Comparison of ordinary reverse transcription real-time polymerase chain reaction (qRT-PCR) with a newly developed one-step single-tube nested real-time RT-PCR (OSN-qRT-PCR) for sensitive detection of SARS-CoV-2 in wastewater.

Wastewater monitoring has proven to be an important approach to detecting and controlling the development of the SARS-CoV-2 pandemic. Various tests based on reverse transcription real-time PCR (qRT-PCR) have been developed and used for the detection of SARS-CoV-2 in wastewater samples. In this study, we attempted to increase the sensitivity of qRT-PCR by developing a one-step single-tube nested qRT-PCR assay (OSN-qRT-PCR). Two variants were developed, oriented to nucleocapsid phosphoprotein gene (N) and to spike protein gene (S), respectively. The performance of conventional qRT-PCR assays oriented to these genes with two novel OSN-qRT-PCR assays were firstly optimized using wastewater artificially contaminated with two encapsidated RNA mimic systems harboring a portion either N or S gene (ENRM and ESRM, respectively). The assays were coupled to a polyethylene glycol-based RNA precipitation/extraction method and applied to detect SARS-CoV-2 in wastewater samples from four cities in Slovakia. Both novel OSN-qRT-PCR assays demonstrated higher detection rates than the ordinary qRT-PCR counterparts. The virus levels in the analyzed wastewater samples had a high or very high relation with the numbers of clinical cases in the monitored regions. In fact, correlation with a 3-, 4-, or 5-day temporal offset was revealed. The OSN-qRT-PCR assays demonstrated robustness, mainly in samples with low viral loads.

Evaluation of enzymatic stamp removal strategies on handmade (cellulose-based) and machine-made (lignin-containing) papers.

Two different biocleaning techniques for stamp removal from different paper samples (handmade and machine-made) were investigated. Cellulose is the main component of handmade paper, while higher concentration of lignin is present in machine-made paper. Biocleaning methods included the direct application on paper surfaces of the extracellular enzymatic mixture (EEM) extracted from the yeast Sporidiobolus metaroseus and the recombinant protein CthediskatG of Chaetomium thermophilum var. dissitum. The produced microbial enzymes (EEM or CthediskatG) were also combined with agarose hydrogels. The effectiveness of the cleaning ability of the individual methods was determined using different spectrophotometer measurements based on colorimetric analysis and by Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (ATR-FTIR). Some tested samples were also subjected to microstructural and chemical analysis using Scanning Electron Microscope-Energy-Dispersive X-ray spectroscopy (SEM-EDX). The analysis showed that the EEM-based approaches were the most suitable, mainly they are less time-consuming and easy to produce, and moreover slight differences were displayed between EEM and CthediskatG during the removal of the stamp by hydrogel-enzyme approaches. Both EEM applications (direct and hydrogel) speed up the stamp removal process from real paper samples. However, for the complete elimination of the stamp smears a quick N,N-dimethylformamide post-treatment is advised too.

Colored stains: Microbial survey of cellulose-based and lignin rich papers.

Over the centuries, various types of paper have been produced, each characterized by a different ratio of natural macromolecules, mainly lignin and cellulose. Handmade paper has a higher content of cellulose with respect to the early machine-made paper, where lignin is the other important component. Microorganisms are able to colonize and deteriorate both types. They can release on their surfaces pigments and colorants which produced anesthetic stains. To better understand the microbiota colonizing these stains, 17 samples were analyzed, from both handmade and machine-made paper surfaces, as well as library and archive environments. Combination of microbiological and high-throughput sequencing (HTS) approaches were applied. The culture-dependent methodology comprised: isolation, DNA identification, hydrolytic and paper staining assays. The HTS was performed by MinION platform and for the mycobiome a more suitable bioinformatics analysis pipeline, MetONTIIME based on QIIME2 framework, was applied. The paper model staining assay permitted the direct recognition of colorizing isolates which in combination with sequencing data evidenced a complex microbial community able to stain the two types of paper. Staining abilities were confirmed by frequently isolated and detected fungi as well as newly discovered ones Roussoella euonymi and Achaetomium. We have also evidenced the staining ability of several bacteria.

Biodegradable Active Packaging Enriched with Essential Oils for Enhancing the Shelf Life of Strawberries.

