Microorganisms

19 pages, 599 KiB

Open AccessReview

Microbial Contributions to Heavy Metal Phytoremediation in Agricultural Soils: A Review

by Zobia Khatoon, Ma. del Carmen Orozco-Mosqueda and Gustavo Santoyo

Microorganisms 2024, 12(10), 1945; https://doi.org/10.3390/microorganisms12101945 (registering DOI) - 25 Sep 2024

Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with [...] Read more.

Phytoremediation is a sustainable technique that employs plants to reinforce polluted environments such as agroecosystems. In recent years, new strategies involving the plant microbiome as an adjuvant in remediation processes have been reported. By leveraging this microbial assistance to remediate soils contaminated with heavy metals such As, Pb, Cd, Hg, and Cr, plants can sequester, degrade, or stabilize contaminants more efficiently. Remarkably, some plant species are known for their hyper-accumulative traits in synergy with their microbial partners and can successfully mitigate heavy metal pollutants. This sustainable biotechnology based on plant–microbe associations not only aids in environmental cleanup but also enhances biodiversity, improves soil structure, and promotes plant growth and health, making it a promising solution for addressing agro-pollution challenges worldwide. The current review article emphasizes the potential of synergistic plant–microbe interactions in developing practical and sustainable solutions for heavy metal remediation in agricultural systems, which are essential for food security. Full article

(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)

11 pages, 723 KiB

Open AccessArticle

Soil Sample Analysis of Bacillus anthracis Contaminated Animal Burial Sites

by Mitat Sahin, Thomas R. Laws, Hugh Dyson, Ozgur Celebi, Mehmet Doganay, Fatih Buyuk and Les Baillie

Microorganisms 2024, 12(10), 1944; https://doi.org/10.3390/microorganisms12101944 (registering DOI) - 25 Sep 2024

Abstract

Environmental contamination with Bacillus anthracis spores poses clear threats to livestock that play key roles in the economies of pastoral communities. Regular monitoring of contaminated sites is particularly important in anthrax-endemic parts of the world, such as Kars province in eastern Türkiye, where [...] Read more.

Environmental contamination with Bacillus anthracis spores poses clear threats to livestock that play key roles in the economies of pastoral communities. Regular monitoring of contaminated sites is particularly important in anthrax-endemic parts of the world, such as Kars province in eastern Türkiye, where the Veterinary Microbiology Department of Kafkas University has conducted an anthrax surveillance programme for over 30 years. We reviewed the microbiological results of 232 soil samples collected during 2009–2023, from sites known to be contaminated with B. anthracis spores following burial or butchering of infected animal carcasses. Twenty-five contaminated sites in 16 villages were studied. Samples were taken from a total of 61 different positions within these sites and viable spores were detected in 136 (58.6%) of the samples examined. Of the 96 samples from which spores were not recovered, subsequent samples from the same positions proved positive on 21 occasions. Using a standardised sampling plan, it was discovered that samples taken 1–2 m on a downward slope from the centre-point of contamination had higher (p < 0.001) spore concentrations than those taken from other positions. Although spore concentrations at some sampling positions varied over time, the overall values remained stable. This finding contrasts with observations in other parts of the world where spore concentrations tend to decline with time and may reflect regional differences in soil composition that permit more prolonged spore persistence. Concentrations of >100 spores/g soil were found in 10 (66.7%) of the 15 samples taken 10–13 years following a contamination event. These results demonstrate the longevity of viable anthrax spores in the soil of agricultural environments following decomposition of infected animal carcasses, and therefore the need for prolonged bacteriological monitoring of contaminated sites. Furthermore, they underline the importance of appropriate decontamination, as burial on its own does not eliminate all spores. Full article

(This article belongs to the Special Issue Bacillus anthracis: Infection Mechanisms, Vaccination and Immune Response)

22 pages, 9959 KiB

Open AccessArticle

Biocontrol Activity of Bacillus altitudinis CH05 and Bacillus tropicus CH13 Isolated from Capsicum annuum L. Seeds against Fungal Strains

by Merle Ariadna Espinosa Bernal, Mayra Paola Mena Navarro, Jackeline Lizzeta Arvizu Gómez, Carlos Saldaña, Miguel Ángel Ramos López, Aldo Amaro Reyes, Monserrat Escamilla García, Juan Ramiro Pacheco Aguilar, Victor Pérez Moreno, José Alberto Rodríguez Morales, Erika Álvarez Hidalgo, Jorge Nuñez Ramírez, José Luis Hernández Flores and Juan Campos Guillén

Microorganisms 2024, 12(10), 1943; https://doi.org/10.3390/microorganisms12101943 (registering DOI) - 25 Sep 2024

Abstract

In this study, seed-surface-associated bacteria from fresh fruits of Capsicum spp. were analyzed to explore potential isolates for biocontrol of phytopathogenic fungal strains. A total of 76 bacterial isolates were obtained from three different species of chili pepper (C. annuum L., C. [...] Read more.

