Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater

The Materials Corrosion Test (MaCoTe) at the Underground Research Laboratory in Grimsel, Switzerland, assesses the microbiology and corrosion behavior of engineered barrier components of a deep geological repository (DGR) for long-term disposal of high-level nuclear waste. Diversity and temporal changes of bentonite-associated microbial community profiles were assessed under DGR-like conditions for compacted Wyoming MX-80 bentonite (1.25 g/cm3 and 1.50 g/cm3 targeted dry densities) exposed to natural groundwater. Using culture-dependent and molecular techniques, samples taken from the outside layer of 5-year borehole modules revealed up to 66% and 23% of 16S rRNA gene sequences affiliated with Desulfosporosinus and Desulfovibrio, respectively. Putatively involved in sulfate reduction, these taxa were almost undetectable within the bentonite core. Instead, microbial profiles of the inner bentonite core were similar to uncompacted bentonite used to pack modules years earlier, and were consistent with a previously published 1-year time point, revealing no detectable microbial growth. Abundances of culturable aerobic and anaerobic heterotrophic bacteria in the uncompacted bentonite were relatively low, with less than 1,000 and 100 colony-forming units (CFUs) per gram dry weight, respectively. Nearly 5 years after emplacement, culturable heterotrophic bacterial CFUs and sulfate-reducing bacteria did not change significantly inside the bentonite core. Phospholipid fatty acid data indicated similar lipid abundance, and corresponding cell abundance estimates, for inner 5-year MaCoTe bentonite samples compared to those previously obtained for 1-year incubations. Collectively, our results provide complementary evidence for microbial stability inside highly compacted bentonite exposed to conditions that mimic engineered barrier components of a deep geological repository. IMPORTANCE The long-term safety of a deep geological repository for used nuclear fuel is dependent on the performance of the engineered and natural barriers. Microbial activity can produce chemical species that can influence the corrosion of the disposal containers for used nuclear fuel. Although previous studies have evaluated the microbiology of compacted bentonite clay within subsurface environments, these have been limited to relatively short incubations (i.e., 1 year). The current study provides a unique 5-year perspective that reinforces previous findings of growth inhibition for bentonite clay exposed to in situ subsurface conditions.

Dielectrophoresis microbial characterization and isolation of Staphylococcus aureus based on optimum crossover frequency

Characterization of antibiotic-resistant bacteria is a significant concern that persists for the rapid classification and analysis of the bacteria. A technology that utilizes the manipulation of antibiotic-resistant bacteria is key to solving the significant threat of these pathogenic bacteria by rapid characterization profile. Dielectrophoresis (DEP) can differentiate between antibiotic-resistant and susceptible bacteria based on their physical structure and polarization properties. In this work, the DEP response of two Gram-positive bacteria, namely, Methicillin-resistant Staphylococcus aureus (MRSA) and Methicillin-susceptible S. aureus (MSSA), was investigated and simulated. The DEP characterization was experimentally observed on the bacteria influenced by oxacillin and vancomycin antibiotics. MSSA control without antibiotics has crossover frequencies (f x 0 ${f_{x0}}$ ) from 6 to 8 MHz, whereas MRSA control is from 2 to 3 MHz. Thef x 0 ${f_{x0}}$ changed when bacteria were exposed to the antibiotic. As for MSSA, thef x 0 ${f_{x0}}$ decreased to 3.35 MHz compared tof x 0 ${f_{x0}}$ MSSA control without antibiotics, MRSA,f x 0 ${f_{x0}}$ increased to 7 MHz when compared to MRSA control. The changes in the DEP response of MSSA and MRSA with and without antibiotics were theoretically proven using MyDEP and COMSOL simulation and experimentally based on the modification to the bacteria cell walls. Thus, the DEP response can be employed as a label-free detectable method to sense and differentiate between resistant and susceptible strains with different antibiotic profiles. The developed method can be implemented on a single platform to analyze and identify bacteria for rapid, scalable, and accurate characterization.

