Cultivating efficiency: high-throughput growth analysis of anaerobic bacteria in compact microplate readers

Anaerobic microbes play crucial roles in environmental processes, industry, and human health. Traditional methods for monitoring the growth of anaerobes, including plate counts or subsampling broth cultures for optical density measurements, are time and resource-intensive. The advent of microplate readers revolutionized bacterial growth studies by enabling high-throughput and real-time monitoring of microbial growth kinetics. Yet, their use in anaerobic microbiology has remained limited. Here, we present a workflow for using small-footprint microplate readers and the Growthcurver R package to analyze the kinetic growth metrics of anaerobic bacteria. We benchmarked the small-footprint Cerillo Stratus microplate reader against a BioTek Synergy HTX microplate reader in aerobic conditions using Escherichia coli DSM 28618 cultures. The growth rates and carrying capacities obtained from the two readers were statistically indistinguishable. However, the area under the logistic curve was significantly higher in cultures monitored by the Stratus reader. We used the Stratus to quantify the growth responses of anaerobically grown E. coli and Clostridium bolteae DSM 29485 to different doses of the toxin sodium arsenite. The growth of E. coli and C. bolteae was sensitive to arsenite doses of 1.3 µM and 0.4 µM, respectively. Complete inhibition of growth was achieved at 38 µM arsenite for C. bolteae and 338 µM in E. coli. These results show that the Stratus performs similarly to a leading brand of microplate reader and can be reliably used in anaerobic conditions. We discuss the advantages of the small format microplate readers and our experiences with the Stratus.

IMPORTANCE

We present a workflow that facilitates the production and analysis of growth curves for anaerobic microbes using small-footprint microplate readers and an R script. This workflow is a cost and space-effective solution to most high-throughput solutions for collecting growth data from anaerobic microbes. This technology can be used for applications where high throughput would advance discovery, including microbial isolation, bioprospecting, co-culturing, host-microbe interactions, and drug/toxin-microbial interactions.

Effect of Plasma-Activated Water (PAW) on the Postharvest Quality of Shepherd's Purse (Capsella bursa-pastoris)

Plasma-activated water (PAW) treatment is an effective technique for the quality retention of fresh vegetables with cold atmospheric plasma using controllable parameters. This study investigated the effect of PAW on the postharvest quality of shepherd's purse (Capsella bursa-pastoris). The results displayed that PAW treatment with an activation time of 5, 10, 15, and 20 min reduced the yellowing rate and weight loss of the shepherd's purse during 9 days of storage. Compared with untreated samples, PAW treatment at different times reduced the number of total bacteria, coliform, yeast, and mold by 0.18-0.94, 0.59-0.97, 0.90-1.18, and 1.03-1.17 Log CFU/g after 9 days of storage, respectively. Additionally, the treatments with PAW-5 and PAW-10 better preserved ascorbic acid, chlorophyll, total phenol, and total flavonoid contents. They also maintained the higher antioxidant and CAT activity and inhibited the formation of terpenes, alcohols, and nitrogen oxide compounds of the shepherd's purse at the end of storage. The microstructural result illustrated that the cells of the shepherd's purse treated with PAW-5 and PAW-10 were relatively intact, with a small intercellular space after storage. This study demonstrated that PAW treatment effectively improved the postharvest quality of shepherd's purse.

"Energy and enthalpy" for microbial energetics in soil

Energy is the driver of all microbial processes in soil. The changes in Gibbs energy are equal to the enthalpy changes during all processes in soil because these processes are ongoing under constant pressure and volume-without work generation. The enthalpy change by transformation of individual organic compounds or of complex organic matter in soil can be exactly quantified by the nominal oxidation state of carbon changes. Consequently, microbial energy use efficiency can be assessed by the complete combustion enthalpy of organic compounds when microorganisms use O2 as the terminal electron acceptor for microbial processes under aerobic conditions.

Effect of beef long-storage under different temperatures and vacuum-packaging conditions on meat quality, oxidation processes and microbial growth

BACKGROUND

The global beef market demands the meat industry to ensure product quality and safety in markets that are often very distant. The present study aimed to evaluate the effects of chilled (CH, 120 d) and chilled-then-frozen (CHF, 28 d + 92 d) storage conditions of beef vacuum packaged (VP) and vacuum packaged with antimicrobial (VPAM) on meat quality, oxidative status and microbial loads. Treatments resulted from the combination of storage condition and packaging type: VP + CH, VP + CHF, VPAM + CH and VPAM + CHF.

RESULTS

Warner-Bratzler shear force values decreased in all treatments after 28 d of chilling. Except for VP + CH, L* values (lightness) of meat color did not differ in each treatment as the storage time increased. Meat from VP + CH had greater a* values than CHF treatments on day 120 of storage. A consumer panel did not detect differences in tenderness, flavor and overall liking between VP and VPAM beef, but they preferred CHF steaks rather than CH beef. TBARS values did not differ between VP and VPAM and between CH and CHF at any time during the storage period. At the end of storage time, all treatments except VP + CHF presented a greater concentration of thiols than at 48 h post-mortem. On day 120 of storage, VP + CH had greater catalase enzyme activity than CHF treatments while VP + CH and VP + CHF showed a greater superoxide dismutase activity than VPAM + CHF. Storage condition (CH or CHF) had a greater impact on microbial counts than the type of packaging.

CONCLUSION

Freezing meat after an ageing period represents a suitable strategy to extend beef storage life without a detrimental impact on its quality. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Limiting resources for soil microbial growth in climate change simulation treatments in the subarctic

The microbial use of resources to sustain life and reproduce influences for example, decomposition and plant nutrient provisioning. The study of "limiting factors" has shed light on the interaction between plants and their environment. Here, we investigated whether carbon (C), nitrogen (N), or phosphorus (P) was limiting for soil microorganisms in a subarctic tundra heath, and how changes in resource availability associated with climate change affected this. We studied samples in which changes in resource availability due to climate warming were simulated by the addition of birch litter and/or inorganic N. To these soils, we supplied factorial C (as glucose), N (as NH4 NO3 ), and P (as KH2 PO4 /K2 HPO4 ) additions ("limiting factor assays," LFA), to determine the limiting factors. The combination of C and P induced large growth responses in all soils and, combined with a systematic tendency for growth increases by C, this suggested that total microbial growth was primarily limited by C and secondarily by P. The C limitation was alleviated by the field litter treatment and strengthened by N fertilization. The microbial growth response to the LFA-C and LFA-P addition was strongest in the field-treatment that combined litter and N addition. We also found that bacteria were closer to P limitation than fungi. Our results suggest that, under a climate change scenario, increased C availability resulting from Arctic greening, treeline advance, and shrubification will reduce the microbial C limitation, while increased N availability resulting from warming will intensify the microbial C limitation. Our results also suggest that the synchronous increase of both C and N availability might lead to a progressive P limitation of microbial growth, primarily driven by bacteria being closer to P limitation. These shifts in microbial resource limitation might lead to a microbial targeting of the limiting element from organic matter, and also trigger competition for nutrients between plants and microorganisms, thus modulating the productivity of the ecosystem.

Heat wave-induced microbial thermal trait adaptation and its reversal in the Subarctic

Climate change predictions suggest that arctic and subarctic ecosystems will be particularly affected by rising temperatures and extreme weather events, including severe heat waves. Temperature is one of the most important environmental factors controlling and regulating microbial decomposition in soils; therefore, it is critical to understand its impact on soil microorganisms and their feedback to climate warming. We conducted a warming experiment in a subarctic birch forest in North Sweden to test the effects of summer heat waves on the thermal trait distributions that define the temperature dependences for microbial growth and respiration. We also determined the microbial temperature dependences 10 and 12 months after the heat wave simulation had ended to investigate the persistence of the thermal trait shifts. As a result of warming, the bacterial growth temperature dependence shifted to become warm-adapted, with a similar trend for fungal growth. For respiration, there was no shift in the temperature dependence. The shifts in thermal traits were not accompanied by changes in α- or β-diversity of the microbial community. Warming increased the fungal-to-bacterial growth ratio by 33% and decreased the microbial carbon use efficiency by 35%, and both these effects were caused by the reduction in moisture the warming treatments caused, while there was no evidence that substrate depletion had altered microbial processes. The warm-shifted bacterial thermal traits were partially restored within one winter but only fully recovered to match ambient conditions after 1 year. To conclude, a summer heat wave in the Subarctic resulted in (i) shifts in microbial thermal trait distributions; (ii) lower microbial process rates caused by decreased moisture, not substrate depletion; and (iii) no detectable link between the microbial thermal trait shifts and community composition changes.

