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18 pages, 1363 KB  
Article
Rosemary Extract: Phytochemical Composition and Potential for Eliminating Polymicrobial Biofilm of Candida albicans and Multidrug-Resistant Bacteria
by Tuana Mendonça Faria Cintra, Raquel Teles de Menezes, Lara Steffany de Carvalho, Leticia de Miguel Nazario, Leandro Wang Hantao, Maria Cristina Marcucci, Luciane Dias de Oliveira and Vanessa Marques Meccatti-Domiciano
BioTech 2025, 14(3), 61; https://doi.org/10.3390/biotech14030061 - 13 Aug 2025
Viewed by 365
Abstract
Herbal medicines can be promising for the treatment of infections caused by multidrug-resistant microorganisms. This study aimed to evaluate Rosmarinus officinalis (Rosemary) hydroalcoholic extract (RHE) regarding its phytochemical composition and potential for eliminating polymicrobial biofilm of Candida albicans with multidrug-resistant bacteria (Acinetobacter [...] Read more.
Herbal medicines can be promising for the treatment of infections caused by multidrug-resistant microorganisms. This study aimed to evaluate Rosmarinus officinalis (Rosemary) hydroalcoholic extract (RHE) regarding its phytochemical composition and potential for eliminating polymicrobial biofilm of Candida albicans with multidrug-resistant bacteria (Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa). The extraction and quantification of the extract (flavonoids and phenols) were performed, and its antioxidant activity (DPPH) and the presence of bio-active compounds were investigated using high-performance liquid chromatography with Diode Array Detection (HPLC-DAD) and Gas Chromatography–Mass Spectrometry (GC-MS). The minimum inhibitory concentration (MIC) and minimum microbicidal concentration (MMC) were determined, and the extract’s action on polymicrobial biofilms was evaluated using the MTT assay. Data were analyzed using one-way ANOVA and Tukey’s tests, as well as Kruskal–Wallis and Dunn’s tests, with a significance level of 5%. RHE showed compatible amounts of flavonoids and phenols, with an EC50 of 19.53 µg/mL. Through HPLC-DAD and GC-MS, biomolecules such as rosmarinic acid and α-Pinene were identified. The extract exhibited microbicidal activity and antibiofilm action, with reduction percentages of up to 69.6% (p < 0.05), showing superior performance compared to 0.12% chlorhexidine against C. albicans + A. baumannii. In conclusion, RHE may be a promising therapeutic agent against multidrug-resistant pathogens. Full article
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10 pages, 1883 KB  
Article
In Vitro Biofilm Formation Kinetics of Pseudomonas aeruginosa and Escherichia coli on Medical-Grade Polyether Ether Ketone (PEEK) and Polyamide 12 (PA12) Polymers
by Susana Carbajal-Ocaña, Kristeel Ximena Franco-Gómez, Valeria Atehortúa-Benítez, Daniela Mendoza-Lozano, Luis Vicente Prado-Cervantes, Luis J. Melgoza-Ramírez, Miguel Delgado-Rodríguez, Mariana E. Elizondo-García and Jorge Membrillo-Hernández
Hygiene 2025, 5(3), 32; https://doi.org/10.3390/hygiene5030032 - 1 Aug 2025
Viewed by 339
Abstract
Biofilms, structured communities of microorganisms encased in an extracellular matrix, are a major cause of persistent infections, particularly when formed on medical devices. This study investigated the kinetics of biofilm formation by Escherichia coli and Pseudomonas aeruginosa, two clinically significant pathogens, on [...] Read more.
Biofilms, structured communities of microorganisms encased in an extracellular matrix, are a major cause of persistent infections, particularly when formed on medical devices. This study investigated the kinetics of biofilm formation by Escherichia coli and Pseudomonas aeruginosa, two clinically significant pathogens, on two medical-grade polymers: polyether ether ketone (PEEK) and polyamide 12 (PA12). Using a modified crystal violet staining method and spectrophotometric quantification, we evaluated biofilm development over time on polymer granules and catheter segments composed of these materials. Results revealed that PEEK surfaces supported significantly more biofilm formation than PA12, with peak accumulation observed at 24 h for both pathogens. Conversely, PA12 demonstrated reduced bacterial adhesion and lower biofilm biomass, suggesting surface characteristics less conducive to microbial colonization. Additionally, the study validated a reproducible protocol for assessing biofilm formation, providing a foundation for evaluating anti-biofilm strategies. While the assays were performed under static in vitro conditions, the findings highlight the importance of material selection and early prevention strategies in the design of infection-resistant medical devices. This work contributes to the understanding of how surface properties affect microbial adhesion and underscores the critical need for innovative surface modifications or coatings to mitigate biofilm-related healthcare risks. Full article
(This article belongs to the Section Hygiene in Healthcare Facilities)
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15 pages, 3942 KB  
Article
Quantitative Evaluation of Endogenous Reference Genes for RT-qPCR and ddPCR Gene Expression Under Polyextreme Conditions Using Anaerobic Halophilic Alkalithermophile Natranaerobius thermophilus
by Xinyi Tao, Qinghua Xing, Yingjie Zhang, Belsti Atnkut, Haozhuo Wei, Silva Ramirez, Xinwei Mao and Baisuo Zhao
Microorganisms 2025, 13(8), 1721; https://doi.org/10.3390/microorganisms13081721 - 23 Jul 2025
Viewed by 372
Abstract
Accurate gene expression quantification using reverse transcription quantitative PCR (RT-qPCR) requires stable reference genes (RGs) for reliable normalization. However, few studies have systematically identified RGs suitable for simultaneous high salt, alkaline, and high-temperature conditions. This study addresses this gap by evaluating the stability [...] Read more.