In this study, seed-surface-associated bacteria from fresh fruits of Capsicum spp. were analyzed to explore potential isolates for biocontrol of phytopathogenic fungal strains. A total of 76 bacterial isolates were obtained from three different species of chili pepper (C. annuum L., C. pubescens R. & P., and C. chinense Jacq.), and two isolates were selected via mycelial growth inhibition assays based on their production of volatile organic compounds (VOCs) against six fungal strains. Genomic analysis identified these isolates as Bacillus altitudinis CH05, with a chromosome size of 3,687,823 bp and with 41.25% G+C, and Bacillus tropicus CH13, with a chromosome size of 5,283,706 bp and with 35.24% G+C. Both bacterial strains showed high mycelial growth inhibition capacities against Sclerotium rolfsii, Sclerotinia sp., Rhizoctonia solani, and Alternaria alternata but lower inhibition capacities against Colletotrichum gloesporoides and Fusarium oxysporum. VOC identification was carried out after 24 h of fermentation with 64 VOCs for B. altitudinis CH05 and 53 VOCs for B. tropicus CH13. 2,5-Dimethyl pyrazine and acetoin had the highest relative abundance values in both bacterial strains. Our findings revealed that seed-surface-associated bacteria on Capsicum spp. have the metabolic ability to produce VOCs for biocontrol of fungal strains and have the potential to be used in sustainable agriculture. Full article

(This article belongs to the Special Issue Microorganisms in Agriculture)

15 pages, 1496 KiB

Open AccessArticle

Molecular Characterization of Carbapenem and Colistin Resistance in Klebsiella pneumoniae Isolates Obtained from Clinical Samples at a University Hospital Center in Algeria

by Riyane Rihane, Abla Hecini-Hannachi, Chafia Bentchouala, Kaddour Benlabed and Seydina M. Diene

Microorganisms 2024, 12(10), 1942; https://doi.org/10.3390/microorganisms12101942 (registering DOI) - 25 Sep 2024

Abstract

The current study aimed to determine the molecular mechanisms of carbapenem and colistin resistance among the clinical isolates of Klebsiella pneumoniae from hospitalized patients admitted to a university hospital in Eastern Algeria. In total, 124 non-duplicate isolates of K. pneumoniae were collected from [...] Read more.

The current study aimed to determine the molecular mechanisms of carbapenem and colistin resistance among the clinical isolates of Klebsiella pneumoniae from hospitalized patients admitted to a university hospital in Eastern Algeria. In total, 124 non-duplicate isolates of K. pneumoniae were collected from September 2018 to April 2019. Bacterial identification was performed using MALDI-TOF MS. The presence of extended spectrum β-lactamase (ESBL) genes, carbapenemase genes, chromosomal mutation and mcr genes in colistin-resistant K. pneumoniae were evaluated by PCR. ESBLs represented a rate of 49.1% and harbored bla_CTX-M, bla_TEM and bla_SHV genes. Concerning carbapenems, 12 strains (9.6%) were resistant to ertapenem (MIC: 1–32 μg/mL), of which one strain (0.8%) was also resistant to imipenem (MIC: 32 μg/mL). Among these strains, nine (75%) harbored bla_OXA-48 gene. Seven strains (5.6%) expressed resistance to colistin (MIC: 2–32 μg/mL), of which two harbored mcr-8 and mgrB genes simultaneously. The existence of a double resistance to colistin in the same strain is new in Algeria, and this could raise concerns about the increase in levels of resistance to this antibiotic (MIC: 32 μg/mL). The mgrB gene alone was observed in five isolates (71.4%), including two strains harboring bla_OXA-48. This is the first report revealing the presence of K. pneumoniae strains carrying the bla_OXA-48 gene as well as a mutation in the mgrB gene. Large-scale surveillance and effective infection control measures are also urgently needed to prevent the outbreak of various carbapenem- and colistin-resistant isolates. Full article

(This article belongs to the Special Issue Bacterial Infections in Clinical Settings)

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7 pages, 471 KiB

Open AccessCase Report

Challenges in Diagnosis of COVID-19 Pneumonia under Ocrelizumab and De-Risking Strategies in Multiple Sclerosis—The Elephant Is (Still) in the Room

by Alice Mariottini, Antonio Lotti, Valentina Damato and Luca Massacesi

Microorganisms 2024, 12(10), 1941; https://doi.org/10.3390/microorganisms12101941 - 25 Sep 2024

Abstract

Severe SARS-CoV-2 infections may still be observed in people bearing risk factors, such as the use of anti-CD20 monoclonal antibodies (mAbs), which are adopted in several autoimmune disorders including multiple sclerosis (MS). COVID-19 diagnosis is routinely based on nasopharyngeal swab testing, but suboptimal [...] Read more.