Subarctic winter warming promotes soil microbial resilience to freeze-thaw cycles and enhances the microbial carbon use efficiency

Climate change is predicted to cause milder winters and thus exacerbate soil freeze-thaw perturbations in the subarctic, recasting the environmental challenges that soil microorganisms need to endure. Historical exposure to environmental stressors can facilitate the microbial resilience to new cycles of that same stress. However, whether and how such microbial memory or stress legacy can modulate microbial responses to cycles of frost remains untested. Here, we conducted an in situ field experiment in a subarctic birch forest, where winter warming resulted in a substantial increase in the number and intensity of freeze-thaw events. After one season of winter warming, which raised mean surface and soil (-8 cm) temperatures by 2.9 and 1.4°C, respectively, we investigated whether the in situ warming-induced increase in frost cycles improved soil microbial resilience to an experimental freeze-thaw perturbation. We found that the resilience of microbial growth was enhanced in the winter warmed soil, which was associated with community differences across treatments. We also found that winter warming enhanced the resilience of bacteria more than fungi. In contrast, the respiration response to freeze-thaw was not affected by a legacy of winter warming. This translated into an enhanced microbial carbon-use efficiency in the winter warming treatments, which could promote the stabilization of soil carbon during such perturbations. Together, these findings highlight the importance of climate history in shaping current and future dynamics of soil microbial functioning to perturbations associated with climate change, with important implications for understanding the potential consequences on microbial-mediated biogeochemical cycles.

Optimal conditions for beef tenderization through radiofrequency heating with cold air

High-temperature (15-37°C) aging can shorten the tenderizing time of beef; however, the use of constant temperature heating can lead to microbial spoilage. This study tested radiofrequency (RF) tenderization (RF-T) to find the appropriate conditions for the aging-like effect of beef without microbial spoilage. After subjecting beef to 22 h RF-T with four different cooling temperatures (15, 5, -10, and -20°C), the proliferated aerobic bacteria on the surface showed a concentration of 6-6.2 log CFU/g at -10 and -20°C, lower than 7-7.5 log CFU/g at 15 and 5°C. When beef was treated with 25 W/kg RF heating power for 48 h RF-T, the estimated reduction rate of the sliced shear force (SSF) and the increase rate of glutamic acid based on the weight before RF-T were 22.6% and 1.51-fold, which were greater than 19.6% and 1.37-fold with 20 W/kg, and 11.0% and 1.11-fold with 15 W/kg. The optimal specific RF heating power was calculated as 30 W/kg from the results' extrapolation. When processed for 48 h under optimal conditions (30 W/kg specific RF heating power, -20°C cooling air), the tenderization rate and the increased rates of free amino acids based on the weight before RF-T of beef reached over 20% and 1.5-fold with 5.22 log CFU/g aerobic bacteria, which was lesser than the Korean regulation value of 6.7 log CFU/g (5 × 106  CFU/g). Therefore, RF-T could be proposed as a promising high-temperature tenderization method with lowered risk of microbial spoilage. PRACTICAL APPLICATION: We showed that lowering the chamber temperature during RF-T was effective in surface drying and inhibiting aerobic bacteria. RF-T for 24-48 h with 30 W/kg specific RF heating power had an aging-like effect given tenderization and increase in FAAs. Moreover, by providing the matching circuit and impedance during RF-T, this method could be industrially reproducible.

The Use of Predictive Microbiology for the Prediction of the Shelf Life of Food Products

Microbial shelf life refers to the duration of time during which a food product remains safe for consumption in terms of its microbiological quality. Predictive microbiology is a field of science that focuses on using mathematical models and computational techniques to predict the growth, survival, and behaviour of microorganisms in food and other environments. This approach allows researchers, food producers, and regulatory bodies to assess the potential risks associated with microbial contamination and spoilage, enabling informed decisions to be made regarding food safety, quality, and shelf life. Two-step and one-step modelling approaches are modelling techniques with primary and secondary models being used, while the machine learning approach does not require using primary and secondary models for describing the quantitative behaviour of microorganisms, leading to the spoilage of food products. This comprehensive review delves into the various modelling techniques that have found applications in predictive food microbiology for estimating the shelf life of food products. By examining the strengths, limitations, and implications of the different approaches, this review provides an invaluable resource for researchers and practitioners seeking to enhance the accuracy and reliability of microbial shelf life predictions. Ultimately, a deeper understanding of these techniques promises to advance the domain of predictive food microbiology, fostering improved food safety practices, reduced waste, and heightened consumer confidence.

Biochemical Stability and Microbial Control of Reconstituted DaxibotulinumtoxinA-lanm for Injection

DaxibotulinumtoxinA-lanm for injection (DAXI) is a unique US Food and Drug Administration-approved product comprising daxibotulinumtoxinA and a stabilizing excipient peptide (RTP004). DAXI has a longer-labeled shelf life (72 h) following reconstitution than other botulinum toxin type A products. Here, we report the stability and microbial control of reconstituted DAXI when stored at 2 °C-8 °C over a period of 36 days (Study 1) and 7 days (Study 2) following reconstitution with unpreserved or preserved saline. The pH and biological activity of reconstituted DAXI in the 50 U/vial and 100 U/vial formats remained stable at the final assessed time point in both preserved and unpreserved saline when refrigerated (2 °C-8 °C). No changes in recoverable 150 kDa neurotoxin (measured by enzyme-linked immunosorbent assay) were observed over 6 days of refrigeration. Bacterial growth or pathogen proliferation was not observed in DAXI reconstituted in preserved or unpreserved saline in both studies.

A procedure to harmonize the hydrodynamic force during microbial cultivation in shaking flasks

Shake flask cultivation is a routine technique in microbiology and biotechnology laboratories where cell growth can be affected by the hydrodynamic conditions, which depend on the agitation velocity, shaking diameter, and shake flask size. Liquid agitation is implemented inherently to increase aeration, substrate transfer to the cells, and prevent sedimentation, disregarding the role of hydrodynamics in microbial growth and metabolism. Here, we present a simple approach to help standardize the hydrodynamic forces in orbital shakers to increase the experimental accuracy and reproducibility and give students a better knowledge of the significance of the agitation process in microbial growth.

Best Practices for Microbial Challenge In-use Studies to Evaluate the Microbial Growth Potential of Parenteral Biological Products; Industry and Regulatory Considerations

Microbial challenge in-use studies are performed to evaluate the potential for microbial proliferation in preservative-free single dose biological products after first puncture and potential accidental contamination during dose preparation (e.g. reconstitution, dilution) and storage. These studies, in addition to physicochemical in-use stability assessments, are used as part of product registration to define in-use hold times in Prescribing Information and in the pharmacy manual in the case of clinical products. There are no formal guidance documents describing regulator expectations on how to conduct microbial challenge in-use studies and interpret microbial data to assign in-use storage hold-times. In lieu of guidance, US Food and Drug Administration (FDA) regulators have authored publications and presentations describing regulator expectations. Insufficient or unavailable microbial challenge data can result in shortened in-use hold times, thus microbial challenge data enables flexibility for health care providers (HCPs) and patients, while ensuring patient safety. A cross-industry/FDA in-use microbial working group was formed through the Innovation & Quality (IQ) Consortium to gain alignment among industry practice and regulator expectations. The working group assessed regulatory guidance, current industry practice via a blinded survey of IQ Consortium member companies, and scientific rationale to align on recommendations for experimental design, execution of microbial challenge in-use studies, and a decision tree for microbial data interpretation to assign in-use hold times. Besides the study execution and data interpretation, additional considerations are discussed including use of platform data for clinical stage products, closed system transfer devices (CSTDs), transport of dose solutions, long infusion times, and the use of USP <797> by HCPs for preparing sterile drugs for administration. The recommendations provided in this manuscript will help streamline biological product development, ensure consistency on assignment of in-use hold times in biological product labels across industry, and provide maximum allowable flexibility to HCPs and patients, while ensuring patient safety.

A coarse-grained resource allocation model of carbon and nitrogen metabolism in unicellular microbes

Coarse-grained resource allocation models (C-GRAMs) are simple mathematical models of cell physiology, where large components of the macromolecular composition are abstracted into single entities. The dynamics and steady-state behaviour of such models provides insights on optimal allocation of cellular resources and have explained experimentally observed cellular growth laws, but current models do not account for the uptake of compound sources of carbon and nitrogen. Here, we formulate a C-GRAM with nitrogen and carbon pathways converging on biomass production, with parametrizations accounting for respirofermentative and purely respiratory growth. The model describes the effects of the uptake of sugars, ammonium and/or compound nutrients such as amino acids on the translational resource allocation towards proteome sectors that maximized the growth rate. It robustly recovers cellular growth laws including the Monod law and the ribosomal growth law. Furthermore, we show how the growth-maximizing balance between carbon uptake, recycling, and excretion depends on the nutrient environment. Lastly, we find a robust linear correlation between the ribosome fraction and the abundance of amino acid equivalents in the optimal cell, which supports the view that simple regulation of translational gene expression can enable cells to achieve an approximately optimal growth state.

