Lessons learned from COVID-19 on potentially pathogenic soil microorganisms

Vertical and seasonal dynamics of bacterial pathogenic communities at an aged organic contaminated site: Insights into microbial diversity, composition, interactions, and assembly processes

Under the background of the Coronavirus Disease 2019 (COVID-19) pandemic, research on pathogens deserves greater attention in the natural environment, especially in the widely distributed contaminated sites with complicated and severe organic pollution. In this study, the community composition and assembly of soil pathogens identified by the newly-developed 16S-based pipeline of multiple bacterial pathogen detection (MBPD) have been investigated on spatiotemporal scales in the selected organic polluted site. We demonstrated that the richness and diversity of the pathogenic communities were primarily controlled by soil depth, while the structure and composition of pathogenic communities varied pronouncedly with seasonal changes, which were driven by the alterations in both physiochemical parameters and organic contaminants over time. Network analysis revealed that the overwhelmingly positive interactions, identified multiple keystone species, and a well-organized modular structure maintained the stability and functionality of the pathogenic communities under environmental pressures. Additionally, the null-model analysis showed that deterministic processes dominated the pathogenic community assembly across soil profiles. In three seasons, stochasticity-dominated processes in spring and summer changed into determinism-dominated processes in winter. These findings extend our knowledge of the response of the bacterial pathogenic community to environmental disruptions brought on by organic contaminated sites.

Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil

Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

Assessment of residual chlorine in soil microbial community using metagenomics

Chlorine-containing disinfectants have been widely used around the world for the prevention and control of the COVID-19 pandemic. However, at present, little is known about the impact of residual chlorine on the soil micro-ecological environment. Herein, we treated an experimental soil-plant-microbiome microcosm system by continuous irrigation with a low concentration of chlorine-containing water, and then analyzed the influence on the soil microbial community using metagenomics. After 14-d continuous chlorine treatment, there were no significant lasting effect on soil microbial community diversity and composition either in the rhizosphere or in bulk soil. Although metabolic functions of the rhizosphere microbial community were affected slightly by continuous chlorine treatment, it recovered to the original status. The abundance of several resistance genes changed by 7 d and recovered by 14 d. According to our results, the chlorine residue resulting from daily disinfection may present a slight long-term effect on plant growth (shoot length and fresh weight) and soil micro-ecology. In general, our study assisted with environmental risk assessments relating to the application ofchlorine-containing disinfectants and minimization of risks to the environment during disease control, such as COVID-19.

Effects of manure fertilization on human pathogens in endosphere of three vegetable plants

Pathogens can colonize plant endosphere and, be transferred into human beings through the food chain. However, our understanding of the influences of agricultural activities, such as fertilization, on endophytic microbial communities and human pathogens is still limited. Here, we conducted a microcosm experiment using the combination of 16 S rRNA gene amplicon sequencing and high-throughput qPCR array to reveal the effects of manure fertilization on microbiomes of soils and plants and how such impact is translated into endophytic pathogens. Our results showed that manure fertilization significantly altered soil microbiomes, whereas with less influence on endophytic microbial communities. Soil is a vital source of both bacterial communities and human pathogens for the plant endosphere. The abundance of pathogens was increased both in soils and endosphere under manure fertilization. These findings provide an integrated understanding of the impact of manure fertilization on endophytic pathogens.

ROS as a key player in quinolone antibiotic stress on Arabidopsis thaliana: From the perspective of photosystem function, oxidative stress and phyllosphere microbiome

With the increasing use of antibiotics, their ecological impacts have received widespread attention. However, research on the toxicity of quinolone antibiotics is still limited, especially regarding the oxidative stress and phyllosphere of plants. In this study, the toxic effects of enrofloxacin, norfloxacin, and levofloxacin on Arabidopsis thaliana and their underlying mechanisms were investigated. The toxicity of the three quinolone antibiotics decreased in the following order: enrofloxacin > norfloxacin > levofloxacin. Physiological cellular changes, such as plasmolysis and chloroplast swelling, were observed using electron microscopy. Photosynthetic efficiency was inhibited with a decline in the effective photochemical quantum yield of photosystem II (Y(II)) and non-photochemical quenching (NPQ), indicating that quinolone antibiotics might reduce light energy conversion efficiency and excess light energy dissipation. Oxidative stress occurred in A. thaliana after quinolone antibiotic treatment, with an increase in reactive oxygen species (ROS) levels and malondialdehyde (MDA) content. High ROS levels stimulated the over-expression of superoxide-responsive genes for self-protection. Structural equation modeling (SEM) analysis showed that photosynthesis inhibition and cellular damage caused by oxidative stress were critical factors for growth inhibition, suggesting that the antioxidant response activated by ROS might be a potential mechanism. Furthermore, the diversity of the phyllospheric microbial communities decreased after enrofloxacin exposure. Additionally, specific microbes were preferentially recruited to the phyllosphere because of the higher ROS levels.