Severe SARS-CoV-2 infections may still be observed in people bearing risk factors, such as the use of anti-CD20 monoclonal antibodies (mAbs), which are adopted in several autoimmune disorders including multiple sclerosis (MS). COVID-19 diagnosis is routinely based on nasopharyngeal swab testing, but suboptimal sensitivity for SARS-CoV-2 detection compared to bronchoalveolar lavage (BAL) may lead to misdiagnosis in some cases. Such diagnostic issues were described in a few MS patients receiving anti-CD20 mAbs, including middle-aged people and lacking information on subsequent MS therapeutic management, a debated topic as no evidence-based guidance on de-risking strategies is currently available. Here, we report the case of a young MS patient who developed severe COVID-19 pneumonia under treatment with the anti-CD20 mAb ocrelizumab, and who was finally diagnosed with SARS-CoV-2 by BAL despite repeatedly negative nasopharyngeal swabs. Ocrelizumab was then discontinued, and treatment with a sphingosine-1 phosphate receptor modulator was started, followed by maintenance of clinical and radiological MS stability. Challenges in diagnosing COVID-19 pneumonia in people without risk factors other than immunomodulatory treatment are hence discussed, as well as potential strategies for de-risking MS therapies. The latter topic is increasingly debated based on raising concerns for potential long-term safety issues of high-efficacy treatments, including anti-CD20 mAbs. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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15 pages, 2676 KiB

Open AccessArticle

Rapid Responses of Greenhouse Gas Emissions and Microbial Communities to Carbon and Nitrogen Addition in Sediments

by Jin-Feng Liang, Bo Yao, Xiao-Ya Zhang and Qi-Wu Hu

Microorganisms 2024, 12(10), 1940; https://doi.org/10.3390/microorganisms12101940 - 25 Sep 2024

Abstract

Massive labile carbon and nitrogen inputs into lakes change greenhouse gas emissions. However, the rapid driving mechanism from eutrophic and swampy lakes is not fully understood and is usually contradictory. Thus, we launched a short-term and anaerobic incubation experiment to explore the response [...] Read more.

Massive labile carbon and nitrogen inputs into lakes change greenhouse gas emissions. However, the rapid driving mechanism from eutrophic and swampy lakes is not fully understood and is usually contradictory. Thus, we launched a short-term and anaerobic incubation experiment to explore the response of greenhouse gas emissions and microbial communities to glucose and nitrate nitrogen (NO₃⁻-N) inputs. Glucose addition significantly increased CH₄ and CO₂ emissions and decreased N₂O emissions, but there were no significant differences. NO₃⁻-N addition significantly promoted N₂O emissions but reduced CH₄ accumulative amounts, similar to the results of the Tax4Fun prediction. Bacterial relative abundance changed after glucose addition and coupled with the abundance of denitrification genes (nirS and nirK) decreased while maintaining a negative impact on N₂O emissions, considerably increasing methanogenic bacteria (mcrA1) while maintaining a positive impact on CH₄ emissions. Structural equation modeling showed that glucose and NO₃⁻-N addition directly affected MBC content and greenhouse gas emissions. Further, MBC content was significantly negative with nirS and nirK, and positive with mcrA1. These results significantly deepen the current understanding of the relationships between labial carbon, nitrogen, and greenhouse emissions, further highlighting that labile carbon input is the primary factor driving greenhouse gas emissions from eutrophic shallow lakes. Full article

(This article belongs to the Section Environmental Microbiology)

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16 pages, 5427 KiB

Open AccessArticle

Biogenic Sulfide-Mediated Iron Reduction at Low pH

by Caryl Ann Becerra, Brendan Murphy, Brittnee V. Veldman and Klaus Nüsslein

Microorganisms 2024, 12(10), 1939; https://doi.org/10.3390/microorganisms12101939 - 25 Sep 2024

Abstract

Acid mine drainage (AMD) pollutes natural waters, but some impacted systems show natural attenuation. We sought to identify the biogeochemical mechanisms responsible for the natural attenuation of AMD. We hypothesized that biogenic sulfide-mediated iron reduction is one mechanism and tested this in an [...] Read more.