The strawberry (Fragaria ananassa) is a nutrient-rich fruit with high content of health-beneficial compounds. However, strawberries are susceptible to mechanical damage and microbiological contamination which can cause changes in fruit sensory properties. These changes consequently effect on ripening and shelf life of the strawberry. In recent years, essential oils (EOs) have been famous for their antimicrobial and antioxidant properties and are promising ecological alternatives to chemical antimicrobial substances. Nowadays, active packaging is one of several techniques developed for slowing down the metabolic processes of fresh fruits. Poly(lactic acid) (PLA) is one of the several polymers suitable for encapsulation EOs, whereas at the same time represent non-toxic, biodegradable, and compostable polymer derived from renewable resources. Suitable packaging prolongs the shelf life of fruit, keeps the products at the highest possible nutrition level, improves quality, and attracts customer attention. In the current study, we encapsulated EOs (lemongrass and oregano) into a PLA and poly(3-hydroxybutyrate) (PHB) packaging film and explored their antimicrobial and antioxidant properties. Moreover, biochemical and quality parameters for strawberry preservation and shelf-life extension were also assessed. Our tested active packaging film with EOs was proven to be useful for postharvest quality maintenance and shelf-life extension of strawberries, with PLA/PHB/ATBC + 5% lemongrass EO being slightly better than PLA/PHB/ATBC + 5% oregano EO.

Protection and Disinfection Activities of Oregano and Thyme Essential Oils Encapsulated in Poly(ε-caprolactone) Nanocapsules.

The biocolonization of building materials by microorganisms is one of the main causes of their degradation. Fungi and bacteria products can have an undesirable impact on human health. The protection and disinfection of sandstone and wood materials are of great interest. In this study, we evaluated the protection and disinfection activity of oregano and thyme essential oils encapsulated in poly(ε-caprolactone) nanocapsules (Or-NCs, Th-NCs) against four types of environmental microorganisms: Pleurotus eryngii, Purpureocillium lilacinum (fungal strains), Pseudomonas vancouverensis, and Flavobacterium sp. (bacterial strains). The surfaces of sandstone and whitewood samples were inoculated with these microorganisms before or after applying Or-NCs and Th-NCs. The concentration-dependent effect of Or-NCs and Th-NCs on biofilm viability was determined by the MTT reduction assay. The results showed that Or-NCs and Th-NCs possess effective disinfection and anti-biofilm activity. Diffuse reflectivity measurements revealed no visible color changes of the materials after the application of the nanoencapsulated essential oils.

Useful molecular tools for facing next pandemic events: Effective sample preparation and improved RT-PCR for highly sensitive detection of SARS-CoV-2 in wastewater environment.

Viral pandemics can be inevitable in the next future. Considering SARS-CoV-2 pandemics as an example, there seems to be a need to develop a surveillance system able to monitor the presence of potential pathogenic agents. The sewage and wastewater environments demonstrated to be suitable targets for such kind of analysis. In addition, it is important to have reliable molecular diagnostic tools and also to develop a robust detection strategy. In this study, an effective sample preparation procedure was selected from four options and combined with a newly developed improved RT-PCR. First, a model viral system was constructed, containing a fragment of the SARS-CoV-2 gene encoding for the Spike protein. The encapsidated S RNA mimic (ESRM) was based on the plum pox virus (PPV) genome with the inserted targeted gene fragment. ESRM was used for seeding wastewater samples in order to evaluate the viral recovery of four different viral RNA concentration/extraction methods. The efficiency of individual approaches was assessed by the use of a quantitative reverse transcription PCR (qRT-PCR) and by a one-step single-tube nested quantitative reverse transcription PCR (OSN-qRT-PCR). For the detection of viruses in wastewater samples with low viral loads, OSN-qRT-PCR assay produced the most satisfactory results and the highest sensitivity.

Wine Yeasts Selection: Laboratory Characterization and Protocol Review.

