Filters
Dose–Response Effect of Nitrogen on Microbial Community during Hydrocarbon Biodegradation in Simplified Model System
Knowledge about the influence of C:N ratio on the biodegradation process of hydrocarbon compounds is of significant importance in the development of biostimulation techniques. The purpose of this study was to assess the impact of nitrogen compounds on the environmental consortium during the process of biological decomposition of hydrocarbons. The experimental variants represented low, moderate, and excessive biostimulation with nitrogen compounds. The metabolic activity of the consortium was tested using the flow cytometry technique. The efficiency of the biodegradation of hydrocarbons of the consortium, based on the gas chromatography method, and metapopulation changes, based on the analysis of V4 16srRNA sequencing data, were assessed. The results of the research confirm the positive effect of properly optimized biostimulation with nitrogen compounds on the biological decomposition of polycyclic aromatic hydrocarbons. The negative impact of excessive biostimulation on the biodegradation efficiency and metabolic activity of microorganisms is also proven. Low resistance to changes in the supply of nitrogen compounds is demonstrated among the orders Xanthomonadales, Burkholderiales, Sphingomonadales, Flavobacteriales, and Sphingobacteriales. It is proven that quantitative analysis of the order of Rhizobiales, characterized by a high-predicted potential for the decomposition of polycyclic aromatic hydrocarbons, may be helpful during biostimulation optimization processes in areas with a high nitrogen deficiency.
Konsorcjum bakteryjno-grzybowe i sposób bioremediacji gleby skażonej substancjami ropopochodnymi
Temperature, Salinity and Garlic Additive Shape the Microbial Community during Traditional Beetroot Fermentation Process
Plant-based traditional fermented products are attracting a lot of interest in global markets. An example of them is beetroot leaven, which is valued for its high bioactive compound content. The variety of production recipes and the spontaneous nature of red beet fermentation favor its high diversity. This study aimed to analyze the impact of external factors—temperature, brine salinity, and garlic dose—on the beetroot fermentation and bacterial metapopulation responsible for this process. The research results confirmed the significant influence of the selected and analyzed factors in shaping the leaven physicochemical profile including organic acid profile and betalain content. Analysis of bacterial populations proved the crucial importance of the first 48 h of the fermentation process in establishing a stable metapopulation structure and confirmed that this is a targeted process driven by the effect of the analyzed factors. Lactobacillaceae, Enterobacteriaceae, and Leuconostocaceae were observed to be the core microbiome families of the fermented red beet. Regardless of the impact of the tested factors, the leaven maintained the status of a promising source of probiotic bacteria. The results of this research may be helpful in the development of the regional food sector and in improving the quality and safety of traditionally fermented products such as beetroot leaven.
Optimization of the flow cytometry method of detection, quantification and qualification of microorganisms in carrot juice
Microbiome of Bovine Milk and Factors Influencing Its Composition
The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.
2,4-D versus 2,4-D based ionic liquids: Effect of cation on herbicide biodegradation, tfdA genes abundance and microbiome changes during soil bioaugmentation.
The Influence of Bacteria Causing Subclinical Mastitis on the Structure of the Cow’s Milk Microbiome
Mastitis is the most expensive disease of dairy cattle across the world and is the main reason for the use of antibiotics in animal husbandry. The aim of this study was to analyze the microbiome of raw milk obtained from a semi-subsistence farm located in the Kuyavian–Pomeranian Voivodeship in Poland. Milk from healthy cows and from cows with subclinical mastitis was analyzed. The following pathogenic bacteria were found in milk from individuals with subclinical mastitis: Escherichia coli or Streptococcus agalactiae. The composition of drinking milk was assessed on the basis of 16S rRNA gene sequencing using the Ion Torrent platform. Based on the conducted research, significant changes in the composition of the milk microbiome were found depending on the physiological state of the cows. The microbiome of milk from healthy cows differed significantly from the milk from cows with subclinical mastitis. Two phyla dominated in the milk from healthy cows: Firmicutes and Proteobacteria, in equal amounts. On the contrary, in the milk from cows with diagnosed subclinical mastitis, one of the types dominated: either Firmicutes or Proteobacteria, and was largely predominant. Moreover, the milk microflora from the ill animals were characterized by lower values of the determined biodiversity indicators than the milk from healthy cows. The presence of pathogenic bacteria in the milk resulted in a significant reduction in the share of lactic acid bacteria in the structure of the population of microorganisms, which are of great importance in the production technology of regional products.
Effect of Processing Treatment and Modified Atmosphere Packing on Carrot’s Microbial Community Structure by Illumina MiSeq Sequencing
The aim of this study was to analyze the microbiome of carrot (Daucus carota subsp. sativus) subjected to minimal pre-treatment (rinsing in organic acid solution) and packaging in a high-oxygen modified atmosphere, and then stored for 17 days under refrigeration conditions (4 °C). The highest levels of bacteria in the carrot microbiome were characterized, at almost 78%, by bacteria belonging to the Enterobacteriaceae and Pseudomonadaceae families. Rinsing in a solution of ascorbic and citric acids resulted in the improvement of microbiological quality in the first day of storage. However, the use of a high-oxygen modified atmosphere extended the shelf life of the minimally processed product. Compared to carrots stored in air, those stored in high oxygen concentration were characterized by a greater ratio of bacteria belonging to the Serratia and Enterobacter genera, and a lower ratio belonging to the Pseudomonas and Pantoea genera. Moreover, the β-biodiversity analysis confirmed that the oxygen concentration was the main factor influencing the differentiation of the metabiomes of the stored carrots. The bacterial strains isolated from carrots identified by molecular methods were mostly pathogenic or potentially pathogenic microorganisms. Neither the minimal pre-treatment nor packaging in high-oxygen atmosphere was able to eliminate the threat of pathogenic bacteria emerging in the product.
