Microbiology Research

21 pages, 3741 KiB

Open AccessReview

Methanotrophy: A Biological Method to Mitigate Global Methane Emission

by Anju Rani, Aarushi Pundir, Medhashree Verma, Samiksha Joshi, Geeta Verma, Snežana Andjelković, Snežana Babić, Jasmina Milenković and Debasis Mitra

Microbiol. Res. 2024, 15(2), 634-654; https://doi.org/10.3390/microbiolres15020042 (registering DOI) - 25 Apr 2024

Abstract

Methanotrophy is a biological process that effectively reduces global methane emissions by utilizing microorganisms that can utilize methane as a source of energy under both oxic and anoxic conditions, using a variety of different electron acceptors. Methanotrophic microbes, which utilize methane as their [...] Read more.

Methanotrophy is a biological process that effectively reduces global methane emissions by utilizing microorganisms that can utilize methane as a source of energy under both oxic and anoxic conditions, using a variety of different electron acceptors. Methanotrophic microbes, which utilize methane as their primary source of carbon and energy, are microorganisms found in various environments, such as soil, sediments, freshwater, and marine ecosystems. These microbes play a significant role in the global carbon cycle by consuming methane, a potent greenhouse gas, and converting it into carbon dioxide, which is less harmful. However, methane is known to be the primary contributor to ozone formation and is considered a major greenhouse gas. Methane alone contributes to 30% of global warming; its emissions increased by over 32% over the last three decades and thus affect humans, animals, and vegetation adversely. There are different sources of methane emissions, like agricultural activities, wastewater management, landfills, coal mining, wetlands, and certain industrial processes. In view of the adverse effects of methane, urgent measures are required to reduce emissions. Methanotrophs have attracted attention as multifunctional bacteria with potential applications in biological methane mitigation and environmental bioremediation. Methanotrophs utilize methane as a carbon and energy source and play significant roles in biogeochemical cycles by oxidizing methane, which is coupled to the reduction of various electron acceptors. Methanotrophy, a natural process that converts methane into carbon dioxide, presents a promising solution to mitigate global methane emissions and reduce their impact on climate change. Nonetheless, additional research is necessary to enhance and expand these approaches for extensive use. In this review, we summarize the key sources of methane, mitigation strategies, microbial aspects, and the application of methanotrophs in global methane sinks with increasing anthropogenic methane emissions. Full article

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8 pages, 2857 KiB

Open AccessCase Report

First Molecular Detection and Characterization of Fowl Aviadenovirus Serotype 11 from Broiler Chickens in Chile

by Leandro Cádiz, Miguel Guzmán, Fernando Navarrete, Paulina Torres and Hector Hidalgo

Microbiol. Res. 2024, 15(2), 626-633; https://doi.org/10.3390/microbiolres15020041 - 23 Apr 2024

Abstract

Fowl aviadenovirus (FAdV) is a member of the Aviadenovirus genus within the Adenoviridae family. FAdVs are divided into five species based on genomic differences: Fowl aviadenovirus A to Fowl aviadenovirus E (FAdV-A to FAdV-E). They are classified into twelve serotypes (FAdV-1 to FAdV-8a [...] Read more.

Fowl aviadenovirus (FAdV) is a member of the Aviadenovirus genus within the Adenoviridae family. FAdVs are divided into five species based on genomic differences: Fowl aviadenovirus A to Fowl aviadenovirus E (FAdV-A to FAdV-E). They are classified into twelve serotypes (FAdV-1 to FAdV-8a and FAdV-8b to FAdV-11) through cross-neutralization tests. FAdVs are mainly associated with hepatitis hydropericardium syndrome (HHS), adenoviral gizzard erosion (AGE), and inclusion body hepatitis (IBH). The serotypes commonly involved in IBH are FAdV-2, FAdV-11, FAdV-8a, and FAdV-8b. IBH causes significant economic losses in the poultry industry, mainly due to high mortality, reduced productivity, and immunosuppression. This is the first case report on IBH in Chile caused—according to post-mortem findings, molecular analysis, sequencing, and phylogenetic analysis—by FAdV-11. Since the serotype had not previously been reported in Chile, continued monitoring of IBH cases is required to determine the serotype of the circulating FAdVs and adapt preventative vaccination programs. Full article

(This article belongs to the Special Issue Evolution of Viral Virulence)

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12 pages, 1951 KiB

Open AccessArticle

Ingested Microplastics Can Act as Microbial Vectors of Ichthyofauna

by Abdulhusein Jawdhari, György Deák, Dan Florin Mihăilescu, Nicolai Crăciun, Andrea Cristina Staicu, Ioana Stanca, Derniza Cozorici, Sergiu Fendrihan, Cristian-Emilian Pop and Maria Mernea

Microbiol. Res. 2024, 15(2), 614-625; https://doi.org/10.3390/microbiolres15020040 - 23 Apr 2024

Abstract

Microplastics (plastic particles < 5 mm) are ubiquitous pollutants that have the ability to carry microbiota, including pathogens. Microbial adhesion is usually a sign of pathogenicity; thus, we investigated the adherent microbiota found on 4 mm nylon strips, which were ingested and excreted [...] Read more.