Wine reflects the specificity of a terroir, including the native microbiota. In contrast to the use of Saccharomyces cerevisiae commercial starters, a way to maintain wines' microbial terroir identities, guaranteeing at the same time the predictability and reproducibility of the wines, is the selection of autochthonous Saccharomyces and non-Saccharomyces strains towards optimal enological characteristics for the chosen area of isolation. This field has been explored but there is a lack of a compendium covering the main methods to use. Autochthonous wine yeasts from different areas of Slovakia were identified and tested, in the form of colonies grown either on nutrient agar plates or in grape must micro-fermentations, for technological and qualitative enological characteristics. Based on the combined results, Saccharomyces cerevisiae PDA W 10, Lachancea thermotolerans 5-1-1 and Metschnikowia pulcherrima 125/14 were selected as potential wine starters. This paper, as a mixture of experimental and review contributions, provides a compendium of methods used to select autochthonous wine yeasts. Thanks to the presence of images, this compendium could guide other researchers in screening their own yeast strains for wine production.

Properties and Degradation Performances of Biodegradable Poly(lactic acid)/Poly(3-hydroxybutyrate) Blends and Keratin Composites.

From environmental aspects, the recovery of keratin waste is one of the important needs and therefore also one of the current topics of many research groups. Here, the keratin hydrolysate after basic hydrolysis was used as a filler in plasticized polylactic acid/poly(3-hydroxybutyrate) blend under loading in the range of 1-20 wt%. The composites were characterized by infrared spectroscopy, and the effect of keratin on changes in molar masses of matrices during processing was investigated using gel permeation chromatography (GPC). Thermal properties of the composites were investigated using thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The effect of keratin loading on the mechanical properties of composite was investigated by tensile test and dynamic mechanical thermal analysis. Hydrolytic degradation of matrices and composites was investigated by the determination of extractable product amounts, GPC, DSC and NMR. Finally, microbial growth and degradation were investigated. It was found that incorporation of keratin in plasticized PLA/PHB blend provides material with good thermal and mechanical properties and improved degradation under common environmental conditions, indicating its possible application in agriculture and/or packaging.

Biofilm inhibition by biocompatible poly(ε-caprolactone) nanocapsules loaded with essential oils and their cyto/genotoxicity to human keratinocyte cell line.

Essential oils (EOs) of Thymus capitatus (Th) carvacrol chemotype and Origanum vulgare (Or) thymol and carvacrol chemotype were encapsulated in biocompatible poly(ε-caprolactone) nanocapsules (NCs). These nanosystems exhibited antibacterial, antifungal, and antibiofilm activities against Staphylococcus aureus, Escherichia coli, and Candida albicans. Th-NCs and Or-NCs were more effective against all tested strains than pure EOs and at the same time were not cytotoxic on HaCaT (T0020001) human keratinocyte cell line. The genotoxic effects of EO-NCs and EOs on HaCaT were evaluated using an alkaline comet assay for the first time, revealing that Th-NCs and Or-NCs did not induce DNA damage compared with untreated control HaCaT cells in vitro after 24 h. The cells morphological changes were assessed by label-free live cell Raman imaging. This study demonstrate the ability of poly(ε-caprolactone) nanocapsules loaded with thyme and oregano EOs to reduce microbial and biofilm growth and could be an ecological alternative in the development of new antimicrobial strategies.

Removal of overpainting from an historical painting of the XVIII Century: A yeast enzymatic approach.

Biocleaning of cultural heritage items is mainly performed using living microorganisms. Approaches utilizing the enzymes of isolated microorganisms have not been frequently investigated. To find an enzymatic alternative for the removal of an oil-based overpainting, we focused on the characterization and use of a yeast Extracellular Enzymatic Mixture (EEM). A historical silk yeast was selected for its lipolytic properties and its EEM was extracted after cultivation on a medium supplemented with linseed oil. The EEM protein content was visualized by SDS-PAGE, its concentration assessed by fluorimeter and the enzymatic activity evaluated by p-NPP spectrophotometric lipase assay. The yeast growth was suppressed by adding diverse metal ions (Cd, Zn, Cr and Cu) in Reasoner's 2A (R2A) broth, while the quantity and activity of EEM were affected by adding Fe and Pb. Various delivery systems (agar-agar, tylose and klucel G) alone or in a combination with EEM were assayed on the historical painting surface. The colorimetric measurements and the ATR-FTIR analysis indicated that the combinations tylose-EEM and klucel G-EEM can be easily and effectively applied as biocleaning procedures to remove oil-based overpainting from fragile and valuable historical painting surfaces.