Accurate gene expression quantification using reverse transcription quantitative PCR (RT-qPCR) requires stable reference genes (RGs) for reliable normalization. However, few studies have systematically identified RGs suitable for simultaneous high salt, alkaline, and high-temperature conditions. This study addresses this gap by evaluating the stability of eight candidate RGs in the anaerobic halophilic alkalithermophile Natranaerobius thermophilus JW/NM-WN-LFT under combined salt, alkali, and thermal stresses. The stability of these candidate RGs was assessed using five statistical algorithms: Delta CT, geNorm, NormFinder, BestKeeper, and RefFinder. Results indicated that recA exhibited the highest expression stability across all tested conditions and proved adequate as a single RG for normalization in both RT-qPCR and droplet digital PCR (ddPCR) assays. Furthermore, recA alone or combined with other RGs (sigA, rsmH) effectively normalized the expression of seven stress-response genes (proX, opuAC, mnhE, nhaC, trkH, ducA, and pimT). This work represents the first systematic validation of RGs under polyextreme stress conditions, providing essential guidelines for future gene expression studies in extreme environments and aiding research on microbial adaptation mechanisms in halophilic, alkaliphilic, and thermophilic microorganisms. Full article
(This article belongs to the Section Environmental Microbiology)
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16 pages, 472 KB  
Article
Evaluation of the Biodegradation Potential of Phytopathogenic Fungi in Sugar Cane (Saccharum officinarum) Waste from the Rural Sector of Milagro, Ecuador
by Sandra Campuzano-Rodríguez, Fabricio Guevara-Viejó, Arturo Guevara-Sandoya, Juan Diego Valenzuela-Cobos and Claudia Pozzi Jantalia
Appl. Sci. 2025, 15(12), 6621; https://doi.org/10.3390/app15126621 - 12 Jun 2025
Viewed by 410
Abstract
In Ecuador, sugarcane (Saccharum officinarum) is a grass of great socioeconomic impact due to the employment rate involved in its cultivation and its use as a raw material for obtaining sugar and other derivatives. The industrial processing of the usable sugarcane [...] Read more.
In Ecuador, sugarcane (Saccharum officinarum) is a grass of great socioeconomic impact due to the employment rate involved in its cultivation and its use as a raw material for obtaining sugar and other derivatives. The industrial processing of the usable sugarcane material generates an excessive amount of waste, including leaves, bagasse, molasses, and other types of organic residues. Waste treatment systems have demonstrated inefficiency in the degradation time with respect to the harmful effects they cause. In this study, the dynamics of two genera of phytopathogenic microorganisms (Colletotrichum spp. and Rhizopus spp.) in the decomposition of sugarcane organic wastes were tested by analyzing the proximate composition, biodegradation characteristics, microbial incidence, and amino acid content. The results showed that inoculation with a combination of 2.00 × 106 spores/mL of Colletotrichum spp. and 2.00 × 106 spores/mL of Rhizopus spp., corresponding to treatment T4, led to a higher degree of biodegradation of the residues and aspartic amino acid content, with an incidence of 14.11 mmol/100 g. The amount of amino acids was not closely related to the addition of microorganisms, since the wastes belonging to the control treatment were not recorded as the wastes with the lowest concentration. On the other hand, the different treatments induced variations in the quantification of microorganisms in each biodegraded waste, reporting an average of 5.43 × 104 CFU/g of mesophilic bacteria and 6.52 × 104 CFU/g of fungi with treatment T2. The amounts obtained highlighted the predominance of cycles of increase and decrease in the concentration of microorganisms in a compost according to the stage of compost maturation. Full article
(This article belongs to the Special Issue Research Progress in Waste Resource Utilization)
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14 pages, 1696 KB  
Article
Development of Multiplex qPCR Method for Accurate Detection of Enzyme-Producing Psychrotrophic Bacteria
by Kidane Yalew, Shuwen Zhang, Solomon Gebreyowhans, Ning Xie, Yunna Wang, Jiaping Lv, Xu Li and Xiaoyang Pang
Foods 2025, 14(11), 1975; https://doi.org/10.3390/foods14111975 - 3 Jun 2025
Viewed by 691
Abstract
Microbial detection in milk is crucial for food safety and quality, as beneficial and harmful microorganisms can affect consumer health and dairy product integrity. Identifying and quantifying these microorganisms helps prevent contamination and spoilage. The study employs advanced molecular techniques to detect and [...] Read more.