Acid mine drainage (AMD) pollutes natural waters, but some impacted systems show natural attenuation. We sought to identify the biogeochemical mechanisms responsible for the natural attenuation of AMD. We hypothesized that biogenic sulfide-mediated iron reduction is one mechanism and tested this in an experimental model system. We found sulfate reduction occurred under acidic conditions and identified a suite of sulfate-reducing bacteria (SRB) belonging to the groups Desulfotomaculum, Desulfobacter, Desulfovibrio, and Desulfobulbus. Iron reduction was not detected in microcosms when iron-reducing bacteria or SRB were selectively inhibited. SRB also did not reduce iron enzymatically. Rather, the biogenic sulfide produced by SRB was found to be responsible for the reduction of iron at low pH. Addition of organic substrates and nutrients stimulated iron reduction and increased the pH. X-ray diffraction and an electron microprobe analysis revealed that the polycrystalline, black precipitate from SRB bioactive samples exhibited a greater diversity of iron chalcogenide minerals with reduced iron oxidation states, and minerals incorporating multiple metals compared to abiotic controls. The implication of this study is that iron reduction mediated by biogenic sulfide may be more significant than previously thought in acidic environments. This study not only describes an additional mechanism by which SRB attenuate AMD, which has practical implications for AMD-impacted sites, but also provides a link between the biogeochemical cycling of iron and sulfur. Full article

(This article belongs to the Section Environmental Microbiology)

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20 pages, 4014 KiB

Open AccessArticle

Endophytic Bacterial Biofilm-Formers Associated with Antarctic Vascular Plants

by Olga Iungin, Yevheniia Prekrasna-Kviatkovska, Oleksandr Kalinichenko, Olena Moshynets, Geert Potters, Marina Sidorenko, Yaroslav Savchuk and Saulius Mickevičius

Microorganisms 2024, 12(10), 1938; https://doi.org/10.3390/microorganisms12101938 - 25 Sep 2024

Abstract

Deschampsia antarctica and Colobantus quitensis are the only two vascular plants colonized on the Antarctic continent, which is usually exposed to extreme environments. Endophytic bacteria residing within plant tissues can exhibit diverse adaptations that contribute to their ecological success and potential benefits for [...] Read more.

Deschampsia antarctica and Colobantus quitensis are the only two vascular plants colonized on the Antarctic continent, which is usually exposed to extreme environments. Endophytic bacteria residing within plant tissues can exhibit diverse adaptations that contribute to their ecological success and potential benefits for their plant hosts. This study aimed to characterize 12 endophytic bacterial strains isolated from these plants, focusing on their ecological adaptations and functional roles like plant growth promotion, antifungal activities, tolerance to salt and low-carbon environments, wide temperature range, and biofilm formation. Using 16S rRNA sequencing, we identified several strains, including novel species like Hafnia and Agreia. Many strains exhibited nitrogen-fixing ability, phosphate solubilization, ammonia, and IAA production, potentially benefiting their hosts. Additionally, halotolerance and carbon oligotrophy were also shown by studied bacteria. While some Antarctic bacteria remain strictly psychrophilic, others demonstrate a remarkable ability to tolerate a wider range of temperatures, suggesting that they have acquired mechanisms to cope with fluctuations in environmental temperature and developed adaptations to survive in intermediate hosts like mammals and/or birds. Such adaptations and high plasticity of metabolism of Antarctic endophytic bacteria provide a foundation for research and development of new promising products or mechanisms for use in agriculture and technology. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 7437 KiB

Open AccessArticle

Comparative Study on Growth and Metabolomic Profiles of Six Lactobacilli Strains by Sodium Selenite

by Longrui Wang, Jiasheng Ju, Huichun Xie, Feng Qiao, Qiaoyu Luo and Lianyu Zhou

Microorganisms 2024, 12(10), 1937; https://doi.org/10.3390/microorganisms12101937 - 24 Sep 2024

Abstract

Selenium (Se) has garnered increasing attention in the field of nutrition, as it is essential for both humans and animals. Certain microorganisms can enrich inorganic selenium and convert it into organic selenium. The growth and metabolomic profiles of six lactobacilli strains exposed to [...] Read more.

