of pesticide use.

Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana.

The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.

Geographic patterns of microbial traits of river basins in China.

River microbiotas contribute to critical geochemical processes and ecological functions of rivers but are sensitive to variations of environmental drivers. Understanding the geographic pattern of river microbial traits in biogeochemical processes can provide important insights into river health. Many studies have characterized river microbial traits in specific situations, but the geographic patterns of these traits and environmental drivers at a large scale are unknown. We reanalyzed 4505 raw 16S rRNA sequences samples for microbiota from river basins in China. The results indicated differences in the diversity, composition, and structure of microbiotas across diverse river basins. Microbial diversity and functional potential in the river basins decreased over time in northern China and increased in southern China due to niche differentiation, e.g., the Yangtze River basin was the healthiest ecosystem. River microbiotas were mainly involved in the cycling of carbon and nitrogen in the river ecosystems and participated in potential organic metabolic functions. Anthropogenic pollutants discharge was the most critical environmental driver for the microbial traits, e.g., antibiotic discharge, followed by climate change. The prediction by machine-learning models indicated that the continuous discharge of antibiotics and climate change led to high ecological risks for the rivers. Our study provides guidelines for improving the health of river ecosystems and for the formulation of strategies to restore the rivers.

Response of microbial antibiotic resistance to pesticides: An emerging health threat.

The spread of microbial antibiotic resistance has seriously threatened public health globally. Non-antibiotic stressors have significantly contributed to the evolution of bacterial antibiotic resistance. Although numerous studies have been conducted on the potential risk of pesticide pollution for bacterial antibiotic resistance, a systematic review of these concerns is still lacking. In the present study, we elaborate the mechanism underlying the effects of pesticides on bacterial antibiotic resistance acquisition as well as the propagation of antimicrobial resistance. Pesticide stress enhanced the acquisition of antibiotic resistance in bacteria via various mechanisms, including the activation of efflux pumps, inhibition of outer membrane pores for resistance to antibiotics, and gene mutation induction. Horizontal gene transfer is a major mechanism whereby pesticides influence the transmission of antibiotic resistance genes (ARGs) in bacteria. Pesticides promoted the conjugation transfer of ARGs by increasing cell membrane permeability and increased the proportion of bacterial mobile gene elements, which facilitate the spread of ARGs. This review can improve our understanding regarding the pesticide-induced generation and spread of ARGs and antibiotic resistant bacteria. Moreover, it can be applied to reduce the ecological risks of ARGs in the future.

Development of a Potentially New Algaecide for Controlling Harmful Cyanobacteria Blooms Which is Ecologically Safe and Selective.

Harmful cyanobacterial blooms (HCBs) caused by Microcystis aeruginosa are of great concern as they negatively affect the aquatic environment and human health. Chemical methods could rapidly eradicate HCBs and have been used for many decades. However, many chemical reagents are not recommended to eliminate HCBs in the long term, given the possible destructive and toxic effects of the chemicals employed on non-target aquatic organisms. We developed a new algaecide, 2-((1,3,4-thiadiazol-2-yl)thio)-N-(4-chlorophenyl) acetamide (Q2), to control harmful cyanobacteria while being environmentally friendly and selective. In our study, Q2 effectively inhibited cyanobacterial growth, especially of M. aeruginosa, but did not affect eukaryotic algae in test concentrations. A critical mechanism was revealed by transcriptome and metagenomic results showing that Q2 affects multiple cellular targets of cyanobacteria for HCB control, including the destruction of organelles, damage in the photosynthesis center, as well as inhibition of gas vesicle growth, and these changes can be highly relevant to the decrease of quorum-sensing functional KEGG pathways. Furthermore, Q2 did not affect the microbial composition and could recover the disrupted aquatic functional pathways in a short period. This is different from the impact on ecosystem functioning of the traditionally used harmful algaecide diuron. All these results verified that Q2 could be friendly to the aquatic environment, providing a new directional choice in managing HCBs in the future.

Effects of chiral herbicide dichlorprop on Arabidopsis thaliana metabolic profile and its implications for microbial communities in the phyllosphere.

