Nanosilver inhibits nitrification and reduces ammonia-oxidising bacterial but not archaealamoAgene abundance in estuarine sediments

Comprehensive response of microbes to Ag and Ag2S nanoparticles and silver spatial distribution in constructed wetlands

This study investigated functional bacteria, key enzymes, and nitrogen metabolism in vertical flow constructed wetlands (CWs) after exposing to silver, silver sulfide nanoparticles (Ag NPs and Ag2S NPs), and silver iron (Ag+), and silver spatial distribution in CWs for 155 days. Ag NPs and Ag2S NPs affected species richness and diversity whereas Ag+ showed the higher the species diversity indices. Sequencing analysis exhibited that Ag NPs or Ag+ significantly inhibited nitrogen metabolic process by hindering the relative activity of functional enzymes, downregulating relative abundances of nrfA, norB and napA for Ag NPs, nxrA gene for Ag+, while Ag2S NPs inhibited relative abundance of nirA. The above results confirmed that NPs or Ag+ significantly reduced nitrogen removal and Ag NPs mainly inhibited NO3--N removal while Ag+ significantly suppressed NH4+-N removal. This study also found that CWs could effectively remove NPs or Ag+ (about 98 %), and nanoparticles showed higher translocation factors (TFs) values (0.81-1.15 or 0.36), indicating nanoparticles transported easily through substrate layers.

Ecological risks of microplastics contamination with green solutions and future perspectives

The rise of plasticulture as mulching material in farming systems has raised concerns about microplastics (MPs) in the agricultural landscape. MPs are emerging pollutants in croplands and water systems with significant ecological risks, particularly over the long term. In the soil systems, MPs polymer type, thinness, shape, and size induces numerous effects on soil aggregates, dissolved organic carbon (C), rapidly oxidized organic C, microbial biomass C, microbial biomass nitrogen (N), microbial immobilization, degradation of organic matter, N cycling, and production of greenhouse gas emissions (GHGs), thereby posing a significant risk of impairing soil physical and biochemical properties over time. Further, toxic chemicals released from polyethylene mulching (PMs) might indirectly harm plant growth by affecting soil wetting-drying cycles, releasing toxic substances that interact with soil matrix, and suppressing soil microbial activity. In the environment, accumulation of MPs poses a risk to human health by accelerating emissions of GHGs, e.g., methane and carbon dioxide, or directly releasing toxic substances such as phthalic acid esters (PAEs) into the soils. Also, larger sizes MPs can adhere to root surface and block stomata could significantly change the shape of root epidermal cells resulting in arrest plant growth and development by restricting water-nutrient uptake, and gene expression and altering the biodiversity of the soil pollutants. In this review, we systematically analyzed the potential risks of MPs to the soil-plant and human body, their occurrence, abundance, and migration in agroecosystems. Further, the impacts of MPs on soil microbial function, nutrient cycling, soil C, and GHGs are mechanistically reviewed, with emphasis on potential green solutions such as organic materials amendments along with future research directions for more eco-friendly and sustainable plastic management in agroecosystems.

Long-term effects of Ag NPs on denitrification in sediment: Importance of Ag NPs exposure ways in aquatic ecosystems

The widespread use of silver nanoparticles (Ag NPs) inevitably leads to their increasing release into aquatic systems, with studies indicating that the mode of Ag NPs entry into water significantly affects their toxicity and ecological risks. However, there is a lack of research on the impact of different exposure ways of Ag NPs on functional bacteria in sediment. This study investigates the long-term influence of Ag NPs on denitrification process in sediments by comparing denitrifies responses to single (pulse injection of 10 mg/L) and repetitive (1 mg/L × 10 times) Ag NPs treatments over 60-day incubation. Results showed that a single exposure of 10 mg/L Ag NPs caused an obvious toxicity on activity and abundance of denitrifying bacteria on the first 30 days, reflecting by the decreased NADH amount, ETS activity, NIR and NOS activity, and nirK gene copy number, which resulted in a significant decline of denitrification rate in sediments (from 0.59 to 0.64 to 0.41-0.47 μmol15N L-1 h-1). While inhibition was mitigated with time and denitrification process recovered to the normal at the end of the experiment, the accumulated nitrate generated in the system showed that the recovery of microbial function did not mean the restoration of aquatic ecosystem after pollution. Differently, the repetitive exposure of 1 mg/L Ag NPs exhibited the evident inhibition on metabolism, abundance, and function of denitrifiers on Day 60, due to the accumulated amount of Ag NPs with the increased dosing number, indicating that the accumulated toxicity on functional microorganic community of repetitive exposure in less toxic concentration. Our study highlights the importance of Ag NPs entry pathways into aquatic ecosystem on their ecological risks, which affected dynamic responses of microbial function to Ag NPs.

Analytical methods for assessing antimicrobial activity of nanomaterials in complex media: advances, challenges, and perspectives

Assessing the antimicrobial activity of engineered nanomaterials (ENMs), especially in realistic scenarios, is of great significance for both basic research and applications. Multiple analytical methods are available for analysis via off-line or on-line measurements. Real-world samples are often complex with inorganic and organic components, which complicates the measurements of microbial viability and/or metabolic activity. This article highlights the recent advances achieved in analytical methods including typical applications and specifics regarding their accuracy, cost, efficiency, and user-friendliness. Methodological drawbacks, technique gaps, and future perspectives are also discussed. This review aims to help researchers select suitable methods for gaining insight into antimicrobial activities of targeted ENMs in artificial and natural complex matrices.