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.

Several major issues concerning the environmental transmission and risk prevention of SARS-CoV-2

Coronavirus disease 2019 (COVID-19) is the most serious infectious disease pandemic in the world in a century, and has had a serious impact on the health, safety, and social and economic development of all mankind. Since the earth entered the “Anthropocene”, human activities have become the most important driving force of the evolution of the earth system. At the same time, the epidemic frequency of major human infectious diseases worldwide has been increasing, with more than 70% of novel diseases having zoonotic origins. The review of several major epidemics in human history shows that there is a common rule, i.e., changes in the natural environment have an important and profound impact on the occurrence and development of epidemics. Therefore, the impact of the natural environment on the current COVID-19 pandemic and its mechanisms have become scientific issues that need to be resolved urgently. From the perspective of the natural environment, this study systematically investigated several major issues concerning the environmental transmission and risk prevention of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). From a macroscopic temporal and spatial scale, the research focus on understand the impact of the destruction of the natural environment and global changes on the outbreak of infectious diseases; the threat of zoonotic diseases to human health; the regularity for virus diffusion, migration and mutation in environmental media; the mechanisms of virus transmission from animals and environmental media to humans; and environmental safety, secondary risk prevention and control of major epidemics. Suggestions were made for future key research directions and issues that need attention, with a view to providing a reference for the prevention and control of the global coronavirus disease 2019, and to improving the ability of response to major public health emergencies.

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.

Viral diversity and potential environmental risk in microplastic at watershed scale: Evidence from metagenomic analysis of plastisphere

Microplastics (MPs) have been considered as a new vector for the long-distance transport of pathogens in aquatic ecosystems. However, the composition of viral communities attached on MPs and their environmental risk are largely unknown. Here, we profiled the viral diversity and potential risk in five different MPs collected from the Beilun River based on metagenomic analysis. Nearly 2863 million raw reads were produced and assembled, and annotation resulted in the identification of 1719 different species of viruses in MPs. Viruses in polypropylene (PP) displayed the highest diversity, with about 250 specific viruses detected. Source tracking of viruses in MPs by the fast expectation-maximization microbial source tracking method (FEAST) demonstrated that viruses in upstream and downstream MPs are two major sources of viruses in estuary. Furthermore, the MP-type-dependent potential environmental risk of viruses was significant based on both antibiotic resistance genes (ARGs) and virulence factors (VFs) detected in viral metagenomes, and PP was confirmed with the highest potential environmental risk. This study reveals the high diversity and potential environmental risk of viruses in different MPs, and provides an important guidance for future environmental monitoring and understanding the potential risks associated with both viral transmission and MPs pollution.

Residual chlorine disrupts the microbial communities and spreads antibiotic resistance in freshwater

Chlorine disinfection is a key global public health strategy for the prevention and control of diseases, such as COVID-19. However, little is known about effects of low levels of residual chlorine on freshwater microbial communities and antibiotic resistomes. Here, we treated freshwater microcosms with continuous low concentrations of chlorine and quantified the effects on aquatic and zebrafish intestinal microbial communities and antibiotic resistomes, using shotgun metagenome and 16S rRNA gene sequencing. Although chlorine rapidly degraded, it altered the aquatic microbial community composition over time and disrupted interactions among microbes, leading to decreases in community complexity and stability. However, community diversity was unaffected. The majority of ecological functions, particularly metabolic capacities, recovered after treatment with chlorine for 14 d, due to microbial community redundancy. There were also increased levels of antibiotic-resistance gene dissemination by horizontal and vertical gene transfer under chlorine treatment. Although the zebrafish intestinal microbial community recovered from temporary dysbiosis, growth and behavior of zebrafish adults were negatively affected by chlorine. Overall, our findings demonstrate the negative effects of residual chlorine on freshwater ecosystems and highlight a possible long-term risk to public health.

