Microbial Survival Research Articles

'Follow the Water': Microbial Water Acquisition in Desert Soils.

Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.

Biochar as functional amendment for antibiotic resistant microbial community survival during hen manure composting

The study aim was to reveal the mechanism of impact of two type biochar on composting of hen manure (HM) and wheat straw (WS). Biochar derived from coconut shell and bamboo used as additives to reduce antibiotic resistant bacteria (ARB) in HM compost. The results manifested that effect of biochar amendment was significant to reduce ARB in HM composting. Compared with control, the microbial activity and abundance were increased in both biochar applied treatment, and bacterial community was changed. Additionally, network analysis revealed that biochar amendment increased the quantity of microorganisms related to organic matter degrading. Among them, coconut shell biochar (CSB) played a pioneering role to mitigate ARB to better exert its effects. Structural correlation analysis showed that CSB reduce ARB mobility and promote organic matter degradation via improving beneficial bacterial community structure. Overall, composting with participation of biochar amendment stimulated antibiotic resistance bacterial dynamics. These results evidence practical value for scientific research and lay the foundation for agricultural promotion of composting.

Prediction of Pseudomonas spp. Population in Food Products and Culture Media Using Machine Learning-Based Regression Methods.

Machine learning approaches are alternative modelling techniques to traditional modelling equations used in predictive food microbiology and utilise algorithms to analyse large datasets that contain information about microbial growth or survival in various food matrices. These approaches leverage the power of algorithms to extract insights from the data and make predictions regarding the behaviour of microorganisms in different food environments. The objective of this study was to apply various machine learning-based regression methods, including support vector regression (SVR), Gaussian process regression (GPR), decision tree regression (DTR), and random forest regression (RFR), to estimate bacterial populations. In order to achieve this, a total of 5618 data points for Pseudomonas spp. present in food products (beef, pork, and poultry) and culture media were gathered from the ComBase database. The machine learning algorithms were applied to predict the growth or survival behaviour of Pseudomonas spp. in food products and culture media by considering predictor variables such as temperature, salt concentration, water activity, and acidity. The suitability of the algorithms was assessed using statistical measures such as coefficient of determination (R2), root mean square error (RMSE), bias factor (Bf), and accuracy (Af). Each of the regression algorithms showed appropriate estimation capabilities with R2 ranging from 0.886 to 0.913, RMSE from 0.724 to 0.899, Bf from 1.012 to 1.020, and Af from 1.086 to 1.101 for each food product and culture medium. Since the predictive capability of RFR was the best among the algorithms, externally collected data from the literature were used for RFR. The external validation process showed statistical indices of Bf ranging from 0.951 to 1.040 and Af ranging from 1.091 to 1.130, indicating that RFR can be used for predicting the survival and growth of microorganisms in food products. Therefore, machine learning approaches can be considered as an alternative to conventional modelling methods in predictive microbiology. However, it is important to highlight that the prediction power of the machine learning regression method directly depends on the dataset size, and it requires a large dataset to be employed for modelling. Therefore, the modelling work of this study can only be used for the prediction of Pseudomonas spp. in specific food products (beef, pork, and poultry) and culture medium with certain conditions where a large dataset is available.

Performance of atrazine adsorption behavior and microbial community structure in Mollisol aggregate fraction