Microbial detection in milk is crucial for food safety and quality, as beneficial and harmful microorganisms can affect consumer health and dairy product integrity. Identifying and quantifying these microorganisms helps prevent contamination and spoilage. The study employs advanced molecular techniques to detect and quantify the genomic DNA for the target hydrolytic enzyme coding genes lipA and aprX based on the multi-align sequence conserved region, specific primer pair, and hydrolysis probes designed using the singleplex qPCR and multiplex qPCR. Cultured isolates and artificially contaminated sterilized ultra-high-temperature (UHT) milk were analyzed for their specificity, cross-reactivity, and sensitivity. The finding indicated that strains with lipA and aprX genes were amplified while the other strains were not amplified. This indicated that the designed primer pairs/probes were very specific to the target gene of interest. The specificity of each design primer pair was checked using SYBR Green qPCR using 16 different isolate strains from the milk sample. The quantification specificity of each strain target gene was deemed to be with a mean Ct value for positive pseudomonas strain > 16.98 ± 1.76 (p < 0.0001), non-pseudomonas positive strain ≥ 27.47 ± 1.25 (p < 0.0001), no Ct for the negative control and molecular grade water. The sensitivity limit of detection (LOD) analyzed based on culture broth and milk sample was >105 and >104 in PCR amplification while it was >104 and >103 in real-time qPCR, respectively. At the same time, the correlation regression coefficient of the standard curve based on the pure culture cell DNA as the DNA concentration serially diluted (20 ng/µL to 0.0002 ng/µL) was obtained in multiplex without interference and cross-reactivity, yielding R2 ≥ 0.9908 slope (−3.2591) and intercepting with a value of 37, where the efficiency reached the level of 95–102% sensitivity reached up to 0.0002 ng/µL concentration of DNA, and sensitivity of microbial load was up to 1.2 × 102 CFU/mL. Therefore, multiplex TaqMan qPCR simultaneous amplification was considered the best method developed for the detection of the lipA and aprX genes in a single tube. This will result in developing future simultaneous (three- to four-gene) detection of spoilage psychrotrophic bacteria in raw milk. Full article
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22 pages, 3577 KB  
Article
Metschnikowia pulcherrima and Lachancea thermotolerans Killer Toxins: Contribution to Must Bioprotection
by Fatima El Dana, Vanessa David, Mohammad Ali Hallal, Raphaëlle Tourdot-Maréchal, Salem Hayar, Marie-Charlotte Colosio and Hervé Alexandre
Foods 2025, 14(9), 1462; https://doi.org/10.3390/foods14091462 - 23 Apr 2025
Viewed by 2373
Abstract
The spoilage of wine caused by Brettanomyces bruxellensis and Hanseniaspora uvarum poses a significant challenge for winemakers, necessitating the development of effective and reliable strategies to control the growth of these yeasts, such as grape must bioprotection. Despite evidence that certain microorganisms can [...] Read more.
The spoilage of wine caused by Brettanomyces bruxellensis and Hanseniaspora uvarum poses a significant challenge for winemakers, necessitating the development of effective and reliable strategies to control the growth of these yeasts, such as grape must bioprotection. Despite evidence that certain microorganisms can inhibit the growth of Brettanomyces bruxellensis and Hanseniaspora uvarum, the specific mechanisms driving this inhibition remain unclear. The primary objective of this study is to elucidate the underlying mechanisms responsible for this inhibitory effect. We analyzed one Metschnikowia pulcherrima (Mp2) and two Lachancea thermotolerans (Lt29 and Lt45) strains, all of which demonstrated significant killing and inhibitory effects on Brettanomyces bruxellensis (B1 and B250) and Hanseniaspora uvarum (Hu3137) in synthetic must at pH 3.5 and 22 °C. The effectiveness of these two strains exhibited varying inhibition kinetics. The strains were monitored for growth and metabolite production (L-lactic acid, ethanol, and acetic acid) in both single and co-cultures. The low levels of these metabolites did not account for the observed bioprotective effect, indicating a different mechanism at play, especially given the different growth profiles observed with added L-lactic acid and ethanol compared to direct bioprotectant addition. Following the production, purification, and quantification of killer toxins, different concentrations of toxins were tested, showing that the semi-purified Mp2Kt, Lt29Kt, and Lt45Kt toxins controlled the growth of both spoilage yeasts in a dose-dependent manner. These bioprotectant strains also showed compatibility with Saccharomyces cerevisiae in co-cultures, suggesting their potential use alongside commercial starter cultures. Full article
(This article belongs to the Section Food Microbiology)
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15 pages, 1630 KB  
Article
Chemical Profile Analysis of Prosopis laevigata Extracts and Their Topical Anti-Inflammatory and Antibacterial Activities
by Manasés González-Cortazar, David Osvaldo Salinas-Sánchez, Maribel Herrera-Ruiz, Paulina Hernández-Hernández, Alejandro Zamilpa, Enrique Jiménez-Ferrer, Beatriz E. Utrera-Hernández, Ma. Dolores Pérez-García, Ana S. Gutiérrez-Roman and Ever A. Ble-González
Plants 2025, 14(7), 1118; https://doi.org/10.3390/plants14071118 - 3 Apr 2025
Cited by 2 | Viewed by 729
Abstract
There are two major global morbidity and mortality problems in the health sector: inflammation, which is the physiological process that, in acute and chronic conditions, gradually causes the loss of the body’s functionality, leading to severe damage to health; and microbial diseases, which [...] Read more.