Advances in characterization of probiotics and challenges in industrial application

An unbalanced diet and poor lifestyle are common reasons for numerous health complications in humans. Probiotics are known to provide substantial benefits to human health by producing several bioactive compounds, vitamins, short-chain fatty acids and short peptides. Diets that contain probiotics are limited to curd, yoghurt, kefir, kimchi, etc. However, exploring the identification of more potential probiotics and enhancing their commercial application to improve the nutritional quality would be a significant step to utilizing the maximum benefits. The complex evolution patterns among the probiotics are the hurdles in their characterization and adequate application in the industries and dairy products. This article has mainly discussed the molecular methods of characterization that are based on the analysis of ribosomal RNA, whole genome, and protein markers and profiles. It also has critically emphasized the emerging challenges in industrial applications of probiotics.

Characterization of a Bacillus cereus strain associated with a large feed-related outbreak of severe infection in pigs

Aims

Bacillus cereus is often responsible for foodborne diseases and both local and systemic infections in humans. Cases of infection in other mammals are rather rare. In this study, we report a B. cereus feed‐related outbreak that caused the death of 6234 pigs in Italy.

Methods and Results

Massive doses of a Gram‐positive, spore‐forming bacterium were recovered from the animal feed, faeces of survived pigs and intestinal content of dead ones. The B. cereus MM1 strain was identified by MALDI‐TOF MS and typified by RAPD‐PCR. The isolate was tested for the production of PC‐PLC, proteases, hemolysins and biofilm, for motility, as well as for the presence of genes encoding tissue‐degrading enzymes and toxins. Antimicrobial resistance and pathogenicity in Galleria mellonella larvae were also investigated. Our results show that the isolated B. cereus strain is swimming‐proficient, produces PC‐PLC, proteases, hemolysins, biofilm and carries many virulence genes. The strain shows high pathogenicity in G. mellonella larvae.

Conclusions

The isolated B. cereus strain demonstrates an aggressive profile of pathogenicity and virulence, being able to produce a wide range of determinants potentially hazardous to pigs' health.

Significance and Impact of Study

This study highlights the proficiency of B. cereus to behave as a devastating pathogen in swine if ingested at high doses and underlines that more stringent quality controls are needed for livestock feeds and supplements.

Functional Characterization of khadi Yeasts Isolates for Selection of Starter Cultures

Yeasts play an important role in spontaneous fermentation of traditional alcoholic beverages. Our previous study revealed that a mixed-consortia of both Saccharomyces and non-Saccharomyces yeasts were responsible for fermentation of khadi, a popular, non-standardized traditional beverage with an immense potential for commercialization in Botswana. Functional characterization of isolated fermenting yeasts from mixed consortia is an indispensable step towards the selection of potential starter cultures for commercialization of khadi. In this study, we report the characterization of 13 khadi isolates for the presence of brewing-relevant phenotypes such as their fermentative capacity, ability to utilize a range of carbon sources and their ability to withstand brewing-associated stresses, as a principal step towards selection of starter cultures. Khadi isolates such as Saccharomyces cerevisiae, Saccharomycodes ludwigii and Candida ethanolica showed good brewing credentials but Lachancea fermentati emerged as the isolate with the best brewing attributes with a potential as a starter culture. However, we were then prompted to investigate the potential of L. fermentati to influence the fruity aromatic flavor, characteristic of khadi. The aroma components of 18 khadi samples were extracted using headspace solid phase micro-extraction (HSSPME) and identified using a GC-MS. We detected esters as the majority of volatile compounds in khadi, typical of the aromatic signature of both khadi and L. fermentati associated fermentations. This work shows that L. fermentati has potential for commercial production of khadi.