Microplastics (plastic particles < 5 mm) are ubiquitous pollutants that have the ability to carry microbiota, including pathogens. Microbial adhesion is usually a sign of pathogenicity; thus, we investigated the adherent microbiota found on 4 mm nylon strips, which were ingested and excreted by wild fish specimens. Retention times were recorded and the polymer analysis of the excreted samples was performed, which showed no signs of degradation, nor did their controls, represented by the nylon strips submerged in the same water tanks. Both the ingested samples and controls presented pathogens in large quantities. Following Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight identification, the dominant genus was represented by Aeromonas, revealing the fact that nylon microplastics can serve as undegradable physical carriers for this pathogen, among others, in the aquatic environment. Full article

(This article belongs to the Special Issue Zoonotic Bacteria: Infection, Pathogenesis and Drugs)

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16 pages, 3512 KiB

Open AccessArticle

Correlation between Aerosol Particulates, Carcass Dirtiness, and Hygiene Indicators of Bovine Carcasses in the Abattoir Environment: Results of a Study in Italy

by Beniamino T. Cenci-Goga, Emma Tedeschini, Egidia Costanzi, Margherita Maranesi, Musafiri Karama, Saeed El-Ashram, Cristina Saraiva, Juan García-Díez, Massimo Zerani, Ebtesam M. Al-Olayan and Luca Grispoldi

Microbiol. Res. 2024, 15(2), 598-613; https://doi.org/10.3390/microbiolres15020039 - 22 Apr 2024

Abstract

The objective of this study was to demonstrate the possible correlation of visible carcass contamination and abattoir aerosol quality with microbial hygiene criteria. A total of 279 bovine carcasses were analyzed on 23 different working days. The aerobic colony count and total coliforms [...] Read more.

The objective of this study was to demonstrate the possible correlation of visible carcass contamination and abattoir aerosol quality with microbial hygiene criteria. A total of 279 bovine carcasses were analyzed on 23 different working days. The aerobic colony count and total coliforms on the carcasses were calculated together with the presence of Escherichia coli. To determine the visible contamination of carcasses, we used a 100 cm² sheet of transparent, adhesive plastic material, applied to the side of the carcass, to collect all the particles, which were then counted against both black and white backgrounds. The daily particulate index in the abattoir aerosol was determined using an air sampler device. The results showed that aerobic colony counts, which ranged from 1.41 to 2.40 log cfu cm⁻², total coliforms (from 0.00 to 0.73 log cfu cm⁻²), and E. coli presence (from 0.00% to 60% of the sampled carcasses per day) are not correlated with the carcasses’ visual dirtiness or the aerosol quality. The factor analysis showed a correlation between the three groups of variables investigated: group 1, representing “aerosol quality”, group 2, representing the “microbiology of the carcass”, and group 3, the “visual dirtiness of the carcass”. Thus, even though microbiology analysis is useful in diagnosing the microorganisms which the official veterinarian is unable to detect during the post-mortem inspection, it is ineffective in evaluating slaughtering procedures. Aerosol monitoring and the visual classification of carcass dirtiness, instead, could provide good indications of the slaughtering process and the quality of the abattoir environment, and guarantee control of manufacturing practices, protecting both animals’ and operators’ health. Full article

(This article belongs to the Special Issue Molecular Microbiology Underlying Foodborne Viruses)

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16 pages, 4483 KiB

Open AccessArticle

Antiviral Activity of Flavonoids from Bauhinia holophylla Leaves against Zika virus

by Rodrigo Michelini de Oliveira Thomasi, Thaiz Rodrigues Teixeira, Gabriela Francine Martins Lopes, Simony Carvalho Mendonça, Brendo Araujo Gomes, Suzana Guimarães Leitão, Tiago Alves de Oliveira, Sara Thamires Dias da Fonseca, Alex Gutterres Taranto, Jaqueline Maria Siqueira Ferreira, Luciana Alves Rodrigues dos Santos Lima and Ana Hortência Fonsêca Castro

Microbiol. Res. 2024, 15(2), 582-597; https://doi.org/10.3390/microbiolres15020038 - 21 Apr 2024

Abstract

Zika virus (ZIKV) is involved in the etiology of serious nervous system pathologies. Currently, there are no specific and effective vaccines or antiviral drugs to prevent the diseases caused by ZIKV. This study aimed to assess the activity of flavonoids present in crude [...] Read more.

Zika virus (ZIKV) is involved in the etiology of serious nervous system pathologies. Currently, there are no specific and effective vaccines or antiviral drugs to prevent the diseases caused by ZIKV. This study aimed to assess the activity of flavonoids present in crude hydroethanolic extract (CHE) and fractions obtained from B. holophylla leaves against ZIKV. O-glycosylated flavonoids were characterized by high-performance liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS). The cytotoxic concentration and the effective concentration for 50% of the cells (CC₅₀ and EC₅₀, respectively) were determined, and the selectivity index (SI) was calculated. Molecular networks were constructed based on the chemical composition of the samples and global antiviral activity data using the Global Natural Products Social Molecular Networking (GNPS) platform. Protein–ligand docking was performed in the NS2B-NS3 protease, NS3 helicase, and NS5 methyltransferase of the ZIKV. CHE showed greater antiviral activity at a multiplicity of infection (MOI) of 1.0, with an EC₅₀ of 11.93 µg/mL, SI = 13.38, and reduced cytopathic effects. Molecular networks indicated that O-glycosylated flavonoids are responsible for the activity against ZIKV, being quercetin-O-deoxyhexoside more selective and effective. Molecular docking confirmed the inhibitory activity of quercetin-O-deoxyhexoside, which showed an affinity for the tested targets, especially for NS2B-NS3 protease. The results showed that B. holophylla has flavonoids with potential for future therapeutic applications against ZIKV. Full article

