Response of soil microbial communities to engineered nanomaterials in presence of maize (Zea mays L.) plants

Iron-containing nanominerals for sustainable phosphate management: A comprehensive review and future perspectives

Adsorption, which is a quick and effective method for phosphate management, can effectively address the crisis of phosphorus mineral resources and control eutrophication. Phosphate management systems typically use iron-containing nanominerals (ICNs) with large surface areas and high activity, as well as modified ICNs (mICNs). This paper comprehensively reviews phosphate management by ICNs and mICNs in different water environments. mICNs have a higher affinity for phosphates than ICNs. Phosphate adsorption on ICNs and mICNs occurs through mechanisms such as surface complexation, surface precipitation, electrostatic ligand exchange, and electrostatic attraction. Ionic strength influences phosphate adsorption by changing the surface potential and isoelectric point of ICNs and mICNs. Anions exhibit inhibitory effects on ICNs and mICNs in phosphate adsorption, while cations display a promoting effect. More importantly, high concentrations and molecular weights of natural organic matter can inhibit phosphate adsorption by ICNs and mICNs. Sodium hydroxide has high regeneration capability for ICNs and mICNs. Compared to ICNs with high crystallinity, those with low crystallinity are less likely to desorb. ICNs and mICNs can effectively manage municipal wastewater, eutrophic seawater, and eutrophic lakes. Adsorption of ICNs and mICNs saturated with phosphate can be used as fertilizers in agricultural production. Notably, mICNs and ICNs have positive and negative effects on microorganisms and aquatic organisms in soil. Finally, this study introduces the following: trends and prospects of machine learning-guided mICN design, novel methods for modified ICNs, mICN regeneration, development of mICNs with high adsorption capacity and selectivity for phosphate, investigation of competing ions in different water environments by mICNs, and trends and prospects of in-depth research on the adsorption mechanism of phosphate by weakly crystalline ferrihydrite. This comprehensive review can provide novel insights into the research on high-performance mICNs for phosphate management in the future.

Nano-Iron Oxide (Fe3O4) Mitigates the Effects of Microplastics on a Ryegrass Soil-Microbe-Plant System

To understand microplastic-nanomaterial interactions in agricultural systems, a randomized block 90-day pot experiment was set up to cultivate ryegrass seedings in a typical red sandy soil amended with compost (1:9 ratio). Polyvinyl chloride (PVC) and polyethylene (PE) microplastic (MP) contaminants were added into pot soils at 0.1 and 10%, whereas nano-Fe3O4 (as nanoenabled agrochemicals) was added at 0.1% and 0.5% in comparison with chemical-free controls. The combination of nano-Fe3O4 and MPs significantly increased the soil pH (+3% to + 17%) but decreased the total nitrogen content (-9% to - 30%; P < 0.05). The treatment group with both nano-Fe3O4 and PE had the highest total soil C (29 g kg-1 vs 20 g kg-1 in control) and C/N ratio (13 vs 8 in control). Increased rhizosphere nano-Fe3O4 concentrations promoted ryegrass growth (+42% dry weight) by enhancing the chlorophyll (+20%) and carotenoid (+15%) activities. Plant leaf and root peroxidase enzyme activity was more significantly affected by nano-Fe3O4 with PVC (+15%) than with PE (+6%). Nano-Fe3O4 significantly changed the ryegrass bacterial community structure from belowground (the rhizoplane and root endosphere) to aboveground (the phylloplane). Under MP contamination, the addition of nano-Fe3O4 increased bacterial diversity (+0.35%) and abundance (+30%) in the phylloplane and further intensified the connectivity of ryegrass aboveground bacterial networks (positive association increased 17%). The structural equation model showed that the change in the plant microbiome was associated with the rhizosphere microbiome. Overall, these findings imply the positive influences of nano-Fe3O4 on the soil-microbe-plant system and establish a method to alleviate the harmful effects of MP accumulation in soils.

