Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure

The good, the bad, and the ugly of metals as antimicrobials

We are now moving into the antimicrobial resistance (AMR) era where more antibiotic resistant bacteria are now the majority, a problem brought on by both misuse and over use of antibiotics. Unfortunately, the antibiotic development pipeline dwindled away over the past decades as they are not very profitable compounds for companies to develop. Regardless researchers over the past decade have made strides to explore alternative options and out of this we see revisiting historical infection control agents such as toxic metals. From this we now see a field of research exploring the efficacy of metal ions and metal complexes as antimicrobials. Such antimicrobials are delivered in a variety of forms from metal salts, alloys, metal complexes, organometallic compounds, and metal based nanomaterials and gives us the broad term metalloantimicrobials. We now see many effective formulations applied for various applications using metals as antimicrobials that are effective against drug resistant strains. The purpose of the document here is to step aside and begin a conversation on the issues of use of such toxic metal compounds against microbes. This critical opinion mini-review in no way aims to be comprehensive. The goal here is to understand the benefits of metalloantimicrobials, but also to consider strongly the disadvantages of using metals, and what are the potential consequences of misuse and overuse. We need to be conscious of the issues, to see the entire system and affect through a OneHealth vision.

Anti-biofilm properties of laser-synthesized, ultrapure silver-gold-alloy nanoparticles against Staphylococcus aureus

Staphylococcus aureus biofilm-associated infections are a common complication in modern medicine. Due to inherent resilience of biofilms to antibiotics and the rising number of antibiotic-resistant bacterial strains, new treatment options are required. For this purpose, ultrapure, spherical silver-gold-alloy nanoparticles with homogenous elemental distribution were synthesized by laser ablation in liquids and analyzed for their antibacterial activity on different stages of S. aureus biofilm formation as well as for different viability parameters. First, the effect of nanoparticles against planktonic bacteria was tested with metabolic activity measurements. Next, nanoparticles were incubated with differently matured S. aureus biofilms, which were then analyzed by metabolic activity measurements and three dimensional live/dead fluorescent staining to determine biofilm volume and membrane integrity. It could be shown that AgAu NPs exhibit antibacterial properties against planktonic bacteria but also against early-stage and even mature biofilms, with a complete diffusion through the biofilm matrix. Furthermore, AgAu NPs primarily targeted metabolic activity, to a smaller extend membrane integrity, but not the biofilm volume. Additional molecular analyses using qRT-PCR confirmed the influence on different metabolic pathways, like glycolysis, stress response and biofilm formation. As this shows clear similarities to the mechanism of pure silver ions, the results strengthen silver ions to be the major antibacterial agent of the synthesized nanoparticles. In summary, the results of this study provide initial evidence of promising anti-biofilm characteristics of silver-gold-alloy nanoparticles and support the importance of further translation-oriented analyses in the future.

Innovative Elastomers with Antimicrobial Activity May Decrease Infection Risks during Milking

Contagious pathogens are very costly to dairy herds, and they may have zoonotic and reverse-zoonotic potentials and may contribute to the spread of antimicrobial resistance. One of the most important risk factors for spreading these infections is milking, when liner contamination may transfer the pathogens from infected to healthy cows. There is no effective protocol to prevent the transmission of infection without the segregation of infected cows. Recently, the availability of elastomers with patented antimicrobial components in their formulations has allowed the exploration of alternative methods to reduce the risk of infection. Two different types of elastomers (rubber and silicone) and nine different formulations were challenged with three major mastitis pathogens (S. aureus, S. agalactiae, and E. coli). The results that were obtained in this study were interesting and unexpected. Indeed, to our knowledge, this is the first study to show that basic rubber materials have intrinsic antimicrobial activity. Silicone elastomers did not exhibit the same levels of bactericidal activity, although they did exhibit some antibacterial capacity. A significant decrease in bacterial survival curves was observed for all the formulations tested when antimicrobial components were added. The different results observed for the various products are likely due to the different formulations and diverse manufacturing processes. The availability of these new materials that significantly reduce the bacterial load on the liner surface may reduce the risk of spreading intramammary infections during milking. This would be an important step forward in achieving global sustainability of dairy herds, consistent with the objectives of One Health, by reducing the risks of zoonotic diseases and antimicrobial treatments.

The Origin of the Intracellular Silver in Bacteria: A Comprehensive Study using Targeting Gold-Silver Alloy Nanoparticles

The bactericidal effects of silver nanoparticles (Ag NPs) against infectious strains of multiresistant bacteria is a well-studied phenomenon, highly relevant for many researchers and clinicians battling bacterial infections. However, little is known about the uptake of the Ag NPs into the bacteria, the related uptake mechanisms, and how they are connected to antimicrobial activity. Even less information is available on AgAu alloy NPs uptake. In this work, the interactions between colloidal silver-gold alloy nanoparticles (AgAu NPs) and Staphylococcus aureus (S. aureus) using advanced electron microscopy methods are studied. The localization of the nanoparticles is monitored on the membrane and inside the bacterial cells and the elemental compositions of intra- and extracellular nanoparticle species. The findings reveal the formation of pure silver nanoparticles with diameters smaller than 10 nm inside the bacteria, even though those particles are not present in the original colloid. This finding is explained by a local RElease PEnetration Reduction (REPER) mechanism of silver cations emitted from the AgAu nanoparticles, emphasized by the localization of the AgAu nanoparticles on the bacterial membrane by aptamer targeting ligands. These findings can deepen the understanding of the antimicrobial effect of nanosilver, where the microbes are defusing the attacking silver ions via their reduction, and aid in the development of suitable therapeutic approaches.

