Pyrosequencing Reveals Soil Enzyme Activities and Bacterial Communities Impacted by Graphene and Its Oxides

Effects of Graphene-Based Nanomaterials on Microorganisms and Soil Microbial Communities

The past decades have witnessed intensive research on the biological effects of graphene-based nanomaterials (GBNs) and the application of GBNs in different fields. The published literature shows that GBNs exhibit inhibitory effects on almost all microorganisms under pure culture conditions, and that this inhibitory effect is influenced by the microbial species, the GBN's physicochemical properties, the GBN's concentration, treatment time, and experimental surroundings. In addition, microorganisms exist in the soil in the form of microbial communities. Considering the complex interactions between different soil components, different microbial communities, and GBNs in the soil environment, the effects of GBNs on soil microbial communities are undoubtedly intertwined. Since bacteria and fungi are major players in terrestrial biogeochemistry, this review focuses on the antibacterial and antifungal performance of GBNs, their antimicrobial mechanisms and influencing factors, as well as the impact of this effect on soil microbial communities. This review will provide a better understanding of the effects of GBNs on microorganisms at both the individual and population scales, thus providing an ecologically safe reference for the release of GBNs to different soil environments.

The influences of graphene oxide and nitrification inhibitor on vegetable growths and soil and endophytic bacterial communities: Double-edge sword effects and nitrate risk controls

Crop yield and quality are substantial indicators of evaluating agricultural nitrogen management practices, and the nitrate (NO3--N) is one of the predominant factors affecting crop quality. The NO3--N accumulation in vegetable crop affects plant growth and quality and human health. Therefore, it is necessary to stimulate vegetable yield but eliminate excessive NO3--N in soils and plants with feasible management strategies. Graphene oxide (GO) is a novel carbon nanomaterial that has attracted great attention, but rare research has been conducted to quantify the effects of GO on plant NO3--N accumulation and microbial communities. This study explored effects of the GO and nitrification inhibitors, dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP), on vegetable yields and NO3--N contents and bacterial communities in soil-cabbage (Brassica rapa subsp. Chinensis) system. The soil NO3--N content was significantly reduced with the single GO application. The cabbage NO3--N content was increased by 60.4 % while the cabbage yield was significantly enhanced by 101.9 % with the single GO application. Meanwhile, the Invsimpson index of soil bacterial community and the ACE and Chao1 richness estimators of endophytic bacterial community were significantly decreased by the GO application. Cabbage NO3--N content was significantly and negatively correlated with the soil Myxococcota, endophytic bacterial community co-occurrence network edge, cabbage soluble sugar and cabbage proline. The GO application generated double-edged sword effects of positively promoting yield but causing risks of NO3--N accumulation and quality deterioration. However, these adverse effects could be mitigated by the extra nitrification inhibitor application. The potential ecological risks of GO application to the vegetable quality and endophytic community should be considered.

Graphene as a nano-delivery vehicle in agriculture - current knowledge and future prospects

Graphene has triggered enormous interest in, and exploration of, its applications in diverse areas of science and technology due to its unique properties. While graphene has displayed great potential as a nano-delivery system for drugs and biomolecules in biomedicine, its application as a nanocarrier in agriculture has only begun to be explored. Conventional fertilizers and agricultural delivery systems have a number of disadvantages, such as: fast release of the active ingredient, low delivery efficiency, rapid degradation and low stability that often leads to their over-application and consequent environmental problems. Advanced nano fertilizers with high carrier efficiency and slow and controlled release are now considered the gold standard for promoting agricultural sustainability while protecting the environment. Graphene's attractive properties include large surface area, chemical stability, mechanical stability, tunable surface chemistry and low toxicity making it a promising material on which to base agricultural delivery systems. Recent research has demonstrated considerable success in the use of graphene for agricultural applications, including its utilization as a delivery vehicle for plant nutrients and crop protection agents, as well as in post-harvest management of crops. This review, therefore, presents a comprehensive overview of the current status of graphene-based nanocarriers in agriculture. Additionally, the review outlines the surface functionalization methods used for effective molecular delivery, various strategies for nano-vehicle design and the underlying features necessary for a graphene-based agro-delivery system. Finally, the review discusses directions for further research in optimization of graphene-based nanocarriers.