Isolation and Characterization of Lactic Acid Bacteria and Yeasts from Typical Bulgarian Sourdoughs

Traditional sourdoughs in Bulgaria were almost extinct during the centralized food production system. However, a rapidly developing trend of sourdough revival in the country is setting the demand for increased production and use of commercial starter cultures. The selection of strains for such cultures is based on geographical specificity and beneficial technological properties. In this connection, the aim of this study was to isolate, identify and characterize lactic acid bacteria (LAB) and yeasts from typical Bulgarian sourdoughs for the selection of strains for commercial sourdough starter cultures. Twelve samples of typical Bulgarian sourdoughs were collected from different geographical locations. All samples were analyzed for pH, total titratable acidity and dry matter content. Enumeration of LAB and yeast was also carried out. Molecular identification by 16S rDNA sequence analysis was performed for 167 LAB isolates, and 106 yeast strains were identified by ITS1-5.8S-ITS2 rRNA gene partial sequence analysis. The LAB strains were characterized according to their amylolytic and proteolytic activity and acidification capacity, and 11 strains were selected for further testing of their antimicrobial properties. The strains with the most pronounced antibacterial and antifungal activity are listed as recommended candidates for the development of starter cultures for sourdoughs or other food products.

Short communication: High-throughput sequencing approach to investigate Italian artisanal cheese production

In this study, high-throughput sequencing (HTS) was used to investigate the microbiota of Robiola di Roccaverano production, an artisanal Protected Designation of Origin soft cheese made with raw goat milk by addition of a natural milk starter (NMS), from the Piedmont region of Italy. Different steps of production of Robiola di Roccaverano cheese at one artisanal dairy were monitored. Matched samples of milk, NMS, curd, and 5-d and 15-d matured cheeses were collected at different periods of the year. The DNA sequences obtained by HTS belonged to 5 phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Tenericutes. In milk, Proteobacteria and Firmicutes were mainly found, and several operational taxonomic units (OTU) belonging to contaminant bacteria such as Pseudomonas, Serratia, and Staphylococcus were observed. However, in NMS, curd, and 5- and 15-d cheeses, Firmicutes were principally observed where OTU of Lactococcus lactis were predominant, followed by Leuconostoc mesenteroides OTU. The results of the analysis showed high bacterial diversity in milk samples compared with NMS, curd, and 5- and 15-d cheeses, suggesting strong action of NMS in driving the characteristics of the final products.

Stability of Microbial Community Profiles Associated with Compacted Bentonite from the Grimsel Underground Research Laboratory

To assess the microbiology and corrosion potential of engineered components of a deep geological repository for long-term storage of high-level nuclear waste, the Materials Corrosion Test is being conducted at the Underground Research Laboratory in Grimsel, Switzerland. Modules containing metal coupons surrounded by highly compacted MX-80 bentonite, at two dry densities (1.25 and 1.50 g/cm3), were emplaced within 9-m-deep boreholes, and the first modules were retrieved after 13 months of exposure. Bentonite and associated module materials were sampled, and microbial communities and their distributions were assessed using 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) analysis. Borehole fluid was dominated by amplicon sequence variants (ASVs) affiliated with Desulfosporosinus and Desulfovibrio, which are putatively involved in sulfate reduction. The relative abundance of these ASVs was lower for samples from inside the borehole module, and they were almost undetectable in samples of the inner bentonite layer. The dominant ASV in case and filter sample sequence data was affiliated with Pseudomonas stutzeri, yet its relative abundance decreased in the inner layer samples. Streptomyces sp. ASVs were relatively abundant in all bentonite core sample data both prior to emplacement and after 13 months of exposure, presumably as metabolically inactive spores or extracellular "relic" DNA. PLFA concentrations in outer and inner layer bentonite samples suggested cellular abundances of 1 × 106 to 3 × 106 cells/g, with similar PLFA distributions within all bentonite samples. Our results demonstrate consistent microbial communities inside the saturated borehole module, providing the first evidence for microbial stability under conditions that mimic a deep geological repository.IMPORTANCE The Materials Corrosion Test in Grimsel Underground Research Laboratory, Switzerland, enables an evaluation of microbiological implications of bentonite clay at densities relevant for a deep geological repository. Our research demonstrates that after 13 months of exposure within a granitic host rock, the microbial 16S rRNA gene signatures of saturated bentonite clay within the modules were consistent with the profiles in the original clay used to pack the modules. Such results provide evidence that densities chosen for this emplacement test are refractory to microbial activity, at least on the relatively short time frame leading to the first time point sampling event, which will help inform in situ engineered barrier system science. This study has important implications for the design of deep geological repository sites under consideration for the Canadian Shield.