Effectiveness of silver nitrate application on plant growth and bioactive compounds in Agastache rugosa (Fisch. & C.A.Mey.) kuntze

The objective of this study was to determine the optimal dose of silver nitrate (AgNO3) for plant growth and to increase the main bioactive compounds in A. rugosa cultivated in a hydroponic system. The application of soaked diniconazole (120 μmol mol-1) to all plants at 7 days after transplanting (DAT) for dwarfing plant height, optimizing cultivation space in the plant factory. Subsequently, plants were soaked with 50, 100, 200, and 400 μmol mol-1 AgNO3 for 10 min at 25 DAT and harvested at 39 DAT. The results indicated that 200 and 400 μmol mol-1 treatments tended to severely decrease plant growth parameters compared to treatments with lower concentrations. The net photosynthetic rate was significantly reduced by the 200 and 400 μmol mol-1 treatments compared to treatments with other concentrations. The 400 μmol mol-1 treatment led to the lowest concentrations of chlorophyll a, chlorophyll a/b, total carotenoid, chlorophyll b, and the total chlorophyll. However, 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity was considerably increased in 50, 100, 200, and 400 μmol mol-1 compared to that of the control plants. A higher rosmarinic acid (RA) concentration in the whole plant was noticed with the 400 μmol mol-1 treatment compared with that of the untreated plants. The 100 μmol mol-1 treatment exhibited the highest concentration and content of tilianin in the whole plant. Concentration of acacetin 1 significantly increased in the whole plant with 100 and 200 μmol mol-1 treatments compared with that of the untreated plants. Concentrations of acacetin 2 and 3 in the whole plant were the highest with 100 and 200 μmol mol-1 treatments, respectively. The results demonstrated that 100 μmol mol-1 treatments can be used to increase bioactive compounds without severely limiting the plant growth and reducing chlorophyll concentrations of A. rugosa. Implementing this optimal dose can enable growers and researchers to cultivate A. rugosa more efficiently, enhancing bioactive compound content and overall plant performance, thus harnessing the potential health benefits of this valuable plant species.

Different responses of Chlorella vulgaris to silver nanoparticles and silver ions under modulation of nitric oxide

Silver nanoparticles (Ag-NPs) are widely used in daily life because of their antibacterial properties. A fraction of Ag-NPs are released into the ecosystem during their production and utilization. The toxicity of Ag-NPs has been reported. However, it is still disputed whether the toxicity is mainly due to the released silver ions (Ag⁺). In addition, few studies have reported the response of algae to metal nanoparticles under modulation of nitric oxide (NO). In this study, Chlorella vulgaris (C. vulgaris) was used as a model organism to study the toxic effects of Ag-NPs and Ag⁺ released from Ag-NPs on algae under the modulation of NO. The results showed that the biomass inhibition rate of Ag-NPs (44.84%) to C. vulgaris was higher than that of Ag⁺ (7.84%). Compared with Ag⁺, Ag-NPs induced more severe damage to photosynthetic pigments, photosynthetic system II (PSII) performance, and lipid peroxidation. More serious damage to cell permeability led to higher internalization of Ag under Ag-NPs stress. Application of exogenous NO reduced the inhibition ratio of photosynthetic pigments and chlorophyll autofluorescence. Further, NO reduced the MDA levels by scavenging reactive oxygen species induced by Ag-NPs. NO modulated the secretion of extracellular polymers and hampered the internalization of Ag. All these results showed that NO alleviates the toxicity of Ag-NPs to C. vulgaris. However, NO did not improve the toxic effects of Ag⁺. Our results provide new insights into the toxicity mechanism of Ag-NPs to algae modulated by the signal molecule NO.

Recent progression of cyanobacteria and their pharmaceutical utility: an update

Cyanobacteria (blue-green algae) are Gram-negative photosynthetic eubacteria that are found everywhere. This largest group of photosynthetic prokaryotes is rich in structurally novel and biologically active compounds; several of which have been utilized as prospective drugs against cancer and other ailments, as well. Consequently, the integument of nanoparticles-synthetic approaches in cyanobacterial extracts should increase pharmacological activity. Moreover, silver nanoparticles (AgNPs) are small materials with diameters below 100 nm that are classified into different classes based on their forms, sizes, and characteristics. Indeed, the biosynthesized AgNPs are generated with a variety of organisms, algae, plants, bacteria, and a few others, for the medicinal purposes, as the bioactive compounds of curio and some proteins from cyanobacteria have the potentiality in the treatment of a wide range of infectious diseases. The critical focus of this review is on the antimicrobial, antioxidant, and anticancer properties of cyanobacteria. This would be useful in the pharmaceutical industries in the future drug development cascades.Communicated by Ramaswamy H. Sarma.

Metabolomics for early detection of stress in freshwater alga Poterioochromonas malhamensis exposed to silver nanoparticles

Silver nanoparticles (AgNPs) are one of the most used engineered nanomaterials. Despite progress in assessing their environmental implications, knowledge gaps exist concerning the metabolic perturbations induced by AgNPs on phytoplankton, essential organisms in global biogeochemical cycles and food-web dynamics. We combine targeted metabolomics, biouptake and physiological response studies to elucidate metabolic perturbations in alga Poterioochromonas malhamensis induced by AgNPs and dissolved Ag. We show time-dependent perturbation of the metabolism of amino acids, nucleotides, fatty acids, tricarboxylic acids, photosynthesis and photorespiration by both Ag-treatments. The results suggest that dissolved Ag ions released by AgNPs are the major toxicity driver; however, AgNPs internalized in food vacuoles contributed to the perturbation of amino acid metabolism, TCA cycle and oxidative stress. The metabolic perturbations corroborate the observed physiological responses. We highlight the potential of metabolomics as a tool for understanding the molecular basis for these metabolic and physiological changes, and for early detection of stress.