Owing to complex pore systems and chemical substances, soil aggregates provide a spatially heterogeneous microenvironment for adsorption capacity and microbial survival. As the widely used pesticide in farmlands, atrazine environmental behavior is not well known at the aggregate scale. In this study, Mollisol soil samples were sieved into four aggregate-size classes: large macroaggregates (>2 mm, LMa), small macroaggregates (1–2 mm, SMa), microaggregates (0.25–1 mm, Mia) and primary particles (<0.25 mm, P). The pore characteristics of each aggregate fraction was visualized by non-invasive X-ray three-dimensional microscopic computed tomography (3D-CT) combined with pore network extraction. The adsorption kinetics of atrazine in each aggregate-size fraction can be described well by a pseudo-second-order kinetic model. The adsorption isothermal process of atrazine can be better fitted by the Langmuir isotherm model than Freundlich isotherm model. There was an obvious linear correlation between the maximum atrazine adsorption capacity and aggregate SOC content as well as TN. In addition, the abundance of bacteria, actinomycetes and anaerobic bacteria in P was totally higher than those in SMa and Mia. Although pH is strongly linked to the bacterial community in the aggregate fraction, aggregate particle size explained 18 % for shaping the microbial community. Therefore, chemical properties and pore characteristics of each soil aggregate fraction both contributed to performance of atrazine adsorption behavior and microbial community.

Antimicrobial and Antioxidant Edible Films and Coatings in the Shelf-Life Improvement of Chicken Meat.

Meat deterioration during processing, distribution, and display can compromise the quality and safety of products, causing several undesirable changes and decreasing products' shelf-life, which has a negative impact on the industry and consumers. In recent years, studies have been carried out using decontamination techniques and new packaging methodologies to overcome deterioration problems, increase sustainability, and reduce waste. Edible films and coatings obtained from biopolymers such as polysaccharides, proteins, and lipids, combined with active compounds, can be an alternative approach. This article focused on recent studies that used alternative biodegradable polymeric matrices in conjunction with natural compounds with antioxidant/antimicrobial activity on chicken meat. Its impact on physicochemical, microbiological, and sensory characteristics was evident, as well as the effect on its shelf-life. In general, different combinations of active edible films or coatings had a positive effect on the chicken meat. Different studies reported that the main results were a decrease in microbial growth and pathogen survival, a slowdown in lipid oxidation evolution, and an improvement in sensory quality and shelf-life (an increase from 4 to 12 days).

Influence of compression kinetics during tableting of fluidized bed-granulated microorganisms on microbiological and physical-mechanical tablet properties

As tablets are convenient to administer to patients, ensure safe dosing and allow cost-effective production on a large scale, they are the favored dosage form for numerous active pharmaceutical ingredients but also for the administration of viable probiotic microorganisms. Granules with viable yeast cells (Saccharomyces cerevisiae) formed by fluidized bed granulation with dicalcium phosphate (DCP), lactose (LAC) or microcrystalline cellulose (MCC) as carrier materials were tableted using a compaction simulator. Besides the compression stress, the compression speed was systematically studied by varying consolidation time and dwell time. The microbial survival as well as physical properties of the tablets, e.g., porosity and tensile strength, were determined. Higher compression stresses result in lower porosities. While on the one hand this has a detrimental effect on microbial survival (due to increased pressure and shear stress during particle rearrangement / densification), on the other hand it results in higher tensile strengths. At the same compression stress, a prolonged dwell time resulted in lower porosity and thus in lower survival rates but higher tensile strength. Against that, consolidation time showed no significant influence on the considered tablet quality attributes. Since changes of the tensile strength related survival rate were negligible (due to opposite but balancing dependence on porosity), high production speeds could be used for tableting of these granules without additional loss of viability, as long as tablets with the same tensile strength are produced.