There are two major global morbidity and mortality problems in the health sector: inflammation, which is the physiological process that, in acute and chronic conditions, gradually causes the loss of the body’s functionality, leading to severe damage to health; and microbial diseases, which are caused by pathogenic microorganisms such as bacteria. In the present study, the anti-inflammatory effects of three extracts of mesquite (Prosopis laevigata)n-hexane (PH), dichloromethane (PD), and methanol (PM)—were assessed in a mouse model of 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced ear oedema, and the antimicrobial effects against 14 microorganisms were assessed using the broth microdilution method. The extracts inhibited ear oedema by 60.81% (PH), 75.96% (PD), and 60.29% (PM). The most active anti-inflammatory extract (PD) was fractionated through chromatography, and three fractions (PDR3, PDR6, and PDR7) were evaluated. One of the most active fractions (PDR7) was purified via column chromatography, and ethyl veratrate (VE, 1) was isolated and identified. VE inhibited ear oedema by 85.1%. The anti-inflammatory effect is evidenced by the quantification of two pro-inflammatory cytokines (IL-10 and TNF-α). The PD extract, the PDR7 fraction, and the compound present an IL-10 concentration of 11.8, 18.9, and 36.5 pg/mg of protein, values significantly higher than the group that received only phorbol ester (* p < 0.05). These treatments also significantly decreased the concentration of TNF-α (* p < 0.05) to 197.6, 241.9, and 247.0 pg/mg protein, respectively. The PM extract showed the most pronounced antimicrobial effect, with a minimum inhibitory concentration (MIC) of <12.5 µg/mL for almost all the 14 tested strains, followed by the PD and PH extracts. Chromatographic fractionation of the PM extract yielded the PMR6, PMR7, and PMR10 fractions that inhibited all tested microorganisms with a MIC between 6.25 and 200 µg/mL. Compound 1 was active on five strains, with a concentration between 2 and 8 µg/mL. High-performance liquid chromatography analysis and comparison with commercial standards allowed for the identification of rutin (2) and quercetin 3-O-glucoside (3). Gas chromatography–mass spectrometry analysis of the PH and PD extracts allowed for the identification of fatty acids, terpenes, and phenols. Full article
(This article belongs to the Section Phytochemistry)
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19 pages, 9067 KB  
Review
The Aroma of Non-Fermented and Fermented Dry-Cured Meat Products: Savory and Toasted Odors
by Lei Li, Carmela Belloch and Mónica Flores
Foods 2025, 14(5), 881; https://doi.org/10.3390/foods14050881 - 5 Mar 2025
Viewed by 1600
Abstract
Volatile chemicals containing nitrogen and sulfur as key odors in dry-cured meat products have extremely low odor thresholds. These compounds play an important part in the overall uniqueness and characteristic flavor of dry-cured meat products, contributing to savory and toasted aroma sensations, respectively. [...] Read more.
Volatile chemicals containing nitrogen and sulfur as key odors in dry-cured meat products have extremely low odor thresholds. These compounds play an important part in the overall uniqueness and characteristic flavor of dry-cured meat products, contributing to savory and toasted aroma sensations, respectively. In this review, we define the different volatiles and aroma compounds related to the flavor of dry-cured meat products. Moreover, the main differences regarding volatiles, aromas, and flavor profiles from non-fermented and fermented dry-cured meat products are summarized. Comparisons using the same volatile extraction techniques revealed that dry loins contained the most sulfur- and nitrogen-containing compounds, while complex flavor and aroma compounds in fermented sausages were greatly impacted by the fermentation process. The screening and quantification of savory and toasted odors showed that methionol, dimethyl sulfide, and 2-methyl-3-(methylthio)furan were mainly reported in non-fermented products, whereas pyrazines were mainly detected in fermented meat products. Finally, the different mechanisms in the generation of savory and toasted aromas, including chemical reactions and biochemical reactions by microorganisms (bacteria, yeast, and molds), are discussed. These discussions will help to better understand the complex flavor of dry-cured meat products. Full article
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10 pages, 244 KB  
Article
New Method for Lawsonia intracelullaris Quantification Based on Optical Density by Spectrophotometry
by Mirtha E. Suarez-Duarte, Ricardo P. Laub, Renato L. Santos, Carlos E. R. Pereira, Talita P. Resende, Matheus D. Araujo, Paula A. Correia, Jessica C. R. Barbosa and Roberto M. C. Guedes
Microorganisms 2025, 13(3), 568; https://doi.org/10.3390/microorganisms13030568 - 3 Mar 2025
Viewed by 780
Abstract
Studies investigating the pathogenesis of Lawsonia intracellularis often require bacterial quantification in suspension. However, due to the organism’s fastidious growth requirements—being both intracellular and microaerophilic—traditional quantification methods, such as colony-forming unit counting, are not feasible. Currently, the only widely available method for quantifying [...] Read more.