Dynamic interplay between nano-enabled agrochemicals and the plant-associated microbiome

The plant-associated microbiome is known to be a critical component for crop growth, nutrient acquisition, resistance to pathogens, and abiotic stress tolerance. Conventional approaches have been attempted to manipulate the plant-soil microbiome to improve plant performance; however, several issues have arisen, such as collateral negative impacts on microbiota composition. The lack of reliability and robustness of conventional techniques warrants efforts to develop novel alternative strategies. Nano-enabled approaches have emerged as promising platforms for enhancing agricultural sustainability and global food security. Specifically, the use of engineered nanomaterials (ENMs) as nanoscale agrochemicals has great potential to modulate the plant-associated microbiome. We review the dynamic interplay between nano-agrochemicals and the plant-associated microbiome for the safe development and use of nano-enabled microbiome engineering.

Iron oxide nanoparticles in the soil environment: Adsorption, transformation, and environmental risk

Iron oxide nanoparticles (IONPs) have great application potential due to their multifunctional excellence properties, leading to the possibility of their release into soil environments. IONPs exhibit different adsorption properties toward environmental pollutants (e.g., heavy metals and organic compounds), thus the adsorption performance for various contaminants and the molecular interactions at the IONPs-pollutants interface are discussed. After solute adsorption, the change in the environmental behavior of IONPs is an important transformation process in the natural environments. The aggregation, aging process, and chemical/biological transformation of IONPs can be altered by soil solution chemistry, as well as by the presence of dissolved organic matter and microorganisms. Upon exposure to soil environments, IONPs have both positive and negative impacts on soil organisms (e.g., bacteria, plants, nematodes, and earthworms). Moreover, we compared the toxicity of IONPs alone to combined toxicity with environmental pollutants and pristine IONPs to aged IONPs, and the mechanisms of IONPs toxicity at the cellular level are also reviewed. Given the unanswered questions, future research should include prediction and design of IONPs, new characterization technology for monitoring IONPs transformation in soil ecosystems, and further refinement the environmental risk assessment of IONPs. This review will greatly enhance our knowledge of the performance and impact of IONPs in soil systems.

Global analysis of the perturbation effects of metal-based nanoparticles on soil nitrogen cycling

Although studies have investigated the effects of metal-based nanoparticles (MNPs) on soil biogeochemical processes, the results obtained thus far are highly variable. Moreover, we do not yet understand how the impact of MNPs is affected by experimental design and environmental conditions. Herein, we conducted a global analysis to synthesize the effects of MNPs on 17 variables associated with soil nitrogen (N) cycling from 62 studies. Our results showed that MNPs generally exerted inhibitory effects on N-cycling process rates, N-related enzyme activities, and microbial variables. The response of soil N cycling varied with MNP type, and exposure dose was the most decisive factor for the variations in the responses of N-cycling process rates and enzyme activities. Notably, Ag/Ag2 S and CuO had dose-dependent inhibitory effects on ammonia oxidation rates, while CuO and Zn/ZnO showed hormetic effects on nitrification and denitrification rates, respectively. Other experimental design factors (e.g., MNP size and exposure duration) also regulated the effect of MNPs on soil N cycling, and specific MNPs, such as Ag/Ag2 S, exerted stronger effects during long-term (>28 days) exposure. Environmental conditions, including soil pH, organic carbon, texture, and presence/absence of plants, significantly influenced MNP toxicity. For instance, the effects of Ag/Ag2 S on the ammonia oxidation rate and the activity of leucine aminopeptidase were more potent in acid (pH <6), organic matter-limited (organic carbon content ≤10 g kg-1 ), and coarser soils. Overall, these results provide new insights into the general mechanisms by which MNPs alter soil N processes in different environments and underscore the urgent need to perform multivariate and long-term in situ trials in simulated natural environments.