Selenium (Se) has garnered increasing attention in the field of nutrition, as it is essential for both humans and animals. Certain microorganisms can enrich inorganic selenium and convert it into organic selenium. The growth and metabolomic profiles of six lactobacilli strains exposed to 50 μg/mL of sodium selenite were performed using gas chromatography tandem time-off light mass spectrometry (GC-TOF-MS) analysis. The addition of selenium significantly increased both the population and weight of the Lacticaseibacillus rhamnosus PS5, Lbs. rhamnosus RT-B, Limosilactobacillus reuteri 3630, and Lmb. reuteri 1663 strains, while those of the other two strains decreased. A total of 271 metabolites were determined, with their concentrations ranked from highest to lowest as follows: organic acids and derivatives, oxygen compounds, lipids and lipid-like molecules, and benzenoids. In certain groups, the concentrations of serine, aspartic acid, trehalose, palmitic acid, methylthreonine, and melibiose increased significantly, whereas glucuronic acid, ribose, ornithine, and methionine were downregulated. The metabolic pathways were significantly associated with ABC transporters, glycine, serine, threonine metabolism, and aminobenzoate degradation and other pathways. Based on these findings, we concluded that the transport, absorption, assimilation, and stress response to selenium by lactobacilli in metabolomic changed. Furthermore, the metabolomic alterations among different types of lactobacilli varied primarily due to their distinct properties. Full article

(This article belongs to the Section Food Microbiology)

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17 pages, 1835 KiB

Open AccessArticle

Bacterial N-Acyl Homoserine Lactone Priming Enhances Leaf-Rust Resistance in Winter Wheat and Some Genomic Regions Are Associated with Priming Efficiency

by Behnaz Soleimani, Heike Lehnert, Adam Schikora, Andreas Stahl, Andrea Matros and Gwendolin Wehner

Microorganisms 2024, 12(10), 1936; https://doi.org/10.3390/microorganisms12101936 - 24 Sep 2024

Abstract

Leaf rust (Puccinia triticina) is a common disease that causes significant yield losses in wheat. The most frequently used methods to control leaf rust are the application of fungicides and the cultivation of resistant genotypes. However, high genetic diversity and associated [...] Read more.

Leaf rust (Puccinia triticina) is a common disease that causes significant yield losses in wheat. The most frequently used methods to control leaf rust are the application of fungicides and the cultivation of resistant genotypes. However, high genetic diversity and associated adaptability of pathogen populations hamper achieving durable resistance in wheat. Emerging alternatives, such as microbial priming, may represent an effective measure to stimulate plant defense mechanisms and could serve as a means of controlling a broad range of pathogens. In this study, 175 wheat genotypes were inoculated with two bacterial strains: Ensifer meliloti strain expR⁺ch (producing N-acyl homoserine lactone (AHL)) or transformed E. meliloti carrying the lactonase gene attM (control). In total, 21 genotypes indicated higher resistance upon bacterial AHL priming. Subsequently, the phenotypic data of 175 genotypes combined with 9917 single-nucleotide polymorphisms (SNPs) in a genome-wide association study to identify quantitative trait loci (QTLs) and associated markers for relative infection under attM and expR⁺ch conditions and priming efficiency using the Genome Association and Prediction Integrated Tool (GAPIT). In total, 15 QTLs for relative infection under both conditions and priming efficiency were identified on chromosomes 1A, 1B, 2A, 3A, 3B, 3D, 6A, and 6B, which may represent targets for wheat breeding for priming and leaf-rust resistance. Full article

(This article belongs to the Special Issue Harnessing Beneficial Microbiota in Sustainable Agriculture)

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13 pages, 3170 KiB

Open AccessArticle

Diversity and Complexity of CTXΦ and Pre-CTXΦ Families in Vibrio cholerae from Seventh Pandemic

by Xiaorui Li, Yu Han, Wenxuan Zhao, Xiao Yue, Siyu Huang, Zhenpeng Li, Fenxia Fan, Weili Liang and Biao Kan

Microorganisms 2024, 12(10), 1935; https://doi.org/10.3390/microorganisms12101935 - 24 Sep 2024

Abstract

CTXΦ is a lysogenic filamentous phage that carries the genes encoding cholera toxin (ctxAB), the main virulence factor of Vibrio cholerae. The toxigenic conversion of environmental V. cholerae strains through CTXΦ lysogenic infection is crucial for the emergence of new [...] Read more.