Studies investigating the pathogenesis of Lawsonia intracellularis often require bacterial quantification in suspension. However, due to the organism’s fastidious growth requirements—being both intracellular and microaerophilic—traditional quantification methods, such as colony-forming unit counting, are not feasible. Currently, the only widely available method for quantifying L. intracellularis is real-time quantitative PCR (RT-qPCR). Unfortunately, the time required to perform RT-qPCR is incompatible with the bacterium’s limited survival outside its intracellular and microaerophilic environment. As a result, bacterial suspensions are typically quantified subjectively, based on the researcher’s experience for immediate use, with RT-qPCR conducted afterward. Optical density (OD) spectrophotometry is a rapid, although indirect, method of estimating bacterial concentrations in suspension, and it has been applied successfully to fast-growing prokaryotic species. Therefore, the objective of this study was to determine the correlation between RT-qPCR results and the optical density of L. intracellularis suspensions, with the goal of enabling the use of spectrophotometry for immediate bacterial quantification in experimental settings. Optical densities (ODs) were measured at 405 nm and 450 nm, using either a cuvette or microplate, while RT-qPCR was employed to establish a standard curve from samples of known concentration and to quantify the concentration of L. intracellularis in the test suspensions. Four comparison variations between OD and RT-qPCR were evaluated: (1) spectrophotometry at 405 nm using a cuvette vs. RT-qPCR; (2) spectrophotometry at 405 nm using a microplate vs. RT-qPCR; (3) spectrophotometry at 450 nm using a cuvette vs. RT-qPCR; and (4) spectrophotometry at 450 nm using a microplate vs. RT-qPCR. The tests were conducted in two independent replications, with each sample analyzed in duplicate. In all variations, the correlation between the bacterial concentrations determined by RT-qPCR and those estimated by OD was greater than 80%, with a statistical significance of p < 0.05. The following OD conversion equations for determining the number of microorganisms/mL were obtained: (1) f(x) = −7.438 × 108 + 1.797 × 1010. x; (2) f(x) = 3.255 × 108 + 3.003 × 109. x; (3) f(x) = −8.006 × 108 + 2.169 × 1010. x; (4) f(x) = 3.107 × 108 + 3.758 × 109. x. Here, “X” is the Ct value obtained by RT-qPCR. These findings enable researchers to improve the accuracy of their L. intracellularis experiments by utilizing optical spectrometry—a straightforward method that provides immediate results for determining bacterial concentration in suspensions. Full article
(This article belongs to the Section Microbial Biotechnology)
18 pages, 6588 KB  
Article
Three-Year Follow-Up Assessment of Anthropogenic Contamination in the Nichupte Lagoon
by Jorge Herrera-Silveira, Flor Arcega-Cabrera, Karina León-Aguirre, Elizabeth Lamas-Cosio, Ismael Oceguera-Vargas, Elsa Noreña-Barroso, Daniela Medina-Euán and Claudia Teutli-Hernández
Appl. Sci. 2024, 14(24), 11889; https://doi.org/10.3390/app142411889 - 19 Dec 2024
Viewed by 1577
Abstract
Tourism still represents a means of generating revenues in the coastal areas in the Mexican Caribbean, despite the growing concern about the social and environmental impacts. The Nichupte Lagoon System (NLS), the most representative lagoon of Quintana Roo State for being in the [...] Read more.