Selenium and Bacillus proteolyticus SES synergistically enhanced ryegrass to remediate Cu-Cd-Cr contaminated soil

Heavy metal compound contaminated soil is an ecological threat, and soil containing copper (Cu), cadmium (Cd) and chromium (Cr) simultaneously is widely distributed. The application of phytoremediation in heavy metal combined contamination is still limited. In this study, to explore whether and how exogenous selenium (Se) and Bacillus proteolyticus SES enhance the remediation of combined Cu-Cd-Cr contaminated soil by ryegrass, pot experiments were carried out. Se alone or in combination with B. proteolyticus SES treatment increased the removal rates of heavy metals in the rhizosphere soil by 17.38%-157.25% relative to the control, while Se + B. proteolyticus SES treatment played a greater role in improving the heavy metals tolerance of ryegrass and increasing the activity of soil acid phosphatase. Moreover, Se and B. proteolyticus SES favored the preferential recruitment of specific taxa with the capacity of plant growth promotion and heavy metals resistance to the rhizosphere. The rhizosphere soil of Se treatment was specifically enriched with Lysobacter, Rhodanobacter, Micrococcales, Paenarthrobacter, and Adhaeribacter, while from class Bacilli to genus Bacillus enriched extensively and specifically in the rhizosphere of B. proteolyticus SES + Se treatment. Furthermore, five functional beneficial rhizosphere microbes including: Microbacterium sp., Pseudomonas extremaustralis, Bacillus amyloliquefaciens, Priestia megaterium, and Bacillus subtilis were isolated from the two treatments with the best remediation effect and synthetic communities (SynComs) were constructed. SynComs inoculation experiment further demonstrated the role of specific beneficial microbes in regulating the bioavailability of heavy metals. Results revealed that Se supplementation efficiently facilitated the phytoextraction of combined Cu-Cd-Cr contaminated soil, and B. proteolyticus SES inoculation showed the synergistical enhancement effect in the presence of Se.

Integrating nanotechnology with plant microbiome for next-generation crop health

Nanotechnology has enormous potential for sustainable agriculture, such as improving nutrient use efficiency, plant health, and food production. Nanoscale modulation of the plant-associated microbiota offers an additional valuable opportunity to increase global crop production and ensure future food and nutrient security. Nanomaterials (NMs) applied to agricultural crops can impact plant and soil microbiota, which offers valuable services to host plants, including the acquisition of nutrients, abiotic stress tolerance, and disease suppression. Dissecting the complex interactions between NMs and plants by integrating multi-omic approaches is providing new insights into how NMs can activate host responses and functionality as well as influence native microbial communities. Such nexus and moving beyond descriptive microbiome studies to hypothesis-driven research will foster microbiome engineering and open up opportunities for the development of synthetic microbial communities to provide agronomic solutions. Herein, we first summarize the significant role of NMs and the plant microbiome in crop productivity and then focus on NMs effects on plant-associated microbiota. We outline three urgent priority research areas and call for a transdisciplinary collaborative approach, involving plant scientists, soil scientists, environmental scientists, ecologists, microbiologists, taxonomists, chemists, physicists, and stakeholders, to advance nano-microbiome research. Detailed understanding of the nanomaterial-plant-microbiome interactions and the mechanisms underlying NMs-mediated shifts in the microbiome assembly and functions may help to exploit the services of both nano-objects and microbiota for next-generation crop health.

Missing symbionts – emerging pathogens? Microbiome management for sustainable agriculture

Plant diversification and co-evolution shaped the plant microbiome and vice versa. This resulted in a specific composition of the plant microbiome and a strong connection with the host in terms of functional interplay. Symbionts are part of the microbiota, and important for the plant’s germination and growth, nutrition, as well as stress protection. However, human activities in the Anthropocene are linked to a significant shift of diversity, evenness and specificity of the plant microbiota. In addition, and very importantly, many plant symbionts are missing or no longer functional. It will require targeted microbiome management to support and reintroduce them. In future agriculture, we should aim at replacing harmful chemicals in the field, as well as post-harvest, by using precision microbiome engineering. This is because the plant microbiome is connected across systems and crucial for human and planetary health. This commentary aims to inspire holistic studies for the development of solutions for sustainable agriculture in framework of the One Health and the Planetary Health concepts.