Composition identification and functional verification of bacterial community in disease-suppressive soils by machine learning

It has been widely reported that probiotic consortia in the rhizosphere can enhance the plant resistance to pathogens. However, the general composition and functional profiles of bacterial community in soils which suppress multiple diseases for various plants remain largely unknown. Here, we combined metadata analysis with machine learning to identify the general patterns of bacterial-community composition in disease-suppressive soils. Disease-suppressive soils significantly enriched Firmicutes and Actinobacteria but showed a decrease in Proteobacteria and Bacteroidetes. Our machine-learning models accurately identified the disease-conducive and -suppressive soils with 54 biomarker genera, 28 of which were potentially beneficial. We further carried out a successive passaging experiment with the susceptible rps2 mutant of Arabidopsis thaliana invaded by Pseudomonas syringae pv. tomato DC3000 (avrRpt2) for functional verification of potential beneficial bacteria. The disease-suppressive ability of Kribbella, Nocardioides and Bacillus was confirmed, and they positively activated the pathogen-associated molecular patterns-triggered immunity pathway. Results also showed that chemical control by pesticides in agricultural production decreased the disease-suppressive ability of soil. This study provides a method for accurately predicting the occurrence of multiple diseases in soil and identified potential beneficial bacteria to guide a wide range of multiple-strain biological control strategies in agricultural management.

Synergetic toxicity of silver nanoparticle and glyphosate on wheat (Triticum aestivum L.)

Silver nanoparticles (AgNPs) are one of the most commonly used nanomaterials in industrial and agricultural production. Glyphosate is a broad-spectrum systemic herbicide, which mainly acts in the phloem of weeds that compete with crop growth and is widely used in agriculture. This study investigated the interactive effects of AgNPs and glyphosate on the physiological morphology, gene transcription, and rhizosphere microorganisms of wheat. Our results demonstrated that wheat growth, and the structure and diversity of rhizosphere microorganisms were slightly influenced by AgNPs and glyphosate single treatment at the test concentration. However, AgNPs and glyphosate (Gly) combined treatment (AgNPs + Gly) strongly inhibited wheat growth and influenced gene transcription. In total, 955, 601, and 1336 genes were determined to be differentially expressed in AgNPs, glyphosate, and combined treatment, respectively. According to KEGG analysis, the combined groups induced an antioxidant response by upregulating the transcription of phenylpropanoid biosynthesis-related genes. In addition, more energy was needed, and disrupted cell membrane was shown in the combined treatment, which displayed in the upregulation of sucrose, starch, and lipid synthesis. Moreover, the relative abundance of Bradyrhizobium, Devosia, Kribbella, Sphingopyxis (nitrogen-fixing bacteria), and Streptomyces (plant growth-promoting bacteria) in soil microbiota were decreased, implicated that nitrogen fixation and some beneficial substance secretions were inhibited by the combined treatment. This study emphasized that the synergetic effects of AgNPs and glyphosate exerted a negative impact on wheat growth.

SARS-CoV-2 and other viruses in soil: An environmental outlook

In the present review, the authors shed light on the SARS-CoV-2 impact, persistence, and monitoring in the soil environment. With this purpose, several aspects have been deepened: i) viruses in soil ecosystems; ii) direct and indirect impact on the soil before and after the pandemic, and iii) methods for quantification of viruses and SARS-CoV-2 monitoring in soil. Viruses are present in soil (i.e. up to 417 × 107 viruses per g TS-1 in wetlands) and can affect the behavior and ecology of other life forms (e.g. bacteria), which are remarkably important for maintaining environmental equilibrium. Also, SARS-CoV-2 can be found in soil (i.e. up to 550 copies·g-1). Considering that the SARS-CoV-2 is very recent, poor knowledge is available in the literature on persistence in the soil and reference has been made to coronaviruses and other families of viruses. For instance, the survival of enveloped viruses (e.g. SARS-CoV) can reach 90 days in soils with 10% of moisture content at ambient. In such a context, the possible spread of the SARS-CoV-2 in the soil was evaluated by analyzing the possible contamination routes.