In Vitro Destruction of Pathogenic Bacterial Biofilms by Bactericidal Metallic Nanoparticles via Laser-Induced Forward Transfer

A novel, successful method of bactericidal treatment of pathogenic bacterial biofilms in vitro by laser-induced forward transfer of metallic nanoparticles from a polyethylene terephthalate polymeric substrate was suggested. Transferred nanoparticles were characterized by scanning and transmission electron microscopy, energy-dispersive X-ray and Raman spectroscopy. The antibacterial modality of the method was tested on Gram-positive (Staphylococcus aureus) and Gram-negative (Pseudomonas Aeruginosa) bacterial biofilms in vitro, revealing their complete destruction. The proposed simple, cost-effective and potentially mobile biofilm treatment method demonstrated its high and broad bactericidal efficiency.

Insights into the transcriptional responses of a microbial community to silver nanoparticles in a freshwater microcosm

Silver nanoparticles (AgNPs) are widely used because of their excellent antibacterial properties. They are, however, easily discharged into the water environment, causing potential adverse environmental effects. Meta-transcriptomic analyses are helpful to study the transcriptional response of prokaryotic and eukaryotic aquatic microorganisms to AgNPs. In the present study, microcosms were used to investigate the toxicity of AgNPs to a natural aquatic microbial community. It was found that a 7-day exposure to 10 μg L^-1 silver nanoparticles (AgNPs) dramatically affected the structure of the microbial community. Aquatic micro eukaryota (including eukaryotic algae, fungi, and zooplankton) and bacteria (i.e., heterotrophic bacteria and cyanobacteria) responded differently to the AgNPs stress. Meta-transcriptomic analyses demonstrated that eukaryota could use multiple cellular strategies to cope with AgNPs stress, such as enhancing nitrogen and sulfur metabolism, over-expressing genes related to translation, amino acids biosynthesis, and promoting bacterial-eukaryotic algae interactions. By contrast, bacteria were negatively affected by AgNPs with less signs of detoxification than in case of eukaryota; various pathways related to energy metabolism, DNA replication and genetic repair were seriously inhibited by AgNPs. As a result, eukaryotic algae (mainly Chlorophyta) dominated over cyanobacteria in the AgNPs treated microcosms over the 7-d exposure. The present study helps to understand the effects of AgNPs on aquatic microorganisms and provides insights into the contrasting AgNPs toxicity in eukaryota and bacteria.

Hazardous effects of silver nanoparticles for primary producers in transitional water systems: The case of the seaweed Ulva rigida C. Agardh

The acute toxicity of citrate capped silver nanoparticles (AgNP) and silver nitrate was evaluated on the marine macroalga Ulva rigida C. Agardh (1823). Silver bioaccumulation, ultrastructural chloroplast damages verified by TEM microscopy, inhibition of primary production, neutral lipid production and oxidative stress were observed after 24 h of exposure to AgNP. The toxic effects of silver nitrate in artificial seawater started from a concentration of 0.05 ppm and was more toxic than AgNP that produced effects from a concentration of 0.1 ppm. However only AgNP induced lipid peroxidation in U. rigida. The addition of natural organic and inorganic ligands, represented by transparent exopolymer particles (TEP) and clay, drastically reduced AgNP acute toxicity in a ratio AgNP:ligand of 1:100 and 1:200, respectively. The findings suggest a marked toxicity of Ag on marine macroalgae which however should be mitigated by the high natural ligand concentrations of the transitional environments.

Efficacy and safety of alpha lipoic acid-capped silver nanoparticles for oral applications

Presentation of the limited cumulative cytotoxic effects of an alpha lipoic-acid capped silver nanoparticle on human gingival fibroblasts, with broad range antimicrobial activity, for potential use in biomaterials.

Silver stress differentially affects growth of phototrophic and heterotrophic chrysomonad flagellate populations

Silver ions are among the predominant anthropogenic introduced pollutants in aquatic systems. As silver has effects on species at all trophic levels the community composition in aquatic habitats can be changed as a result of silver stress. The response of planktonic protists to environmental stressors is particularly important as they act both as producers and consumers in complex planktonic communities. Chrysomonad flagellates are of major interest, since this group includes heterotrophic, mixotrophic and phototrophic taxa, and therefore allows analysis of silver stress in organisms with contrasting nutritional strategies independent of a potential taxonomic bias. In a series of lab experiments, we compared the response of different trophic chrysophyte strains to low (5 μg L^-1), medium (10 μg L^-1) and high (20 μg L^-1) nominal Ag concentrations in combination with changes in temperature and light intensity (phototrophs), temperature and food concentration (heterotrophs), or a combination of the above settings (mixotrophs). All tested strains were negatively affected by silver in their growth rates. The phototrophic strains reacted strongly to silver stress, whereas light intensity and temperature had only minor effects on growth rates. For heterotrophic strains, high food concentration toned down the effect of silver, whereas temperatures outside the growth optimum had a combined stress effect. The mixotrophic strains reacted differently depending on whether their nutritional mode was dominated by heterotrophy or by phototrophy. The precise response pattern across all variables was uniquely different for every single species we tested. The present work contributes to a deeper understanding of the effects of environmental stressors on complex planktonic communities. It indicates that silver will negatively impact planktonic communities and may create shifts in their composition and functioning.