The impact of silver nanoparticles on microbial communities and antibiotic resistance determinants in the environment

Nanosilver (NAg) is currently one of the major alternative antimicrobials to control microorganisms. With its broad-spectrum efficacy and lucrative commercial values, NAg has been used in medical devices and increasingly, in consumer products and appliances. This widespread use has inevitably led to the release and accumulation of the nanoparticle in water and sediment, in soil and even, wastewater treatment plants (WWTPs). This Article describes the physical and chemical transformations of NAg as well as the impact of the nanoparticle on microbial communities in different environmental settings; how the nanoparticle shifts not only the diversity and abundance of microbes, including those that are important in nitrogen cycles and decomposition of organic matters, but also their associated genes and in turn, the key metabolic processes. Current findings on the microbiological activity of the leached soluble silver, solid silver particulates and their respective transformed products, which underpin the mechanism of the nanoparticle toxicity in environmental microbes, is critically discussed. The Article also addresses the emerging evidence of silver-driven co-selection of antibiotic resistance determinants. The mechanism has been linked to the increasing pools of many antibiotic resistance genes already detected in samples from different environmental settings, which could ultimately find their ways to animals and human. The realized ecological impact of NAg calls for more judicial use of the nanoparticle. The generated knowledge can inform strategies for a better 'risks versus benefits' assessment of NAg applications, including the disposal stage.

Silver nanoparticles in aquatic sediments: Occurrence, chemical transformations, toxicity, and analytical methods

Sediments represent the major sink for released silver nanoparticles (AgNPs) in aquatic environments. It is well known that the environmental behavior and toxicity of AgNPs in sediments are governed by their specific chemical species instead of their total concentration. This review focuses on various chemical transformations of AgNPs in sediments, which have not been well outlined before. We first outline the concentrations of AgNPs in sediments. The predicted concentrations are 1-5 µg kg^-1 in most model studies. Once enter sediments, AgNPs are transformed to different species (e.g., Ag₂S, Ag-humic substance complexes, AgCl, and Ag⁺) during multiple chemical transformations, such as oxidative dissolution, sulfidation, chlorination, and complexation. Those chemical behaviors mitigate the toxicity of AgNPs by reducing their availability and decreasing Ag⁺ release. Benthic invertebrates and microbes are prone to be affected by AgNPs. AgNPs are found to be accumulated in sediment-dwelling organisms and transferred to higher trophic levels along the food web. Besides X-ray absorption spectroscopy, reliable separation procedures coupled with detection techniques, are powerful tools that characterize the speciation of AgNPs in sediments. More research is needed to investigate diverse chemical transformations in various sediments through development of novel techniques and mathematical models.

Impacts of Ag and Ag2S nanoparticles on the nitrogen removal within vertical flow constructed wetlands treating secondary effluent

In this study, the effects of silver (Ag NPs) and sliver sulfide nanoparticles (Ag₂S NPs) on nitrogen removal and nitrogen functional microbes in constructed wetlands were investigated. The obtained results demonstrated that inhibition extent on nitrogen removal relied on NPs types and high concentrations NPs showed higher negative effects. 0.5 mg/L Ag NPs had no influence on NH₄⁺-N removal, amoA and nxrA gene copies, whereas Ag₂S NPs and Ag⁺ decreased NH₄⁺-N removal by reducing abundances of nitrifying genes. The concentrations of NO₃^--N and TN in all 0.5 mg/L obviously increased compared with control, resulting from decreasing functional genes and denitrifying bacteria. And 0.5 mg/L Ag NPs exhibited largest inhibitory effects, with the highest NO₃^--N effluent concentrations. 2 mg/L Ag NPs decreased NH₄⁺-N removal, but adverse effects gradually vanished with extension of time, whereas both Ag₂S NPs and Ag⁺ at 2 mg/L influenced NH₄⁺-N transformation and decreased the abundance of amoA and nxrA genes and the AOB Nitrosomonas in CWs. Moreover, 2 mg/L of Ag NPs reduced NO₃^--N removal by decreasing abundance of nirS and key denitrifying bacteria. To sum up, the inhibition mechanisms concluded from current results were possibly in that Ag NPs exhibited nanotoxicity rather than ionic toxicity.

Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline

Tree decline is a global concern and the primary cause is often unknown. Complex interactions between fluctuations in nitrogen (N) and acidifying compounds have been proposed as factors causing nutrient imbalances and decreasing stress tolerance of oak trees. Microorganisms are crucial in regulating soil N available to plants, yet little is known about the relationships between soil N-cycling and tree health. Here, we combined high-throughput sequencing and qPCR analysis of key nitrification and denitrification genes with soil chemical analyses to characterise ammonia-oxidising bacteria (AOB), archaea (AOA) and denitrifying communities in soils associated with symptomatic (declining) and asymptomatic (apparently healthy) oak trees (Quercus robur and Q. petraea) in the United Kingdom. Asymptomatic trees were associated with a higher abundance of AOB that is driven positively by soil pH. No relationship was found between AOA abundance and tree health. However, AOA abundance was driven by lower concentrations of NH₄⁺, further supporting the idea of AOA favouring lower soil NH₄⁺ concentrations. Denitrifier abundance was influenced primarily by soil C:N ratio, and correlations with AOB regardless of tree health. These findings indicate that amelioration of soil acidification by balancing C:N may affect AOB abundance driving N transformations, reducing stress on declining oak trees.

A novel method to estimate cellular internalization of nanoparticles into gram-negative bacteria: Non-lytic removal of outer membrane and cell wall

Bacteria efficiently take up small organic molecules and ions. However, the internalization of particulate forms, specifically nanoparticles (NPs) has been understudied and is a newly-emerging area of interest. However, determination of true cellular internalization is challenging owing to the difficulty of separating the aqueous phase from bacteria-associated NPs and, more importantly, of differentiating between internalized and NPs sorbed on bacteria surfaces. In this work, we developed and validated an extraction method which can operationally estimate internalization of metal NPs into Gram-negative bacteria. The outer cell membrane and cell wall, collectively called the periplasm, was successfully removed from bacteria using ethylenediaminetetraacetic acid (EDTA) at an optimized exposure period and concentration, without lysis of bacteria. This was followed by standard digestion and metal measurements. Verification of each step of the methodology was conducted by assessing both cellular and metal behavior. Specifically, the combined approaches of live/dead staining of bacteria, optical density measurements, transmission electron microscopy (TEM) and metal analyses of the supernatant indicated that the method operationally separated externally-sorbed NPs from those internalized actually localized within the bacterial cytoplasm. However, this new method is ideally used alongside other methods in a multi-method approach, to provide improved data quality. Therefore, it should be used with CSLM, FACS, TEM and other available methods.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis