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Graphical abstract

15 pages, 2023 KiB

Open AccessArticle

Molecular Biological Methods to Assess Different Botrytis cinerea Strains on Grapes

by Louis Backmann, Katharina Schmidtmann, Pascal Wegmann-Herr, Andreas Jürgens and Maren Scharfenberger-Schmeer

Microbiol. Res. 2024, 15(2), 567-581; https://doi.org/10.3390/microbiolres15020037 - 19 Apr 2024

Abstract

Botrytis cinerea is a well-known pathogen that can be challenging to control in crops, such as wine grapes. To adapt to the increasing problems of climate change and strain resistance, it is important to find new methods to detect Botrytis cinerea and differentiate [...] Read more.

Botrytis cinerea is a well-known pathogen that can be challenging to control in crops, such as wine grapes. To adapt to the increasing problems of climate change and strain resistance, it is important to find new methods to detect Botrytis cinerea and differentiate strains. These methods include strain differentiation and classification by simple sequence repeats (SSRs) and early detection of the fungus by qPCR. Various strains were analysed using SSR markers and either agarose gel electrophoresis or capillary sequencing via PCR. A sensitive qPCR method was refined to achieve an early detection method for the pathogen. The results demonstrate promising ways to distinguish between strains using both agarose gel electrophoresis and capillary sequencing as well as to detect infection before it becomes visible on grapes. This can be used to further understand and analyse different Botrytis cinerea strain characteristics such as laccase activity, regional or annual effects. The early detection method can be used to better prepare growers for an impending infection so that targeted efforts can be made. Full article

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17 pages, 4016 KiB

Open AccessArticle

Altered Cytostructure and Lignolytic Enzymes of Ganoderma boninense in Response to Phenolic Compounds

by Yasmeen Siddiqui and Daarshini Ganapathy

Microbiol. Res. 2024, 15(2), 550-566; https://doi.org/10.3390/microbiolres15020036 - 16 Apr 2024

Abstract

Ganoderma boninense is a white-rot fungus that causes basal stem rot (BSR) disease in the oil palm. Potential natural inhibitors, such as gallic acid, thymol, propolis, and carvacrol, were assessed for their antagonistic effects against G. boninense. These naturally occurring phenolic compounds [...] Read more.

Ganoderma boninense is a white-rot fungus that causes basal stem rot (BSR) disease in the oil palm. Potential natural inhibitors, such as gallic acid, thymol, propolis, and carvacrol, were assessed for their antagonistic effects against G. boninense. These naturally occurring phenolic compounds have also been utilised to inhibit hydrolytic and ligninolytic enzymes produced by the pathogen. Mycelial inhibition was dose-dependent in the presence of different concentrations of phenolic compounds, including, for example, in cellulase enzyme inhibition (GA mg/mL = 94%, THY 0.25 mg/mL = 90%, PRO 3.5 mg/mL = 92.5%, and CARV 0.15 mg/mL = 90.3%). A significant difference was observed revealing that gallic acid had the greatest inhibitory effect on the secretion of hydrolytic and ligninolytic enzymes, especially at 40 mM GA (cellulase = 0.337 U/mL, amylase = 0.3314 U/mL, xylanase = 0.211 U/mL, laccase = 0.4885 U/mL, lignin peroxidase = 0.218 U/mL, and manganese peroxidase = 0.386 U/mL). The growth and secretion of enzymes (inhibitory action) are inversely proportional to the concentration of phenolic compounds. Phenolic compounds have a greater potential as inhibitory agents and suppress the production of hydrolytic and ligninolytic enzymes. The selected phenolic compounds were evaluated for their ability to alter the morphology and integrity of G. boninense mycelia. The reduction in cell viability of G. boninense has been explained by research on morphological disruption, such as branching patterns, hyphal length, and rigidity of fungal cells, which eventually interrupt the secretion of enzymes. These studies highlight the efficacy of phenolic compounds in treating Ganoderma. In addition, these findings proved that naturally occurring phenolic compounds could be a substitute for chemical controls and other synthetic fungicides to eradicate the occurrence of BSR in oil palms, thus avoiding a situation that is difficult to overcome. Full article

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25 pages, 1393 KiB

Open AccessReview

Polysaccharides and Lectins: A Natural Complementary Approach against the SARS-CoV-2 Pandemic

by Radu Lefter, Prairna Balyan, Ioana-Miruna Balmus, Abdellah Ech-Chahad, Ahmad Ali, Alin Ciobica, Antoneta Dacia Petroaie, Gabriela Halitchi, Bogdan Novac, Catalina Ionescu and Fatima Zahra Kamal

Microbiol. Res. 2024, 15(2), 525-549; https://doi.org/10.3390/microbiolres15020035 - 09 Apr 2024

Abstract

Infection with the novel coronavirus SARS-CoV-2, the cause of coronavirus disease (COVID-19), has emerged as a global pandemic, with a high toll on casualties, economic impact, and human lifestyle. Despite the recent approval of various vaccines against the virus, challenges remain, including the [...] Read more.

