Biogenic silver nanoparticles: understanding the antimicrobial mechanism using Confocal Raman Microscopy

The antimicrobial properties of silver nanoparticles (AgNPs) have made them ubiquitous in a number of real-world industrial applications; however, the antimicrobial mode of action of biogenic AgNPs is not entirely understood. The use of Raman spectroscopy can provide molecular fingerprint information on various chemical and biochemical components in complex systems like microbial cultures, without the need for any complex sample pre-treatment. Consequently, the antimicrobial mechanism of AgNPs can be inferred through morphological and compositional changes of microbial cells that are monitored via changes in Raman band profiles. Here we show the synthesis of biogenic AgNPs using the extracellular cell-free filtrates of Penicillium expansum. The antimicrobial activity of the Penicillium expansum synthesized silver nanoparticles (hereafter PeNPs) was evaluated and the interactions between the nanoparticles and Escherichia coli were studied using Transmission Electron Microscopy (TEM) and Environmental Scanning Electron Microscopy (ESEM), showing the attachment of PeNPs to the surface of the bacteria and rupture of the bacterial cell membrane. Importantly, we show how Confocal Raman Microscopy can be used as an innovative approach to study the antimicrobial mechanisms, the results of which confirm that the PeNPs induce damage to bacterial and fungal cells, resulting in critical changes to polysaccharides, lipids, proteins and nucleic acids.


Introduction
In recent years, the biological synthesis of nanoparticles, including the intracellular or extracellular production of nanoparticles by microorganisms [1,2] has gained interest over other chemical and physical methods [3]. Extracellular biosynthesis using fungi could also make downstream processing much easier than the intracellular biosynthesis [4]. In particular, silver nanoparticles (AgNPs) have attracted considerable attention due to their applications as antimicrobial agents [5,6]. The antimicrobial action mechanisms of AgNPs are known to be complex [7] and depend on many factors such as the physicochemical properties of the type of nanoparticle (for example, their size, shape and surface charge) or type of microorganism [8].
The use of Raman spectroscopy is an important vibrational spectroscopic tool that can provide molecular fingerprint information on various chemical and biochemical components in complex systems like microbial cultures, without any complex sample pre-treatment. Changes in cellular composition, such as proteins, lipids and nucleic acids, can be monitored using changes in Raman band profiles, which can be associated with the morphological changes of microbial cells, providing an image of the antimicrobial effect [9]. In recent times, Raman difference spectroscopy has been shown to provide molecular details on changes within E. coli cells caused by antibiotics, hydrogen peroxide [10,11] or graphene oxide [9]. The objective of the present study was to produce silver nanoparticles (AgNPs) using the extracellular cell-free filtrates of Penicillium expansum, evaluate their antimicrobial activity and study nanoparticle-microorganism interactions. Furthermore, we propose a new approach using Confocal Raman Microscopy to study the antimicrobial mechanism of silver nanoparticles.

Material and methods
2.1. Synthesis of silver nanoparticles Strain of Penicillium expansum (14 S) from the Cátedra de Microbiología General Collection of CCMG, Facultad de Química, Montevideo, Uruguay, was used for the nanoparticle biosynthesis.
The mycelia were grown in Potato Dextrose Agar (PDA, BD Difco) at 28°C and two plugs of 0.9 cm in diameter were then transferred to 500 mL flasks containing 100 mL Potato Dextrose Broth (PDB, BD Difco). Fermentations were carried out at 28°C, with agitation on an orbital shaker operating at 150 rpm for 72 h. The biomass from cultures was harvested by filtration and then washed extensively with sterilized distilled water to remove any remaining media components. Then, synthesis of silver nanoparticles was carried out as described in Sanguiñedo et al 2018 [12]. Wet fungal mycelia were suspended in sterilized distilled water (0.1 g ml −1 ) and incubated with agitation on an orbital shaker operating at 150 rpm. Then, the cell-free filtrate was collected by filtration of this suspension through membrane filter with 0.45 μm pore size. Finally, 50 ml of the cell-free filtrate was added to 50 ml of a silver nitrate solution. The mixture was incubated in dark. The absorbance spectrum was measured in the range of 250-800 nm and the maximum peak was determined, at different times. The reaction was stopped when there was no increase in the maximum absorption peak of silver nanoparticles. The remaining cell-free filtrate was used as control.
To evaluate the incidence of the reaction variables in the biosynthesis of the nanoparticles, the following experimental conditions were modified: incubation time of the mycelium with water, concentration of AgNO 3 and incubation temperature in the synthesis reaction.
After synthesis reaction, the samples were centrifuged at 10000 rpm for 10 min. The supernatant was removed and nanoparticles (PeNPs) were washed twice using sterilized distilled water, by centrifuging the nanoparticles for 5 min at 10000 rpm. The absorbance peak of the purified silver nanoparticles was measured and the concentration was estimated according to Paramelle et al [13].