Potential of Medicago sativa and Perilla frutescens for overcoming the soil sickness caused by ginseng cultivation

There are serious soil sickness in ginseng cultivation. Crop rotation is an effective agricultural management to improve soil sustainability and reduce soil sickness. To explore an appropriate ginseng rotation system, Medicago sativa (alfalfa) and Perilla frutescens (perilla) were planted on ginseng cultivation soil for 1 year to evaluate the improvement effect of both. Through chemical analysis and high-throughput sequencing technology, we found that after alfalfa and perilla cultivation for one-year, various nutrients and enzyme activities in ginseng cultivation soil were significantly improved. In addition, perilla significantly increased the diversity and richness of soil fungal communities. Cultivation of alfalfa and perilla significantly changed the composition of soil bacterial and fungal communities and significantly reduced the abundance of the potentially pathogenic fungi Ilyonectria. Further pot experiments also showed that the improved soil could significantly increase root activity of ginseng plant after two plants were planted. It should be noted that, unlike alfalfa, perilla decreased soil electrical conductivity, increased soil organic matter, soil urease, and may significantly improve the diversity and richness of soil fungal community. Moreover, in the pot experiment, the root fresh weight of ginseng cultured in perilla treated soil increased significantly. This study highlights that perilla may have better soil improvement effect than alfalfa and it has the potential to be used in the soil improvement of ginseng cultivation.

A 24-epibrassinolide treatment and intercropping willow with alfalfa increase the efficiency of the phytoremediation of cadmium-contaminated soil

Cadmium contamination in agricultural soils threatens food security and human health, and that has caused widespread concern worldwide. Willow and alfalfa are widely used for the phytoremediation of cadmium (Cd)-contaminated soil, and willow NJU513 is the promising plant for remediating Cd-contaminated soil. In order to discuss the effect of intercropping willow NJU513 with alfalfa on the phytoremediation of Cd-contaminated soil, a pot-culture experiment was conducted in the greenhouse. The result showed that the phytoremediation of Cd-contaminated soil was enhanced by this intercropping because of the 25.90 % increase in the available Cd content. In order to increase the phytoremediation efficiency of Cd in the intercropping treatment, a 24-epibrassinolide (Brs) treatment was designed in the current study. The results showed that the phytoremediation of Cd-contaminated soil by willow and alfalfa improved following a Brs treatment because of the 16.32-74.15 % and 16.91-44.48 % increases in the plant biomass and available Cd content, respectively. Additionally, the extracted Cd by plants in the intercropping treatments with and without Brs was 0.56 and 0.31 mg pot-1, respectively. Transcriptome analyses of willow leaves revealed that Brs up-regulated the expression of genes related to calcium channel activity, calcium and zinc transmembrane transport, photosynthesis, catalase/antioxidant activity, glutathione metabolic processes and detoxification, phagosomes, and vacuoles, and that these upregulated genes promoted plant remediation efficiency and resistance to Cd stress. Brs promoted the phosphate ion transporter activity in willow leaves, which may have enhanced the solubilization of insoluble phosphate minerals by bacterial species (e.g., Vicinamibacterales, Bacillus, and Gaiella) to release Cd, ultimately leading to increased phytoremediation efficiency. In addition, plants with and without Brs treatments induced the bacteria-mediated transformation of available Cd to stable Cd. The study findings may be useful for improving the phytoremediation of Cd-contaminated paddy soil.

Fe-Based Nanomaterial-Induced Root Nodulation Is Modulated by Flavonoids to Improve Soybean (Glycine max) Growth and Quality