Infection with the novel coronavirus SARS-CoV-2, the cause of coronavirus disease (COVID-19), has emerged as a global pandemic, with a high toll on casualties, economic impact, and human lifestyle. Despite the recent approval of various vaccines against the virus, challenges remain, including the limited availability of these vaccines, the prevalent rejection of vaccination by a large proportion of the population, and the recurrent appearance of new variants of the virus due to mutations. This context raises the alarm for scientists and clinicians to seek alternative and complementary therapies. In this context, natural products and their derivatives serve as reservoirs for potential therapeutic compounds that can be exploited in the research and production of antiviral drugs against COVID-19. Among these substances, lectin and polysaccharides isolated from fauna and flora emerge as complementary strategies for treating coronavirus infection. The review objective is to cover and analyze the specific role of polysaccharides and lectins and their synergy in the fight against this deadly SARS-CoV-2 virus. For this purpose, a primary literature search was conducted on Google Scholar, PubMed, and Web of Sciences using relevant keywords like “SARS-CoV-2 Variants”; “Antiviral Strategies”; “Antiviral Polysaccharides”; “Antiviral Lectins”; and “Synergistic effect”. The results demonstrate that lectins and polysaccharides exhibit antiviral activities against SARS-CoV-2 via mechanisms related to binding and steric blocking, the binding of glycan-based decoys, chemical reactions, virus particle disruption strategies, and steric blocking for competitive inhibition to block SARS-CoV-2 and its variants’ entry. In addition, this review analyzes the rationale behind combining polysaccharides and lectins, emphasizing complementary mechanisms of action. By simultaneously targeting multiple stages of the viral life cycle, this dual strategy aims to comprehensively inhibit viral propagation and enhance the durability of antiviral strategies over time. Full article

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17 pages, 21389 KiB

Open AccessArticle

Transcription Factors Mcm1 and Sfp1 May Affect [PSI⁺] Prion Phenotype by Altering the Expression of the SUP35 Gene

by Andrew G. Matveenko, Anastasiia S. Mikhailichenko, Polina B. Drozdova and Galina A. Zhouravleva

Microbiol. Res. 2024, 15(2), 508-524; https://doi.org/10.3390/microbiolres15020034 - 08 Apr 2024

Abstract

Mcm1 is an essential Q/N-rich transcription factor. Q/N-rich proteins interact with each other, and many affect the [PSI⁺] prion formed by the translation termination factor Sup35 (eRF3). We found that transient MCM1 overexpression increased nonsense suppression in [PSI⁺ [...] Read more.

Mcm1 is an essential Q/N-rich transcription factor. Q/N-rich proteins interact with each other, and many affect the [PSI⁺] prion formed by the translation termination factor Sup35 (eRF3). We found that transient MCM1 overexpression increased nonsense suppression in [PSI⁺] strains and SUP35 transcription. As we had discovered similar effects of another Q/N-rich transcription factor, Sfp1, here we focus on the roles of Mcm1 and Sfp1 in SUP35 expression, as well as on the effects of Sfp1 on the expression of the gene encoding another release factor, Sup45 (eRF1). Mutations in the SUP35 promoter showed that none of the potential Mcm1 binding sites affected the Sup35 protein level or nonsense suppression, even during MCM1 overexpression. Mcm1 itself neither formed aggregates in vivo nor affected Sup35 aggregation. In contrast, a mutation in the Sfp1-binding site decreased Sup35 production and [PSI⁺] toxicity of excess Sfp1. Mutation of the Sfp1 binding site in the SUP45 promoter lowered SUP45 expression and increased nonsense suppression even more drastically. Our data indicate that the mechanisms of Mcm1 and Sfp1 action differ. While Mcm1 seems unlikely to directly regulate SUP35 expression, Sfp1 appears to act through its binding sites and to directly activate SUP35 expression, which in turn may influence the [PSI⁺] prion phenotype and toxicity. Full article

(This article belongs to the Special Issue Current Progress in Prion Research)

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19 pages, 2335 KiB

Open AccessReview

The Role of the Gut Microbiota in Neurodegenerative Diseases

by Arshilin Philip Mani, Balamuralikrishnan Balasubramanian, Linsha A. Mali, Kadanthottu Sebastian Joseph, Arun Meyyazhagan, Manikantan Pappuswamy and Biljo V. Joseph

Microbiol. Res. 2024, 15(2), 489-507; https://doi.org/10.3390/microbiolres15020033 - 05 Apr 2024

Abstract

The human gut has a rich and dynamic microbial population that plays an important role in many physiological activities. This review explores the complex interaction between the gut microbiota and human health, with an emphasis on its effect on neurodegenerative illnesses. The makeup [...] Read more.