BACKGROUND

The beneficial use of nanoparticle silver or nanosilver may be confounded when its potent antimicrobial properties impact non-target members of natural microbiomes such as those present in soil or the plant rhizosphere. Agricultural soils are a likely sink for nanosilver due to its presence in agrochemicals and land-applied biosolids, but a complete assessment of nanosilver's effects on this environment is lacking because the impact on the natural soil microbiome is not known. In a study assessing the use of nanosilver for phytopathogen control with maize, we analyzed the metatranscriptome of the maize rhizosphere and observed multiple unintended effects of exposure to 100 mg kg-1 nanosilver in soil during a growth period of 117 days.

RESULTS

We found several unintended effects of nanosilver which could interfere with agricultural systems in the long term. Firstly, the archaea community was negatively impacted with a more than 30% decrease in relative abundance, and as such, their involvement in nitrogen cycling and specifically, nitrification, was compromised. Secondly, certain potentially phytopathogenic fungal groups showed significantly increased abundances, possibly due to the negative effects of nanosilver on bacteria exerting natural biocontrol against these fungi as indicated by negative interactions in a network analysis. Up to 5-fold increases in relative abundance have been observed for certain possibly phytopathogenic fungal genera. Lastly, nanosilver exposure also caused a direct physiological impact on maize as illustrated by increased transcript abundance of aquaporin and phytohormone genes, overall resulting in a stress level with the potential to yield hormetically stimulated plant root growth.

CONCLUSIONS

This study indicates the occurrence of significant unintended effects of nanosilver use on corn, which could turn out to be negative to crop productivity and ecosystem health in the long term. We therefore highlight the need to include the microbiome when assessing the risk associated with nano-enabled agriculture. Video Abstract.

The effects of silver nanoparticles on the microbial nitrogen cycle: a review of the known risks

The nitrogen cycle is an integral biogeochemical function for maintaining healthy environments. Nitrogen is a key nutrient that must be continuously replenished through recycling mechanisms to sustain ecosystems, disruption to which can result in compromised ecosystem functioning. Certain stages in the microbial conversion of nitrogen compounds are performed by a limited range of micro-organisms making these key functional species in ecosystems. The growing industrial use of silver nanoparticles (AgNPs) potentially poses significant risks for microbial nitrogen cycling species. AgNPs possess potent antimicrobial properties and are expected to reach a range of natural environments through several routes of exposure. Certain functional nitrogen cycling microbes have been shown to be highly susceptible to AgNP toxicity. The current literature indicates that AgNPs can negatively affect certain nitrogen fixing, nitrifying and denitrifying microbes in vitro. In vivo studies investigating the effect of AgNPs on nitrogen cycling microbial communities and nitrogen transformation rates in soil, sediment and sludge environments have also indicated disruption of these functional processes. This review provides a comprehensive description of the current state of knowledge regarding the toxicity of AgNPs to nitrogen cycling communities. The aim of the review is to highlight the most susceptible stages in the nitrogen cycle and the implications for the affected ecosystems.

Environmentally relevant concentrations of silver nanoparticles diminish soil microbial biomass but do not alter enzyme activities or microbial diversity

The increasing use of silver nanoparticles (AgNPs) due to their well-known antimicrobial activity, has led to their accumulation in soil ecosystems. However, the impact of environmental realistic concentrations of AgNPs on the soil microbial community has been scarcely studied. In this work, we have assessed the impact of AgNPs, that mimic real concentrations in nature, on tropical soils cultivated with Coffea arabica under conventional and organic management systems. We evaluated the biomass, extracellular enzyme activities, and diversity of the soil microbial community, in a microcosm experiment as a function of time. After seven days of incubation, we found an increase in microbial biomass in an AgNPs-concentration-independent manner. In contrast, after 60-day-incubation, there was a decrease in Gram+ and actinobacterial biomass, in both soils and all AgNPs concentrations. Soil physico-chemical properties and enzyme activities were not affected overall by AgNPs. Regarding the microbial community composition, only some differences in the relative abundance at phylum and genus level in the fungal community were observed. Our results suggest that environmental concentrations of AgNPs affected microbial biomass but had little impact on microbial diversity and may have little effects on the soil biogeochemical cycles mediated by extracellular enzyme activities.

Microplastics affect sedimentary microbial communities and nitrogen cycling

Microplastics are ubiquitous in estuarine, coastal, and deep sea sediments. The impacts of microplastics on sedimentary microbial ecosystems and biogeochemical carbon and nitrogen cycles, however, have not been well reported. To evaluate if microplastics influence the composition and function of sedimentary microbial communities, we conducted a microcosm experiment using salt marsh sediment amended with polyethylene (PE), polyvinyl chloride (PVC), polyurethane foam (PUF) or polylactic acid (PLA) microplastics. We report that the presence of microplastics alters sediment microbial community composition and nitrogen cycling processes. Compared to control sediments without microplastic, PUF- and PLA-amended sediments promote nitrification and denitrification, while PVC amendment inhibits both processes. These results indicate that nitrogen cycling processes in sediments can be significantly affected by different microplastics, which may serve as organic carbon substrates for microbial communities. Considering this evidence and increasing microplastic pollution, the impact of plastics on global ecosystems and biogeochemical cycling merits critical investigation.