The Metabolomics Changes in Luria-Bertani Broth Medium under Different Sterilization Methods and Their Effects on Bacillus Growth

Luria-Bertani broth (LB) culture medium is a commonly used bacterial culture medium in the laboratory. The nutrient composition, concentration, and culture conditions of LB medium can influence the growth of microbial strains. The purpose of this article is to demonstrate the impact of LB liquid culture medium on microbial growth under different sterilization conditions. In this study, LB medium with four different treatments was used, as follows: A, LB medium without treatments; B, LB medium with filtration; C, LB medium with autoclaving; and D, LB medium with autoclaving and cultured for 12 h. Subsequently, the protein levels and antioxidant capacity of the medium with different treatments were measured, and the effects of the different LB medium treatments on the growth of microorganisms and metabolites were determined via 16s rRNA gene sequencing and metabolomics analysis, respectively. Firmicutes and Lactobacillus were the dominant microorganisms, which were enriched in fermentation and chemoheterotrophy. The protein levels and antioxidant capacity of the LB medium with different treatments were different, and with the increasing concentration of medium, the protein levels were gradually increased, while the antioxidant capacity was decreased firstly and then increased. The growth trend of Bacillus subtilis, Bacillus paralicheniformis, Micrococcus luteus, and Alternaria alternata in the medium with different treatments was similar. Additionally, 220 and 114 differential metabolites were found between B and C medium, and between C and D medium, which were significantly enriched in the "Hedgehog signaling pathway", "biosynthesis of plant secondary metabolites", "ABC transporters", "arginine and proline metabolism", and "linoleic acid metabolism". LB medium may be a good energy source for Lactobacillus growth with unsterilized medium, and LB medium filtered with a 0.22 μm filter membrane may be used for bacterial culture better than culture medium after high-pressure sterilization. LB medium still has the ability for antioxidation and to keep bacteria growth whether or not autoclaved, indicating that there are some substances that can resist a high temperature and pressure and still maintain their functions.

Garlic Extracts: Effect of pH on Inhibition of Helicobacter pylori

The present work studies the influence of pH on the stability of thiosulfinates, compounds responsible for the bacteriostatic properties shown by ethanolic and acetonic garlic extracts (EGE and AGE) against the in vitro growth of Helicobacter pylori (Hp), a bacterium which is implicated in the etiology of diverse gastrointestinal diseases. The influence of pH and time on the stability of thiosulfinates and the microbiological activities of EGE and AGE has been evaluated at human body temperature (37 °C) and in a pH range of 0.9-4.7. A marked decrease in thiosulfinate concentration was observed in a relatively short time at pH values below 2.0. However, at pH values over 2.0, the samples maintained 70% of thiosulfinate concentration for 12 h. The inhibition halo diameters showed a maximum value at pH 2.50, with an inhibition halo of 28.94 ± 0.61 mm. The reduction in the activity at pH values below 2.0 was particularly remarkable. These results suggest that, for medical application, the pH of the selected extracts must only be maintained above 2 to maintain a high level of antibacterial activity. This fact would overcome the need for proton pump inhibitors and/or antibiotics during the treatment of Hp infections in human patients.

Microbial Growth under Limiting Conditions-Future Perspectives

Microorganisms rule the functioning of our planet and each one of the individual macroscopic living creature. Nevertheless, microbial activity and growth status have always been challenging tasks to determine both in situ and in vivo. Microbial activity is generally related to growth, and the growth rate is a result of the availability of nutrients under adequate or adverse conditions faced by microbial cells in a changing environment. Most studies on microorganisms have been carried out under optimum or near-optimum growth conditions, but scarce information is available about microorganisms at slow-growing states (i.e., near-zero growth and maintenance metabolism). This study aims to better understand microorganisms under growth-limiting conditions. This is expected to provide new perspectives on the functions and relevance of the microbial world. This is because (i) microorganisms in nature frequently face conditions of severe growth limitation, (ii) microorganisms activate singular pathways (mostly genes remaining to be functionally annotated), resulting in a broad range of secondary metabolites, and (iii) the response of microorganisms to slow-growth conditions remains to be understood, including persistence strategies, gene expression, and cell differentiation both within clonal populations and due to the complexity of the environment.

"Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture

The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.

Variation in Temperature Dependences across Europe Reveals the Climate Sensitivity of Soil Microbial Decomposers

Temperature is a major determinant of biological process rates, and microorganisms are key regulators of ecosystem carbon (C) dynamics. Temperature controls microbial rates of decomposition, and thus warming can stimulate C loss, creating positive feedback to climate change. If trait distributions that define temperature relationships of microbial communities can adapt to altered temperatures, they could modulate the strength of this feedback, but if this occurs remains unclear. In this study, we sampled soils from a latitudinal climate gradient across Europe. We established the temperature relationships of microbial growth and respiration rates and used these to investigate if and with what strength the community trait distributions for temperature were adapted to their local environment. Additionally, we sequenced bacterial and fungal amplicons to link the variance in community composition to changes in temperature traits. We found that microbial temperature trait distributions varied systematically with climate, suggesting that an increase in mean annual temperature (MAT) of 1°C will result in warm-shifted microbial temperature trait distributions equivalent to an increase in temperature minimum (T_min) of 0.20°C for bacterial growth, 0.07°C for fungal growth, and 0.10°C for respiration. The temperature traits for bacterial growth were thus more responsive to warming than those for respiration and fungal growth. The microbial community composition also varied with temperature, enabling the interlinkage of taxonomic information with microbial temperature traits. Our work shows that the adaptation of microbial temperature trait distributions to a warming climate will affect the C-climate feedback, emphasizing the need to represent this to capture the microbial feedback to climate change. IMPORTANCE One of the largest uncertainties of global warming is if the microbial decomposer feedback will strengthen or weaken soil C-climate feedback. Despite decades of research effort, the strength of this feedback to warming remains unknown. We here present evidence that microbial temperature relationships vary systematically with environmental temperatures along a climate gradient and use this information to forecast how microbial temperature traits will create feedback between the soil C cycle and climate warming. We show that the current use of a universal temperature sensitivity is insufficient to represent the microbial feedback to climate change and provide new estimates to replace this flawed assumption in Earth system models. We also demonstrate that temperature relationships for rates of microbial growth and respiration are differentially affected by warming, with stronger responses to warming for microbial growth (soil C formation) than for respiration (C loss from soil to atmosphere), which will affect the atmosphere-land C balance.

Does long-term soil warming affect microbial element limitation? A test by short-term assays of microbial growth responses to labile C, N and P additions

Increasing global temperatures have been reported to accelerate soil carbon (C) cycling, but also to promote nitrogen (N) and phosphorus (P) dynamics in terrestrial ecosystems. However, warming can differentially affect ecosystem C, N and P dynamics, potentially intensifying elemental imbalances between soil resources, plants and soil microorganisms. Here, we investigated the effect of long-term soil warming on microbial resource limitation, based on measurements of microbial growth (18 O incorporation into DNA) and respiration after C, N and P amendments. Soil samples were taken from two soil depths (0-10, 10-20 cm) in control and warmed (>14 years warming, +4°C) plots in the Achenkirch soil warming experiment. Soils were amended with combinations of glucose-C, inorganic/organic N and inorganic/organic P in a full factorial design, followed by incubation at their respective mean field temperatures for 24 h. Soil microbes were generally C-limited, exhibiting 1.8-fold to 8.8-fold increases in microbial growth upon C addition. Warming consistently caused soil microorganisms to shift from being predominately C limited to become C-P co-limited. This P limitation possibly was due to increased abiotic P immobilization in warmed soils. Microbes further showed stronger growth stimulation under combined glucose and inorganic nutrient amendments compared to organic nutrient additions. This may be related to a prolonged lag phase in organic N (glucosamine) mineralization and utilization compared to glucose. Soil respiration strongly positively responded to all kinds of glucose-C amendments, while responses of microbial growth were less pronounced in many of these treatments. This highlights that respiration-though easy and cheap to measure-is not a good substitute of growth when assessing microbial element limitation. Overall, we demonstrate a significant shift in microbial element limitation in warmed soils, from C to C-P co-limitation, with strong repercussions on the linkage between soil C, N and P cycles under long-term warming.