Silver nanoparticles: Their role as antibacterial agent against Aeromonas salmonicida subsp. salmonicida in rainbow trout (Oncorhynchus mykiss)

The rise of bacterial resistance to antibiotics is one of the great challenges of our age. One of the strategies to limit the development of antibiotics resistance is the investigation of alternative antimicrobials. As silver nanoparticles demonstrated a potent bactericidal activity in vitro, the aim of this study was to evaluate the in vivo antibacterial activity of silver nanoparticles against Aeromonas salmonicida subsp. salmonicida. Rainbow trout (n = 120) were divided into four groups of 30 fish each. First group was challenged with A. salmonicida (Positive control), the second group was challenged with A. salmonicida and exposed to silver nanoparticles by immersion for three hours (100 μg/L), the third group was challenged with A. salmonicida and intraperitoneally injected with silver nanoparticles (17 μg/mL) and the fourth group was sham-treated and served as a negative control group. At the 7th day post challenge, histopathology of the positive control group revealed the presence of bacterial aggregates in tissues with degenerative and necrotic changes, while at the 35th day post challenge, only liver necrosis persisted. Silver nanoparticles-treated and negative control groups did not show any clinical signs, mortalities or histopathological alterations and they were tested negative for A. salmonicida. The immersion in silver nanoparticles did not result in detectable residues of silver in the muscles 35 days after treatment. These findings demonstrate the antibacterial properties of silver nanoparticles against A. salmonicida infection. Therefore, they could be used for development of antibacterial agents in aquaculture.

Synchrony of Eukaryotic and Prokaryotic Planktonic Communities in Three Seasonally Sampled Austrian Lakes

Freshwater systems are characterized by an enormous diversity of eukaryotic protists and prokaryotic taxa. The community structures in different lakes are thereby influenced by factors such as habitat size, lake chemistry, biotic interactions, and seasonality. In our study, we used high throughput 454 sequencing to study the diversity and temporal changes of prokaryotic and eukaryotic planktonic communities in three Austrian lakes during the ice-free season. In the following year, one lake was sampled again with a reduced set of sampling dates to observe reoccurring patterns. Cluster analyses (based on SSU V9 (eukaryotic) and V4 (prokaryotic) OTU composition) grouped samples according to their origin followed by separation into seasonal clusters, indicating that each lake has a unique signature based on OTU composition. These results suggest a strong habitat-specificity of microbial communities and in particular of community patterns at the OTU level. A comparison of the prokaryotic and eukaryotic datasets via co-inertia analysis (CIA) showed a consistent clustering of prokaryotic and eukaryotic samples, probably reacting to the same environmental forces (e.g., pH, conductivity). In addition, the shifts in eukaryotic and bacterioplanktonic communities generally occurred at the same time and on the same scale. Regression analyses revealed a linear relationship between an increase in Bray-Curtis dissimilarities and elapsed time. Our study shows a pronounced coupling between bacteria and eukaryotes in seasonal samplings of the three analyzed lakes. However, our temporal resolution (biweekly sampling) and data on abiotic factors were insufficient to determine if this was caused by direct biotic interactions or by reacting to the same seasonally changing environmental forces.

Effects of low dose silver nanoparticle treatment on the structure and community composition of bacterial freshwater biofilms

The application of engineered silver nanoparticles (AgNPs) in a considerable amount of registered commercial products inevitably will result in the continuous release of AgNPs into the natural aquatic environment. Therefore, native biofilms, as the prominent life form of microorganisms in almost all known ecosystems, will be subjected to AgNP exposure. Despite the exponentially growing research activities worldwide, it is still difficult to assess nanoparticle-mediated toxicity in natural environments. In order to obtain an ecotoxicologically relevant exposure scenario, we performed experiments with artificial stream mesocosm systems approaching low dose AgNP concentrations close to predicted environmental concentrations. Pregrown freshwater biofilms were exposed for 14 days to citrate-stabilized AgNPs at a concentration of 600 μg l^-1 in two commonly used sizes (30 and 70 nm). Sublethal effects of AgNP treatment were assessed with regard to biofilm structure by gravimetric measurements (biofilm thickness and density) and by two biomass parameters, chlorophyll a and protein content. The composition of bacterial biofilm communities was characterized by t-RFLP fingerprinting combined with phylogenetic studies based on the 16S gene. After 14 days of treatment, the structural parameters of the biofilm such as thickness, density, and chlorophyll a and protein content were not statistically significantly changed by AgNP exposure. Furthermore, t-RFLP fingerprint analysis showed that the bacterial diversity was not diminished by AgNPs, as calculated by Shannon Wiener and evenness indices. Nevertheless, t-RFLP analysis also indicated that AgNPs led to an altered biofilm community composition as was shown by cluster analysis and multidimensional scaling (MDS) based on the Bray Curtis index. Sequence analysis of cloned 16S rRNA genes further revealed that changes in community composition were related with the displacement of putatively AgNP-sensitive bacterial taxa Actinobacteria, Chloroflexi, and Cyanobacteria by taxa known for their enhanced adaptability towards metal stress, such as Acidobacteria, Sphingomonadales, and Comamonadaceae. This measurable community shift, even after low dose AgNP treatment, causes serious concerns with respect to the broad application of AgNPs and their potentially adverse impact on the ecological function of lotic biofilms, such as biodegradation or biostabilization.