Sposób usuwania zanieczyszczeń ropopochodnych z gleby na drodze biodegradacji przy użyciu kwasów humusowych i hydrolizatu drożdżowego
Analysis of the Effect of Various Potential Antimicrobial Agents on the Quality of the Unpasteurized Carrot Juice
Short shelf-life and poor microbial quality of minimally processed foods of plant origin pose a serious problem for the food industry. Novel techniques of minimal treatment combined with disinfection are being researched, and, for fresh juice, the addition of antimicrobial agents appears to be a promising route. In this research, fresh, nonfiltered, unpasteurized carrot juice was mixed with four potential antimicrobials (bourbon vanilla extract, peppermint extract, cannabidiol oil, and grapefruit extract). All four variants and the reference pure carrot juice were analyzed for metapopulational changes, microbial changes, and physicochemical changes. The potential antimicrobials used in the research have improved the overall microbial quality of carrot juice across 4 days of storage. However, it is important to notice that each of the four agents had a different spectrum of effectiveness towards the groups identified in the microflora of carrot juice. Additionally, the antimicrobials have increased the diversity of the carrot juice microbiome but did not prevent the occurrence of pathogenic bacteria. In conclusion, the use of antimicrobial agents such as essential oils or their derivatives may be a promising way of improving the microbial quality and prolonging the shelf-life of minimally processed foods, such as fresh juices, but the technique requires further research.
Fungi of the Trichoderma Genus: Future Perspectives of Benefits in Sustainable Agriculture
The negative impact of chemical pesticides on the environment and human health has contributed to the introduction of legal regulations that ensure the reduction in the use of agrochemicals in favor of biological products. The existing review of the literature, including our research, clearly shows that the ideal biocontrol agents are Trichoderma fungi. The production of antibiotics, lytic enzymes degrading the cell walls of plant pathogens, or inducing a defense response in plants are just some of the features supporting the wide use of these microorganisms in sustainable agriculture. It is estimated that currently about 60% of biofungicides used to eliminate fungal pathogens are produced based on Trichoderma sp. strains.
Development and Validation of the LC–MS/MS Method for Determination of 130 Natural and Synthetic Cannabinoids in Cannabis Oil
Dietary supplements are widely available products used by millions of people around the world. Unfortunately, the procedure of adding pharmaceutical and psychoactive substances has recently been observed, in order to increase the effectiveness of supplements in the form of hemp oils. For this reason, it is extremely important to develop analytical methods for the detection of substances prohibited in dietary supplements and food products. In the present study, using the LC–MS/MS technique, an innovative method for the detection and quantification of 117 synthetic cannabinoids and 13 natural cannabinoids in dietary supplements and food products in the form of oils during one 13-min chromatographic run was developed. Each method was fully validated by characterization of the following parameters: The limit of detection was set to 0.1 ng/mL (100 µg/g, 0.01%). The limit of quantification ranged from 0.05 ng/mL to 50 ng/mL. The criteria assumed for systematic error caused by methodological bias (±20%) resulting from the recovery of analytes after the extraction process, as well as the coefficient of variation (CV) (≤20%), were met for all 130 tested compounds. The positive results of the validation confirmed that the developed methods met the requirements related to the adequacy of their application in a given scope. Additionally, methods developed using the LC–MS/MS technique were verified via proficiency tests. The developed analytical procedure was successfully used in the analysis of hemp oils and capsules containing them in the studied dietary supplements.
Grapevine and Horseradish Leaves as Natural, Sustainable Additives for Improvement of the Microbial, Sensory, and Antioxidant Properties of Traditionally Fermented Low-Salt Cucumbers
The agro-food industry produces large amounts of secondary by-products, which can act as a source of bio-active ingredients. These ingredients can be used as valuable additives to support the sustainable circular economy concept. This study aimed to analyze the potential application of horseradish and grapevine leaves in the fermentation process of low-salt pickled cucumbers to improve their sensory and functional properties. The pour plate technique, RT-qPCR, HPLC, and a nine-point hedonic scale test with penalty analysis were used to analyze the traditionally fermented product. The research showed that the addition of both horseradish and grapevine leaves did not negatively affect the kinetics of fermentation and had a positive effect on the overall desirability. Moreover, they contributed to an increase in the concentration of antioxidant compounds, namely gallic acid (grape leaves) and ellagic acid (grapevine and horseradish leaves). Bacterial metabiome analysis showed the positive effect of all analyzed additives on an increase in the relative expression of genes responsible for the synthesis of selected bacteriocins (plantaricin and acidocin). Research results indicated a high potential for sustainable use of by-products (horseradish and grapevine leaves) in the production of traditional low-salt fermented cucumbers with high health-promoting potential.