Adaptive mechanisms of Bacillus to near space extreme environments

Earth's near space is an extreme atmosphere environment with high levels of radiation, low atmospheric pressure and dramatic temperature fluctuations. The region is above the flight altitude of aircraft but below the orbit of satellites, which has special and Mars-like conditions for investigating the survival and evolution of life. Technical limitations including flight devices, payloads and technologies/methodologies hinder microbiological research in near space. In this study, we investigated microbial survival and adaptive strategies in near space using a scientific balloon fight mission and multi-omics analyses. Methods for sample preparation, storage, protector and vessel were optimized to prepare the exposed microbial samples. After 3 h 17 min of exposure at a float altitude of ~32 km, only Bacillus strains were alive with survival efficiencies of 0–10−6. Diverse mutants with significantly altered metabolites were generated, firstly proving that Earth's near space could be used as a new powerful microbial breeding platform. Multi-omics analyses of mutants revealed cascade changes at the genome, transcriptome and proteome levels. In response to environmental stresses, two mutants had similar proteome changes caused by different genomic mutations and mRNA expression levels. Metabolic network analysis combined with proteins' expression levels revealed that metabolic fluxes of EMP, PPP and purine synthesis-related pathways were significantly altered to increase/decrease inosine production. Further analysis showed that proteins related to translation, molecular chaperones, cell wall/membrane, sporulation, DNA replication/repair and anti-oxidation were significantly upregulated, enabling cells to efficiently repair DNA/protein damages and improve viability against environmental stress. Overall, these results revealed genetic and metabolic responses of Bacillus to the harsh conditions in near space, providing a research basis for bacterial adaptive mechanisms in extreme environments.

Tableting of fluidized bed granules containing living microorganisms

Tablets are the favored dosage form for numerous active pharmaceutical ingredients, among others because they are easy to take, ensure safe dosing and allow cost-effective production on a large scale. This dosage form is also frequently chosen for the administration of viable probiotic microorganisms. Saccharomyces cerevisiae cells granulated in a fluidized bed process, with dicalcium phosphate (DCP), lactose (LAC) and microcrystalline cellulose (MCC) as carrier materials, were tableted using a compaction simulator, varying the compression stress. The tablets were analyzed regarding physical properties, e.g., porosity and tensile strength, as well as microbial survival. Carrier material and compression stress showed a significant influence on survival rate and physical tablet properties. The dependencies were related to material specific deformation characteristics and linked to mechanistic approaches to explain the different sensitivities.

Stay or Go: Sulfolobales Biofilm Dispersal Is Dependent on a Bifunctional VapB Antitoxin.

A type II VapB14 antitoxin regulates biofilm dispersal in the archaeal thermoacidophile Sulfolobus acidocaldarius through traditional toxin neutralization but also through noncanonical transcriptional regulation. Type II VapC toxins are ribonucleases that are neutralized by their proteinaceous cognate type II VapB antitoxin. VapB antitoxins have a flexible tail at their C terminus that covers the toxin's active site, neutralizing its activity. VapB antitoxins also have a DNA-binding domain at their N terminus that allows them to autorepress not only their own promoters but also distal targets. VapB14 antitoxin gene deletion in S. acidocaldarius stunted biofilm and planktonic growth and increased motility structures (archaella). Conversely, planktonic cells were devoid of archaella in the ΔvapC14 cognate toxin mutant. VapB14 is highly conserved at both the nucleotide and amino acid levels across the Sulfolobales, extremely unusual for type II antitoxins, which are typically acquired through horizontal gene transfer. Furthermore, homologs of VapB14 are found across the Crenarchaeota, in some Euryarchaeota, and even bacteria. S. acidocaldarius vapB14 and its homolog in the thermoacidophile Metallosphaera sedula (Msed_0871) were both upregulated in biofilm cells, supporting the role of the antitoxin in biofilm regulation. In several Sulfolobales species, including M. sedula, homologs of vapB14 and vapC14 are not colocalized. Strikingly, Sulfuracidifex tepidarius has an unpaired VapB14 homolog and lacks a cognate VapC14, illustrating the toxin-independent conservation of the VapB14 antitoxin. The findings here suggest that a stand-alone VapB-type antitoxin was the product of selective evolutionary pressure to influence biofilm formation in these archaea, a vital microbial community behavior. IMPORTANCE Biofilms allow microbes to resist a multitude of stresses and stay proximate to vital nutrients. The mechanisms of entering and leaving a biofilm are highly regulated to ensure microbial survival, but are not yet well described in archaea. Here, a VapBC type II toxin-antitoxin system in the thermoacidophilic archaeon Sulfolobus acidocaldarius was shown to control biofilm dispersal through a multifaceted regulation of the archaeal motility structure, the archaellum. The VapC14 toxin degrades an RNA that causes an increase in archaella and swimming. The VapB14 antitoxin decreases archaella and biofilm dispersal by binding the VapC14 toxin and neutralizing its activity, while also repressing the archaellum genes. VapB14-like antitoxins are highly conserved across the Sulfolobales and respond similarly to biofilm growth. In fact, VapB14-like antitoxins are also found in other archaea, and even in bacteria, indicating an evolutionary pressure to maintain this protein and its role in biofilm formation.