Bioremediation system consisted with Leclercia adecarboxylata and nZVI@Carbon/Phosphate for lead immobilization: The passivation mechanisms of chemical reaction and biological metabolism in soil

Bioremediation is one of the most promising strategies for heavy metal immobilization. A new remediation system was demonstrated in this research, which combined phosphate solubilizing bacteria (PSB) with nZVI@Carbon/Phosphate (nZVI@C/P) composite to remediate lead contaminated soil. Experimental results indicated that the new system (nZVI@C/P + PSB) could effectively convert the labile Pb into the stable fraction after 30 days of incubation, which increased the maximum residual fraction percentage of Pb by 70.58%. The characterization results showed that lead may exist in the forms of Pb₅(PO₄)₃Cl, PbSO₄ and 3PbCO₃·2Pb(OH)₂·H₂O in the soil treated with nZVI@C/P + PSB. Meanwhile, soil enzyme activities and Leclercia abundance were enhanced in the treated soil compared with CK during the incubation time. In addition, the specialized functions (e.g. ABC transporters, siderophore metabolism, sulfur metabolism and phosphorus metabolism) in PSB and nZVI@C/P + PSB group were also enhanced. These phenomena proved that the key soil metabolic functions may be maintained and enhanced through the synergistic effect of incubated PSB and nZVI@C/P. The study demonstrated that this new bioremediation system provided feasible way to improve the efficacy for lead contaminated soil remediation.

The combined effect of graphene oxide and elemental nano-sulfur on soil biological properties and lettuce plant biomass

The impact of graphene oxide (GO) nanocarbon on soil properties is mixed, with both negative and positive effects. Although it decreases the viability of some microbes, there are few studies on how its single amendment to soil or in combination with nanosized sulfur benefits soil microorganisms and nutrient transformation. Therefore, an eight-week pot experiment was carried out under controlled conditions (growth chamber with artificial light) in soil seeded with lettuce (Lactuca sativa) and amended with GO or nano-sulfur on their own or their several combinations. The following variants were tested: (I) Control, (II) GO, (III) Low nano-S + GO, (IV) High nano-S + GO, (V) Low nano-S, (VI) High nano-S. Results revealed no significant differences in soil pH, dry plant aboveground, and root biomass among all five amended variants and the control group. The greatest positive effect on soil respiration was observed when GO was used alone, and this effect remained significant even when it was combined with high nano-S. Low nano-S plus a GO dose negatively affected some of the soil respiration types: NAG_SIR, Tre_SIR, Ala_SIR, and Arg_SIR. Single GO application was found to enhance arylsulfatase activity, while the combination of high nano-S and GO not only enhanced arylsulfatase but also urease and phosphatase activity in the soil. The elemental nano-S probably counteracted the GO-mediated effect on organic carbon oxidation. We partially proved the hypothesis that GO-enhanced nano-S oxidation increases phosphatase activity.

Graphene oxide decreases the abundance of nitrogen cycling microbes and slows nitrogen transformation in soils

Graphene oxide (GO) has been widely used in many applications due to its excellent properties. Given the extensive production and use of this nanomaterial, its release into the environment is inevitable. However, little is known about the effects of GO on microbial nitrogen transformation and the related processes after GO enters the soil environment. The present study showed that GO significantly reduced soil microbial biomass and caused a decline in microbial diversity after the soils were subjected to various GO concentrations (10, 100, and 1000 mg kg^-1) for 4 months. Among them, the abundances of nitrogen transformation related bacteria such as Firmicutes, Nitrospirota, Proteobacteria, Planctomycetota, and Cyanobacteria were significantly decreased with GO incubation. Among the enzymes that are related to nitrogen transformation, nitrate reductase was the most sensitive even at low concentrations of GO, followed by ammonia monooxygenase and urease, which were reduced by 13-31%, 5-26%, and 9-19% respectively, than those of the control. We found that high concentrations of GO significantly increased the retention of soil urea by 32-59%, and the contents of ammonium and nitrate were 22-28% and 55-69% lower compared to those of the control, respectively. Moreover, the response of most of the indicators in the above process to multilayer GO was more significant than that to single layer GO. Overall, this study provides new insights into the comprehensive understanding of GO's impacts on the soil nitrogen cycle.

Relationship between graphene and pedosphere: A scientometric analysis

The mass production and application of graphene have gradually expanded from academic research to industrial applications, which will inevitably lead to graphene entering the soil actively and passively. Therefore, the relationship between graphene and the pedosphere has attracted a lot of attention in the last decade. The most important question is whether graphene will harm soil health. Fortunately, the evidence is that graphene can alter soil physicochemical properties and microbial communities to some extent, but not dramatically. On this basis, the role of graphene in soil has been investigated in all directions. This review summarizes the literature on the relationship between graphene and soils. Topics include remediation and sensing of soil using graphene materials, the effects of graphene on soil, and the effects of graphene in soil on plant growth. At the same time, this review also uses bibliometrics to review the history of the topic. The number of papers published each year, participating countries, participating institutions and important articles were analyzed in detail. Finally, based on the published literature, we described the future perspectives of graphene and the pedosphere.