Nanoencapsulated Essential Oils with Enhanced Antifungal Activity for Potential Application on Agri-Food, Material and Environmental Fields.

Nanotechnology is a new frontier of this century that finds applications in various fields of science with important effects on our life and on the environment. Nanoencapsulation of bioactive compounds is a promising topic of nanotechnology. The excessive use of synthetic compounds with antifungal activity has led to the selection of resistant fungal species. In this context, the use of plant essential oils (EOs) with antifungal activity encapsulated in ecofriendly nanosystems could be a new and winning strategy to overcome the problem. We prepared nanoencapsules containing the essential oils of Origanum vulgare (OV) and Thymus capitatus (TC) by the nanoprecipitation method. The colloidal suspensions were characterized for size, polydispersity index (PDI), zeta potential, efficiency of encapsulation (EE) and loading capacity (LC). Finally, the essential oil nanosuspensions were assayed against a panel of fourteen fungal strains belonging to the Ascomycota and Basidiomycota phyla. Our results show that the nanosystems containing thyme and oregano essential oils were active against various fungal strains from natural environments and materials. In particular, the minimum inhibitory concentration (MIC) and minimum fungicidal concentration (MFC) values were two to four times lower than the pure essential oils. The aqueous, ecofriendly essential oil nanosuspensions with broad-spectrum antifungal activity could be a valid alternative to synthetic products, finding interesting applications in the agri-food and environmental fields.

Comparison of microbial diversity during two different wine fermentation processes.

Wine production is a complex procedure in which an important role is played by many microorganisms, particularly yeasts and bacteria. In modern wineries, alcoholic fermentation is usually carried out by adding microbial starter cultures of Saccharomyces cerevisiae strains for precisely controlled production. Nowadays, in the Slovak Republic, autochthonous vinification is getting more popular. The present article deals with the comparison of two vinification approaches, namely spontaneous fermentation and fermentation controlled by a standard commercial S. cerevisiae starter, from the point of view of microbiota dynamics and the chemical characteristics of the wines produced. The dynamics of microbial populations were determined during the fermentation process by a 16S and 28S rRNA next-generation sequencing approach. A profile of the volatile compounds during these fermentation processes was identified by solid-phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS). In summary, the microbial diversity in the m1 phase (initial must) was higher, despite the presence of the starter culture. In the m3 phase (young wine), the microbiome profiles of both batches were very similar. It seems that the crucial phase in order to study the relationship of the microbiome and the resulting product should be based on the m2 phase (fermented must), where the differences between the autochthonous and inoculated batches were more evident.

The antifungal activity of vapour phase of odourless thymol derivate.

Thymol is a substance with a great therapeutic potential possessing antibacterial and antifungal activity, with a characteristic odour that remains long after application but is not pleasant at higher concentrations. In this study, attention has been focused on describing the chemical and biological properties of the simply prepared trimethylsilyl ether of thymol (kubicin). Interestingly, kubicin has similar volatility as thymol, undergoes hydrolysis in the water (moisture; forming thymol and trimethylsilanol) and can be used at 6,000 times higher concentration than thymol without any negative and irritating odour. Kubicin showed diverse fungistatic and fungicidal activities when tested by direct contact assay, or in vapour phase. The volatile vapour of kubicin was effective on all tested fungal strains. These results suggest that vapours of kubicin might provide an alternative way to fight against fungal contamination.

Studying the Gene Expression of Penicillium rubens Under the Effect of Eight Essential Oils.

Essential oils (EOs) are well-known for their beneficial properties against a broad range of microorganisms. For the better understanding of their mechanism of action in fungi, a microarray approach was used in order to evaluate the gene expression of Penicillium chrysogenum (recently renamed P. rubens) exposed to the indirect contact (vapors) of eight EOs. The selection of assayed EOs was based on their antifungal activity. The extraction of RNA and the microarray hybridization procedure were optimized for the analysis of P. rubens. Gene ontology annotation was performed to investigate the functional analysis of the genes. To uncover the metabolic pathway of these differentially expressed genes, they were mapped into the KEGG BRITE pathway database. The transcriptomic analysis showed that, from a total of 12,675 genes, only 551 genes are annotated, and the other 12,124 genes encoded hypothetical proteins. Further bioinformatic analysis demonstrated that 1350 genes were upregulated and 765 downregulated at least with half (four) of the utilizing EOs. A microarray investigation has confirmed the main impact of EOs to metabolic processes in P. rubens involved in vital functions. Presumably, this is the first time that a microarray hybridization analysis was performed in order to evaluate the gene expression of P. rubens exposed to various EOs.