Innovative technology to increase efficient nitrogen (N) use while avoiding environmental damages is needed because of the increasing food demand of the rapidly growing global population. Soybean (Glycine max) has evolved a complex symbiosis with N-fixing bacteria that forms nodules to fix N. Herein, foliar application of 10 mg L^-1 Fe₇(PO₄)₆ and Fe₃O₄ nanomaterials (NMs) (Fe-based NMs) promoted soybean growth and root nodulation, thus improving the yield and quality over that of the unexposed control, EDTA-control, and 1 and 5 mg L^-1 NMs. Mechanistically, flavonoids, key signaling molecules at the initial signaling steps in nodulation, were increased by more than 20% upon exposure to 10 mg L^-1 Fe-based NMs, due to enhanced key enzyme (phenylalanine ammonia-lyase, PAL) activity and up-regulation of flavonoid biosynthetic genes (GmPAL, GmC4H, Gm4CL, and GmCHS). Accumulated flavonoids were secreted to the rhizosphere, recruiting rhizobia for colonization. Fe₇(PO₄)₆ NMs increased Allorhizobium by 87.3%, and Fe₃O₄ NMs increased Allorhizobium and Mesorhizobium by 142.2% and 34.9%, leading to increased root nodules by 50.0% and 35.4% over the unexposed control, respectively. Leghemoglobin content was also noticeably improved by 8.2-46.5% upon Fe-based NMs. The higher levels of nodule number and leghemoglobin content resulted in enhanced N content by 15.5-181.2% during the whole growth period. Finally, the yield (pod number and grain biomass) and quality (flavonoids, soluble protein, and elemental nutrients) were significantly increased more than 14% by Fe-based NMs. Our study provides an effective nanoenabled strategy for inducing root nodules to increase N use efficiency, and then both yield and quality of soybean.

Effects of planting of two common crops, Allium fistulosum and Brassica napus, on soil properties and microbial communities of ginseng cultivation in northeast China

Background

Long-term cultivation of ginseng can cause severe crop disorders and soil sickness. Crop rotation is an effective agricultural management measure to improve soil sustainability and decrease pathogens. However, the suitable ginseng rotation system and the changes in soil microbial community and soil characteristics under the rotation system need to be further explored.

Methods

To explore suitable ginseng crop rotation systems and improve soil utilization, Allium fistulosum and Brassica napus were planted on ginseng cultivation soil for one year. The effects of the two crops on the chemical properties and enzyme activities of the ginseng cultivation soil were evaluated by chemical analysis. In addition, amplicon sequencing targeting 16 s rDNA genes of bacteria and ITS of fungi has been used to characterize the functional and compositional diversity of microbial communities.

Results

The results elucidated that the levels of available phosphorus (AP) and available potassium (AK) in the soil increased significantly after one year of cultivation for both crops and Allium fistulosum cultivation may also have reduced soil salinity. In addition, the effects of the two crops on the activities of key soil enzymes were different. Catalase (CAT), urease (URE), and acid phosphatase (A-PHO) activities were significantly reduced and sucrase (SUC), and laccase (LAC) activities were significantly increased after Allium fistulosum planting. While A-PHO activity was significantly increased and LAC activity was significantly decreased after Brassica napus planting. Allium fistulosum significantly reduced the abundance of soil fungal communities. The cultivation of Allium fistulosum and Brassica napus significantly altered the composition of soil bacterial and fungal communities, where changes in the abundance of dominant microorganisms, such as Ascomycota, and Mortierellomycota, etc., were closely related to soil chemistry and enzyme activity. Moreover, both significantly reduced the abundance of the pathogenic fungus Ilyonectria.

Conclusions

Our study clarified the effects of Allium fistulosum and Brassica napus on the microbial community and physicochemical properties of ginseng cultivated soil and provides a basis for the sustainable application of ginseng cultivation soil and the development of ginseng crop rotation systems.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-022-02592-0.

Rhizosphere microbial community composition and survival strategies in oligotrophic and metal(loid) contaminated iron tailings areas

In this study, the metal(loid) fractions in two alkaline iron tailings areas with similar physico-chemical properties and the enrichment ability of dominant plants in these areas were investigated. Additionally, high-throughput sequencing and metagenome analysis were used to examine the rhizosphere microbial community structures and their strategies and potential for carbon fixation, nitrogen metabolism, and metal(loid) resistance in mining areas. Results showed that Salsola collina, Setaria viridis, and Xanthium sibiricum have strong enrichment capacity for As, and the maximum transport factor for Mn can reach 4.01. The richness and diversity of bacteria were the highest in rhizosphere tailings, and the dominant phyla were Proteobacteria, Actinobacteria, Ascomycota, and Thaumarchaeota. The key taxa present in rhizosphere tailings were generally metal(loid) resistant, especially Sphingomonas, Pseudomonas, Nocardioides, and Microbacterium. The reductive citrate cycle was the main carbon fixation pathway of microorganisms in tailings. Rhizosphere microorganisms have evolved a series of survival strategies and can adapt to oligotrophic and metal(loid) polluted mining environments. The results of this study provide a basis for the potential application of plant-microbial in situ remediation of alkaline tailings.