The human gut has a rich and dynamic microbial population that plays an important role in many physiological activities. This review explores the complex interaction between the gut microbiota and human health, with an emphasis on its effect on neurodegenerative illnesses. The makeup of the gut microbiome and its impact on brain function through the gut–brain axis is highlighted. Dysbiosis, characterized by changes in the gut microbiota’s composition, has been linked to the development of neurodegenerative diseases such as Alzheimer’s, Parkinson’s, Huntington’s, and amyotrophic lateral sclerosis. A Bidirectional communication between the stomach and the brain takes place via a variety of channels, including neurotransmitters and metabolites generated by gut bacteria. We investigate the processes through which dysbiosis causes neuroinflammation, oxidative stress, and neuronal damage, which drive disease development. Potential therapeutic approaches that focus on the gut microbiota, such as antibiotics, probiotics, prebiotics, and fecal microbiota transplantation, are reviewed, with promising preclinical and clinical findings. Overall, this study emphasizes the relevance of gut microbiota to neurodegenerative illnesses, as well as the need to understand and target the gut-brain axis for future treatment options. Full article

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21 pages, 8713 KiB

Open AccessReview

Medicinal Plants Used in Sri Lankan Traditional Medicine for Dengue Fever

by Jayani K. Handagala, Nishantha Kumarasinghe, Charitha L. Goonasekara and Anchala I. Kuruppu

Microbiol. Res. 2024, 15(2), 468-488; https://doi.org/10.3390/microbiolres15020032 - 03 Apr 2024

Abstract

Dengue fever, a mosquito-borne viral infectious disease caused by the dengue virus, is a significant global health concern, especially in tropical and subtropical regions. Despite preventive efforts, Sri Lanka faces recurring dengue outbreaks, with the Western province being the most affected. Current treatments [...] Read more.

Dengue fever, a mosquito-borne viral infectious disease caused by the dengue virus, is a significant global health concern, especially in tropical and subtropical regions. Despite preventive efforts, Sri Lanka faces recurring dengue outbreaks, with the Western province being the most affected. Current treatments primarily focus on supportive care, as specific antiviral therapies remain elusive. This review presents an overview of dengue, its clinical presentations, the dengue burden in Sri Lanka, and the potential of Sri Lankan medicinal plants used in traditional medicine for treating dengue. Several plants, such as Munronia pinnata, Azardirachta indica, Cissampelos pareira L., Carica papaya, Zingiber officinale, Curcuma longa, and Bambusa vulgaris, show antiviral properties against dengue. The utilization of these medicinal plants in dengue treatment could offer a promising avenue for further research and drug development. Full article

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11 pages, 2543 KiB

Open AccessArticle

The Effect of Conserved Histidine on the Proximity of Fe-S Clusters in Adenosine-5′-Phosphosulfate Reductases from Pseudomonas aeruginosa and Enteromorpha intestinalis

by Jung-Sung Chung, Sung-Kun Kim and Thomas Leustek

Microbiol. Res. 2024, 15(2), 457-467; https://doi.org/10.3390/microbiolres15020031 - 30 Mar 2024

Abstract

This study investigates the impact of conserved histidine (His) residue mutations on the adenosine 5′-phosphosulfate (APS) reductase enzymes Pseudomonas aeruginosa APR (PaAPR) and Enteromorpha intestinalis APR (EiAPR), focusing on the effects of His-to-alanine (Ala) and His-to-arginine (Arg) substitutions on enzyme activity, iron–sulfur [4Fe-4S] [...] Read more.

This study investigates the impact of conserved histidine (His) residue mutations on the adenosine 5′-phosphosulfate (APS) reductase enzymes Pseudomonas aeruginosa APR (PaAPR) and Enteromorpha intestinalis APR (EiAPR), focusing on the effects of His-to-alanine (Ala) and His-to-arginine (Arg) substitutions on enzyme activity, iron–sulfur [4Fe-4S] cluster stability, and APS binding affinity. Using recombinant His-tagged wild-types (WTs) and variants expressed in Escherichia coli, analyses revealed that both PaAPR and EiAPR enzymes exhibit a distinct absorption peak associated with their [4Fe-4S] clusters, which are critical for their catalytic functions. Notably, the His-to-Ala variants displayed reduced enzymatic activities and lower iron and sulfide contents compared to their respective WTs, suggesting alterations in the iron–sulfur cluster ligations and thus affecting APS reductase catalysis. In contrast, His-to-Arg variants maintained similar activities and iron and sulfide contents as their WTs, highlighting the importance of a positively charged residue at the conserved His site for maintaining structural integrity and enzymatic function. Further kinetic analyses showed variations in Vmax and Km values among the mutants, with significant reductions observed in the His-to-Ala variants, emphasizing the role of the conserved His in enzyme stability and substrate specificity. This study provides valuable insights into the structural and functional significance of conserved His residues in APS reductases, contributing to a better understanding of sulfur metabolism and its regulation in bacterial and plant systems. Future investigations into the structural characterization of these enzymes and the exploration of other critical residues surrounding the [4Fe-4S] cluster are suggested to elucidate the complete mechanism of APS reduction and its biological implications. Full article

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10 pages, 1419 KiB

Open AccessCommunication

Comparative Analysis of Cyanotoxins in Fishponds in Nigeria and South Africa

by Odo J. Bassey, Jabulani R. Gumbo, Munyaradzi Mujuru, Adeeyo Adeyemi and Farai Dondofema

Microbiol. Res. 2024, 15(2), 447-456; https://doi.org/10.3390/microbiolres15020030 - 24 Mar 2024

Abstract

Over the decades, the aquaculture sector has witnessed substantial growth, contributing significantly to the nation’s economy. However, the menace of CyanoHABs threatens the sustainability of fish farming. Considering the possible hazards linked to cyanotoxins in food and water, a comparative study design between [...] Read more.