Lead soaps formation and biodiversity in a XVIII Century wax seal coloured with minium.

A multidisciplinary approach was carried out in order to study the biodeterioration and the associated microbiome of a XVIII Century wax seal coloured with minium. A small wax seal fragment was observed by scanning electron microscopy combined with energy dispersive spectroscopy in non-destructive mode. The same object was analysed by Raman and Fourier-transform infrared spectroscopy. The identification of the microbiota growing on the seal was performed with both a culture-dependent strategy, combined with hydrolytic assays, and high-throughput sequencing using the MinION platform. The whole bacterial 16S rRNA gene and the fungal markers ITS and 28S rRNA were targeted. It was observed that the carnauba wax coloured with lead tetroxide (minium) was covered by a biofilm consisting of a network of filaments and other structures of microbial origin. The culture-dependent and culture-independent investigations showed the presence of a complex microbiota composed mainly by fungal members, which demonstrated interesting properties related to lipids and lead processing. The formation of lead soaps and secondary biogenic minerals was also described.

The Effect of Ten Essential Oils on Several Cutaneous Drug-Resistant Microorganisms and Their Cyto/Genotoxic and Antioxidant Properties.

In this study, we determined the antimicrobial activity of ten essential oils (EOs)-oregano, thyme, clove, arborvitae, cassia, lemongrass, melaleuca, eucalyptus, lavender, and clary sage-against drug-resistant microorganisms previously isolated from patients with skin infections. The essential oil compositions were determined using gas chromatography coupled to mass spectrometry (GC/MS). The assayed bacteria included Pseudomonas aeruginosa, Proteus vulgaris, Citrobacter koseri, and Klebsiella pneumoniae. Two drug-resistant yeasts (Candida albicans and Candida parapsilosis) were also involved in our survey. Oregano, thyme, cassia, lemongrass and arborvitae showed very strong antibacterial and antifungal activity against all tested strains. These results show that these essential oils may be effective in preventing the growth of the drug-resistant microorganisms responsible for wound infections. In this study, the genotoxic effects of tested essential oils on healthy human keratinocytes HaCaT were evaluated using the comet assay for the first time. These results revealed that none of the essential oils induced significant DNA damage in vitro after 24 h. Moreover, the treatment of HaCaT cells with essential oils increased the total antioxidant status (TAS) level. The obtained results indicate that EOs could be used as a potential source of safe and potent natural antimicrobial and antioxidant agents in the pharmaceutical and food industries.

Biogas production: evaluation of the influence of K2FeO4 pretreatment of maple leaves (Acer platanoides) on microbial consortia composition.

The potential of K2FeO4 as a pretreatment agent of a lignocellulosic material was examined on leaves of Acer platanodides as the sole substrate for biogas production by anaerobic digestion carried out through modelling laboratory-scaled semi-continuous reactors differing in loading rates and substrate (pretreated and untreated leaves). The quality of bioagas produced by K2FeO4-pretreated leaves was significantly better in terms of higher methane content and lower content of H2S. K2FeO4 had no crucial influence on growth inhibition of biogas-producing bacteria, which were analysed by comprehensive culture-independent methods utilising high-throughput sequencing of specific genes [bacterial and archaeal 16S rRNA, formyltetrahydrofolate synthetase gene (fhs), methyl-coenzyme M reductase α subunit gene (mcrA) and fungal internal transcribed spacers (ITS)]. The higher amount of CH4 in biogas utilising pretreated leaves as substrate could be caused by a shift to acetoclastic methanogenesis pathway, which was indicated by the higher amount of homoacetogenic bacteria and acetotrophic methanogens detected in those reactors.