Fruit and vegetable snacks as carriers of probiotics and bioactive compounds: a review

SummaryVegetable and fruit snacks emerge as an innovative non‐dairy functional food of probiotic carriers and a valuable alternative to consumers with dietary restrictions. However, enriching snacks with probiotics is challenging as several factors may affect cell viability making it difficult to maintain adequate microbial doses at consumption time. This article aimed to review the most recent advances in the design of probiotic fruit and vegetable snacks to provide the current state of knowledge on this cutting‐edge topic. In particular, the technologies applied to introduce probiotics into the food matrix, classical and novel drying methods, and strategies to improve microbial survival during processing, storage and gastrointestinal passage, are discussed. Most of the published works report bacterial counts above 7 log cfu g−1 in snacks, which is a proper dose of probiotics to promote health benefits. However, many of these studies did not evaluate the survival rate during storage or considered short periods. The design of fruit‐ or vegetable‐based snacks enriched with probiotics appears to be a worthwhile strategy at laboratory scale but further studies to validate results both at pilot and industrial scale are necessary.

Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils.

Stable soil organic carbon (SOC) formation in coastal saline soils is important to improve arable land quality and mitigate greenhouse gas emissions. However, how microbial life-history strategies and metabolic traits regulate SOC turnover in coastal saline soils remains unknown. Here, we investigated the effects of microbial life history strategy tradeoffs on microbial carbon use efficiency (CUE) and microbial-derived SOC formation using metagenomic sequencing technology in different salinity soils. The results showed that high-salinity is detrimental to microbial CUE and microbial-derived SOC formation. Moreover, the regulation of nutrients stoichiometry could not mitigate adverse effects of salt stress on microbial CUE, which indicated that microbial-derived SOC formation is independent of stoichiometry in high-salinity soil. Low-salinity soil is dominated by a high growth yield (Y) strategy, such as higher microbial biomass carbon and metabolic traits which are related to amino acid metabolism, carbohydrate metabolism, and cell processes. However, high-salinity soil is dominated by stress tolerance (S) (e.g., higher metabolic functions of homologous recombination, base excision repair, biofilm formation, extracellular polysaccharide biosynthesis, and osmolytes production) and resource acquisition (A) strategies (e.g., higher alkaline phosphatase activity, transporters, and flagellar assembly). These trade-offs of strategies implied that resource reallocation took place. The high-salinity soil microbes diverted investments away from growth yield to microbial survival and resource capture, thereby decreasing biomass turnover efficiency and impeding microbial-derived SOC formation. Moreover, altering the stoichiometry in low-salinity soil caused more investment in the A-strategy, such as the production of more β-glucosidase and β-N-acetyl-glucosaminidase, and increasing bacterial chemotaxis, which thereby reduced microbial-derived SOC formation. Our research reveals that shift the microbial community from S- and A- strategies to the Y-strategy is important to increase the microbial CUE, and thus enhance SOC turnover in coastal saline soils.

Microbial Protocols for Spacecraft: 3. Spore Monolayer Preparation Methods for Ultraviolet Irradiation Exposures.