Over the decades, the aquaculture sector has witnessed substantial growth, contributing significantly to the nation’s economy. However, the menace of CyanoHABs threatens the sustainability of fish farming. Considering the possible hazards linked to cyanotoxins in food and water, a comparative study design between commercial fish in Nigeria and South Africa was employed to investigate cyanotoxins in the water from fishponds. Six commercial fishponds in Calabar Municipality—Nigeria and Duthuni—South Africa with varying climatic zones were selected. Water samples from the ponds were collected at intervals during different seasons (summer, winter, dry, and wet seasons) to capture climate-induced variation. Liquid chromatography–mass spectrometry (LCMS) in combination with the metabolites database was used for the identification of toxic cyanometabolites in water samples. The molecular networking approach, coupled with the Global Natural Products Social Molecular Networking (GNPS) database and CANOPUS annotation, enabled the putative identification of cyanometabolites. The resulting molecular network unveiled discernible clusters representing related molecule families, aiding in the identification of both known cyanotoxins and unfamiliar analogues. Furthermore, the molecular network revealed that water samples from different fishponds shared specific metabolites, including ethanesulfonic acid, pheophorbide A, cholic acid, phenylalanine, amyl amine, phosphocholine (PC), and sulfonic acid, despite variations in location, local climatic factors, and sampling sites. The fishponds in Nigeria showed the presence of multiple cyanotoxin classes in the dry, wet, and summer seasons in the water. Aflatoxin was identified in all sampling sites in Nigeria (N1, N2, and N3). The Duthuni, South Africa, sampling sites (P1, P2, and P3) exhibited the presence of microginins and microcystins. All the fishponds displayed a widespread occurrence of anabaenopeptins, aplysiatoxins, aflatoxin, microcolins, and marabmids during the selected summer. In conclusion, the untargeted metabolome analysis, guided by GNPS, proved highly effective in identifying both toxic and non-toxic metabolites in fishponds. Full article

(This article belongs to the Special Issue Bioactive Secondary Metabolites of Microbial Symbionts)

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16 pages, 1091 KiB

Open AccessArticle

Serum Calcium and Magnesium Levels in Patients with Type 2 Diabetes and COVID-19 Infection Requiring Hospitalization—Correlations with Various Parameters

by Patricia-Andrada Reștea, Ștefan Tigan, Luminita Fritea, Laura Grațiela Vicaș, Eleonora Marian, Mariana Eugenia Mureșan and Liana Stefan

Microbiol. Res. 2024, 15(2), 431-446; https://doi.org/10.3390/microbiolres15020029 - 23 Mar 2024

Abstract

The purpose of this research was to analyze the impact of SARS-CoV-2 infection on ionic calcium, total calcium and serum magnesium upon hospital admission, taking into account the association of type 2 diabetes as a metabolic comorbidity. Our study included 57 patients: a [...] Read more.

The purpose of this research was to analyze the impact of SARS-CoV-2 infection on ionic calcium, total calcium and serum magnesium upon hospital admission, taking into account the association of type 2 diabetes as a metabolic comorbidity. Our study included 57 patients: a group of 28 patients without diabetes, but with SARS-CoV-2 virus infection, and a second group of 29 patients with type 2 diabetes and SARS-CoV-2 virus infection. The serum level of calcium and magnesium of the patients included in the study did not differ statistically significantly in those with type 2 diabetes compared to those without type 2 diabetes who were infected with the SARS-CoV-2 virus at the time of hospitalization. Ionic calcium, total calcium, and serum magnesium did not statistically significantly influence the survival of the patients with COVID-19 infection included in this research, but the type of infection severity (mild or moderate) did influence the survival rate. Concerning the diabetic patients, a statistically significant correlation was found between serum total calcium and total serum proteins, and another one between ionic calcium and uric acid, urea, and total cholesterol. Serum total calcium and D-dimers were statistically significantly correlated with being transferred to the intensive care unit. On the other hand, magnesium significantly correlated with lipids (triglycerides, total lipids) and inflammatory (fibrinogen, ESR) biomarkers. Full article

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9 pages, 687 KiB

Open AccessBrief Report

An Evaluation of a SARS-CoV-2 Pseudovirus Neutralization Test and A Comparison to a SARS-CoV-2 Surrogate Virus Neutralization Test in a COVID-19 Long-Term Follow-Up Cohort

by Constant Gillot, Julien Favresse, Clara David, Vincent Maloteau, Jean-Michel Dogne and Jonathan Douxfils

Microbiol. Res. 2024, 15(1), 422-430; https://doi.org/10.3390/microbiolres15010028 - 21 Mar 2024

Abstract

Background: The detection of neutralizing anti-SARS-CoV-2 antibodies is important since they represent the subset of antibodies able to prevent the virus to invade human cells. The aim of this study is to evaluate the clinical performances of an in-house pseudovirus neutralization test (pVNT) [...] Read more.