Characterization of silver nanoparticles 2.2.1. UV-vis spectroscopy
The absorbance spectrum was measured in the range of 250-800 nm as evidence for silver nanoparticles formation.

Small angle x-ray scattering (SAXS)
For the Small Angle x-ray Scattering measurements, an x-ray Powder Diffractometer, Rigaku Ultima IV model, using radiation CuK α =1.5418 Å was used. The measurements were made at low angle, in Bragg-Brentano geometry, applying an offset of 0.2 Å −1 on nanoparticle deposits on silicon substrate. The measurement ranges of q=0.05 Å −1 to 1.50 Å −1 .

Dynamic light scattering (DLS) and ζ-potential
The hydrodynamic diameter and the ζ-potential of the nanoparticles were determined by Dynamic Light Scattering (DLS) utilizing a Malvern Instruments Zetasizer. Samples were prepared at pH 6, in Milli-Q water. For DLS determination, each sample was measured at 25°C, 10 times, combining 5 runs per measurement. In the case of ζ-potential, each sample was measured at 25°C, three times, combining 10 runs per measurement. Results were treated using the Malvern software Zetasizer.

Confocal raman microscopy
An aliquot of PeNPs was deposited on an aluminum support and dried at room temperature for a further analysis by Confocal Raman Microscopy. The measurements were made on an Alpha 300 RA WITec Raman Microscope using a λ=532 nm excitation laser and focused through a 100X objective.

Colloidal stability assays
The nanoparticles colloidal stability was studied at different pH (3-10) and ionic strength (10-500 mM NaCl) conditions by the measurement of the absorbance spectrum.
2.3. Antimicrobial activity of PeNPs against E. coli 2.3.1. Resazurin cell viability assays Cell viability was analyzed using a Resazurin (7-Hydroxy-3H-phenoxazin-3-one 10-oxide) assay in a 96-well plate. A bacterial inoculum (1×10 6 CFU ml −1 ) of E. coli DH5α in LB media was supplemented with different concentrations of PeNPs and a blank sample (bacteria without PeNPs) was also included in the assay as negative control. Once the microbial cultures had been grown for a total of 24 h, 30 μl of 0.1 mg ml −1 Resazurin in LB media was added to each well and incubated in the dark at 37°C for 1 h under stirring.

Environmental scanning electron microscopy (ESEM)
Bacterial cells were incubated with PeNPs (0.11 nM and 0.15 nM), in the same way as in the Resazurin assay. Then, three wells of 200 μl each were mixed into an Eppendorf and centrifuged at 1400 rpm (300 G) for 10 min. The supernatant was removed and the pellet was resuspended into 1.5 ml of 2.5% glutaraldehyde in phosphate buffer 10 mM pH 7.2 for fixation of the cells. The solutions were left for 2 h in the wheel. Afterwards, the cells were washed once with 1.5 ml of sterile PBS and three times with sterile distilled water to remove glutaraldehyde. Finally, the pellets were resuspended in 200 μl of sterile MilliQ water. Data were collected on a Quanta FEG-250 (FEI Company) field emission SEM for high-resolution imaging working in ESEM mode using a GSED detector under high relative humidity conditions.

Transmission electron microscopy (TEM)
Samples were prepared in the same way as in the ESEM assay, including the PeNPs concentrations. After de pellets were resuspended in sterile distilled water, 4 μl of the sample was deposited onto a carbon-coated copper grid (Cu200 mesh) and left to dry in air for several hours at room temperature. TEM analysis was carried out in a TECNAI T20 electron microscope (FEI) working at 60 kV.

Microorganism-nanoparticle interactions by confocal raman microscopy
Studies of the phenotypic profile of microbial cells before and after treatment with silver nanoparticles were carried out using Confocal Raman Microscopy according to the methodology described for antibiotics [14]. The cell suspensions were deposited on an aluminum support and dried at room temperature. The measurements were made using a 532 nm laser focused through a 100 X objective. The data processing and statistical analysis was performed by principal component analysis (PCA) using a script to be executed with the MATLAB software. The changes obtained in the Raman spectra (phenotypic profile) of the cells treated with the nanoparticles were evaluated by comparing them with those of the untreated cells (control).

Results
3.1. Synthesis of silver nanoparticles (PeNPs) using Penicillium expansum Penicillium expansum synthesized silver nanoparticles (hereafter PeNPs) were synthesized by incubating an aqueous cell-free filtrate with silver nitrate solution in the dark. A color change in the reaction mixtures, characterised by the appearance of absorption bands between 400 and 450 nm, were indicative of silver plasmon resonances associated with the production of AgNPs ( figure 1(b)). No color change was observed in the cell-free supernatant alone used as control ( figure 1(a)). The spectroscopic signature associated with the biosynthesis of PeNPs (plasmon band at 440 nm) is shown in figure 1(c).
The samples were centrifuged and the nanoparticles in the pellet were washed with water to remove unwanted reagents. After centrifugation, UV-vis spectroscopy was used to determine the stability of the PeNPs, which displayed an absorption band at 439 nm corresponding to the resonance bands of the PeNPs (figure 2).