Dichlorprop (2-(2,4-dichlorophenoxy) propionic acid, DCPP), a commonly used herbicide for weed control, can be residually detected in soil. It is still unclear whether chiral DCPP exerts an enantioselective adverse effect on plant metabolism and the microbial community of the phyllosphere. In this study, we selected Arabidopsis thaliana as a model plant to explore the effects of R- and S-DCPP enantiomers on plant physiological activities, metabolism, and associated changes in the phyllosphere microbial community. Results indicated that the fresh weight of plants decreased by 37.6% after R-DCPP treatment, whereas it increased by 7.6% after S-DCPP treatment. The R-DCPP enantiomer also caused stronger disturbance to leaf morphology, mesophyll cell structure, and leaf metabolites compared with S-DCPP. GC-MS analysis of DCPP-treated Arabidopsis leaves pointed out a differential profile mostly in carbohydrates, organic acids, and fatty acids, between S-DCPP and R-DCPP treatments. The diversity of phyllospheric microorganisms decreased and the stability of microbial community in the phyllosphere increased after R-DCPP treatment, whereas the opposite result was detected after S-DCPP exposure. The correlation analysis revealed that chiral herbicides may affect microbial communities in the phyllosphere by influencing leaf metabolism, while sugars and terpenoids were considered the main factors in reshaping the microbial community structure in the phyllosphere. Our study provides a new perspective for evaluating the effect of residual DCPP enantiomers on plant physiology and corresponding phyllosphere microorganism changes via the regulation of leaf metabolism, and clarifies the ecological risk of DCPP enantiomer application in agriculture.

Machine learning predicts ecological risks of nanoparticles to soil microbial communities.

With the rapid development of nanotechnology in agriculture, there is increasing urgency to assess the impacts of nanoparticles (NPs) on the soil environment. This study merged raw high-throughput sequencing (HTS) data sets generated from 365 soil samples to reveal the potential ecological effects of NPs on soil microbial community by means of metadata analysis and machine learning methods. Metadata analysis showed that treatment with nanoparticles did not have a significant impact on the alpha diversity of the microbial community, but significantly altered the beta diversity. Unfortunately, the abundance of several beneficial bacteria, such as Dyella, Methylophilus, Streptomyces, which promote the growth of plants, and improve pathogenic resistance, was reduced under the addition of synthetic nanoparticles. Furthermore, metadata demonstrated that nanoparticles treatment weakened the biosynthesis ability of cofactors, carriers, and vitamins, and enhanced the degradation ability of aromatic compounds, amino acids, etc. This is unfavorable for the performance of soil functions. Besides the soil heterogeneity, machine learning uncovered that a) the exposure time of nanoparticles was the most important factor to reshape the soil microbial community, and b) long-term exposure decreased the diversity of microbial community and the abundance of beneficial bacteria. This study is the first to use a machine learning model and metadata analysis to investigate the relationship between the properties of nanoparticles and the hazards to the soil microbial community from a macro perspective. This guides the rational use of nanoparticles for which the impacts on soil microbiota are minimized.

Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets.

The development of machine learning and deep learning provided solutions for predicting microbiota response on environmental change based on microbial high-throughput sequencing. However, there were few studies specifically clarifying the performance and practical of two types of binary classification models to find a better algorithm for the microbiota data analysis. Here, for the first time, we evaluated the performance, accuracy and running time of the binary classification models built by three machine learning methods - random forest (RF), support vector machine (SVM), logistic regression (LR), and one deep learning method - back propagation neural network (BPNN). The built models were based on the microbiota datasets that removed low-quality variables and solved the class imbalance problem. Additionally, we optimized the models by tuning. Our study demonstrated that dataset pre-processing was a necessary process for model construction. Among these 4 binary classification models, BPNN and RF were the most suitable methods for constructing microbiota binary classification models. Using these 4 models to predict multiple microbial datasets, BPNN showed the highest accuracy and the most robust performance, while the RF method was ranked second. We also constructed the optimal models by adjusting the epochs of BPNN and the n_estimators of RF for six times. The evaluation related to performances of models provided a road map for the application of artificial intelligence to assess microbial ecology.

Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts.

The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.