Background: The detection of neutralizing anti-SARS-CoV-2 antibodies is important since they represent the subset of antibodies able to prevent the virus to invade human cells. The aim of this study is to evaluate the clinical performances of an in-house pseudovirus neutralization test (pVNT) versus a commercial surrogate neutralization test (sVNT). Material and Methods: A total of 114 RT-PCR positives samples from 75 COVID-19 patients were analyzed using a pVNT and an sVNT technique. Fifty-six pre-pandemic samples were also analyzed to assess the specificity of the two techniques. An analysis of the repeatability and the reproducibility of the pVNT was also performed. Results: A coefficient of variation (CV) of 10.27% for the repeatability of the pVNT was computed. For the reproducibility test, CVs ranged from 16.12% for low NAbs titer to 6.40% for high NAbs titer. Regarding the clinical sensitivity, 90 RT-PCR positive samples out of 114 were positive with the pVNT (78.94%), and 97 were positive with the sVNT (84.21%). About the clinical specificity, all 56 pre-pandemic samples were negative in both techniques. When comparing the sVNT to the pVNT, the specificity and sensibility were 66.67% (95%CI: 47.81–85.53%) and 98.88% (95%CI: 96.72–99.99%), respectively. Conclusions: The results obtained with the automated sVNT technique are consistent with those obtained with the pVNT technique developed in-house. The results of the various repeatability and reproducibility tests demonstrate the good robustness of the fully manual pVNT technique. Full article

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18 pages, 2121 KiB

Open AccessArticle

Effects of Biochar and Arbuscular Mycorrhizal Fungi on Soil Health in Chinese Kale (Brassica oleracea var. alboglabra L.) Cultivation

by Kritsana Jatuwong, Worawoot Aiduang, Tanongkiat Kiatsiriroat, Wassana Kamopas and Saisamorn Lumyong

Microbiol. Res. 2024, 15(1), 404-421; https://doi.org/10.3390/microbiolres15010027 - 12 Mar 2024

Abstract

Biochar and arbuscular mycorrhizal fungi (AMF), a promising environmentally friendly soil enhancer and biostimulant, play a crucial role in sustainable agriculture by influencing soil properties and plant growth. This research investigates the chemical properties of three biochar types [bamboo (BB-char), corn cob (CC-char), [...] Read more.

Biochar and arbuscular mycorrhizal fungi (AMF), a promising environmentally friendly soil enhancer and biostimulant, play a crucial role in sustainable agriculture by influencing soil properties and plant growth. This research investigates the chemical properties of three biochar types [bamboo (BB-char), corn cob (CC-char), and coffee grounds (CG-char)] derived from different biomass sources and their impact on soil quality and Chinese kale growth. The results reveal significant differences in chemical properties among different types of biochar. Particularly, CG-char showed the greatest pH value and phosphorus content, with an average of 10.05 and 0.44%, respectively. On the other hand, CC-char had the highest potassium content, with an average of 2.16%. Incorporating biochar into degraded soil enhances soil structure, promoting porosity and improved texture, as evidenced by scanning electron microscope images revealing distinct porous structures. Soil chemistry analyses in treatment T2–T14 after a 42-day cultivation demonstrate the impact of biochar on pH, electrical conductivity, organic matter, and organic carbon levels in comparison to the control treatment (T1). Furthermore, the research assesses the impact of biochar on Chinese kale growth and photosynthetic pigments. Biochar additions, especially 5% BB-char with AMF, positively influence plant growth, chlorophyll content, and photosynthetic pigment levels. Notably, lower biochar concentrations (5%) exhibit superior effects compared to higher concentrations (10%), emphasizing the importance of optimal biochar application rates. The study also delves into the total phenolic content in Chinese kale leaves, revealing that the synergistic effect of biochar and AMF enhances phenolic compound accumulation. The combination positively influences plant health, soil quality, and nutrient cycling mechanisms. Overall, the research indicates the multifaceted impact of biochar on soil and plant dynamics, emphasizing the need for tailored application strategies to optimize benefits in sustainable agriculture. Full article

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19 pages, 3658 KiB

Open AccessArticle

Virulence and Antimicrobial Resistance Profiles of Shiga Toxin-Producing Escherichia coli from River Water and Farm Animal Feces near an Agricultural Region in Northwestern Mexico

by Bianca A. Amézquita-López, Marcela Soto-Beltrán, Bertram G. Lee, Edgar F. Bon-Haro, Ofelia Y. Lugo-Melchor and Beatriz Quiñones

Microbiol. Res. 2024, 15(1), 385-403; https://doi.org/10.3390/microbiolres15010026 - 08 Mar 2024

Abstract

Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens linked to human gastroenteritis worldwide. To aid the development of pathogen control efforts, the present study characterized the genotypic diversity and pathogenic potential of STEC recovered from sources near agricultural fields in Northwest Mexico. [...] Read more.