Developing robust microbial survival models for interplanetary and planetary spacecraft requires precise inactivation kinetics for vehicle bioburdens. To generate such data, reliable protocols are required for preparing, testing, and assaying microbial cells or spores on simulated spacecraft materials. New data are presented on the utility of the liquid droplet protocol for applying Bacillus subtilis spores to aluminum coupons. Results indicate that low-density spore monolayers should be created between 2 and 5 × 106 spores per cm2 on individual coupons to prevent the formation of aggregates or multilayers of spores. Such aggregation or multilayers will interfere with the precision of characterizing the effects of UV irradiation on spore survival. Optimum spore monolayers are defined as spore monolayers without overlapping or clustered cells and in which all spores will receive UV photons during assays. The best spore monolayers were created with sterile deionized water (SDIW) on uncoated aluminum coupons, or with SDIW + Triton X-100 (at 0.5 × of the critical micellar concentration) on either uncoated Al-coupons or on Chemfilm Class 1A-coated coupons. The Triton X-100 surfactant improved the uniformity of the monolayers without affecting the sensitivity of the spores to UV irradiation. Furthermore, spore layers created at either 2 × 107 or 2 × 108 spores/cm2 created multi-stacking effects that clearly reduced the precision of the UV irradiation assays. A set of standardized protocols is suggested for spacecraft processing and planetary protection communities to permit directly comparing results from divergent labs.

Using simulated wildland fire to assess microbial survival at multiple depths from biocrust and bare soils.

Surface soil microbial communities are directly exposed to the heat from wildland fires. Due to this, the microbial community composition may be stratified within the soil profile with more heat tolerant microbes near the surface and less heat tolerant microbes, or mobile species found deeper in the soil. Biological soil crusts, biocrusts, are found on the soil surface and contain a diverse microbial community that is directly exposed to the heat from wildland fires. Here, we used a simulated fire mesocosm along with a culture-based approach and molecular characterization of microbial isolates to understand the stratification of biocrust and bare soil microbes after low severity (450°C) and high severity (600°C) fires. We cultured and sequenced microbial isolates from 2 to 6 cm depth from both fire types. The isolates were stratified along the soil depth. Green algal isolates were less thermotolerant and found in the deeper depths (4-6 cm) and the control soils, while several cyanobacteria in Oscillatoriales, Synechococcales, and Nostocales were found at 2-3 cm depth for both fire temperatures. An Alphaproteobacteria isolate was common across several depths, both fire types, and both fire temperatures. Furthermore, we used RNA sequencing at three depths after the high severity fire and one control to determine what microbial community is active following a fire. The community was dominated by Gammaproteobacteria, however some Cyanobacteria ASVs were also present. Here we show evidence of stratification of soil and biocrust microbes after a fire and provide evidence that these microbes are able to survive the heat from the fire by living just below the soil surface. This is a steppingstone for future work on the mechanisms of microbial survival after fire and the role of soil insulation in creating resilient communities.

Fresh Produce as a Potential Vector and Reservoir for Human Bacterial Pathogens: Revealing the Ambiguity of Interaction and Transmission.

The consumer demand for fresh produce (vegetables and fruits) has considerably increased since the 1980s for more nutritious foods and healthier life practices, particularly in developed countries. Currently, several foodborne outbreaks have been linked to fresh produce. The global rise in fresh produce associated with human infections may be due to the use of wastewater or any contaminated water for the cultivation of fruits and vegetables, the firm attachment of the foodborne pathogens on the plant surface, and the internalization of these agents deep inside the tissue of the plant, poor disinfection practices and human consumption of raw fresh produce. Several investigations have been established related to the human microbial pathogens (HMPs) interaction, their internalization, and survival on/within plant tissue. Previous studies have displayed that HMPs are comprised of several cellular constituents to attach and adapt to the plant's intracellular niches. In addition, there are several plant-associated factors, such as surface morphology, nutrient content, and plant-HMP interactions, that determine the internalization and subsequent transmission to humans. Based on documented findings, the internalized HMPs are not susceptible to sanitation or decontaminants applied on the surface of the fresh produce. Therefore, the contamination of fresh produce by HMPs could pose significant food safety hazards. This review provides a comprehensive overview of the interaction between fresh produce and HMPs and reveals the ambiguity of interaction and transmission of the agents to humans.