Effects of silver nanoparticles on coupled nitrification-denitrification in suspended sediments

The effects of varying concentrations of Ag NPs on coupled nitrification and denitrification (CND) in two suspended sediments (SPSs) sizes were investigated using isotopic tracer method. In general, 0.5 and 5 mg/L Ag NPs had less effect on CND, while 2 and 10 mg/L Ag NPs exhibited the improvement and inhibition effect, respectively. The CND improvement by 2 mg/L NPs was mainly due to the enhanced nitrifying and denitrifying enzyme activity. However, 10 mg/L Ag NPs inhibited NH₄⁺ oxidation by directly reducing the AMO activity and AOB abundance. The inhibition on NAR and NIR activity and their encoding narG and nirK gene abundance further inhibited NO₃^- and NO₂^- reduction, leading to a dramatic decrease in the ¹⁵N-N₂ production. The above inhibition effects were attributed to the nano-effects of Ag NPs, which led to the excessive ROS amount and the decreased T-AOC level in microbial systems. But the connection between nitrification and denitrification was not broken after Ag NPs exposure. Moreover, the results indicated that N-cycling in clay and silt-type SPS systems could be more sensitive than sand-type SPS systems to NP exposure. The findings provide a basis for evaluating the environmental risks of Ag NPs in water-sediment systems.

Silver nanoparticles and Fe(III) co-regulate microbial community and N2O emission in river sediments

The effects of environmental concentration silver nanoparticles (ecAgNPs) on microbial communities and the nitrogen cycling in river sediments remain largely uncharacterized. As a fundamental component of sediments, Fe(III) can interact with AgNPs and participate in nitrogen transformation processes. N₂O is an important intermediate in nitrogen transformation processes and can be a potent greenhouse gas with significant environmental effects. However, the impacts of the co-existence of AgNPs and Fe(III) on microbial communities and N₂O emission in river sediments are still unclear. In the present study, mesocosm experiments were conducted to assess the changes of microbial communities and N₂O emission in response to the co-existence of AgNPs and environmental concentration Fe(III). Our results revealed that the microbial community diversity and N₂O emission in river sediments responded differently to ecAgNPs (0.05 mg/kg) and high-polluting concentration AgNPs (hcAgNPs, 5 mg/kg), which was further regulated by the environmental concentration Fe(III) (1 mg/g and 10 mg/g). After ecAgNPs treatments, a marked increase was observed in microbial diversity compared to hcAgNPs treatments, regardless of the Fe(III) concentration in the sediment. The β-NTI index indicated that AgNPs had stronger impacts on phylogenetic distance of bacterial communities in sediments containing 1 mg/g Fe(III) than that containing 10 mg/g Fe(III). In sediments containing 1 mg/g Fe(III), ecAgNPs did not affect N₂O emission, but hcAgNPs significantly inhibited the emission of N₂O. However, in sediments containing 10 mg/g Fe(III), N₂O emission was significantly stimulated upon exposure to ecAgNPs, but the inhibition effect of hcAgNPs was barely observed. Functional prediction and real-time PCR analyses indicated that AgNPs and Fe(III) predominantly affected N₂O emissions by affecting the abundance of the nirK gene. Our results provide new insights into the ecological impacts of the co-existence of environmental concentration AgNPs and Fe(III) in altering microbial communities and nitrogen transformation functions in river sediments.

Effects of PVP-coated silver nanoparticles on enzyme activity, bacterial and archaeal community structure and function in a yellow-brown loam soil

The undesirable effects of silver nanoparticles (AgNPs) on soil environment have caused much concern. The previous studies, however, focused on sandy soil, with little known on others. In present study, the effects of polyvinylpyrrolidone-coated AgNPs (0, 1, 10, and 100 mg kg^- 1 soil) on enzyme activities (urease and dehydrogenase), ammonia-oxidizing bacteria (AOB) and archaea (AOA), bacterial and archaeal communities, and microbial function profile in a yellow-brown loam soil were investigated. The significant dose-response inhibitions of AgNPs on enzyme activities were observed, with dehydrogenase more susceptible to AgNPs. Both of bacterial and archaeal amoA genes were reduced by AgNPs above 10 mg kg^- 1, with AOB more susceptible to AgNPs than AOA. AgNPs at 100 mg kg^- 1 caused reductions on the dominant Nitrosospira and Nitrosomonas, and even disappearance on Nitrosovibrio, while increase on Nitrososphaera significantly. AgNPs also changed bacterial and archaeal community structure. Exposure to AgNPs at 100 mg kg^- 1 caused significant increases by 186.79% and 44.89% for Bacteroidetes and Proteobacteria, while decreases by 47.82%, 44.09%, 43.67%, and 80.44% for Actinobacteria, Chloroflexi, Planctomycetes, and Verrucomicrobia, respectively. Moreover, three dominant archaeal phyla (Thaumarchaeota, Euryarchaeota, and Parvarchaeota) were also reduced in the presence of AgNPs, especially Thaumarchaeota with the significant reduction of 13.71%. PICRUSt prediction revealed that AgNPs indeed had the potential to change soil microbial community's functional contributions. It must be cautious on the interference of AgNPs to soil ecological functions in the future.

Nitrogen oxidation consortia dynamics influence the performance of full-scale rotating biological contactors

Ammonia oxidising microorganisms (AOM) play an important role in ammonia removal in wastewater treatment works (WWTW) including rotating biological contactors (RBCs). Environmental factors within RBCs are known to impact the performance of key AOM, such that only some operational RBCs have shown ability for elevated ammonia removal. In this work, long-term treatment performance of seven full-scale RBC systems along with the structure and abundance of the ammonia oxidising bacteria (AOB) and archaea (AOA) communities within microbial biofilms were examined. Long term data showed the dominance of AOB in most RBCs, although two RBCs had demonstrable shift toward an AOA dominated AOM community. Next Generation Sequencing of the 16S rRNA gene revealed diverse evolutionary ancestry of AOB from RBC biofilms while nitrite-oxidising bacteria (NOBs) were similar to reference databases. AOA were more abundant in the biofilms subject to lower organic loading and higher oxygen concentration found at the distal end of RBC systems. Modelling revealed a distinct nitrogen cycling community present within high performing RBCs, linked to efficient control of RBC process variables (retention time, organic loading and oxygen concentration). We present a novel template for enhancing the resilience of RBC systems through microbial community analysis which can guide future strategies for more effective ammonia removal. To best of the author's knowledge, this is the first comparative study reporting the use of next generation sequencing data on microbial biofilms from RBCs to inform effluent quality of small WWTW.