Trophic transfer of citrate, PVP coated silver nanomaterials, and silver ions in a paddy microcosm

We used replicated paddy microcosm systems to estimate the tropic transfer of citrate-coated silver nanoparticles (AgNP citrate), polyvinylpyrrolidone (PVP)-coated AgNP (AgNP PVP), and silver ions (AgNO₃) for 14 days under two exposure regimes (a single high-dose exposure; 60 μg L^-1 and a sequential low-dose exposure at 1 h, 4 days and 9 days; 20 μg L^-1 × 3 = 60 μg L^-1). Most Ag ions from AgNO₃ had dispersed in the water and precipitated partly on the sediment, whereas the two Ag NPs rapidly coagulated and precipitated on the sediment. The bioconcentration factors (BCFs) of Ag from AgNPs and AgNO₃ in Chinese muddy loaches and biofilms were higher than those of river snails in both exposure conditions. These BCFs were more prominent for 14 days exposure (7.30 for Chinese muddy loach; 4.48 for biofilm) in the low-dose group than in the single high-dose group. Their retention of AgNPs and Ag ions differed between the two exposure conditions, and uptake and elimination kinetics of Ag significantly differed between AgNP citrate and AgNP PVP in the sequential low-dose exposure. Stable isotopes analyses indicated that the trophic levels between Chinese muddy loaches and biofilms and between river snails and biofilms were 2.37 and 2.27, respectively. The biomagnification factors (BMFs) of AgNPs and AgNO₃ between Chinese muddy loaches and biofilms were significantly higher than those between river snails and biofilms under both exposure settings. The BMFs of AgNP citrate and AgNO₃ between Chinese muddy loaches and biofilms were greater than those of AgNP PVP for 14 days in the single high-dose group, whereas the BMFs of AgNP PVP were greater than those of AgNP citrate and AgNO₃ in the sequential low-dose group. These microcosm data suggest that AgNPs have the potential to impact on ecological receptors and food chains.

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

Background

High-throughput sequencing (HTS) technologies are increasingly applied to analyse complex microbial ecosystems by mRNA sequencing of whole communities, also known as metatranscriptome sequencing. This approach is at the moment largely limited to prokaryotic communities and communities of few eukaryotic species with sequenced genomes. For eukaryotes the analysis is hindered mainly by a low and fragmented coverage of the reference databases to infer the community composition, but also by lack of automated workflows for the task.

Results

From the databases of the National Center for Biotechnology Information and Marine Microbial Eukaryote Transcriptome Sequencing Project, 142 references were selected in such a way that the taxa represent the main lineages within each of the seven supergroups of eukaryotes and possess predominantly complete transcriptomes or genomes. From these references, we created an annotated microeukaryotic reference database. We developed a tool called TaxMapper for a reliably mapping of sequencing reads against this database and filtering of unreliable assignments. For filtering, a classifier was trained and tested on each of the following: sequences of taxa in the database, sequences of taxa related to those in the database, and random sequences. Additionally, TaxMapper is part of a metatranscriptomic Snakemake workflow developed to perform quality assessment, functional and taxonomic annotation and (multivariate) statistical analysis including environmental data. The workflow is provided and described in detail to empower researchers to apply it for metatranscriptome analysis of any environmental sample.

Conclusions

TaxMapper shows superior performance compared to standard approaches, resulting in a higher number of true positive taxonomic assignments. Both the TaxMapper tool and the workflow are available as open-source code at Bitbucket under the MIT license: https://bitbucket.org/dbeisser/taxmapperand as a Bioconda package: https://bioconda.github.io/recipes/taxmapper/README.html.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4168-6) contains supplementary material, which is available to authorized users.

Nanoparticulate versus ionic silver: Behavior in the tank water, bioaccumulation, elimination and subcellular distribution in the freshwater mussel Dreissena polymorpha

Zebra mussels (Dreissena polymorpha) were exposed to polyvinylpyrrolidone (PVP)-coated silver nanoparticles (AgNP; hydrodynamic diameter 80 nm; solid diameter 50 nm) to investigate the behavior of Ag in the tank water with respect to its uptake, bioaccumulation, elimination and subcellular distribution in the mussel soft tissue. Parallel experiments were performed with ionic Ag (AgNO₃) to unravel possible differences between the metal forms. The recovery of the applied Ag concentration (500 μg/L) in the tank water was clearly affected by the metal source (AgNP < AgNO₃) and water type (reconstituted water < tap water). Filtration (<0.45 μm) of water samples showed different effects on the quantified metal concentration depending on the water type and Ag form. Ag accumulation in the mussel soft tissue was neither influenced by the metal source nor by the water type. Ag concentrations in the mussel soft tissue did not decrease during 14 days of depuration. For both metal forms the Ag distribution within different subcellular fractions, i.e. metal-rich granules (MRG), cellular debris, organelles, heat-sensitive proteins (HSP) and metallothionein-like proteins (MTLP), revealed time-dependent changes which can be referred to intracellular Ag translocation processes. The results provide clear evidence for the uptake of Ag by the mussel soft tissue in nanoparticulate as well as in ionic form. Thus, zebra mussels could be used as effective accumulation indicators for environmental monitoring of both Ag forms.