The "comfort timing" strategy: a potential pathway for the cultivation of uncultured microorganisms and a possible adaptation for environmental colonisation

Efforts to isolate uncultured microorganisms over the last century and a half, as well as the advanced 'omics' technologies developed over the last three decades, have greatly increased the knowledge and resources of microbiology. However, many cellular functions such as growth remain unknown in most of the microbial diversity identified through genomic sequences from environmental samples, as evidenced by the increasingly precise observations of the phenomenon known as the 'great plate count anomaly'. Faced with the many microbial cells recalcitrant to cultivation present in environmental samples, Epstein proposed the 'scout' model, characterised by a dominance of dormant cells whose awakening would be strictly stochastic. Unfortunately, this hypothesis leaves few exploitable possibilities for microbial cultivation. This review proposes that many microorganisms follow the 'comfort timing' strategy, characterised by an exit from dormancy responding to a set of environmental conditions close to optimal for growth. This 'comfort timing' strategy offers the possibility of designing culture processes that could isolate a larger proportion of uncultured microorganisms. Two methods are briefly proposed in this article. In addition, the advantages of dormancy, of the 'scout' model and of the 'comfort timing' strategy for survival under difficult conditions, but also for colonisation of environments, are discussed.

Effect of pH on Adsorption of Tetracycline Antibiotics on Graphene Oxide

Graphene oxide (GO) has good dispersibility and adsorption capacity for antibiotics adsorption, a complex process influenced by many factors. In this work, the adsorption mechanism of GO on tetracycline antibiotics at different pH was studied to address its attenuated effects on the microbial growth. The results showed that the adsorption process of GO on three antibiotics, namely, tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC), followed the pseudo-second-order kinetic model. The maximum adsorption capacities were observed at pH5 which were 133.0 mg/g for TC, 125.4 mg/g for OTC, and 167.0 mg/g for CTC. Furthermore, the reaction was uniform adsorption with a single layer on the surface of GO, and heating was conducive to the reaction. In the microbial growth experiment, the growth of E. coli and B. subtilis senses was optimal at pH5, which was consistent with the adsorption experiment. This study analyzed the effect of pH on the adsorption of antibiotics by GO and provided a theoretical basis for the further application of GO in various aquatic environments.

Video frame prediction of microbial growth with a recurrent neural network

The recent explosion of interest and advances in machine learning technologies has opened the door to new analytical capabilities in microbiology. Using experimental data such as images or videos, machine learning, in particular deep learning with neural networks, can be harnessed to provide insights and predictions for microbial populations. This paper presents such an application in which a Recurrent Neural Network (RNN) was used to perform prediction of microbial growth for a population of two Pseudomonas aeruginosa mutants. The RNN was trained on videos that were acquired previously using fluorescence microscopy and microfluidics. Of the 20 frames that make up each video, 10 were used as inputs to the network which outputs a prediction for the next 10 frames of the video. The accuracy of the network was evaluated by comparing the predicted frames to the original frames, as well as population curves and the number and size of individual colonies extracted from these frames. Overall, the growth predictions are found to be accurate in metrics such as image comparison, colony size, and total population. Yet, limitations exist due to the scarcity of available and comparable data in the literature, indicating a need for more studies. Both the successes and challenges of our approach are discussed.

Cause and Effect Analysis between Influencing Factors Related to Environmental Conditions, Hunting and Handling Practices and the Initial Microbial Load of Game Carcasses

Environmental, hunting and handling factors affect the microbial load of hunted game and the resulting meat products. The aim of this study was to systematically investigate the influence of several factors on the initial microbial load (IML) of game carcasses during the early hunting chain. Eviscerated roe deer body cavities (n = 24) were investigated in terms of total viable count and the levels of Pseudomonas spp., Lactobacillus spp., Enterobacteriaceae and Escherichia coli (E. coli). Furthermore, a risk analysis based on the obtained original IML data, literature search and a Failure Mode and Effects Analysis (FMEA) was performed. The IML could be explained in a regression model by factors including the higher body weight (BW), damaged gastrointestinal tract by the shot, ambient temperature or rain. The levels of Lactobacillus spp. (p = 0.0472), Enterobacteriaceae (p = 0.0070) and E. coli (p = 0.0015) were lower on the belly flap surface when gloves were used during evisceration. The literature search revealed that studies examining influencing factors (IF) on the IML of game carcasses found contradictory effects of the comparable IF on IML. Potential handling failures may lead to a higher IML of game carcasses during the early hunting chain ranked by FMEA. Several handling practices for game carcasses are recommended, such as ensuring efficient cooling of heavier BW carcasses to limit bacterial growth or eviscerating heavier carcasses before lighter ones.

High-Energy-Density Organic Amendments Enhance Soil Health

Soil microbial biomass (SMB) and soil microbial communities (SMCs) are the key factors in soil health and agricultural sustainability. We hypothesized that low bioavailable carbon (C) and energy were the key limiting factors influencing soil microbial growth and developed a new fertilization system to address this: the simultaneous application of mineral fertilizers and high-energy-density organic amendments (HED-OAs). A microcosm soil incubation experiment and a Brassica rapa subsp. chinensis pot culture experiment were used to test the effects of this new system. Compared to mineral fertilizer application alone, the simultaneous input of fertilizers and vegetable oil (SIFVO) achieved a bacterial abundance, fungal abundance, and fungal:bacterial ratio that were two orders of magnitude higher, significantly higher organic C and nitrogen (N) content, significantly lower N loss, and nearly net-zero N₂O emissions. We proposed an energy and nutrient threshold theory to explain the observed bacterial and fungal growth characteristics, challenging the previously established C:N ratio determination theory. Furthermore, SIFVO led to microbial community improvements (an increased fungal:bacterial ratio, enriched rhizosphere bacteria and fungi, and reduced N-transformation bacteria) that were beneficial for agricultural sustainability. A low vegetable oil rate (5 g/kg) significantly promoted Brassica rapa subsp. chinensis growth and decreased the shoot N content by 35%, while a high rate caused severe N deficiency and significantly inhibited growth of the crop, confirming the exceptionally high microbial abundance and indicating severe microbe-crop competition for nutrients in the soil.

Occurrence of mycotoxins in pulses

Pulses, dry grains of the Fabaceae family used for food and feed, are particularly important agricultural products with increasing commercial and nutritional relevance. Similar to other plant commodities, pulses can be affected by fungi in the field and during postharvest. Some of these fungi produce mycotoxins, which can seriously threaten human and animal health by causing acute poisoning and chronic effects. In this review, information referring to the analysis and occurrence of these compounds in pulses is summarized. An overview of the aims pursued, and of the methodologies employed for mycotoxin analysis in the different reports is presented, followed by a comprehensive review of relevant articles on mycotoxins in pulses, categorized according to the geographical region, among other considerations. Moreover, special attention was given to the effect of climatic conditions on microorganism infestation and mycotoxin accumulation. Furthermore, the limited literature available was considered to look for possible correlations between the degree of fungal infection and the mycotoxin incidence in pulses. In addition, the potential effect of certain phenolic compounds on reducing fungi infestation and mycotoxin accumulation was reviewed with examples on beans. Emphasis was also given to a specific group of mycotoxins, the phomopsins, that mainly impact lupin. Finally, the negative consequences of mycotoxin accumulation on the physiology and development of contaminated seeds and seedlings are presented, focusing on the few reports available on pulses. Given the agricultural and nutritional potential that pulses offer for human well-being, their promotion should be accompanied by attention to food safety issues, and mycotoxins might be among the most serious threats. Practical Application: According to the manuscript template available in the website, this section is for "JFS original research manuscripts ONLY; optional". Since we are publishing in CRFSFS this requirement will not be done.