Tourism still represents a means of generating revenues in the coastal areas in the Mexican Caribbean, despite the growing concern about the social and environmental impacts. The Nichupte Lagoon System (NLS), the most representative lagoon of Quintana Roo State for being in the middle of Cancun’s hotel development, has experienced a continuous drop-off in its water quality due to several factors, including dredging and wastewater discharges from different anthropogenic activities, which modify the flux of nutrients, increase the number of pathogenic microorganisms, and promote physicochemical changes in this ecosystem. Three sampling campaigns (2018, 2019, and 2020) were carried out in the NLS in August, which is the month of greatest tourist occupancy. To evidence the presence of anthropogenic wastewater in the NLS, the caffeine tracer was used, and to determine the water quality, 43 sampling stations were monitored for “in situ” physicochemical parameters (salinity and dissolved oxygen), and water samples were collected for the quantification of nutrients (NO2 + NO3, NH4+, SRP and SRSi) and chlorophyll-a (Chl-a). For data analysis, the lagoon was subdivided into five zones (ZI, ZII, ZIII, ZIV, and ZV). Caffeine spatial and time variation evidence (1) the presence of anthropogenic wastewater in all areas of the NLS probably resulting from the tourist activity, and (2) wastewater presence is directly influenced by the coupling of the hydrological changes driven by anomalous rain events and the number of tourists. This same tendency was observed for nutrients that increased from 2018 to 2019 and the trophic state changed from oligotrophic to hypertrophic in all areas, as a result of previous anomalous precipitations in 2018, followed by normal precipitations in 2019. From 2019 to 2020, the nutrients decreased due to the drop in tourism due to COVID-19, promoting fewer nutrients in the lagoon, but, also coupled with an anomalous precipitation event (Cristobal storm), resulted in a dilution phenomenon and an oligotrophic state. The cluster analysis indicated that the least similar zones in the lagoon were the ZI and ZV due to their geomorphology that restricts the connection with the rest of the system. Principal component analysis revealed that wastewater presence evidenced by the caffeine tracer had a positive association with dissolved oxygen and chlorophyll-a, indicating that the arrival of nutrients from wastewater amongst other sources promotes algal growth, but this could develop into an eutrophic or hypertrophic state under normal precipitation conditions as seen in 2019. This study shows the relevance of monitoring in time of vulnerable karstic systems that could be affected by anthropogenic contamination from wastewater inputs, stressing the urgent need for efficient wastewater treatment in the area. The tourist industry in coastal karstic lagoons such as the NLS must have a Wastewater Treatment Program as a compensation measure for the anthropic pressure that is negatively changing the water quality of this highly relevant socio-environmental system. Full article
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14 pages, 1377 KB  
Article
The Effects of Predominantly Chemoautotrophic Versus Heterotrophic Biofloc Systems on Nitrifying Bacteria, Planktonic Microorganisms, and Growth of Penaeus vannamei, and Oreochromis niloticus in an Integrated Multitrophic Culture
by Raysa Pâmela Oliveira Sena, Dariano Krummenauer, Wilson Wasielesky, Otávio Augusto Lacerda Ferreira Pimentel, Aline Bezerra, Jorge Renato Tagliaferro dos Santos Junior, Andrezza Carvalho, Elisa Ravagnan, Andrea Bagi and Luis H. S. Poersch
Fishes 2024, 9(12), 478; https://doi.org/10.3390/fishes9120478 - 26 Nov 2024
Cited by 1 | Viewed by 1672
Abstract
The aim of this study was to evaluate the effect of predominantly chemoautotrophic and heterotrophic biofloc systems on ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and planktonic microorganisms in an integrated Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. Shrimp and tilapia were stocked [...] Read more.
The aim of this study was to evaluate the effect of predominantly chemoautotrophic and heterotrophic biofloc systems on ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), and planktonic microorganisms in an integrated Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. Shrimp and tilapia were stocked at a density of 400 shrimp m−2 and 45 fish m−3, respectively. The trial consisted of two biofloc treatments, with three replicates each: chemoautotrophic and heterotrophic. The identification and quantification of the planktonic microorganisms (ciliates, flagellates, microalgae, and total bacteria) and nitrifying bacteria were carried out through direct counting and fluorescence in situ hybridization, respectively. At the end of the trial, heterotrophic treatment had resulted in higher total abundance of bacteria. The relative abundance of AOB and NOB in relation to the total abundance was less than 0.1% for both treatments. The system was dominated by flagellates in both treatment groups. The abundance of microalgae and ciliates was higher with chemoautotrophic treatment. After 43 days, the shrimp weights were higher in the chemoautotrophic group, while the final weights of the tilapia were not significantly different between the two treatments. The type of biofloc system (Chemoautotrophic vs. Heterotrophic) did not significantly alter the establishment of AOB and NOB in a Penaeus vannamei and Oreochromis niloticus integrated multitrophic culture. The two treatments proved to be equally efficient for maintaining good water quality, but the chemoautotrophic treatment resulted in better shrimp growth. Thus, our study demonstrated that chemoautotrophic biofloc is a promising approach in integrated multitrophic aquaculture. Full article
(This article belongs to the Special Issue Biofloc Technology in Aquaculture)
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13 pages, 4189 KB  
Article
Spatiotemporal Distribution of nirS-Type Denitrifiers in Cascade Reservoir Sediments of the Qinghai Plateau
by Yi Wu, Xufeng Mao, Hongyan Yu, Hongyan Li, Feng Xiao, Yuhua Mo, Haichuan Ji and Yuanjie Ma
Diversity 2024, 16(11), 656; https://doi.org/10.3390/d16110656 - 24 Oct 2024
Viewed by 931
Abstract
Compared to single damming, the impact of cascade damming on nitrogen-related microorganisms in river ecosystems exhibits greater complexity. However, there is still a lack of research on the response of denitrifiers to the construction of cascade reservoirs. A study was conducted on 10 [...] Read more.