Laser Synthesis and Processing of Colloids: Fundamentals and Applications

Driven by functionality and purity demand for applications of inorganic nanoparticle colloids in optics, biology, and energy, their surface chemistry has become a topic of intensive research interest. Consequently, ligand-free colloids are ideal reference materials for evaluating the effects of surface adsorbates from the initial state for application-oriented nanointegration purposes. After two decades of development, laser synthesis and processing of colloids (LSPC) has emerged as a convenient and scalable technique for the synthesis of ligand-free nanomaterials in sealed environments. In addition to the high-purity surface of LSPC-generated nanoparticles, other strengths of LSPC include its high throughput, convenience for preparing alloys or series of doped nanomaterials, and its continuous operation mode, suitable for downstream processing. Unscreened surface charge of LSPC-synthesized colloids is the key to achieving colloidal stability and high affinity to biomolecules as well as support materials, thereby enabling the fabrication of bioconjugates and heterogeneous catalysts. Accurate size control of LSPC-synthesized materials ranging from quantum dots to submicrometer spheres and recent upscaling advancement toward the multiple-gram scale are helpful for extending the applicability of LSPC-synthesized nanomaterials to various fields. By discussing key reports on both the fundamentals and the applications related to laser ablation, fragmentation, and melting in liquids, this Article presents a timely and critical review of this emerging topic.

Silver Sink Effect of Humic Acid on Bacterial Surface Colonization in the Presence of Silver Ions and Nanoparticles

Silver nanoparticles (AgNPs) released from consumer products may enter the environment and possibly harm microbial communities. Prior research showed that surface-adherent AgNPs inhibit bacterial surface colonization, a precursor to biofilm formation, only when planktonic bacterial inoculum concentrations are less than a threshold level ( Wirth and co-workers, J. Colloid Interface Sci. 2016 , 467 , 17 - 27 ). This inoculum effect is due to a decrease in free silver ion concentration associated with sublethal binding to bacteria. Natural organic matter can be an additional silver sink in environmental systems. Using Pseudomonas fluorescens as a model biofilm-forming bacterium, we find significant increases in minimum bactericidal concentrations for AgNP suspensions and Ag⁺ in solution when adding humic acid (HA) to bacterial suspensions. When HA is present, planktonic bacteria survive and colonize AgNP-laden glass surfaces at lower bacterial inoculum concentrations than were needed for survival and colonization in its absence. This occurs despite the observed tendency of HA to inhibit colonization on bare glass surfaces when silver is absent. Results are interpreted through equilibrium Ag⁺ binding isotherms to HA and suspended bacteria. These results indicate that silver ion sinks may lessen AgNP impacts on natural microbial ecology relative to the disruption observed in pristine laboratory conditions.

Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis

Aquatic environments are heavily impacted by human activities including climate warming and the introduction of xenobiotics. Due to the application of silver nanoparticles as bactericidal agent the introduction of silver into the environment strongly has increased during the past years. Silver ions affect the primary metabolism of algae, in particular photosynthesis. Mixotrophic algae are an interesting test case as they do not exclusively rely on photosynthesis which may attenuate the harmful effect of silver. In order to study the effect of silver ions on mixotrophs, cultures of the chrysophyte Poterioochromonas malhamensis were treated in a replicate design in light and darkness with silver nitrate at a sub-lethal concentration. At five time points samples were taken for the identification and quantitation of proteins by mass spectrometry. In our analysis, relative quantitative protein mass spectrometry has shown to be a useful tool for functional analyses in conjunction with transcriptome reference sequences. A total of 3,952 proteins in 63 samples were identified and quantified, mapping to 4,829 transcripts of the sequenced and assembled transcriptome. Among them, 720 and 104 proteins performing various cellular functions were differentially expressed after eight days in light versus darkness and after three days of silver treatment, respectively. Specifically pathways of the energy and primary carbon metabolism were differentially affected by light and the utilization of expensive reactions hints to an energy surplus of P. malhamensis under light conditions. The excess energy is not invested in growth, but in the synthesis of storage metabolites. The effects of silver were less explicit, observable especially in the dark treatments where the light effect could not mask coinciding but weaker effects of silver. Photosynthesis, particularly the light harvesting complexes, and several sulphur containing enzymes were affected presumably due to a direct interference with the silver ions, mainly affecting energy supply.

Sublethal concentrations of silver nanoparticles affect the mechanical stability of biofilms

Bacterial biofilms are most likely confronted with silver nanoparticles (Ag NPs) as a pollutant stressor in aquatic systems. In this study, biofilms of Aquabacterium citratiphilum were exposed for 20 h to 30 and 70 nm citrate stabilized Ag NPs in low-dose concentrations ranging from 600 to 2400 μg l^-1, and the Ag NP-mediated effects on descriptive, structural, and functional biofilm characteristics, including viability, protein content, architecture, and mechanical stability, were investigated. Viability, based on the bacterial cell membrane integrity of A. citratiphilum, as determined by epifluorescence microscopy, remained unaffected after Ag NP exposure. Moreover, in contrast to information in the current literature, protein contents of cells and extracellular polymeric substances (EPS) and biofilm architecture, including dry mass, thickness, and density, were not significantly impacted by exposure to Ag NPs. However, the biofilms themselves served as effective sinks for Ag NPs, exhibiting enrichment factors from 5 to 8. Biofilms showed a greater capacity to accumulate 30 nm sized Ag NPs than 70 nm Ag NPs. Furthermore, Ag NPs significantly threatened the mechanical stability of biofilms, as determined by a newly developed assay. For 30 nm Ag NPs, the mechanical stability of biofilms decreased as the Ag NP concentrations applied to them increased. In contrast, 70 nm Ag NPs produced a similar decrease in mechanical stability for each applied concentration. Overall, this finding demonstrates that exposure to Ag NPs triggers remarkable changes in biofilm adhesion and/or cohesiveness. Because of biofilm-mediated ecological services, this response raises environmental concerns regarding Ag NP release into freshwater systems, even in sublethal concentrations.