Nitrogen addition to soil affects microbial carbon use efficiency: Meta-analysis of similarities and differences in 13 C and 18 O approaches

The carbon use efficiency (CUE) of soil microorganisms is a critical parameter for the first step of organic carbon (C) transformation by and incorporation into microbial biomass and shapes C cycling in terrestrial ecosystems. As C and nitrogen (N) cycles interact closely and N availability affects microbial metabolism, N addition to soil may shift the microbial CUE. We conducted a meta-analysis (100 data pairs) to generalize information about the microbial CUE response to N addition in soil based on the two most common CUE estimation approaches: (i) ¹³ C-labelled substrate addition (¹³ C-substrate) and (ii) ¹⁸ O-labelled water addition (¹⁸ O-H₂ O). The mean microbial CUE in soils across all biomes and approaches was 0.37. The effects of N addition on CUE, however, were depended on the approach: CUE decreased by 12% if measured by the ¹³ C-substrate approach, while CUE increased by 11% if measured by the ¹⁸ O-H₂ O approach. These differences in the microbial CUE response depending on the estimation approach are explained by the divergent reactions of microbial growth to N addition: N addition decreases the ¹³ C incorporation into microbial biomass (this parameter is in the numerator by CUE calculation based on the ¹³ C-substrate approach). In contrast, N addition slightly increases (although statistically insignificant) the microbial growth rate (in the numerator of the CUE calculation when assessed by the ¹⁸ O-H₂ O approach), significantly raising the CUE. We explained these N addition effects based on CUE regulation mechanisms at the metabolic, cell, community, and ecosystem levels. Consequently, the differences in the microbial responses (microbial growth, respiration, C incorporation, community composition, and dormant or active states) between the ¹³ C-substrate and ¹⁸ O-H₂ O approaches need to be considered. Thus, these two CUE estimation approaches should be compared to understand microbially mediated C and nutrient dynamics under increasing anthropogenic N input and other global change effects.

Nitrogen input enhances microbial carbon use efficiency by altering plant-microbe-mineral interactions

Microbial growth and respiration are at the core of the soil carbon (C) cycle, as these microbial physiological performances ultimately determine the fate of soil C. Microbial C use efficiency (CUE), a critical metric to characterize the partitioning of C between microbial growth and respiration, thus controls the sign and magnitude of soil C-climate feedback. Despite its importance, the response of CUE to nitrogen (N) input and the relevant regulatory mechanisms remain poorly understood, leading to large uncertainties in predicting soil C dynamics under continuous N input. By combining a multi-level field N addition experiment with a substrate-independent ¹⁸ O-H₂ O labelling approach as well as high-throughput sequencing and mineral analysis, here we elucidated how N-induced changes in plant-microbial-mineral interactions drove the responses of microbial CUE to N input. We found that microbial CUE increased significantly as a consequence of enhanced microbial growth after 6-year N addition. In contrast to the prevailing view, the elevated microbial growth and CUE were not mainly driven by the reduced stoichiometric imbalance, but strongly associated with the increased soil C accessibility from weakened mineral protection. Such attenuated organo-mineral association was further linked to the N-induced changes in the plant community and the increased oxalic acid in the soil. These findings provide empirical evidence for the tight linkage between mineral-associated C dynamics and microbial physiology, highlighting the need to disentangle the complex plant-microbe-mineral interactions to improve soil C prediction under anthropogenic N input.

Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth

Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (N_Inorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and N_Inorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.

The CIAMIB: a Large and Metabolically Diverse Collection of Inflammation-Associated Bacteria from the Murine Gut

Gut inflammation directly impacts the growth and stability of commensal gut microbes and can lead to long-lasting changes in microbiota composition that can prolong or exacerbate disease states. While mouse models are used extensively to investigate the interplay between microbes and the inflamed state, the paucity of cultured mouse gut microbes has hindered efforts to determine causal relationships. To address this issue, we are assembling the Collection of Inflammation-Associated Mouse Intestinal Bacteria (CIAMIB). The initial release of this collection comprises 41 isolates of 39 unique bacterial species, covering 4 phyla and containing 10 previously uncultivated isolates, including 1 novel family and 7 novel genera. The collection significantly expands the number of available Muribaculaceae, Lachnospiraceae, and Coriobacteriaceae isolates and includes microbes from genera associated with inflammation, such as Prevotella and Klebsiella. We characterized the growth of CIAMIB isolates across a diverse range of nutritional conditions and predicted their metabolic potential and anaerobic fermentation capacity based on the genomes of these isolates. We also provide the first metabolic analysis of species within the genus Adlercreutzia, revealing these representatives to be nitrate-reducing and severely restricted in their ability to grow on carbohydrates. CIAMIB isolates are fully sequenced and available to the scientific community as a powerful tool to study host-microbiota interactions. IMPORTANCE Attempts to explore the role of the microbiota in animal physiology have resulted in large-scale efforts to cultivate the thousands of microbes that are associated with humans. In contrast, relatively few lab mouse-associated bacteria have been isolated, despite the fact that the overwhelming number of studies on the microbiota use laboratory mice that are colonized with microbes that are quite distinct from those in humans. Here, we report the results of a large-scale isolation of bacteria from the intestines of laboratory mice either prone to or suffering from gut inflammation. This collection comprises dozens of novel isolates, many of which represent the only cultured representatives of their genus or species. We report their basic growth characteristics and genomes and are making them widely available to the greater research community.

What Worth the Garlic Peel

Plants have two types of reproduction: sexual, resulting in embryo production, and asexual, resulting in vegetative bodies commonly derived from stems and roots (e.g., bulb, tuber). Dead organs enclosing embryos (DOEEs, such as seed coat and pericarp) are emerging as central components of the dispersal unit acting to nurture the embryo and ensure its survival in the habitat. Here we wanted to investigate the properties of dead organs enclosing plant asexual reproductive bodies, focusing on the garlic (Allium sativum) bulb. We investigated the biochemical and biological properties of the outer peel enclosing the bulb and the inner peel enclosing the clove using various methodologies, including bioassays, proteomics, and metabolomics. The garlic peels differentially affected germination and post-germination growth, with the outer peel demonstrating a strong negative effect on seed germination of Sinapis alba and on post-germination growth of Brassica juncea. Proteome analysis showed that dead garlic peels possess 67 proteins, including chitinases and proteases, which retained their enzymatic activity. Among primary metabolites identified in garlic peels, the outer peel accumulated multiple sugars, including rhamnose, mannitol, sorbitol, and trehalose, as well as the modified amino acid 5-hydroxylysine, known as a major component of collagen, at a higher level compared to the clove and the inner peel. Growth of Escherichia coli and Staphylococcus aureus was promoted by garlic peel extracts but inhibited by clove extract. All extracts strongly inhibited spore germination of Fusarium oxysporum f.sp. melonis. Thus, the garlic peels not only provide physical protection to vegetative offspring but also appear to function as a refined arsenal of proteins and metabolites for enhancing growth and development, combating potential pathogens, and conferring tolerance to abiotic stresses.

Effect of 0.4% Triphala and 0.12% chlorhexidine mouthwash on dental plaque, gingival inflammation, and microbial growth in 14-15-year-old schoolchildren: A randomized controlled clinical trial

Context:

A strong correlation exists between plaque and dental caries and periodontal diseases. Ayurvedic drugs have been used since ancient times; oral rinses made from these are used in periodontal therapy. Triphala is one of these with wide spectrum of activity.

Aims:

To assess and compare the effect of 0.4% Triphala and 0.12% chlorhexidine (CHX) mouthwash on dental plaque, gingival inflammation, and microbial count of Streptococcus mutans, Streptococcus sanguinis, and Lactobacilli from dental plaque sample of 14–15-year-old schoolchildren of Pune city during 90 days supervised use.

Settings and Design:

A randomized, controlled, double-blind, parallel-group clinical trial was conducted among 72 schoolchildren aged 14–15 years.

Subjects and Methods:

Children were divided into two study groups: Group A with 0.4% Triphala mouthwash (n = 36) and Group B with 0.12% CHX mouthwash (n = 36). The plaque Index (Loe H [1967]), gingival index (Loe H and Silness J [1963]), and microbial analysis were recorded at baseline, 30 days, and 90 days interval.

Statistical Analysis Used:

Statistical analysis was done using unpaired t-test for group-wise comparison and one-way analysis of variance test, followed by Tukey's post hoc test for intragroup comparison. P < 0.05 was considered statistically significant.

Results:

The results showed that 0.4% Triphala and 0.12% CHX have similar inhibitory effect on plaque accumulation, gingivitis, and growth of S. mutans, S. sanguinis, and Lactobacilli.

Conclusion:

Herbal mouthwash proved to be helpful in reducing plaque microbial counts, plaque, and gingival inflammation and opens new arenas in the field of herbal dentistry and chemical plaque control.

Distinguishing different modes of growth using single-cell data

Collection of high-throughput data has become prevalent in biology. Large datasets allow the use of statistical constructs such as binning and linear regression to quantify relationships between variables and hypothesize underlying biological mechanisms based on it. We discuss several such examples in relation to single-cell data and cellular growth. In particular, we show instances where what appears to be ordinary use of these statistical methods leads to incorrect conclusions such as growth being non-exponential as opposed to exponential and vice versa. We propose that the data analysis and its interpretation should be done in the context of a generative model, if possible. In this way, the statistical methods can be validated either analytically or against synthetic data generated via the use of the model, leading to a consistent method for inferring biological mechanisms from data. On applying the validated methods of data analysis to infer cellular growth on our experimental data, we find the growth of length in E. coli to be non-exponential. Our analysis shows that in the later stages of the cell cycle the growth rate is faster than exponential.