Evaluation of the reaction conditions in the biosynthesis of PeNPs
The AgNO 3 concentration, the reaction temperature and the incubation time of the mycelium with water were evaluated. 5 mM AgNO 3 was found to be the concentration that gave the highest yield for the nanoparticle   3(a)). This concentration was selected for all subsequent biosyntheses. Moreover, results indicated that the biosynthesis reaction allowing greatest nanoparticle production in the shortest time was at 37°C ( figure 3(b)). Figure 3(c) shows the evolution of silver nanoparticle synthesis over time (by measuring absorbance at 440 nm) at different incubation times. The highest biosynthesis yield of PeNPs was obtained by incubating the mycelium with water for 72 h at 37°C.  4(a)) showed a single nanoparticle population with a hydrodynamic diameter of ca. 15 nm (see Online Resource 1). According to the Small Angle x-ray Scattering measurements, the curve was fitted with a two-size-distribution model, corresponding to two-correlation lengths: one at 16 nm and another at 40 nm, the nanoparticle diameter and the distance between nanoparticles, respectively ( figure 4(b)). These differences arise on the preparation of the samples, since DLS is obtained in solution, while SAXS is applied on a dried deposit from the nanoparticle solution. It is likely that during the drying process, the proximity effects of the PeNPs contributed to the second peak in the SAXS measurements.

ζ-potential
The stability of the PeNPs were evaluated by ζ-potential, which corresponded to −18.5 mV, indicating a relatively stable colloidal charge (see Online Resource 1)

Confocal raman microscopy
In order to further characterize the synthetized nanoparticles, Confocal Raman Microscopy was used to obtain more information about the nature of the surface functional groups capping the PeNPs. The presence of the band positioned at 230 cm −1 can be attributed to the Ag-N stretching mode, which may originate from the fungal extract, providing the nitrogen atoms that will finally take part of the capping of the silver nanoparticle. Additionally, the bands positioned at 1320 and 1586 cm −1 could be attributed to the D-and G-band of a carbonaceous component ( figure 5).

Colloidal stability assays
In order to further evaluate the colloidal stability of PeNPs, we analyzed the shift in wavelength (nm) of the colloidal suspension at different pH (3-9) and ionic strength ([NaCl]=10-500 mM). According to the results,    Table 1 shows the MIC values obtained for the PeNPs and the AgNO 3 solution against the gram-negative bacteria Escherichia coli, gram-positive Staphylococcus aureus and the yeast Candida albicans. All the microorganisms tested were more sensitive to the PeNPs than to AgNO 3 solution.

Nanoparticle-microorganism interactions
Phenotypic changes in E. coli, S. aureus and C. albicans cells treated with PeNPs were analyzed by means of Confocal Raman Microscopy (table 2). In the case of E. coli, the interaction with the nanoparticles induces an increase in the intensity of some Raman bands, while others decrease or disappear. The interaction of the nanoparticles with S. aureus causes a decrease in the intensity of all the bands of the Raman spectrum and for the case of C. albicans some bands decrease and others remain with the same intensity. In addition, hyperspectral images were obtained in order to visualize the main characteristics of the interaction between the PeNPs and the microorganisms (see figure 9). These images are obtained from the combination of the bands corresponding to the C-H stretching of the microorganisms and the bands corresponding to the Ag-N stretching of the PeNPs (Raman spectra are shown in Online Resource 1).