Intravenous administration of silver nanoparticles causes organ toxicity through intracellular ROS-related loss of inter-endothelial junction

Background

Administration of silver nanoparticles (AgNPs) to mice could result in their distribution and accumulation in multiple organs, with notable prominence in liver, lungs, and kidneys. However, how AgNPs transport through blood vesicular system to reach the target organs is unclear, and the precise differences in the mechanisms of toxicity between AgNPs and silver ions still remain elusive. In the present research, the pathological changes on these target organs with a focus on inter-endothelial junction was investigated to gain a new insight of AgNPs toxicity by comparing the mechanisms of action of AgNPs and AgNO₃.

Methods

We investigated the in vitro cytotoxicity of either citrated-coated AgNPs (10, 75, and 110 nm) or silver nitrate (AgNO₃) following 24 h incubations (1–40 μg/mL) in the presence of primary human umbilical vein endothelial cells (HUVEC). Meanwhile, we detected the effects of AgNPs on intercellular conjunction and intracellular ROS by VE-cadherin staining and 2′, 7′-dichlorodihydrofluorescein diacetate (DCFH-DA) assay, respectively. To assess in vivo toxicity, we administered single or multiple intravenous injections (25 μg Ag for AgNPs and 2.5 μg Ag for AgNO₃ per dose) to mice.

Results

In the in vitro study, the TEM observation showed that AgNPs were taken up by endothelial cells while AgNO₃ was taken up little. Meanwhile AgNPs incubation induced the elevation of intracellular ROS and down-regulation of VE-cadherin between the endothelial cells and affected the cytoskeleton actin reorganization, which could be rescued by antioxidant N-acetylcysteine. In contrast, AgNO₃ caused direct cell death when the concentration was higher than 20 μg/mL and without ROS induction at lower concentration. The release of AgNPs from leaking vessels induced peripheral inflammation in the liver, lungs, and kidneys, and the severity increased in proportion to the diameter of the AgNPs used.

Conclusion

It is AgNPs but not AgNO₃ that were taken up by vascular endothelial cells and induced intracellular ROS elevated, which was closely related to disruption of the integrity of endothelial layer. The AgNPs-induced leakiness of endothelial cells could mediate the common peripheral inflammation in liver, kidney and lung through intravenous exposure.

Electronic supplementary material

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Impact of silver nanoparticles on marine diatom Skeletonema costatum

When silver nanoparticles (AgNPs) are used commercially at a large scale, they infiltrate the environment at a rapid pace. However, the impact of large quantities of AgNPs on aquatic ecosystems is still largely unknown. In aquatic ecosystems, the phytoplanktons have a vital ecological function and, therefore, the potential impact of AgNPs on the microalgae community has elicited substantial concern. Therefore, in this study, the impacts of AgNPs on a marine diatom, the Skeletonema costatum, are investigated, with a focus on their photosynthesis and associated mechanisms. Exposure to AgNPs at a concentration of 0.5 mg l(-1) significantly induces excess intracellular reactive oxygen species (ROS, 122%) and reduces 28% of their cell viability. More importantly, exposure to AgNPs reduces the algal chlorophyll-a content. Scanning electron microscopy (SEM) was conducted, which revealed that AgNPs obstruct the light absorption of algae because they adhere to their surface. The maximum photochemical efficiency of photosystem II (Fv/Fm) demonstrates that exposure to AgNPs significantly inhibits the conversion of light energy into photosynthetic electron transport. Moreover, the genes of the photosystem II reaction center protein (D1) are significantly down-regulated (P < 0.05) upon exposure to 5 mg l(-1) AgNPs. These results suggest that the physical adhesion and effects of shading of AgNPs on algae might affect their light energy delivery system and damage the crucial protein function of PSII. The photosynthesis inhibition effect of AgNPs is largely different from Ag(+) . This study shows that AgNPs at higher concentrations might have serious consequences for the succession of the phytoplankton communities and aquatic ecosystem equilibrium. Copyright © 2016 John Wiley & Sons, Ltd.

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

High throughput sequencing (HTSeq) of small ribosomal subunit amplicons has the potential for a comprehensive characterization of microbial community compositions, down to rare species. However, the error-prone nature of the multi-step experimental process requires that the resulting raw sequences are subjected to quality control procedures. These procedures often involve an abundance cutoff for rare sequences or clustering of sequences, both of which limit genetic resolution. Here we propose a simple experimental protocol that retains the high genetic resolution granted by HTSeq methods while effectively removing many low abundance sequences that are likely due to PCR and sequencing errors. According to this protocol, we split samples and submit both halves to independent PCR and sequencing runs. The resulting sequence data is graphically and quantitatively characterized by the discordance between the two experimental branches, allowing for a quick identification of problematic samples. Further, we discard sequences that are not found in both branches (“AmpliconDuo filter”). We show that the majority of sequences removed in this way, mostly low abundance but also some higher abundance sequences, show features expected from random modifications of true sequences as introduced by PCR and sequencing errors. On the other hand, the filter retains many low abundance sequences observed in both branches and thus provides a more reliable census of the rare biosphere. We find that the AmpliconDuo filter increases biological resolution as it increases apparent community similarity between biologically similar communities, while it does not affect apparent community similarities between biologically dissimilar communities. The filter does not distort overall apparent community compositions. Finally, we quantitatively explain the effect of the AmpliconDuo filter by a simple mathematical model.