Energetic scaling in microbial growth

Microbial growth is a clear example of organization and structure arising in nonequilibrium conditions. Due to the complexity of the microbial metabolic network, elucidating the fundamental principles governing microbial growth remains a challenge. Here, we present a systematic analysis of microbial growth thermodynamics, leveraging an extensive dataset on energy-limited monoculture growth. A consistent thermodynamic framework based on reaction stoichiometry allows us to quantify how much of the available energy microbes can efficiently convert into new biomass while dissipating the remaining energy into the environment and producing entropy. We show that dissipation mechanisms can be linked to the electron donor uptake rate, a fact leading to the central result that the thermodynamic efficiency is related to the electron donor uptake rate by the scaling law [Formula: see text] and to the growth yield by [Formula: see text] These findings allow us to rederive the Pirt equation from a thermodynamic perspective, providing a means to compute its coefficients, as well as a deeper understanding of the relationship between growth rate and yield. Our results provide rather general insights into the relation between mass and energy conversion in microbial growth with potentially wide application, especially in ecology and biotechnology.

Physicochemical Parameters Limiting Growth of Debaryomyces hansenii in Solutions of Hygroscopic Compounds and Their Effects on the Habitability of Martian Brines

The availability of liquid water is a prerequisite for all lifeforms on Earth. In hyperarid subzero environments like the Dry Valleys in Antarctica or the near-subsurface of Mars liquid water might be provided temporarily by hygroscopic substances that absorb water from the atmosphere and lower the freezing point of water. To evaluate the potential of hygroscopic compounds to serve as a habitat, it is necessary to explore the microbial tolerances towards these substances and their life-limiting properties. Here we present a study investigating the tolerances of the halotolerant yeast Debaryomyces hansenii to various solutes. Growth experiments were conducted via counting colony forming units (CFUs) after inoculation of a liquid growth medium containing a specific solute concentration. The lowest water activities (a_w) enabling growth were determined to be ~0.83 in glycerol and fructose-rich media. For all other solutes the growth-enabling a_w was higher, due to additional stress factors such as chaotropicity and ionic strength. Additionally, we found that the solute tolerances of D. hansenii correlate with both the eutectic freezing point depressions and the deliquescence relative humidities of the respective solutes. Our findings strongly impact our understanding of the habitability of solute-rich low a_w environments on Earth and beyond.

Silicate minerals as a direct source of limiting nutrients: Siderophore synthesis and uptake promote ferric iron bioavailability from olivine and microbial growth

Iron is a micronutrient critical to fundamental biological processes including respiration and photosynthesis, and it can therefore impact primary and heterotrophic productivity. Yet in oxic environments, iron is highly insoluble, rendering it, in principle, unavailable as a nutrient for biological growth. Life has "solved" this problem via the invention of iron chelates, known as siderophores, that keep iron available for microbial productivity. In this work, we examined the impact of siderophore synthesis on the speciation, mobility, and bioavailability of iron from rock-forming silicate minerals-shedding new light on the mechanisms by which microbes use mineral substrates to support primary productivity, as well as the consequent effects on silicate dissolution. Growth experiments were performed with Shewanella oneidensis MR-1 in an oxic, iron-depleted minimal medium, amended with olivine minerals as the sole source of iron. Experiments included the wild-type strain MR-1, and a siderophore synthesis gene deletion mutant strain (ΔMR-1). Relative to MR-1, ΔMR-1 exhibited a very pronounced growth penalty and an extended lag phase. However, substantial growth of ΔMR-1, comparable to MR-1 growth, was observed when the mutant strain was provided with siderophores in the form of either filtrate from a well-grown MR-1 culture, or commercially available deferoxamine. These observations suggest that siderophores are critical for S. oneidensis to acquire iron from olivine. Growth-limiting concentrations of deferoxamine amendments were observed to be ≤5-10 µM, concentrations significantly lower than previously recorded as necessary to impact mineral dissolution rates. X-ray photoelectric spectroscopy analyses of the incubated olivine surfaces suggest that siderophores deplete mineral surface layers of ferric iron. Combined, these results demonstrate that low micromolar concentrations of siderophores can effectively mobilize iron bound within silicate minerals, supporting very significant biological growth in limiting environments. The specific mechanism would involve siderophores removing a protective layer of nanometer-thick iron oxides, enhancing silicate dissolution and nutrient bioavailability.

A Holling Functional Response Model for Mapping QTLs Governing Interspecific Interactions

Genes play an important role in community ecology and evolution, but how to identify the genes that affect community dynamics at the whole genome level is very challenging. Here, we develop a Holling type II functional response model for mapping quantitative trait loci (QTLs) that govern interspecific interactions. The model, integrated with generalized Lotka-Volterra differential dynamic equations, shows a better capacity to reveal the dynamic complexity of inter-species interactions than classic competition models. By applying the new model to a published mapping data from a competition experiment of two microbial species, we identify a set of previously uncharacterized QTLs that are specifically responsible for microbial cooperation and competition. The model can not only characterize how these QTLs affect microbial interactions, but also address how change in ecological interactions activates the genetic effects of the QTLs. This model provides a quantitative means of predicting the genetic architecture that shapes the dynamic behavior of ecological communities.

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

Despite the wide perception that microbes have rapid growth rates, many environments like seawater and soil are often dominated by microorganisms that can only grow very slowly. Our knowledge about growth is necessarily biased toward easily culturable organisms, which tend to be those that grow fast, because microbial growth rates have traditionally been measured using laboratory growth experiments. However, how are potential growth rates distributed in nature? Using genomic data, we predicted the growth rates of over 200,000 organisms, including many as yet uncultivated species. These data reveal how current culture collections are strongly biased toward fast-growing organisms. Finally, we noticed a bimodal distribution of maximal growth rates, suggesting a natural division of microbial growth strategies into two classes.

Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth rates are typically measured using laboratory culture experiments. Yet, we lack sufficient understanding of the physiology of most microbes to design appropriate culture conditions for them, severely limiting our ability to assess the global diversity of microbial growth rates. Genomic estimators of maximal growth rate provide a practical solution to survey the distribution of microbial growth potential, regardless of cultivation status. We developed an improved maximal growth rate estimator and predicted maximal growth rates from over 200,000 genomes, metagenome-assembled genomes, and single-cell amplified genomes to survey growth potential across the range of prokaryotic diversity; extensions allow estimates from 16S rRNA sequences alone as well as weighted community estimates from metagenomes. We compared the growth rates of cultivated and uncultivated organisms to illustrate how culture collections are strongly biased toward organisms capable of rapid growth. Finally, we found that organisms naturally group into two growth classes and observed a bias in growth predictions for extremely slow-growing organisms. These observations ultimately led us to suggest evolutionary definitions of oligotrophy and copiotrophy based on the selective regime an organism occupies. We found that these growth classes are associated with distinct selective regimes and genomic functional potentials.

Dynamic Modeling of Carnobacterium maltaromaticum CNCM I-3298 Growth and Metabolite Production and Model-Based Process Optimization

Carnobacterium maltaromaticum is a species of lactic acid bacteria found in dairy, meat, and fish, with technological properties useful in food biopreservation and flavor development. In more recent years, it has also proven to be a key element of biological time–temperature integrators for tracking temperature variations experienced by perishable foods along the cold-chain. A dynamic model for the growth of C. maltaromaticum CNCM I-3298 and production of four metabolites (formic acid, acetic acid, lactic acid, and ethanol) from trehalose in batch culture was developed using the reaction scheme formalism. The dependence of the specific growth and production rates as well as the product inhibition parameters on the operating conditions were described by the response surface method. The parameters of the model were calibrated from eight experiments, covering a broad spectrum of culture conditions (temperatures between 20 and 37 °C; pH between 6.0 and 9.5). The model was validated against another set of eight independent experiments performed under different conditions selected in the same range. The model correctly predicted the growth kinetics of C. maltaromaticum CNCM I-3298 as well as the dynamics of the carbon source conversion, with a mean relative error of 10% for biomass and 14% for trehalose and the metabolites. The paper illustrates that the proposed model is a valuable tool for optimizing the culture of C. maltaromaticum CNCM I-3298 by determining operating conditions that favor the production of biomass or selected metabolites. Model-based optimization may thus reduce the number of experiments and substantially speed up the process development, with potential applications in food technology for producing starters and improving the yield and productivity of the fermentation of sugars into metabolites of industrial interest.