CTXΦ is a lysogenic filamentous phage that carries the genes encoding cholera toxin (ctxAB), the main virulence factor of Vibrio cholerae. The toxigenic conversion of environmental V. cholerae strains through CTXΦ lysogenic infection is crucial for the emergence of new pathogenic clones. A special allelic form of CTXΦ, called pre-CTXΦ, is a precursor of CTXΦ and without ctxAB. Different members of the pre-CTXΦ and CTXΦ families are distinguished by the sequence of the transcriptional repressor-coding gene rstR. Multiple rstR alleles can coexist within a single strain, demonstrating the diverse structure and complex genomic integration patterns of CTXΦ/pre-CTXΦ prophage on the chromosome. Exploration of the diversity and co-integration patterns of CTXΦ/pre-CTXΦ prophages in V. cholerae can help to understand the evolution of this phage family. In this study, 21 V. cholerae strains, which were shown to carry the CTXΦ/pre-CTXΦ prophages as opposed to typical CTX^ETΦ-RS1 structure, were selected from approximately 1000 strains with diverse genomes. We identified two CTXΦ members and six pre-CTXΦ members with distinct rstR alleles, revealing complex chromosomal DNA integration patterns and arrangements of different prophages in these strains. Promoter activity assays showed that the transcriptional repressor RstR protected against CTXΦ superinfection by preventing the replication and integration of CTXΦ/pre-CTXΦ phages containing the same rstR allele, supporting the co-integration of the diverse CTXΦ/pre-CTXΦ members observed. The numbers and types of prophages and their co-integration arrangements in serogroup O139 strains were more complex than those in serogroup O1 strains. Also, these CTXΦ/pre-CTXΦ members were shown to present the bloom period of the CTXΦ/pre-CTXΦ family during wave 2 of the seventh cholera pandemic. Together, these analyses deepen our comprehension of the genetic variation of CTXΦ and pre-CTXΦ and provide insights into the evolution of the CTXΦ/pre-CTXΦ family in the seventh cholera pandemic. Full article

(This article belongs to the Special Issue Enteric Disease-Associated Pathogens)

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13 pages, 1617 KiB

Open AccessArticle

Changes in Periodontal Parameters and Microbiome Composition of Periodontal Pocket in Patients with Chronic Inflammatory Diseases Receiving Targeted Anti-Cytokine Therapy

by Juliane Wagner, Luisa Haker, Louisa Mewes, Corinna Bang, Malte Rühlemann, Hendrik Naujokat, Johannes Heinrich Spille, Wolfgang Lieb, Andre Franke, Stefan Schreiber, Matthias Laudes, Christof Dörfer, Jörg Wiltfang, Christian Graetz and Dominik Maria Schulte

Microorganisms 2024, 12(10), 1934; https://doi.org/10.3390/microorganisms12101934 - 24 Sep 2024

Abstract

Periodontitis is associated with systemic chronic inflammatory diseases. There is limited evidence on the influence of anti-cytokine therapies on the periodontal condition and microbiome in the tooth pocket of such patients, so the aim of this study was to elucidate this issue. In [...] Read more.

Periodontitis is associated with systemic chronic inflammatory diseases. There is limited evidence on the influence of anti-cytokine therapies on the periodontal condition and microbiome in the tooth pocket of such patients, so the aim of this study was to elucidate this issue. In this observational trial, the periodontal status and the gingival crevicular fluid of 13 patients with different chronic inflammatory diseases were obtained before the initiation of anti-cytokine treatment and 14 weeks after. Gingival crevicular fluid was collected for 16S rRNA gene sequencing from a clinically healthy tooth and the deepest measured pocket. The Shannon Diversity Index significantly increased in the deepest pockets of patients (p = 0.039). The data showed alterations in the diversity of the subgingival microbiome over the course of the study, implying a shift towards a healthier condition after starting anti-cytokine therapy. Additional investigations are needed to analyze whether the administration of selective biologicals can improve periodontal conditions in patients with or without chronic inflammatory diseases. Full article

(This article belongs to the Special Issue Oral Microorganisms and Biofilm)

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15 pages, 2335 KiB

Open AccessArticle

A Mouse Model of Mild Clostridioides difficile Infection for the Characterization of Natural Immune Responses

by Assaf Mizrahi, Gauthier Péan de Ponfilly, Diane Sapa, Antonia Suau, Irène Mangin, Aurélie Baliarda, Sandra Hoys, Benoît Pilmis, Sylvie Lambert, Anaïs Brosse and Alban Le Monnier

Microorganisms 2024, 12(10), 1933; https://doi.org/10.3390/microorganisms12101933 - 24 Sep 2024

Abstract

(1) Background: We describe a model of primary mild-Clostridioides difficile infection (CDI) in a naïve host, including gut microbiota analysis, weight loss, mortality, length of colonization. This model was used in order to describe the kinetics of humoral (IgG, IgM) and mucosal [...] Read more.