Compared to single damming, the impact of cascade damming on nitrogen-related microorganisms in river ecosystems exhibits greater complexity. However, there is still a lack of research on the response of denitrifiers to the construction of cascade reservoirs. A study was conducted on 10 cascade reservoirs in the upper reaches of the Yellow River to investigate the impact of cascade reservoir construction on nirS-type denitrifying bacteria in sediments. Sediment samples were collected in May (dry season) and August (wet season) of 2023. The spatiotemporal characteristics of the nirS-type denitrifying bacterial community and gene abundance were analyzed using Illumina high-throughput sequencing and real-time fluorescence quantification PCR (qPCR). Redundancy analysis (RDA) and variation partitioning (VP) were utilized to assess the impact of environmental factors on these communities. The results showed the following: (1) Proteobacteria was the predominant phylum of nirS-type denitrifying bacteria in cascade reservoir sediments. At the genus level, unclassified Proteobacteria (69.51–95.64%) showed the highest relative abundance, followed by Paracoccus, Rhodanobacter, and Pseudomonas, indicating that unclassified Proteobacteria may dominate denitrification in these reservoir sediments. (2) The α and β diversity indices of nirS-type denitrifying bacteria were higher in the dry season than in the wet season, and also higher in young reservoirs compared to old reservoirs (p < 0.05). (3) Temporally, the abundance of the nirS gene was significantly higher in the wet season (12.71 × 107 copies/g dry sediment) compared to the dry season (66.35 × 105 copies/g dry sediment). Spatially, the abundance of the nirS gene was higher in the central region, while relatively lower at both ends. (4) RDA and VP analysis indicated that the community structure and abundance of nirS-type denitrifying bacteria were significantly influenced by the total nitrogen in sediments (19.31%) and water temperature (14.13%). Spearman correlation analysis showed that organic carbon significantly affected the diversity of nirS-type denitrifying bacteria (p < 0.05). The results contribute to a better understanding of the nitrogen-related microbial community in cascade reservoir sediments of the Yellow River, providing a scientific basis for reservoir management. Full article
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25 pages, 1319 KB  
Article
Multitarget Phytocomplex: Focus on Antibacterial Profiles of Grape Pomace and Sambucus ebulus L. Lyophilisates Against Extensively Drug-Resistant (XDR) Bacteria and In Vitro Antioxidative Power
by Vladimir S. Kurćubić, Vesna Đurović, Slaviša B. Stajić, Marko Dmitrić, Saša Živković, Luka V. Kurćubić, Pavle Z. Mašković, Jelena Mašković, Milan Mitić, Vladimir Živković and Vladimir Jakovljević
Antibiotics 2024, 13(10), 980; https://doi.org/10.3390/antibiotics13100980 - 17 Oct 2024
Cited by 2 | Viewed by 1848
Abstract
Objectives: This study was conceived with the aim of translating the experience and knowledge of the research group into the design and creation of multi-active phytocomplex cocktails from lyophilised winery by-products (Grape Pomace—GP) and weeds (Sambucus ebulus L., Dwarf Elder—DE). Methods: Quantification [...] Read more.
Objectives: This study was conceived with the aim of translating the experience and knowledge of the research group into the design and creation of multi-active phytocomplex cocktails from lyophilised winery by-products (Grape Pomace—GP) and weeds (Sambucus ebulus L., Dwarf Elder—DE). Methods: Quantification of bioactive molecules was performed by high-performance liquid chromatography (HPLC) method. Results: In the extract obtained from lyophilised GP, the most dominant component that was quantified was petunidin-3-glucoside. Prominent compounds that were quantified in DE extract were cyanidin derivatives. The total number of microorganisms in lyophilisates is low, but some of them still survive lyophilisation. Antibacterial activity was determined by microdilution, the minimum inhibitory concentration (MIC) of the tested bacteria ranged from 0.78 mg/mL to 25.00 mg/mL. Antibacterial susceptibility testing (AST) revealed that Klebsiella spp. and Acinetobacter baumannii complex are extensively drug-resistant (XDR). Conclusions: The GP + DE cocktail showed very strong AB power against both tested XDR bacteria. The total phenolic content and antioxidative effect (determined spectrophotometrically) indicate their linear correlation. Full article
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16 pages, 1425 KB  
Article
Use of a Mobile Methodology for the Bio-Mapping of Microbial Indicators and RT-PCR-Based Pathogen Quantification in Commercial Broiler Processing Facilities in Honduras
by Gabriela K. Betancourt-Barszcz, Sabrina E. Blandon, David A. Vargas, Rossy Bueno López, Daniela R. Chavez-Velado, Angelica Sánchez, Valeria Larios, Nadira J. Espinoza-Rock, Mirian Bueno-Almendarez and Marcos X. Sanchez-Plata
Poultry 2024, 3(4), 330-345; https://doi.org/10.3390/poultry3040025 - 24 Sep 2024
Viewed by 1826
Abstract
Poultry bio-mapping helps identify microbial contamination and process optimization opportunities such as sanitary dressing procedures, equipment adjustments, cross-contamination controls, and chemical intervention applications in commercial poultry processing operations. This study focuses on the development of a preliminary microbiological baseline of microbial indicators, including [...] Read more.