Discussion
The silver nanoparticles synthesised with Penicillium expansum were stable after their purification by centrifugation [12]. The evaluation of the biosynthesis conditions of PeNPs was carried out in order to produce more stable nanoparticles in higher yield in less time, for their potential use in biotechnological applications requiring large quantities.
The size of the PeNPs was determined by Dynamic Light Scattering (DLS) and x-ray diffraction at low angles (SAXS). The average hydrodynamic diameter obtained from DLS was 14 nm. Dispersity Parameter (PDI) showed a moderate polydisperse distribution (<0.4) from DLS results. In addition, Small Angle x-ray Scattering (SAXS) analysis showed two peaks associated with populations of spherical nanoparticles. The characteristic distances obtained from the adjustment correspond to 15 nm and 40 nm (figure 5). The first population could be attributed to the size of the single nanoparticles, while the second could correspond to a second larger population, resulting from the drying process necessary to make the preparation on silicon substrate. ζ-potential determination showed that PeNPs had net negative surface charge (−18.5 mV), indicating their stability. Nanoparticle suspensions showing ζ-potential net charges close to neutrality do not possess sufficient electrostatic repulsion to remain stable in solution.
In addition, the absorption spectrum of the nanoparticle solutions showed that the nanoparticles were stable to pH and high ionic strength. However, for the most extreme pH conditions (pH=3 and pH=9), a decrease in the plasmon resonance band suggested mild aggregation. Furthermore, a slight broadening of the peak is observed at pH 3 which could be attributed to the neutralization of surface charges of the PeNPs, which presented negative net charge at pH 6, resulting in their aggregation.
The characterization of the PeNPs was complemented by Confocal Raman Microscopy studies which indicated that this biological synthesis first produces AgNPs coordinated with N or O atoms, coming from the protein matrix, which enable their synthesis. In addition, the bands associated with the vibrational modes corresponding to the C-C stretching of the D-and G-bands of the carbonaceous matrix were found. These bands can be attributed to oxidized organic matter. In particular, the nature of silver nanoparticles gives rise to SERS phenomenon (Surface-Enhanced Raman Scattering), which produces a local effect. Due to this antenna and amplifier effect, it is possible to enhance the Raman signal of those molecular fragments near the surface of the nanoparticles of great importance to assess the nature of the stabilizing agent [16].
The application of biogenic PeNPs as antimicrobial agents was evaluated. The in vitro antimicrobial activity assays showed promising results, with MIC values lower than silver nitrate solution against bacteria and yeasts.
A first approach on the interaction between the PeNPs and Escherichia coli was carried out using electron microscopy techniques (TEM and ESEM). The first step in the interaction seems to be the attachment of the silver nanoparticles to the surface of the bacteria, as seen in TEM images. Thereafter, both ESEM and TEM show a decrease in the integrity of the cell membrane, probably as a consequence of the loss of cytoplasmic components due to de generation of pores on the cell, as shown in the ESEM images. In summary, the interaction of these silver nanoparticles and Escherichia coli seems to occur in three main stages: (i) the attachment of the silver nanoparticles to the bacterial surface, (ii) the generation of pores and the damage of the cell wall, and (iii) the loss of cytoplasmic components and the death of the bacteria.
In order to advance in the knowledge of the antimicrobial mechanisms of action of the PeNPs against different microorganisms, Confocal Raman Microscopy studies were carried out. For this purpose, Principal Components Analysis (PCA) was used. This systematic and statistical power tool was able to demonstrate the existence of significant changes in the phenotypic profile of the microorganisms evaluated against the PeNPs (Escherichia coli, Staphylococcus aureus and Candida albicans). The results suggest that the AgNPs produce cellular damage, producing changes at polysaccharides, lipids, proteins and nucleic acids. Although these studies had already been addressed in studies against antibiotics, this is the first report made with biogenic silver nanoparticles, which allows to advance in the knowledge of the target sites of nanoparticles. Changes in the phenotypic profile of the Raman spectra could be associated with the generation of reactive oxygen species (ROS) and intermediate nitrogen species (RNI) since they are extremely toxic and can cause damage to proteins, lipids and DNA. Previous studies have reported that the oxidative stress would be one of the mechanisms by which the nanoparticles synthetized by P. aeruginosa exert their toxicity [17]. On the other hand, Raman studies on antibiotics against microorganisms showed DNA fragmentation. The decrease of the band associated with DNA in E. coli and S. aureus and the disappearance of the same Raman band for the case of C. albicans can be attributed to a combination of mechanisms, possibly associated with the generation of ROS, which lead to the fragmentation and death of the microbial cells [18].

Conclusions
Extracellular cell-free filtrates of Penicillium expansum were used for the biosynthesis of monodisperse 15-nm diameter silver nanoparticles (PeNPs). Here we reported the optimum biosynthesis conditions to obtain the highest production of PeNPs in the shortest time for their potential use in biotechnological applications requiring large quantities of silver nanoparticles. The size, surface charge and stabilizing agent of the PeNPs were characterized, showing that the biogenic PeNPs were stable over a wide range of pH and ionic strength. The in vitro antimicrobial activity assays showed promising results for the application of biogenic nanoparticles as antimicrobial agents with MICs in the nM range. The interaction between the PeNPs and Escherichia coli was characterized using TEM and ESEM, showing the attachment of silver nanoparticles to the surface of the bacteria, which was accompanied by a coresponding decrease in the integrity of the cell wall. Importantly, a new approach to study the antimicrobial mechanism of biogenic silver nanoparticles, using Confocal Raman Microscopy allowed us to suggest that the damage to bacterial and fungal cells produced by the PeNPs induces changes to polysaccharides, lipids, proteins and nucleic acids. Table 2. Raman band assignment of microbial cells, control and treated cells with PeNPs. The band assignment was made based on previous work [15].