Evidence for positive response of soil bacterial community structure and functions to biosynthesized silver nanoparticles: An approach to conquer nanotoxicity?

The environmental impacts of biosynthesized nanoparticles on the soil bacterial community assemblage and functions are not sufficiently understood. Given the broad application of silver nanoparticles (AgNPs), the present study aims to reveal the effects of biosynthesized AgNPs (~12 nm) on the soil bacterial community structure and functions. Specifically, we used a quantitative real-time PCR (qPCR) approach to quantify the relative abundance of bacterial taxon/group and representative functional genes (AOA, AOB, NirK, NirS, NosZ, and PhoD). Results showed high relative abundance of Actinobacteria (1.53 × 10⁷, p = 0.000) followed by Alphaproteobacteria (1.18 × 10⁶, p = 0.000) and Betaproteobacteria (2.01 × 10⁶, p = 0.000) in the soil exposed to biosynthesized AgNPs (100 mg/kg soil) after 30 days of treatment. Bacteroidetes group was observed to be negatively affected by AgNPs treatment. In the case of functional genes abundance, more pronounced impact was observed after 30 days of application. The biosynthesized AgNPs treatment accounted for significant increase in the relative abundance of all targeted functional genes except NirS. We conclude that the biosynthesized AgNPs did not cause toxic effects on nitrifiers, denitrifiers and organic phosphorus metabolizing bacterial community. While AgNO₃ caused higher toxicity in the soil bacterial community structure and function. Based on our findings, we propose two key research questions for further studies; (i) is there any adaptation strategy or silver resistance embraced by the soil microbial community? and (ii) are biosynthesized nanoparticles environmentally safe and do not pose any risk to the soil microbial community? There is a necessity to address these questions to predict the environmental safety of biosynthesized AgNPs and to apply appropriate soil management policies to avoid nanotoxicity. Since this study provides preliminary evidence for the positive response of the soil bacterial community structure and functions to biosynthesized AgNPs, additional investigations under different soil conditions with varying soil physico-chemical properties are required to authenticate their environmental impact.

Metagenomic analysis exhibited the co-metabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment

The bacterial community from estuarine sediment undertakes the bioremediation and energy transformation of anthropogenic pollutants especially polycyclic aromatic hydrocarbons (PAHs). However, information and studies on bacterial synergism and related metabolic profiles under the stress of PAHs are limited. In this study, sediments from estuarine were collected and co-incubated with a classical PAH, pyrene. The results showed that Alpha- and Gammaproteobacteria became abundant at the late domesticating phase with the dominant genus of ZD0117, the uncultivated bacteria affiliated into Gammaproteobacteria. Functional gene analysis based on metagenomic sequencing showed that quantitatively changes of genes directly related to the degradation of aromatic hydrocarbon coordinated with genes involved into various metabolic pathways such as acylglycerol degradation, nitrogen fixation, sulfate transport system, Arnon-Buchanan cycle, and Calvin cycle (P < 0.01 and |ρ| > 0.8). Fifty-six metagenome-assembled genomes (MAGs) were reconstructed, which were primarily composed by Alpha- and Gammaproteobacteria. Bacteria belonging to the phylum Proteobacteria were found to be abundant in MAGs and contained genes encoding for dehydrogenase, which are key enzymes for pyrene degradation. In addition, genomes of uncultivated bacteria were successfully reconstructed and were proven to carry genes of synergistically metabolizing pyrene. Based on analysis of typical MAGs, the metabolic pathways involved in syntrophic associations of a pyrene-degrading consortium were reconstructed. The results in this study could make us fully understand the metabolic patterns of pyrene-degrading consortium from the estuarine sediment and widen the scope of functional bacteria.

Biological Particles in the Indoor Environment

Airborne microorganisms are very difficult to assess accurately under field conditions owing to differences in the sample collection efficiency of the selected sampler and variations in DNA extraction efficiencies. Consequently, bioaerosol abundance and biodiversity can be underestimated, making it more difficult to link specific bioaerosol components to diseases and human health risk. Owing to the low biomass in air samples, it remains a challenge to obtain a representative microbiological sample to recover sufficient DNA for downstream analyses. Improved sampling methods are particularly crucial, especially for investigating viral communities, owing to the extremely low biomass of viral particles in the air compared with other environments. Without detailed information about sampling, characterization and enumeration techniques, interpretation of exposure level is very difficult. Despite this, bioaerosol research has been enhanced by molecular tools, especially next-generation sequencing approaches that have allowed faster and more detailed characterization of air samples.

Functional sustainability of periphytic biofilms in organic matter and Cu2+ removal during prolonged exposure to TiO2 nanoparticles

Responses of microbial communities to nanotoxicity in aquatic ecosystems are largely unknown, particularly with respect to relationship between community dynamics and functions. Here, periphytic biofilms were selected as a model of species-rich microbial communities to elucidate their responses when exposed to titanium dioxide nanoparticles (TiO₂-NPs). Especially, the relationships between the functions (e.g. organic matter and Cu²⁺ removal) and community dynamics after long-term exposure to TiO₂-NPs were assessed systematically. After 5days exposure to TiO₂-NPs (5mgL^-1), periphytic biofilms showed sustainable functions in pollutant removal and strong plasticity in defensing the toxic disturbance of TiO₂-NPs, including photosynthesis and carbon metabolic diversity. The sustainable pollutant removal functions of periphytic biofilms were attributed to their functional redundancy. Specifically, periphytic biofilms altered their composition with cyanobacteria, Sphingobacteriia and Spirochaetes being the newly dominant taxa, and changed the carbon substrate utilization pattern to maintain high photosynthesis and metabolic rates. Moreover, extracellular polymeric substances (EPS) especially proteins were overproduced to bind the NPs and thereby reduce the nanotoxicity. The information obtained in this study may greatly help to understand the interactions between microbial community dynamics and function under NPs exposure conditions and functional redundancy is an important mechanism of periphytic biofilms to maintain sustainable functions.