Informative and corrective responsive packaging: Advances in farm-to-fork monitoring and remediation of food quality and safety

Microbial growth and fluctuations in environmental conditions have been shown to cause microbial contamination and deterioration of food. Thus, it is paramount to develop reliable strategies to effectively prevent the sale and consumption of contaminated or spoiled food. Responsive packaging systems are designed to react to specific stimuli in the food or environment, such as microorganisms or temperature, then implement an informational or corrective response. Informative responsive packaging is aimed at continuously monitoring the changes in food or environmental conditions and conveys this information to the users in real time. Meanwhile, packaging systems with the capacity to control contamination or deterioration are also of great interest. Encouragingly, corrective responsive packaging attempting to mitigate the adverse effects of condition fluctuations on food has been investigated. This packaging exerts its effects through the triggered release of active agents by environmental stimuli. In this review, informative and corrective responsive packaging is conceptualized clearly and concisely. The mechanism and characteristics of each type of packaging are discussed in depth. This review also summarized the latest research progress of responsive packaging and objectively appraised their advantages. Evidently, the mechanism through which packaging systems respond to microbial contamination and associated environmental factors was also highlighted. Moreover, risk concerns, related legislation, and consumer perspective in the application of responsive packaging are discussed as well. Broadly, this comprehensive review covering the latest information on responsive packaging aims to provide a timely reference for scientific research and offer guidance for presenting their applications in food industry.

Stability of Aprepitant Injectable Emulsion in Alternate Infusion Bags, in Refrigerated Storage, and Admixed with Dexamethasone and Palonosetron

Purpose

The stability of aprepitant injectable emulsion is evaluated in various admixture bags and solutions, under different storage conditions, and when combined with other antiemetics.

Methods

A volume of 18 mL aprepitant injectable emulsion was added to infusion bags (either non-di-(2-ethylhexyl) phthalate [DEHP], polyvinyl chloride [PVC]-containing bags or non-DEHP, non-PVC bags) containing 100, 130, or 250 mL of 0.9% normal saline solution (NSS) or 5% dextrose in water (D5W). Bags were stored at controlled room temperature (20–25°C) for up to 12 hours or refrigerated (2–8°C) for up to 72 hours. Compatibility/stability was also assessed in admixtures combined with either dexamethasone or palonosetron. At specified time points, bags were tested for appearance, pH, assay for aprepitant (ie, percent label claim of aprepitant) and aprepitant-related substances, Z-average particle size, globule size distribution, particulate matter, and DEHP content (PVC bags). In separate analyses to assess microbial burden, bags containing aprepitant were inoculated with seven different organisms and assessed for microbial growth.

Results

There was no detectable impact on the physicochemical properties or potential to promote microbial growth of aprepitant when diluted with various amounts of either NSS or D5W and when admixed with either dexamethasone or palonosetron at room temperature for at least 6 hours or during refrigeration for up to 72 hours in either PVC- or non-PVC-containing bags.

Conclusion

Aprepitant-containing admixtures are stable under these conditions, a finding that may improve patient and provider convenience and reduce medication wastage.

A novel relationship for the maximum specific growth rate of a microbial guild

One of the major parameters that characterizes the kinetics of microbial processes is the maximum specific growth rate. The maximum specific growth rate for a single microorganism (${\mu _{max}}$) is fairly constant. However, a certain microbial process is typically catalyzed by a group of microorganisms (guild) that have various ${\mu _{max}}$ values. In many occasions, it is not feasible to breakdown a guild into its constituent microorganisms. Therefore, it is a common practice to assume a constant maximum specific growth rate for the guild ($\acute{\mu}_{max}$) and determine its value by fitting experimental data. This assumption is valid for natural environments, where microbial guilds are stabilized and dominated by microorganisms that grow optimally in those environments' conditions. However, a change in an environment's conditions will trigger a community shift by favoring some of the microorganisms. This shift leads to a variable ${\acute{\mu}_{max}}$ as long as substrate availability is significantly higher than substrate affinity constant. In this work, it is illustrated that the assumption of constant ${\acute{\mu}_{max}}$ may underestimate or overestimate microbial growth. To circumvent this, a novel relationship that characterizes changes in ${\acute{\mu}_{max}}$ under abundant nutrient availability is proposed. The proposed relationship is evaluated for various random microbial guilds in batch experiments.

The effect of resin coating on the quality characteristics of chicken eggs during storage

In this study, after washing, changes in the quality characteristics of chicken eggs coated with apricot, almond, and sour cherry tree resins were examined during two different temperatures (4 °C and 22 °C) storage for 60 days. While air cell height, weight loss, albumen and yolk pH and a* (redness) values increased in all samples during storage, Haugh unit, albumen and yolk index, shell fracture and vitelline membrane strength, albumen and yolk L* (lightness) and b* (yellowness) values decreased (P < 0.05). The lowest weight loss (0.54 g) and air cell height (2.89 mm), highest Haugh unit (73.95 HU), albumen index (8.81%), and yolk index (40.37%) were found in the samples coated with sour cherry wood resin stored at 4 °C. The shell breakage and vitelline membrane strength of the coated samples were determined to be higher than the control samples and the samples stored after washing. Higher weight loss, air cell height, and pH values, while lower Haugh unit, Albumen and yolk index were found in samples stored at 22 °C (P < 0.05). At the end of storage, the maximum increase in the counts of total aerobic mesophilic and psychrophilic bacteria was found in the albumin and egg yolk of washed samples stored at ambient temperature. As a result, the coating materials prepared with the resin of apricot, almond, and sour cherry trees were suitable for eggshell's shelf life extension. PRACTICAL APPLICATION: The consumers demand the eggs be in their freshest condition, but the currently available storage conditions are not sufficient to maintain freshness in many regions of Turkey. The physical, chemical and, microbiological qualities of the eggs coated with wood resins were determined to be superior compared to other samples. Because resins have good barrier properties, it is recommended to conduct extensive studies on their applicability in different products.

Active Packaging-Releasing System with Foeniculum vulgare Essential Oil for the Quality Preservation of Ready-to-Cook (RTC) Globe Artichoke Slices

Two globe artichoke genotypes, “Spinoso sardo” and “Opera F1”, have been processed as ready-to-cook (RTC) slices and refrigerated at 4 °C for 12 days (i) to evaluate the suitability to be processed as RTC slices; (ii) to evaluate the effect of a Foeniculum vulgare essential oil (EO) emitter, within an active package system, to delay quality decay, thus extending shelf life; (iii) to estimate the impact of EO emitter on the sensory profile of the RTC slices after cooking. Results revealed that both globe artichoke genotypes possess a good attitude to be processed as RTC product. “Opera F1” showed the best performances for color parameters, texture and chemical indexes, while “Spinoso sardo” showed lower mass loss (ML) over the storage time. The addition of EO emitter slowed down the consumption of O₂, better preserved texture when compared to the control and more effectively control polyphenol oxidase (PPO) activity and antioxidants’ retention during the cold storage. Microbial counts in control globe artichoke RTC slices were significantly higher than those packed with EO emitter, confirming the inhibiting role played by EO of F. vulgare. In addition, the EO emitter did not influence negatively the sensory profile of RTC globe artichoke slices after microwave cooking.

Kinetics and modeling of growth and lactic acid production in Gundruk, a Himalayan fermented vegetable dish

Gundruk is a fermented green leafy vegetable product prepared from fresh leaves of local vegetables called Rayo-sag (Brassica campestris), mustard (Brassica juncea), and cauliflower (Brassica oleracea) indigenous to the Nepali people. Fresh gundruk was prepared in a glass jar by fermenting the Brassica juncea leaves anaerobically for 16 days and the changes in biomass, lactic acid, and pH were evaluated after every 24 hr. The viable cell count increased from 6.03 × 104 cfu/g to 9.55 × 108 cfu/g after 3 days and then decreased gradually to remain constant after 8 days with 6.31 × 107 cfu/g until the end of fermentation. The lactic acid increased by about 12.58 times in 12 days and remained constant for the rest of the fermentation period. Unlike this, pH decreased from 6.59 to 3.71 on the 9th day of fermentation and then increased slightly till the last day of fermentation. The data obtained were fitted to two most widely accepted microbial growth models: Modified Gompertz, and Logistic model and three well-known lactic acid production models: Luedeking- Piret, Monteagudo et al., and Balannec et al. model for lactic acid fermentation. Based on nonlinear regression analysis, Modified Gompertz, and Monteagudo et al. model gave a better fit to describe microbial growth and lactic acid production, respectively. The growth-associated and non-growth-associated coefficients were determined to be 0.1104 and 0.0042, respectively, using Monteagudo et al. model. The findings revealed that lactic acid production in gundruk is a mixed type.