The Effects of Graphene-Family Nanomaterials on Plant Growth: A Review

Numerous reports of graphene-family nanomaterials (GFNs) promoting plant growth have opened up a wide range of promising potential applications in agroforestry. However, several toxicity studies have raised growing concerns about the biosafety of GFNs. Although these studies have provided clues about the role of GFNs from different perspectives (such as plant physiology, biochemistry, cytology, and molecular biology), the mechanisms by which GFNs affect plant growth remain poorly understood. In particular, a systematic collection of data regarding differentially expressed genes in response to GFN treatment has not been conducted. We summarize here the fate and biological effects of GFNs in plants. We propose that soil environments may be conducive to the positive effects of GFNs but may be detrimental to the absorption of GFNs. Alterations in plant physiology, biochemistry, cytological structure, and gene expression in response to GFN treatment are discussed. Coincidentally, many changes from the morphological to biochemical scales, which are caused by GFNs treatment, such as affecting root growth, disrupting cell membrane structure, and altering antioxidant systems and hormone concentrations, can all be mapped to gene expression level. This review provides a comprehensive understanding of the effects of GFNs on plant growth to promote their safe and efficient use.

Leaching of graphene oxide nanosheets in simulated soil and their influences on microbial communities

With the wide use of graphene-like nanosheets, especially in agriculture, their release into the environment, it is crucial to grasp the fate of nanosheets in soil and minimum ecological risks. The present work discovered that leaching and migration of nanosheets (rGO) in soil is affected by soil porosity and adsorption processes. And the contents of rGO-Pd in soil layers and leachate increased and then decreased with the decreased of soil porosity. Moreover, physicochemical properties of rGO-Pd nanosheets changed by leaching processes, especially the changes of morphology, thickness and oxygen functional groups. Leaching of rGO-Pd also interfered the soil microbial homeostasis accompanied by the increase of microbial species richness and community diversity. In addition, rGO-Pd altered the usage of carbon sources by edaphon. The utilization of carbon sources by soil microbes, such as polymers, sugars, phenolic acids, carboxylic acids, amino acids, and amines, was also reduced by nanosheets. These findings provide new insights into environmental behaviors of nanomaterials and nanogeochemistry.

Vegetation alleviate the negative effects of graphene oxide on benzo[a]pyrene dissipation and the associated soil bacterial community

Graphene oxide (GO) will enter the soil environment in increasing amounts. The effects of GO on the dissipation of benzo[a]pyrene (B[a]P) from contaminated soil and their phytoremediation system have been explored in this study. B[a]P is a ubiquitous soil pollutant used as a representative indicator of polycyclic aromatic hydrocarbons. A pot experiment was performed to investigate the effects of GO or/and vegetation (Tagetes patula) on B[a]P dissipation and the associated bacterial communities in soil. The bacterial communities in soil were investigated by Illumina sequencing analysis. The presence of vegetation significantly enhanced the dissipation of B[a]P from soil. The addition of GO (100 mg/kg) significantly decreased the B[a]P dissipation. When vegetation and GO coexisted, the inhibition effects of GO on B[a]P dissipation were alleviated by vegetation. Compared with the control treatment, the presence of GO or vegetation had no significant effects on the richness and diversity of bacterial communities in B[a]P-contaminated soil. Compared with the presence of only vegetation, the richness and diversity all significantly decreased when vegetation and GO coexisted. And, vegetation had a greater influence on the bacterial community composition than GO. Vegetation alleviated the inhibition effects of GO on B[a]P dissipation and had a greater influence on the associated bacterial communities than GO. This work helps to understand the interactive effects of GO and vegetation on B[a]P dissipation and the associated bacterial communities in contaminated soil.