Rare-earth metal oxide nanoparticles decouple the linkage between soil bacterial community structure and function by selectively influencing potential keystone taxa

Excessive production and application of rare-earth metal oxide nanoparticles warrants assessment of their environmental risks. Little is known about the impact of these nanoparticles on soil bacterial communities. We quantified the effects of nano-Gd₂O₃ and nano-La₂O₃, at the different concentrations and exposure regimes, on soil bacterial community structure and function as well as the structure-function relationship. Further, we constructed and analyzed a co-occurrence network to identify and characterize potential keystone taxa that were related to the enzyme activities and responded to the increasing concentrations of nanoparticles. Both nano-Gd₂O₃ and nano-La₂O₃ significantly altered the bacterial community structure and function in a concentration-dependent manner; however, these negative effects were observed on day 1 or day 7 but not on day 60, indicating that these effects were transient and the bacterial communities can mitigate the effect of these nanoparticles over time. Interestingly, the nanoparticle exposure decoupled the relationship between the structure and function of the soil bacterial communities. The decoupling was due to changes in the composition and relative abundances of potential keystone taxa related to bacterial community functions. Altogether, we provide insights into the interactions between the rare-earth metal oxide nanoparticles and soil bacterial communities. Our results facilitate the environmental risk assessment and safe usage of rare-earth metal oxide nanoparticles.

The plant microbiota signature of the Anthropocene as a challenge for microbiome research

BACKGROUND

One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.

RESULTS

Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.

CONCLUSIONS

Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health. Video abstract.

Impact of engineered nanomaterials on rice (Oryza sativa L.): A critical review of current knowledge

After use, a large number of engineered materials (ENMs) are directly or indirectly released into the environment. This may threaten the agricultural ecosystem, especially with crops under high demand for irrigation water, such as rice (Oryza sativa L.), a crop that feeds nearly half of the world's population. However, consistent and detailed information on the effects of nanoparticles in rice is limited. This review is a systematic exploration of the effects of ENMs on rice, with a critical evaluation of the mechanisms reported in the literature by which different nanomaterials cause toxicity in rice. The physiological and biochemical effects engendered by the nanoparticles are highlighted, focusing on rice growth and development, ENMs uptake and translocation, gene expression changes, enzyme activity modifications, and secondary metabolite alterations.

Effect of the Nanoparticle Exposures on the Tomato Bacterial Wilt Disease Control by Modulating the Rhizosphere Bacterial Community

Ralstonia Solanacearum is one of the most infectious soil-borne bacterial plant pathogens, causing tomato bacterial wilt (TBW). Nanotechnology is an emerging area of research, particularly the application of nanoparticles (NPs) as nanopesticides to manage plant disease is gaining attention nowadays. However, the interaction between NPs and rhizosphere bacterial communities remains largely elusive. This study indicated that metal NPs (CuO, ZnO, and FeO) reduced the incidence of bacterial wilt to varying degrees and affected the composition and structure of the rhizosphere bacterial community. The results revealed that the application of metal oxide NPs can improve the morphological and physiological parameters of TBW infected tomato plants. Among all, CuONPs amendments significantly increase the Chao1 and Shannon index. In the early stage (the second week), it significantly reduces the relative abundance of pathogens. However, the relative abundance of beneficial Streptomyces bacteria increased significantly, negatively correlated with the relative abundance of pathogenic bacteria. In addition, the nano-treatment group will enrich some potential beneficial bacteria such as species from Sphingomonadaceae, Rhizobiaceae, etc. In general, our research provides evidence and strategies for preventing and controlling soil-borne disease tomato bacterial wilt with metal oxide NPs.