Functional and structural diversification of incomplete phosphotransferase system in cellulose-degrading clostridia.

Carbohydrate utilization is critical to microbial survival. The phosphotransferase system (PTS) is a well-documented microbial system with a prominent role in carbohydrate metabolism, which can transport carbohydrates through forming a phosphorylation cascade and regulate metabolism by protein phosphorylation or interactions in model strains. However, those PTS-mediated regulated mechanisms have been underexplored in non-model prokaryotes. Here, we performed massive genome mining for PTS components in nearly 15,000 prokaryotic genomes from 4,293 species and revealed a high prevalence of incomplete PTSs in prokaryotes with no association to microbial phylogeny. Among these incomplete PTS carriers, a group of lignocellulose degrading clostridia was identified to have lost PTS sugar transporters and carry a substitution of the conserved histidine residue in the core PTS component, HPr (histidine-phosphorylatable phosphocarrier). Ruminiclostridium cellulolyticum was then selected as a representative to interrogate the function of incomplete PTS components in carbohydrate metabolism. Inactivation of the HPr homolog reduced rather than increased carbohydrate utilization as previously indicated. In addition to regulating distinct transcriptional profiles, PTS associated CcpA (Catabolite Control Protein A) homologs diverged from previously described CcpA with varied metabolic relevance and distinct DNA binding motifs. Furthermore, the DNA binding of CcpA homologs is independent of HPr homolog, which is determined by structural changes at the interface of CcpA homologs, rather than in HPr homolog. These data concordantly support functional and structural diversification of PTS components in metabolic regulation and bring novel understanding of regulatory mechanisms of incomplete PTSs in cellulose-degrading clostridia.

Zinc-Based Nanoparticles Reduce Bacterial Biofilm Formation.

Biofilm formation is important for microbial survival in hostile environments and a phenotype that provides microorganisms with antimicrobial resistance. Zinc oxide (ZnO) and Zinc sulfide (ZnS) nanoparticles (NPs) present potential antimicrobial properties for biomedical and food industry applications. Here, we aimed to analyze, for the first time, the bactericidal and antibiofilm activity of ZnS NPs against Staphylococcus aureus, Klebsiella oxytoca, and Pseudomonas aeruginosa, all medically important bacteria in developed countries. We compared ZnS NPs antimicrobial activity to ZnO NPs, which have been extensively studied. Using the colorimetric XTT reduction assay to observe the metabolic activity of bacterial cells and the crystal violet assay to measure biofilm mass, we demonstrated that ZnS and ZnO had similar efficacy in killing planktonic bacterial cells and reducing biofilm formation, with S. aureus being more susceptible to both therapeutics than K. oxytoca and P. aeruginosa. Crystal violet staining and confocal microscopy validated that Zn NPs inhibit biofilm formation and cause architectural damage. Our findings provide proof of principle that ZnS NPs have antibiofilm activity, and can be potentially used in medical and food industry applications, such as treatment of wound infections or package coating for food preservation. IMPORTANCE Zinc (Zn)-based nanoparticles (NPs) can be potentially used in medical and food preservation applications. As proof of principle, we investigated the bactericidal and antibiofilm activity of zinc oxide (ZnO) and zinc sulfide (ZnS) NPs against medically important bacteria. Zn-based NPs were similarly effective in killing planktonic and biofilm-associated Staphylococcus aureus, Klebsiella oxytoca, and Pseudomonas aeruginosa cells. However, S. aureus was more susceptible to these investigational therapeutics. Although further studies are warranted, our findings suggest the possibility of future use of Zn-based NPs in the treatment of skin infections or preservation of food.

Scientific novelty beyond the experiment.