Bioaerosol biomonitoring: Sampling optimization for molecular microbial ecology

Bioaerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimization, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine -scale temporal/spatial ecological studies. To prevent bias for the recovery of Gram-positive bacteria, we found that the matrix for impingement should be phosphate-buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in-field recovery of bioaerosols from impingement samples, without compromising microbial diversity for high -throughput sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question.

Size and coating of engineered silver nanoparticles determine their ability to growth-independently inhibit aflatoxin biosynthesis in Aspergillus parasiticus

Recent studies from our laboratory indicate that engineered silver nanoparticles can inhibit aflatoxin biosynthesis even at concentrations at which they do not demonstrate antifungal activities on the aflatoxin-producing fungus. Whether such inhibition can be modified by altering the nanoparticles' physical properties remains unclear. In this study, we demonstrate that three differently sized citrated-coated silver nanoparticles denoted here as NP1, NP2, and NP3 (where, sizes of NP1 < NP2 < NP3) inhibit aflatoxin biosynthesis at different effective doses in Aspergillus parasiticus, the plant pathogenic filamentous fungus. Recapping NP2 with polyvinylpyrrolidone coating (denoted here as NP2p) also altered its ability to inhibit aflatoxin production. Dose-response experiments with NP concentrations ranging from 10 to 100 ng mL^-1 indicated a non-monotonic relationship between aflatoxin inhibition and NP concentration. The maximum inhibitory concentrations differed between the NP types. NP1 demonstrated maximum inhibition at 25 ng mL^-1. Both NP2 and NP3 showed maximum inhibition at 50 ng mL^-1, although NP2 resulted in a significantly higher inhibition than NP3. While both NP2 and NP2p demonstrated greater aflatoxin inhibition than NP1 and NP3, NP2p inhibited aflatoxin over a significantly wider concentration range as compared to NP2. Our results, therefore, suggest that nano-fungal interactions can be regulated by altering certain NP physical properties. This concept can be used to design NPs for mycotoxin prevention optimally.

Cytotoxic and genotoxic effects of silver nanoparticles on meristematic cells of Allium cepa roots: A close analysis of particle size dependence

The use of silver nanoparticles (AgNPs) in commercial products has increased significantly in recent years. However, findings on the toxic effects of the AgNPs are still limited. This paper reports an investigation on the cytotoxic and genotoxic potential of the AgNPs on root cells of Allium cepa. Germination (GI), root elongation (REI), mitotic (MI), nuclear abnormality (NAI), and micronucleus index (MNI) were determined for seeds exposed to various AgNPs diameters (10, 20, 51, and 73 nm) as well as to the silver bulk (AgBulk) (micrometer-size particles) at the concentration of 100 mg·L^-1. Transmission electron microscopy (TEM) provided the particle size distribution, while dynamic light scattering (DLS) was used to get the hydrodynamic size, polydispersity index, and zeta potential of the AgNPs. Laser-induced breakdown spectroscopy (LIBS) and inductively coupled plasma/optical emission spectrometry (ICP OES) were applied for quantifying the AgNPs content uptake by roots. Silver dissolution was determined by dialysis experiment. Results showed that the AgNPs penetrated the roots, affecting MI, GI, NAI, and MNI in meristematic cells. Changes in these indicators were AgNPs diameter-dependent so that cytotoxic and genotoxic effects in Allium cepa increased with the reduction of the particle diameter. The results also revealed that the AgNPs were the main responsible for the cytotoxicity and genotoxicity since negligible silver dissolution was observed.

The effect of biogenic and chemically manufactured silver nanoparticles on the benthic bacterial communities in river sediments

This study was conducted to determine and compare the effect of chemically-synthesised and biogenic silver nanoparticles on the benthic bacterial community structure in mesocosms containing sediment from three rivers in geographical sites with different population densities (low, medium, high), and therefore likely to be associated with respective low, moderate and high degrees of anthropogenic input. The nanoparticles were applied at the upper limit expected to accumulate in impacted environments (4 μg kg_sed^-1). The biomass, concentrations of elements, including selection metals (P, K, Na, K, Ca, Mg, Zn, Cu, Al, Ag) were all significantly higher at the high density than at the low density sites. Bacterial community profiling (terminal restriction fragment length polymorphism and amplicon sequencing) showed that the bacterial community structure in the sediments from the high population density site were resilient to environmental perturbations [adjustment from in-situ to ex-situ (laboratory) conditions], as well as to exposure to silver nanoparticles, with the converse being true for the low population density site. Results obtained from amplicon sequencing were interrogated to the lowest taxonomic level with a relative abundance >5%. Proteobacteria was the most abundant phylum in all the sediments. Notable resistance (increased relative abundance) to one or both forms of silver nanoparticles was seen in the class Thermoleophilia, and the orders Myxococcales, Bacteriodales, Pirellules CCU21 and iii 1-15 (class Acidobacteria 6). Conversely, sensitivity was demonstrated in the family Koribacteraceae and the orders Rhizobiales, Ellin 329 and Gemmatales. It is recommended that pro-active environmental monitoring is performed in aquatic systems receiving point source pollution from wastewater treatment plants in order to assess the accumulation of silver nanoparticles. If necessary, measures should be implemented to mitigate the entry of silver nanoparticles, especially into more vulnerable environments.