Poultry bio-mapping helps identify microbial contamination and process optimization opportunities such as sanitary dressing procedures, equipment adjustments, cross-contamination controls, and chemical intervention applications in commercial poultry processing operations. This study focuses on the development of a preliminary microbiological baseline of microbial indicators, including total viable counts (TVC), Enterobacteriaceae (EB), and the quantification and detection of pathogens such as Salmonella and Campylobacter spp. in four commercial broiler processing facilities in Honduras. Whole chicken and wing rinses were collected from four poultry processing plants at different locations: live receiving, rehanger, post-evisceration, post-chiller, and wings. The MicroSnap® system was used for the enumeration of microbial indicators, the BAX®-System-SalQuant® was used for the quantification of Salmonella, and the BAX®-System-CampyQuant™ was used for Campylobacter spp. Negative samples after enumeration were tested with BAX®-System Salmonella and BAX®-System Campylobacter for prevalence analysis, respectively. The TVC and EB counts were continuously reduced from the live receiving to the post-chiller location, presenting a statistically significant increase (p < 0.01) at the wings location. The Salmonella counts were significantly different between stages (p < 0.01). The prevalence of Salmonella was highest in the live receiving stage, with 92.50%, while that at the post-chiller stage was the lowest, at 15.38%. Campylobacter spp. counts were lower than that at the other stages at wings 1.61 Log CFU/sample; however, Campylobacter spp.’s prevalence was higher than 62.5% in all stages. Microbial bio-mapping using novel technologies suitable for mobile applications was conducted in this study to establish statistical process control parameters for microorganisms. A nationwide microbial baseline for commercial broiler processing facilities in Honduras was developed. In-country data serve as a benchmark for continuous improvement at each facility evaluated and can assist regulatory officers in the development of risk-based performance standards aimed at reducing the risk of exposure to consumers. Full article
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17 pages, 3449 KB  
Review
Review of the Proteomics and Metabolic Properties of Corynebacterium glutamicum
by Juhwan Park and Sooa Lim
Microorganisms 2024, 12(8), 1681; https://doi.org/10.3390/microorganisms12081681 - 15 Aug 2024
Cited by 2 | Viewed by 4998
Abstract
Corynebacterium glutamicum (C. glutamicum) has become industrially important in producing glutamic acid and lysine since its discovery and has been the subject of proteomics and central carbon metabolism studies. The proteome changes depending on environmental conditions, nutrient availability, and stressors. Post-translational [...] Read more.
Corynebacterium glutamicum (C. glutamicum) has become industrially important in producing glutamic acid and lysine since its discovery and has been the subject of proteomics and central carbon metabolism studies. The proteome changes depending on environmental conditions, nutrient availability, and stressors. Post-translational modification (PTMs), such as phosphorylation, methylation, and glycosylation, alter the function and activity of proteins, allowing them to respond quickly to environmental changes. Proteomics techniques, such as mass spectrometry and two-dimensional gel electrophoresis, have enabled the study of proteomes, identification of proteins, and quantification of the expression levels. Understanding proteomes and central carbon metabolism in microorganisms provides insight into their physiology, ecology, and biotechnological applications, such as biofuels, pharmaceuticals, and industrial enzyme production. Several attempts have been made to create efficient production strains to increase productivity in several research fields, such as genomics and proteomics. In addition to amino acids, C. glutamicum is used to produce vitamins, nucleotides, organic acids, and alcohols, expanding its industrial applications. Considerable information has been accumulated, but recent research has focused on proteomes and central carbon metabolism. The development of genetic engineering technologies, such as CRISPR-Cas9, has improved production efficiency by allowing precise manipulation of the metabolic pathways of C. glutamicum. In addition, methods for designing new metabolic pathways and developing customized strains using synthetic biology technology are gradually expanding. This review is expected to enhance the understanding of C. glutamicum and its industrial potential and help researchers identify research topics and design studies. Full article
(This article belongs to the Special Issue Advances in Metabolic Engineering of Industrial Microorganisms)
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