Changes in soil bacterial communities and diversity in response to long-term silver exposure

Silver-induced selective pressure is becoming increasingly important due to the growing use of silver (Ag) as an antimicrobial agent in biomedical and commercial products. With demonstrated links between environmental resistomes and clinical pathogens, it is important to identify microbial profiles related to silver tolerance/resistance. We investigated the effects of ionic Ag stress on soil bacterial communities and identified resistant/persistent bacterial populations. Silver treatments of 50-400 mg Ag kg(-1) soil were established in five soils. Chemical lability measurements using diffusive gradients in thin-film devices confirmed that significant (albeit decreasing) labile Ag concentrations were present throughout the 9-month incubation period. Synchrotron X-ray absorption near edge structure spectroscopy demonstrated that this decreasing lability was due to changes in the Ag speciation to less soluble forms such as Ag(0) and Ag2S. Real-time PCR and Illumina MiSeq screening of 16S rRNA bacterial genes showed β-diversity changes, increasing α-diversity in response to Ag pressure, and immediate and significant reductions in 16S rRNA gene counts with varying degrees of recovery. These effects were more strongly influenced by exposure time than by Ag dose at these rates. Ag-selected dominant OTUs principally resided in known persister taxa (mainly Gram positive), including metal-tolerant bacteria and slow-growing Mycobacteria.

Biocompatibility of silver containing silica films on Bioverit® II middle ear prostheses in rabbits

For several centuries silver is known for its antibacterial effects. The middle ear is an interesting new scope for silver application since chronic inflammations combined with bacterial infection cause complete destruction of the fragile ossicle chain and tympanic membrane. The resulting conductive deafness requires tympanoplasty for reconstruction. Strategies to prevent bacterial growth on middle ear prostheses are highly recommended. In this study, rabbits were implanted with Bioverit® II middle ear prostheses functionalized with silver containing dense and nanoporous silica films which were compared with pure silica coatings as well as silver sulfadiazine cream applied on nanoporous silica coating. The health status of animals was continuously monitored; blood was examined before and after implantation. After 21 days, the middle ears were inspected; implants and mucosal samples were processed for electron microscopy. Autopsies were performed and systemic spreading of silver was chemically analyzed exemplarily in liver and kidneys. For verification of direct cytotoxicity, NIH 3T3 cells were cultured on similar silver containing silica coatings on glass up to 3 days. In vitro a reduced viability of fibroblasts adhering directly on the samples was detected compared to cells growing on the surrounding plastic of the same culture dish. In transmission electron microscopy, phagocytosed silver silica fragments, silver sulfadiazine cream as well as silver nanoparticles were noticed inside endosomes. In vivo, clinical and post mortem examinations were inconspicuous. Chemical analyses showed no increased silver content compared to controls. Mucosal coverages on almost all prostheses were found. But reduction of granulation tissue was only obvious around silver-coated implants. Single necroses and apoptosis in the mucosa were correlated by intracellular accumulation of metallic silver. For confirming supportive healing effects of middle ear implants, silver ion aggregates need to be tested in the future to optimize biocompatibility while assuring bactericidal effects in the middle ear.

Harmful Effects of Nanoparticles on Animals

Since several years nanoparticles (NPs) are produced by industries and used in several fields of activities. They are finally found in aquatic and terrestrial environments, where they are ingested by living organisms in which they accumulate, before being eliminated. In organisms, NPs represent foreign elements with their own physicochemical properties due to their small size. So NPs may interfere with the normal physiological mechanisms of the embryos, growing animals, and adults, and it is indispensable to understand their potentially direct or indirect harmful effects on living organisms. It has been already shown that NPs could be toxic to bacteria, algae, invertebrates, and vertebrates. In this review, several examples of recent studies are given. We will examine successively the effects of NPs on terrestrial and semiaquatic and aquatic vertebrate and invertebrate animals.

PVP-coated, negatively charged silver nanoparticles: A multi-center study of their physicochemical characteristics, cell culture and in vivo experiments

PVP-capped silver nanoparticles with a diameter of the metallic core of 70 nm, a hydrodynamic diameter of 120 nm and a zeta potential of -20 mV were prepared and investigated with regard to their biological activity. This review summarizes the physicochemical properties (dissolution, protein adsorption, dispersability) of these nanoparticles and the cellular consequences of the exposure of a broad range of biological test systems to this defined type of silver nanoparticles. Silver nanoparticles dissolve in water in the presence of oxygen. In addition, in biological media (i.e., in the presence of proteins) the surface of silver nanoparticles is rapidly coated by a protein corona that influences their physicochemical and biological properties including cellular uptake. Silver nanoparticles are taken up by cell-type specific endocytosis pathways as demonstrated for hMSC, primary T-cells, primary monocytes, and astrocytes. A visualization of particles inside cells is possible by X-ray microscopy, fluorescence microscopy, and combined FIB/SEM analysis. By staining organelles, their localization inside the cell can be additionally determined. While primary brain astrocytes are shown to be fairly tolerant toward silver nanoparticles, silver nanoparticles induce the formation of DNA double-strand-breaks (DSB) and lead to chromosomal aberrations and sister-chromatid exchanges in Chinese hamster fibroblast cell lines (CHO9, K1, V79B). An exposure of rats to silver nanoparticles in vivo induced a moderate pulmonary toxicity, however, only at rather high concentrations. The same was found in precision-cut lung slices of rats in which silver nanoparticles remained mainly at the tissue surface. In a human 3D triple-cell culture model consisting of three cell types (alveolar epithelial cells, macrophages, and dendritic cells), adverse effects were also only found at high silver concentrations. The silver ions that are released from silver nanoparticles may be harmful to skin with disrupted barrier (e.g., wounds) and induce oxidative stress in skin cells (HaCaT). In conclusion, the data obtained on the effects of this well-defined type of silver nanoparticles on various biological systems clearly demonstrate that cell-type specific properties as well as experimental conditions determine the biocompatibility of and the cellular responses to an exposure with silver nanoparticles.