Transcription activity of lactic acid bacterial proteolysis-related genes during cheese maturation.

The catabolism of milk protein in cheese is one way how the microorganisms influence the sensorial characteristics of the final product. In this investigation, we paid attention to four genes [prtP (cell-envelope proteinase gene), pepX (X-prolyl dipeptidyl aminopeptidase gene), pepN (aminopeptidase gene) and bcaT (branched chain aminotransferase gene)] responsible for the production of volatile aroma-active compounds from milk proteins by lactic acid bacteria (LAB). We studied the dynamics of these genes and their corresponding LAB host, during the maturation of a raw ewes' milk-based cheese, using metagenomics and metatranscriptomics approaches. The transcriptome-oriented experiments included the analysis of total RNA (at three stages of cheese maturation) and also the construction of specific cDNA sub-libraries of the abovementioned genes. The proteolytic transcriptome analysis was supported by following the transcription activity of 16S rRNA gene and by metagenomic investigation. The combination of the described methods permitted to screen the dynamics of targeted genes throughout the cheese production. Lactococci were the major players in the LAB group, but the analysis provided also information on the role and properties of members of the genus Lactobacillus, such as Lb. rhamnosus, Lb. helveticus, Lb. pentosus, Lb. curvatus, Lb. parabuchneri, Lb. plantarum, Lb. brevis, Lb. delbrueckii, Lb. paracasei, Lb. fermentum and Lb. heilongjiangensis, proteolysis-related genes of which were active during cheese ripening.

The microbiomes of a XVIII century mummy from the castle of Krásna Hôrka (Slovakia) and its surrounding environment.

This microbiological survey was performed to determine the conservation state of a mummy in the Slovak castle of Krásna Hôrka and its surrounding environment. Culture-dependent identification was coupled with biodegradation assays on keratin, gelatin and cellulose. Next Generation Sequencing (NGS) using Illumina platform was used for a deeper microbial investigation. Three environmental samples were collected: from the glass of the sarcophagus, from the air inside it, and from the air of the chapel where the mummy is located. Seven different samples were taken from mummy's surface: from the left ear, left-hand palm, left-hand nail, left instep, right hand, abdomen and mineral crystals embedded within the skin. Three internal organ samples, from the lung, pleura and stomach, were also included in this study. Together, the culture-dependent and culture-independent analyses revealed that the bacterial communities present had fewer taxa than the fungal ones. The mycobiome showed the largest variability and included Epicoccum nigrum, Penicillium spp., Alternaria spp., Aspergillus spp., Cladosporium spp. and Aureobasidium pullulans; many other Ascomycota and Basidiomycota genera were detected by NGS. The most interesting results came from the skin mineral crystals and the internal organs. The hydrolytic assays revealed those microorganisms which might be considered dangerous 'mummy pathogens'. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) blend mulches in soil burial respirometric tests.

The microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) (PLA/PHB) blend foils were investigated in 1 year long laboratory soil burial experiments. Different PLA/PHB foils were tested: (a) PLA/PHB original transparent foil, (b) PLA/PHB carbon black filled foil and (c) PLA/PHB black foil previously exposed for 90 days to sun light. The microbiome diversity of these three types of foil was compared with that identified from soil/perlite sample at the beginning of experiment and that developed on a cellulose mat. Culture-dependent and culture-independent (DGGE-cloning) approaches together with PLA, PHB and PLA/PHB degradation plate assays were employed. The cultivation strategy combined with degradation tests permitted the isolation and evaluation of several PLA/PHB blend degrading microorganisms such as members of the genera Bacillus, Paenibacillus, Streptomyces, Rhodococcus, Saccharothrix, Arthrobacter, Aureobasidium, Mortierella, Absidia, Actinomucor, Bjerkandera, Fusarium, Trichoderma and Penicillium. The DGGE-cloning investigation increased the information about the microbial communities occurring during bioplastic degradation detecting several bacterial and fungal taxa and some of them (members of the orders Anaerolineales, Selenomonadales, Thelephorales and of the genera Pseudogymnoascus and Pseudeurotium) were revealed here for the first time. This survey showed the microbiome colonizing PLA/PHB blend foils and permitted the isolation of several microorganisms able to degrade the tested polymeric blends.