Assessing the Impacts of Cu(OH)2 Nanopesticide and Ionic Copper on the Soil Enzyme Activity and Bacterial Community

Nanopesticides are being introduced in agriculture, and the associated environmental risks and benefits must be carefully assessed before their widespread agricultural applications. We investigated the impacts of a commercial Cu(OH)₂ nanopesticide formulation (NPF) at different agricultural application doses (e.g., 0.5, 5, and 50 mg of Cu kg^-1) on enzyme activities and bacterial communities of loamy soil (organic matter content of 3.61%) over 21 days. Results were compared to its ionic analogue (i.e., CuSO₄) and nano-Cu(OH)₂, including both the commercial unformulated active ingredient of NPF (AI-NPF) and synthesized Cu(OH)₂ nanorods (NR). There were negligible changes in the activity of acid phosphatase, regardless of exposure dose, whereas significant (p < 0.05) variations in activities of invertase, urease, and catalase were observed at a dose of 5 mg kg^-1 or higher. Invertase activity decreased with an increasing bioavailable Cu concentration in soil under various treatments. In comparison to CuSO₄, both Cu(OH)₂ nanopesticide (i.e., NPF) and nano-Cu(OH)₂ (i.e., AI-NPF and NR) caused a significant (p < 0.05) inhibition of urease activity, wherein a significant (p < 0.05) increase in the activity of catalase was observed, representing serious oxidative stress. Accordingly, NPF, AI-NPF, and NR differently affected soil bacterial abundance, diversity, and community compared to CuSO₄, which could have resulted from the changes in the bioavailable Cu concentration as a result of the distinct nature of copper spiked (i.e., nano form versus salt). Moreover, minor differences in the soil enzyme activity and bacterial community were observed between NPF and AI-NPF, reflecting that the impact of the Cu(OH)₂ nanopesticide was primarily attributed to the presence of nano-Cu(OH)₂. In total, the impacts of nano-Cu(OH)₂ on the soil bacterial community and enzyme activity tested in this study differed from CuSO₄, shedding light on the environmental risks of the Cu(OH)₂ nanopesticide in the long run.

Modification-Free Fabricating Ratiometric Nanoprobe Based on Dual-Emissive Carbon Dots for Nitrite Determination in Food Samples

Great challenges still exist for facilely fabricating ratiometric fluorescent nanoprobes. Fortunately, the appearance of dual-emissive carbon dots (CDs) offers a glimmer of hope for the fabrication of modification-free ratiometric nanoprobe. The chemical and electronic structure characteristics of the dual-emissive CDs might be modulated by conjugated structures of carbon sources and the doped nitrogen and sulfur atoms, and the surface state also contributed to the fluorescence properties via surface functional groups. Herein, we report a one-pot strategy for simultaneous preparation of two kinds of CDs named RYDE CDs and RODE CDs, showing dual-emissive fluorescent peaks with long wavelength by 2,3-diaminobenzoic acid hydrochloride for the first time. Notably, trace nitrite determination with high sensitivity and selectivity was realized for the first time based on the modification-free ratiometric fluorescent nanoprobe fabricated rapidly and directly by the as-prepared RYDE CDs at constant room temperature (20 °C). Under the optimal conditions, the limit of detection for nitrite was 31.61 nM, with a wide concentration linear range of 0.1-100 μM. Furthermore, this ratiometric nanoprobe was successfully applied for nitrite analysis in bacon, sausage, pickle, and milk samples. Additionally, the nanoprobe was also capable of visually monitoring temperature fluctuations and cell imaging.

Nanotoxicity of engineered nanomaterials (ENMs) to environmentally relevant beneficial soil bacteria - a critical review

Deposition of engineered nanomaterials (ENMs) in various environmental compartments is projected to continue rising exponentially. Terrestrial environments are expected to be the largest repository for environmentally released ENMs. Because ENMs are enriched in biosolids during wastewater treatment, agriculturally applied biosolids facilitate ENM exposure of key soil micro-organisms, such as plant growth-promoting rhizobacteria (PGPR). The ecological ramifications of increasing levels of ENM exposure of terrestrial micro-organisms are not clearly understood, but a growing body of research has investigated the toxicity of ENMs to various soil bacteria using a myriad of toxicity end-points and experimental procedures. This review explores what is known regarding ENM toxicity to important soil bacteria, with a focus on ENMs which are expected to accumulate in terrestrial ecosystems at the highest concentrations and pose the greatest potential threat to soil micro-organisms having potential indirect detrimental effects on plant growth. Knowledge gaps in the fundamental understanding of nanotoxicity to bacteria are identified, including the role of physicochemical properties of ENMs in toxicity responses, particularly in agriculturally relevant micro-organisms. Strategies for improving the impact of future research through the implementation of in-depth ENM characterization and use of necessary experimental controls are proposed. The future of nanotoxicological research employing microbial ecoreceptors is also explored, highlighting the need for continued research utilizing bacterial isolates while concurrently expanding efforts to study ENM-bacteria interactions in more complex environmentally relevant media, e.g. soil. Additionally, the particular importance of future work to extensively examine nanotoxicity in the context of bacterial ecosystem function, especially of plant growth-promoting agents, is proposed.