Practical experiments drive important scientific discoveries in biology, but theory-based research studies also contribute novel-sometimes paradigm-changing-findings. Here, we appraise the roles of theory-based approaches focusing on the experiment-dominated wet-biology research areas of microbial growth and survival, cell physiology, host-pathogen interactions, and competitive or symbiotic interactions. Additional examples relate to analyses of genome-sequence data, climate change and planetary health, habitability, and astrobiology. We assess the importance of thought at each step of the research process; the roles of natural philosophy, and inconsistencies in logic and language, as drivers of scientific progress; the value of thought experiments; the use and limitations of artificial intelligence technologies, including their potential for interdisciplinary and transdisciplinary research; and other instances when theory is the most-direct and most-scientifically robust route to scientific novelty including the development of techniques for practical experimentation or fieldwork. We highlight the intrinsic need for human engagement in scientific innovation, an issue pertinent to the ongoing controversy over papers authored using/authored by artificial intelligence (such as the large language model/chatbot ChatGPT). Other issues discussed are the way in which aspects of language can bias thinking towards the spatial rather than the temporal (and how this biased thinking can lead to skewed scientific terminology); receptivity to research that is non-mainstream; and the importance of theory-based science in education and epistemology. Whereas we briefly highlight classic works (those by Oakes Ames, Francis H.C. Crick and James D. Watson, Charles R. Darwin, Albert Einstein, James E. Lovelock, Lynn Margulis, Gilbert Ryle, Erwin R.J.A. Schrödinger, Alan M. Turing, and others), the focus is on microbiology studies that are more-recent, discussing these in the context of the scientific process and the types of scientific novelty that they represent. These include several studies carried out during the 2020 to 2022 lockdowns of the COVID-19 pandemic when access to research laboratories was disallowed (or limited). We interviewed the authors of some of the featured microbiology-related papers and-although we ourselves are involved in laboratory experiments and practical fieldwork-also drew from our own research experiences showing that such studies can not only produce new scientific findings but can also transcend barriers between disciplines, act counter to scientific reductionism, integrate biological data across different timescales and levels of complexity, and circumvent constraints imposed by practical techniques. In relation to urgent research needs, we believe that climate change and other global challenges may require approaches beyond the experiment.

Biocompatible Ti3Au–Ag/Cu thin film coatings with enhanced mechanical and antimicrobial functionality

BackgroundBiofilm formation on medical device surfaces is a persistent problem that shelters bacteria and encourages infections and implant rejection. One promising approach to tackle this problem is to coat the medical device with an antimicrobial material. In this work, for the first time, we impart antimicrobial functionality to Ti3Au intermetallic alloy thin film coatings, while maintaining their superior mechanical hardness and biocompatibility.MethodsA mosaic Ti sputtering target is developed to dope controlled amounts of antimicrobial elements of Ag and Cu into a Ti3Au coating matrix by precise control of individual target power levels. The resulting Ti3Au-Ag/Cu thin film coatings are then systematically characterised for their structural, chemical, morphological, mechanical, corrosion, biocompatibility-cytotoxicity and antimicrobial properties.ResultsX-ray diffraction patterns reveal the formation of a super hard β-Ti3Au phase, but the thin films undergo a transition in crystal orientation from (200) to (211) with increasing Ag concentration, whereas introduction of Cu brings no observable changes in crystal orientation. Scanning and transmission electron microscopy analysis show the polyhedral shape of the Ti3Au crystal but agglomeration of Ag particles between crystal grains begins at 1.2 at% Ag and develops into large granules with increasing Ag concentration up to 4.1 at%. The smallest doping concentration of 0.2 at% Ag raises the hardness of the thin film to 14.7 GPa, a 360% improvement compared to the ∼4 GPa hardness of the standard Ti6Al4V base alloy. On the other hand, addition of Cu brings a 315—330% improvement in mechanical hardness of films throughout the entire concentration range of 0.5—7.1 at%. The thin films also show good electrochemical corrosion resistance and a > tenfold reduction in wear rate compared to Ti6Al4V alloy. All thin film samples exhibit very safe cytotoxic profiles towards L929 mouse fibroblast cells when analysed with Alamar blue assay, with ion leaching concentrations lower than 0.2 ppm for Ag and 0.08 ppm for Cu and conductivity tests reveal the positive effect of increased conductivity on myogenic differentiation. Antimicrobial tests show a drastic reduction in microbial survival over a short test period of < 20 min for Ti3Au films doped with Ag or Cu concentrations as low as 0.2—0.5 at%.ConclusionTherefore, according to these results, this work presents a new antimicrobial Ti3Au-Ag/Cu coating material with excellent mechanical performance with the potential to develop wear resistant medical implant devices with resistance to biofilm formation and bacterial infection.Graphical