Impact of nanoparticles on transcriptional regulation of catabolic genes of petroleum hydrocarbon-degrading bacteria in contaminated soil microcosms

This study was conducted to determine what effects nanoparticles (NPs) like TiO₂ , ZnO, and Ag may pose on natural attenuation processes of petroleum hydrocarbons in contaminated soils. The solid NPs used were identified using x-ray diffraction technique and their average size was certified as 18.2, 16.9, and 18.3 nm for Ag-NPs, ZnO-NPs, and TiO₂ -NPs, respectively. NPs in soil microcosms behave differently where it was dissolved as in case of Ag-NPs, partially dissolved as in ZnO-NPs or changed into other crystalline phase as in TiO₂ -NPs. In this investigation, catabolic gene encoding catechol 2,3 dioxygenase (C23DO) was selected specifically as biomarker for monitoring hydrocarbon biodegradation potential by measuring its transcripts by RT-qPCR. TiO₂ -NPs amended microcosms showed almost no change in C23DO expression profile or bacterial community which were dominated by Bacillus sp., Mycobacterium sp., Microbacterium sp., Clostridium sp., beside uncultured bacteria, including uncultured proteobacteria, Thauera sp. and Clostridia. XRD pattern suggested that TiO₂ -NPs in microcosms were changed into other non-inhibitory crystalline phase, consequently, showing the maximum degradation profile for most low molecular weight oil fractions and partially for the high molecular weight ones. Increasing ZnO-NPs concentration in microcosms resulted in a reduction in the expression of C23DO with a concomitant slight deteriorative effect on bacterial populations ending up with elimination of Clostridium sp., Thauera sp., and uncultured proteobacteria. The oil-degradation efficiency was reduced compared to TiO₂ -NPs amended microcosms. In microcosms, Ag-NPs were not detected in the crystalline form but were available in the ionic form that inhibited most bacterial populations and resulted in a limited degradation profile of oil, specifically the low molecular weight fractions. Ag-NPs amended microcosms showed a significant reduction (80%) in C23DO gene expression and a detrimental effect on bacterial populations including key players like Mycobacterium sp., Microbacterium sp., and Thauera sp. involved in the biodegradation of petroleum hydrocarbons.

Nanomaterials in the environment: Behavior, fate, bioavailability, and effects-An updated review

The present review covers developments in studies of nanomaterials (NMs) in the environment since our much cited review in 2008. We discuss novel insights into fate and behavior, metrology, transformations, bioavailability, toxicity mechanisms, and environmental impacts, with a focus on terrestrial and aquatic systems. Overall, the findings were that: 1) despite substantial developments, critical gaps remain, in large part due to the lack of analytical, modeling, and field capabilities, and also due to the breadth and complexity of the area; 2) a key knowledge gap is the lack of data on environmental concentrations and dosimetry generally; 3) substantial evidence shows that there are nanospecific effects (different from the effects of both ions and larger particles) on the environment in terms of fate, bioavailability, and toxicity, but this is not consistent for all NMs, species, and relevant processes; 4) a paradigm is emerging that NMs are less toxic than equivalent dissolved materials but more toxic than the corresponding bulk materials; and 5) translation of incompletely understood science into regulation and policy continues to be challenging. There is a developing consensus that NMs may pose a relatively low environmental risk, but because of uncertainty and lack of data in many areas, definitive conclusions cannot be drawn. In addition, this emerging consensus will likely change rapidly with qualitative changes in the technology and increased future discharges. Environ Toxicol Chem 2018;37:2029-2063. © 2018 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

Multivariate relationships between microbial communities and environmental variables during co-composting of sewage sludge and agricultural waste in the presence of PVP-AgNPs

This study evaluated the contributions of environmental variables to the variations in bacterial 16S rDNA, nitrifying and denitrifying genes abundances during composting in the presence of polyvinylpyrrolidone coated silver nanoparticles (PVP-AgNPs). Manual forward selection in redundancy analysis (RDA) indicated that the variation in 16S rDNA was significantly explained by NO₃^--N, while nitrifying genes were significantly related with pH, and denitrifying genes were driven by NO₃^--N and TN. Partial RDA further revealed that NO₃^--N solely explained 28.8% of the variation in 16S rDNA abundance, and pH accounted for 61.8% of the variation in nitrifying genes. NO₃^--N and TN accounted for 34.2% and 9.2% of denitrifying genes variation, respectively. The RDA triplots showed that different genes shared different relationships with environmental parameters. Based on these findings, a composting with high efficiency and quality may be conducted in the future work by adjusting the significant environmental variables.

CuO and ZnO Nanoparticles Modify Interkingdom Cell Signaling Processes Relevant to Crop Production

As the world population increases, strategies for sustainable agriculture are needed to fulfill the global need for plants for food and other commercial products. Nanoparticle formulations are likely to be part of the developing strategies. CuO and ZnO nanoparticles (NPs) offer potential as fertilizers, as they provide bioavailable essential metals, and as pesticides, because of dose-dependent toxicity. Effects of these metal oxide NPs on rhizosphere functions are the focus of this review. These NPs at doses of ≥10 mg metal/kg change the production of key metabolites involved in plant protection in a root-associated microbe, Pseudomonas chlororaphis O6. Altered synthesis occurs in the microbe for phenazines, which function in plant resistance to pathogens, the pyoverdine-like siderophore that enhances Fe bioavailability in the rhizosphere and indole-3-acetic acid affecting plant growth. In wheat seedlings, reprogramming of root morphology involves increases in root hair proliferation (CuO NPs) and lateral root formation (ZnO NPs). Systemic changes in wheat shoot gene expression point to altered regulation for metal stress resilience as well as the potential for enhanced survival under stress commonly encountered in the field. These responses to the NPs cross kingdoms involving the bacteria, fungi, and plants in the rhizosphere. Our challenge is to learn how to understand the value of these potential changes and successfully formulate the NPs for optimal activity in the rhizosphere of crop plants. These formulations may be integrated into developing practices to ensure the sustainability of crop production.