(1) Background: We describe a model of primary mild-Clostridioides difficile infection (CDI) in a naïve host, including gut microbiota analysis, weight loss, mortality, length of colonization. This model was used in order to describe the kinetics of humoral (IgG, IgM) and mucosal (IgA) immune responses against toxins (TcdA/TcdB) and surface proteins (SlpA/FliC). (2) Methods: A total of 10⁵ CFU vegetative forms of C. difficile 630Δerm were used for challenge by oral administration after dysbiosis, induced by a cocktail of antibiotics. Gut microbiota dysbiosis was confirmed and described by 16S rDNA sequencing. We sacrificed C57Bl/6 mice after different stages of infection (day 6, 2, 7, 14, 21, 28, and 56) to evaluate IgM, IgG against TcdA, TcdB, SlpA, FliC in blood samples, and IgA in the cecal contents collected. (3) Results: In our model, we observed a reproducible gut microbiota dysbiosis, allowing for C. difficile digestive colonization. CDI was objectivized by a mean weight loss of 13.1% and associated with a low mortality rate of 15.7% of mice. We observed an increase in IgM anti-toxins as early as D7 after challenge. IgG increased since D21, and IgA anti-toxins were secreted in cecal contents. Unexpectedly, neither anti-SlpA nor anti-FliC IgG or IgA were observed in our model. (4) Conclusions: In our model, we induced a gut microbiota dysbiosis, allowing a mild CDI to spontaneously resolve, with a digestive clearance observed since D14. After this primary CDI, we can study the development of specific immune responses in blood and cecal contents. Full article

(This article belongs to the Special Issue Latest Research on Clostridioides difficile)

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11 pages, 1106 KiB

Open AccessArticle

Trends in Enterococcus faecium Bacteremia: Exploring Risk Factors with Emphasis on Prior Antibiotic Exposure

by Erik Sörstedt, Gustaf Ahlbeck and Ulrika Snygg-Martin

Microorganisms 2024, 12(10), 1932; https://doi.org/10.3390/microorganisms12101932 - 24 Sep 2024

Abstract

Enterococcal bacteremia (EB) is on the rise both in Sweden and globally. While Enterococcus faecalis (E. faecalis) is susceptible to ampicillin and piperacillin/tazobactam (pip/taz), Enterococcus faecium (E. faecium) is not. Historically, most enterococcal infections have been caused by E. [...] Read more.

Enterococcal bacteremia (EB) is on the rise both in Sweden and globally. While Enterococcus faecalis (E. faecalis) is susceptible to ampicillin and piperacillin/tazobactam (pip/taz), Enterococcus faecium (E. faecium) is not. Historically, most enterococcal infections have been caused by E. faecalis, but the epidemiology is changing with increasing recognition of enterococci as nosocomial pathogens and the emergence of resistance to commonly used antimicrobial agents. The use of pip/taz has increased dramatically in Sweden, but it is unknown if this has affected the relative incidence of E. faecalis/E. faecium bacteremia. Here, we investigate whether the number and proportion of E. faecium bacteremia (EfmB) cases have increased. Additionally, risk factors associated with EfmB with a focus on prior antibiotic exposure are analyzed. Medical journals of 360 patients with EB admitted to Sahlgrenska University Hospital are reviewed. The proportion of EfmB cases increased from 41% in 2015 to 51% in 2021. Hospital-acquired infection, previous exposure to pip/taz, and carbapenems are identified as independent risk factors for EfmB. There are considerable patient-related differences between the EfmB and EfsB groups, but there is no difference in mortality rates. In conclusion, the increasing proportion of EfmB cases is concerning and is seen parallel to the expanding use of pip/taz, one possible contributing factor. Our findings suggest that a cautious approach to antibiotic use is essential to prevent the spread of antibiotic-resistant bacteria. Full article

(This article belongs to the Special Issue Bacteremia and Sepsis)

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20 pages, 3864 KiB

Open AccessArticle

Analysis of the Respiratory Activity in the Antarctic Yeast Rhodotorula mucilaginosa M94C9 Reveals the Presence of Respiratory Supercomplexes and Alternative Elements

by Daniel Reyes-Rosario, Juan Pablo Pardo, Guadalupe Guerra-Sánchez, Héctor Vázquez-Meza, Georgina López-Hernández, Genaro Matus-Ortega, James González, Marcelo Baeza and Lucero Romero-Aguilar

Microorganisms 2024, 12(10), 1931; https://doi.org/10.3390/microorganisms12101931 - 24 Sep 2024

Abstract

The respiratory activities of mitochondrial complexes I, II, and IV were analyzed in permeabilized Rhodotorula mucilaginosa cells and isolated mitochondria, and the kinetic parameters K_0.5 and V_max were obtained. No difference in substrate affinities were found between mitochondria and permeabilized cells. [...] Read more.