Shiga toxin-producing Escherichia coli (STEC) are zoonotic enteric pathogens linked to human gastroenteritis worldwide. To aid the development of pathogen control efforts, the present study characterized the genotypic diversity and pathogenic potential of STEC recovered from sources near agricultural fields in Northwest Mexico. Samples were collected from irrigation river water and domestic animal feces in farms proximal to agricultural fields and were subjected to enrichment followed by immunomagnetic separation and plating on selective media for the recovery of the STEC isolates. Comparative genomic analyses indicated that the recovered STEC with the clinically relevant serotypes O157:H7, O8:H19, and O113:H21 had virulence genes repertoires associated with host cell adherence, iron uptake and effector protein secretion. Subsequent phenotypic characterization revealed multidrug resistance against aminoglycoside, carbapenem, cephalosporin, fluoroquinolone, penicillin, phenicol, and tetracycline, highlighting the need for improved surveillance on the use of antimicrobials. The present study indicated for the first time that river water in the agricultural Culiacan Valley in Mexico is a relevant key route of transmission for STEC O157 and non-O157 with a virulence potential. In addition, feces from domestic farm animals near surface waterways can act as potential point sources of contamination and transport of diverse STEC with clinically relevant genotypes. Full article

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14 pages, 1697 KiB

Open AccessArticle

Antagonistic Activity of Macrolepiota sp. CS185 against Post-Harvest Fungi of Fig Fruits (Ficus carica L.)

by Guadalupe Gutiérrez-Soto, Iosvany López-Sandin, Jesús Salvador Hernández Ochoa, Carlos Eduardo Hernadez-Luna, Juan Francisco Contreras-Cordero and Carlos Alberto Hernández-Martínez

Microbiol. Res. 2024, 15(1), 371-384; https://doi.org/10.3390/microbiolres15010025 - 07 Mar 2024

Abstract

Macrolepiota sp. CS185 is a basidiomycete with high potential as a biocontrol agent against various phytopathogenic fungi. Regardless of its pronounced potential as a post-harvest fungi biocontrol agent, its activity in tomato seedlings infected with Alternaria alternata has not been well studied. Thus, [...] Read more.

Macrolepiota sp. CS185 is a basidiomycete with high potential as a biocontrol agent against various phytopathogenic fungi. Regardless of its pronounced potential as a post-harvest fungi biocontrol agent, its activity in tomato seedlings infected with Alternaria alternata has not been well studied. Thus, the present work aimed to evaluate the cultures and supernatants’ antagonistic activity against fig fruits’ post-harvest fungi and antifungal activity production kinetics. The culture antagonistic characteristics were assessed through multiple confrontations, the supernatant concentration effect, and the kinetics of antagonistic action. The multiple confrontations showed differences (p ≤ 0.05) among phytopathogens and over time, with Colletotrichum sp. 2 being the most susceptible. Based on the 9-day incubation profile, the treatment fractions supplemented with a 50% concentration of Macrolepiota sp. CS185 supernatants showed a higher inhibition percentage (%In). Except for Alternaria alternata 1 and 2, the rest of the isolates showed a similar decrease in antagonistic activity up to a certain extent over time. Among all tested strains, Colletotrichum sp. 2 was found with a higher susceptibility. Regarding the production kinetics of antagonistic activity, a triple interaction was observed between the phytopathogen, the age of the Macrolepiota sp. CS 185 culture, and incubation time. In addition, changes in the mycelium growth rate (p ≤ 0.05) along with the higher activity in the supernatants of 20 and 30 days were observed and suggested the production of multiple bioactive metabolites. These results indicate that Macrolepiota sp. CS185 produces antifungal metabolites at different times and could be a suitable candidate to control fig fruits’ post-harvest fungi issues. Full article

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17 pages, 4706 KiB

Open AccessArticle

Design and Development of Molecular Beacon-Based Real-Time PCR Assays to Identify Clostridioides difficile Types of Main Evolutionary Clades

by Enrico Maria Criscuolo, Fabrizio Barbanti and Patrizia Spigaglia

Microbiol. Res. 2024, 15(1), 354-370; https://doi.org/10.3390/microbiolres15010024 - 05 Mar 2024

Abstract

C. difficile infection (CDI) has an important impact on both human and animal health. The rapid detection and monitoring of C. difficile PCR-ribotypes (RTs) cause of CDI is critical to control and prevent this infection. This study reports the first application of the [...] Read more.

C. difficile infection (CDI) has an important impact on both human and animal health. The rapid detection and monitoring of C. difficile PCR-ribotypes (RTs) cause of CDI is critical to control and prevent this infection. This study reports the first application of the Molecular Beacon (MB)-based real-time PCR method in genotyping important C. difficile RTs of the main evolutionary clades. The cdtR gene was used as target and the cdtR sequences were analyzed after extraction from deposited genomes or were obtained after sequencing from strains of different origin. cdtR alleles were identified after sequence comparisons and MB-based real-time PCR assays were developed to discriminate them. In total, 550 cdtR sequences were compared, 38 SNPs were found, and five different cdtR alleles were identified. In total, one or two alleles were associated to the RTs grouped in the same evolutionary clade. A MB-based real-time assay was designed for each allele and for optimized testing of the C. difficile strains. The results obtained demonstrated that the MB-based real-time PCR assays developed in this study represent a powerful, original, and versatile tool to identify C. difficile types/clades and to monitor changes in the population structure of this important pathogen. Full article

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