Quantification of Au Nanoparticle Biouptake and Distribution to Freshwater Algae Using Single Cell - ICP-MS

Quantifying metal and nanoparticle (NP) biouptake and distribution on an individual cellular basis has previously been impossible, given available techniques which provide qualitative data that are laborious to acquire and prone to artifacts. Quantifying metal and metal NP uptake and loss processes in environmental organisms will lead to mechanistic understanding of biouptake and improved understanding of potential hazards and risks of metals and NPs. In this work, we present a new technique, single cell inductively coupled plasma mass spectrometry (SC-ICP-MS), which allows quantification of metal concentrations on an individual cell basis down to the attogram (ag) per cell level. We present data validating the novel method, along with the mass of metal per cell. Finally, we use SC-ICP-MS, with ancillary cell counting methods, to quantify the biouptake and strong sorption and distribution of both dissolved Au and Au NPs in a freshwater alga (Cyptomonas ovate). The data suggests differences between dissolved and NP uptake and loss. In the case of NPs, there was a dose and time dependent uptake, but individual cellular variations; at the highest realistic exposure conditions used in this study up to 40-50% of cells contained NPs, while 50-60% of cells did not.

Effect of TiO2 and CeO2 nanoparticles on the metabolic activity of surficial sediment microbial communities based on oxygen microelectrodes and high-throughput sequencing

Environmental concerns regarding the potential ecological risks of metallic oxide nanoparticles (MNPs) in aquatic ecosystems are increasing; sediment is considered a sink for these MNPs. Although several studies have studied the potential impact of MNPs on microbial communities in freshwater and estuarine sediments, limited information is available regarding the influence of MNPs on the metabolic activity of surficial sediment microbial communities and related biogeochemical conditions. To address these issues, a microcosm approach was established to study the metabolic response of surficial sediment microbial communities to a single addition of TiO₂ or CeO₂ NPs (5 mg/L) using oxygen microelectrodes, enzyme activity measurements, and high-throughput sequencing. Rapid sedimentation of MNPs (regardless of NP type) was observed in freshwater samples, and most (up to 85%) accumulated in surface sediments (<5 mm). Microelectrode profile measurements in pre-incubated sediments treated with MNPs showed that the oxygen concentration decreased at a slower rate with increasing sediment depth compared to that in untreated controls. Biological oxygen consumption in the uppermost sediment layer (0-1500 μm) was significantly inhibited by MNPs, as calculated from steady-state microprofiles, with CeO₂ NPs resulting in enhanced acute toxicity than TiO₂ NPs. High-throughput sequencing showed that MNP exposure increased the bacterial diversity and altered the bacterial community structure, regardless of NP type. The abundance of three dominant bacterial genera, Methylotenera, Cytophagceae_uncultured (classified as an aerobic bacterium), and Cyanobacteria_norank (a facultative bacterium), was markedly reduced by MNPs, which was primarily responsible for inhibiting microbial-mediated oxygen consumption in surficial sediments. In summary, short-term exposure to MNPs negatively affected the metabolic activity of benthic microbial communities, which could influence the biogeochemical functions along the sediment-water interface.

Silver nanoparticles or free silver ions work? An enantioselective phytotoxicity study with a chiral tool

Nowadays, silver nanoparticles (AgNP) have been widely used and there are raising concerns about their potential adverse effects on organism. As for the exact toxicity mechanism of AgNP, opinions still vary and whether the released silver ions (Ag⁺) or AgNP themselves are responsible for the toxicity remains debatable. In the present study, we have designed two exposure systems where Ag⁺ and AgNP coexisted but differed in quantification by using photo-reduced method with cysteine enantiomers, and their toxicities to freshwater microalgae Scenedesmus obliquus and model plant Arabidopsis thaliana were determined. In the results, Ag⁺ was in suit photo-reduced by cysteine enantiomers, and the UV-Vis and circular dichroism spectrum evidence confirmed the quantification difference between Ag-l-cysteine (Ag-l-Cys) and Ag-d-cysteine (Ag-d-Cys), where there was more AgNP and less Ag⁺ in Ag-l-Cys. Furthermore, the toxicity assay data revealed that Ag-d-Cys was more toxic to S. obliquus but A. thaliana was more susceptible to Ag-l-Cys. The metal element distribution in Arabidopsis leaves was also influenced in an enantioselective manner, which was related to the oxidative stress. Considering the quantification difference between Ag-l-Cys and Ag-d-Cys, it can be concluded that AgNP exhibited their toxicity to S. obliquus by the action of Ag⁺, but toxicity brought to A. thaliana was attributed to AgNP themselves rather than Ag⁺. The results of the present study help to better clarify the role of Ag⁺ in AgNP toxicity and offer a chiral tool and a new sight to investigate the toxicity mechanism of AgNP.

Citrate-Coated Silver Nanoparticles Growth-Independently Inhibit Aflatoxin Synthesis in Aspergillus parasiticus

Manufactured silver nanoparticles (Ag NPs) have long been used as antimicrobials. However, little is known about how these NPs affect fungal cell functions. While multiple previous studies reveal that Ag NPs inhibit secondary metabolite syntheses in several mycotoxin producing filamentous fungi, these effects are associated with growth repression and hence need sublethal to lethal NP doses, which besides stopping fungal growth, can potentially accumulate in the environment. Here we demonstrate that citrate-coated Ag NPs of size 20 nm, when applied at a selected nonlethal dose, can result in a >2 fold inhibition of biosynthesis of the carcinogenic mycotoxin and secondary metabolite, aflatoxin B₁ in the filamentous fungus and an important plant pathogen, Aspergillus parasiticus, without inhibiting fungal growth. We also show that the observed inhibition was not due to Ag ions, but was specifically associated with the mycelial uptake of Ag NPs. The NP exposure resulted in a significant decrease in transcript levels of five aflatoxin genes and at least two key global regulators of secondary metabolism, laeA and veA, with a concomitant reduction of total reactive oxygen species (ROS). Finally, the depletion of Ag NPs in the growth medium allowed the fungus to regain completely its ability of aflatoxin biosynthesis. Our results therefore demonstrate the feasibility of Ag NPs to inhibit fungal secondary metabolism at nonlethal concentrations, hence providing a novel starting point for discovery of custom designed engineered nanoparticles that can efficiently prevent mycotoxins with minimal risk to health and environment.