The Attenuation of Microbial Reduction in Blueberry Fruit Following UV-LED Treatment

Ultraviolet-C (UV-C) irradiation is a well-recognized technology for improving blueberry postharvest quality, and previous literature indicates that it has the potential for dual-use as an antimicrobial intervention for this industry. However, the practicality and feasibility of deploying this technology in fresh blueberry fruit are significantly hindered by the shadowing effect occurring at the blossom-end scar of the fruit. The purpose of this study was to determine if treating the blueberry fruit within a chamber fitted with UV-Light Emitting Diodes (LEDs) emitting a peak UV-C at 275 nm could minimize this shadowing and result in improved treatment efficacy. Ten blueberry fruits were dip-inoculated with E. coli at a concentration of 105 CFU/mL and irradiated within the system at doses of 0, 1.617, 3.234, 9.702, and 16.17 mJ/cm2 (0, 30, 60, 180, and 300 s). Statistical analysis was performed to characterize the extent of microbial survival as well as the UV-C inactivation kinetics. A maximum of 0.91–0.95 log reduction was observed, which attenuated after 60 s of treatment. The microbial inactivation and survival were thus modeled using the Geeraerd-tail model in Microsoft Excel with the GInaFIt add-in (RMSE = 0.2862). Temperatures fluctuated between 23 ± 0.5°C and 39.5°C ± 0.5°C during treatment but did not statistically impact the treatment efficacy (P = 0.0823). The data indicate that the design of a UV-LED system may improve the antimicrobial efficacy of UV-C technology for the surface decontamination of irregularly shaped fruits, and that further optimization could facilitate its use in the industry.

Fiber-based food packaging materials in view of bacterial growth and survival capacities.

Understanding interactions of bacteria with fiber-based packaging materials is fundamental for appropriate food packaging. We propose a laboratory model to evaluate microbial growth and survival in liquid media solely consisting of packaging materials with different fiber types. We evaluated food contaminating species (Escherichia coli, Staphylococcus aureus, Bacillus cereus), two packaging material isolates and bacterial endospores for their growth abilities. Growth capacities differed substantially between the samples as well as between bacterial strains. Growth and survival were strongest for the packaging material entirely made of recycled fibers (secondary food packaging) with up to 10.8 log10 CFU/ml for the packaging isolates. Among the food contaminating species, B. cereus and E. coli could grow in the sample of entirely recycled fibers with maxima of 6.1 log10 and 8.6 log10 CFU/mL, respectively. Escherichia coli was the only species that was able to grow in bleached fresh fibers up to 7.0 log10 CFU/mL. Staphylococcus aureus perished in all samples and was undetectable after 1-6 days after inoculation, depending on the sample. The packaging material strains were isolated from recycled fibers and could grow only in samples containing recycled fibers, indicating an adaption to this environment. Spores germinated only in the completely recycled sample. Additionally, microbial digestion of cellulose and xylan might not be a crucial factor for growth. This is the first study describing bacterial growth in food packaging materials itself and proposing functionalization strategies toward active food packaging through pH-lowering.