Growth conditions and survival kinetics during storage of Lactobacillus rhamnosus GG for the design of a sustainable probiotic whey-based beverage containing Costa Rican guava fruit pulp

The finding of economical and practical applications for milk whey is still a challenge for dairy industries. This paper presents information about the development of a probiotic-prebiotic beverage based on Lactobacillus rhamnosus GG (LGG) and Costa Rican guava (CRG) fruit pulp with industrial potential. First, a supplemented whey media was developed for LGG growth, and the whey-supplemented media was used for fermentation in bioreactors. LGG reached a maximum growth rate of 0.32 hr^-1 after 48 hr of fermentation. The whey-grown probiotics were then mixed with CRG pulp to produce the probiotic-prebiotic beverage. The survival kinetics of LGG in the formulated drink was not affected by the addition of CRG pulp (P > 0.05), and the shelf-life of the inoculated beverage surpassed 40 days with a minimum population of 10⁶ colony forming units (CFU)/mL. Properties as pH, fructose, glucose, sucrose, and proanthocyanidins (PACs) content exhibited a significant difference after storage time (P < 0.05). Finally, three different formulas of the beverage with different whey content were compared through sensory evaluation. The prototype with 50% whey content was one of the most valuable beverage formulas according to the organoleptic parameters, which remarks about the possibility of developing a probiotic whey-based beverage containing CRG pulp. Furthermore, this is the first report about CRG beverages as a probiotic vector. PRACTICAL APPLICATION: This research focuses on the evaluation of the properties of a probiotic beverage, with a promissory industrial application using whey, as a dairy industry byproduct, combined with the pulp of the highly nutritious and subutilized Costa Rican guava (CRG) fruit.

Quantifying microbial growth and carbon use efficiency in dry soil environments via 18 O water vapor equilibration

Soil microbial physiology controls large fluxes of C to the atmosphere, thus, improving our ability to accurately quantify microbial physiology in soil is essential. However, current methods to determine microbial C metabolism require liquid water addition, which makes it practically impossible to measure microbial physiology in dry soil samples without stimulating microbial growth and respiration (namely, the "Birch effect"). We developed a new method based on in vivo ¹⁸ O-water vapor equilibration to minimize soil rewetting effects. This method allows the isotopic labeling of soil water without direct liquid water addition. This was compared to the main current method (direct ¹⁸ O-liquid water addition) in moist and air-dry soils. We determined the time kinetics and calculated the average ¹⁸ O enrichment of soil water over incubation time, which is necessary to calculate microbial growth from ¹⁸ O incorporation in genomic DNA. We tested isotopic equilibration patterns in three natural and six artificially constructed soils covering a wide range of soil texture and soil organic matter content. We then measured microbial growth, respiration and carbon use efficiency (CUE) in three natural soils (either air-dry or moist). The proposed ¹⁸ O-vapor equilibration method provided similar results as the current method of liquid ¹⁸ O-water addition when used for moist soils. However, when applied to air-dry soils the liquid ¹⁸ O-water addition method overestimated growth by up to 250%, respiration by up to 500%, and underestimated CUE by up to 40%. We finally describe the new insights into biogeochemical cycling of C that the new method can help uncover, and we consider a range of questions regarding microbial physiology and its response to global change that can now be addressed.

The In Vitro Analysis of Prebiotics to Be Used as a Component of a Synbiotic Preparation

Prebiotics are food components that are selectively fermented by beneficial microbiota and which confer a health benefit. The aim of the study was to select a prebiotic for the chosen probiotic strains to create a synbiotic. The impact of prebiotics (inulin, maltodextrin, corn starch, β-glucan, and apple pectin) on five Lactobacillus spp. strains' growth and metabolites synthesis (lactic, acetic, propionic, and butyric acids, ethanol, and acetaldehyde) was tested by the plate count method and by high-performance liquid chromatography, respectively. Moreover, the differences in the ratio of D(-) and L(+) lactate isomers produced by Lactobacillus spp., as well as variations in the probiotics' enzymatic profiles associated with the prebiotic used for cultivation, were determined with a Megazyme rapid assay kit and API® ZYM assay, accordingly. Finally, the influence of the carbon source (prebiotic) used on the antagonistic activity of the probiotic strains towards pathogenic bacteria, such as Salmonella spp. or Listeria monocytogenes was analyzed in the co-cultures. The results showed that the growth, metabolic profile, and antagonistic activity of the probiotics towards selected pathogens were the most favorable when 2% (w/v) of inulin was used. Therefore, the combination of inulin with selected probiotics is a promising synbiotic mixture.

A New Record for Microbial Perchlorate Tolerance: Fungal Growth in NaClO4 Brines and its Implications for Putative Life on Mars

The habitability of Mars is strongly dependent on the availability of liquid water, which is essential for life as we know it. One of the few places where liquid water might be found on Mars is in liquid perchlorate brines that could form via deliquescence. As these concentrated perchlorate salt solutions do not occur on Earth as natural environments, it is necessary to investigate in lab experiments the potential of these brines to serve as a microbial habitat. Here, we report on the sodium perchlorate (NaClO₄) tolerances for the halotolerant yeast Debaryomyces hansenii and the filamentous fungus Purpureocillium lilacinum. Microbial growth was determined visually, microscopically and via counting colony forming units (CFU). With the observed growth of D. hansenii in liquid growth medium containing 2.4 M NaClO₄, we found by far the highest microbial perchlorate tolerance reported to date, more than twice as high as the record reported prior (for the bacterium Planococcus halocryophilus). It is plausible to assume that putative Martian microbes could adapt to even higher perchlorate concentrations due to their long exposure to these environments occurring naturally on Mars, which also increases the likelihood of microbial life thriving in the Martian brines.

Microbial Growth on the Nails of Direct Patient Care Nurses Wearing Nail Polish

OBJECTIVES

To determine whether nurses wearing nail polish pose a greater infection risk to patients than nurses who are not wearing nail polish.

SAMPLE & SETTING

89 direct patient care oncology nurses at a large midwestern National Cancer Institute-designated comprehensive cancer center.

METHODS & VARIABLES

The investigators assigned participants' three middle fingers of their dominant hand to three groups.

RESULTS

Comparison of colony-forming units revealed that one-day-old polish exhibited fewer gram-positive microorganisms than the unpolished nail (p = 0.04). The four-day-old polish showed significantly more microorganisms than the one-day-old polish (p = 0.03). The same trend was demonstrated for gram-negative microorganisms, but the difference was not statistically significant (p = 0.3 and p = 0.17, respectively).

IMPLICATIONS FOR NURSING

The results should be interpreted and applied to expert nursing practice in the care of vulnerable patient populations. Each institution and practitioner should make their own decisions and interpretation of evidence into practice.

Glucose triggers strong taxon-specific responses in microbial growth and activity: insights from DNA and RNA qSIP

Growth of soil microorganisms is often described as carbon limited, and adding labile carbon to soil often results in a transient and large increase in respiration. In contrast, soil microbial biomass changes little, suggesting that growth and respiration are decoupled in response to a carbon pulse. Alternatively, measuring bulk responses of the entire community (total respiration and biomass) could mask ecologically important variation among taxa in response to the added carbon. Here, we assessed taxon-specific variation in cellular growth (measured as DNA synthesis) and metabolic activity (measured as rRNA synthesis) following glucose addition to soil using quantitative stable isotope probing with H₂ ¹⁸ O. We found that glucose addition altered rates of DNA and rRNA synthesis, but the effects were strongly taxon specific: glucose stimulated growth and rRNA transcription for some taxa, and suppressed these for others. These contrasting taxon-specific responses could explain the small and transient changes in total soil microbial biomass. Responses to glucose were not well predicted by a priori assignments of taxa into copiotrophic or oligotrophic categories. Across all taxa, rates of DNA and rRNA synthesis changed in parallel, indicating that growth and activity were coupled, and the degree of coupling was unaffected by glucose addition. This pattern argues against the idea that labile carbon addition causes a large reduction in metabolic growth efficiency; rather, the large pulse of respiration observed with labile substrate addition is more likely to be the result of rapid turnover of microbial biomass, possibly due to trophic interactions. Our results support a strong connection between rRNA synthesis and bacterial growth, and indicate that taxon-specific responses among soil bacteria can buffer responses at the scale of the whole community.