The respiratory activities of mitochondrial complexes I, II, and IV were analyzed in permeabilized Rhodotorula mucilaginosa cells and isolated mitochondria, and the kinetic parameters K_0.5 and V_max were obtained. No difference in substrate affinities were found between mitochondria and permeabilized cells. The activities of the components of the mitochondrial respiratory chain of the Antarctic yeast R. mucilaginosa M94C9 were identified by in-gel activity and SDS-PAGE. The mitochondria exhibited activity for the classical components of the electron transport chain (Complexes I, II, III, and IV), and supercomplexes were formed by a combination of the respiratory complexes I, III, and IV. Unfortunately, the activities of the monomeric and dimeric forms of the F1F0-ATP synthase were not revealed by the in-gel assay, but the two forms of the ATP synthase were visualized in the SDS-PAGE. Furthermore, two alternative pathways for the oxidation of cytosolic NADH were identified: the alternative NADH dehydrogenase and the glycerol-3-phosphate dehydrogenase. In addition, an NADPH dehydrogenase and a lactate cytochrome b2 dehydrogenase were found. The residual respiratory activity following cyanide addition suggests the presence of an alternative oxidase in cells. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 1981 KiB

Open AccessReview

Unravelling the Roles of Bacterial Nanomachines Bistability in Pathogens’ Life Cycle

by Romain Gory, Nicolas Personnic and Didier Blaha

Microorganisms 2024, 12(9), 1930; https://doi.org/10.3390/microorganisms12091930 - 23 Sep 2024

Abstract

Bacterial nanomachines represent remarkable feats of evolutionary engineering, showcasing intricate molecular mechanisms that enable bacteria to perform a diverse array of functions essential to persist, thrive, and evolve within ecological and pathological niches. Injectosomes and bacterial flagella represent two categories of bacterial nanomachines [...] Read more.

Bacterial nanomachines represent remarkable feats of evolutionary engineering, showcasing intricate molecular mechanisms that enable bacteria to perform a diverse array of functions essential to persist, thrive, and evolve within ecological and pathological niches. Injectosomes and bacterial flagella represent two categories of bacterial nanomachines that have been particularly well studied both at the molecular and functional levels. Among the diverse functionalities of these nanomachines, bistability emerges as a fascinating phenomenon, underscoring their dynamic and complex regulation as well as their contribution to shaping the bacterial community behavior during the infection process. In this review, we examine two closely related bacterial nanomachines, the type 3 secretion system, and the flagellum, to explore how the bistability of molecular-scale devices shapes the bacterial eco-pathological life cycle. Full article

(This article belongs to the Special Issue Insight into Bacterial Pathogens: Pathogenesis and Host Response)

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20 pages, 10480 KiB

Open AccessArticle

Hass Avocado (Persea americana Mill) Peel Extract Reveals Antimicrobial and Antioxidant Properties against Verticillium theobromae, Colletotrichum musae, and Aspergillus niger Pathogens Affecting Musa acuminata Colla Species, in Ecuador

by Caterine Donoso, Mihai A. Raluca, Stephanie Chávez-Jinez and Edwin Vera

Microorganisms 2024, 12(9), 1929; https://doi.org/10.3390/microorganisms12091929 - 23 Sep 2024

Abstract

The utilization of agroindustrial residues, such as avocado peel, as a source of bioactive compounds with antioxidant properties has garnered significant attention. In this study, we investigated the antioxidant potential using the DPPH (2,2-diphenyl-1-picrylhydrazyl) and ORAC (oxygen radical absorbance capacity) methods, along with [...] Read more.

The utilization of agroindustrial residues, such as avocado peel, as a source of bioactive compounds with antioxidant properties has garnered significant attention. In this study, we investigated the antioxidant potential using the DPPH (2,2-diphenyl-1-picrylhydrazyl) and ORAC (oxygen radical absorbance capacity) methods, along with the antimicrobial activity of phenolic compounds extracted from Hass avocado peel. These soluble polyphenols were quantified and identified using high-performance liquid chromatography (HPLC). The research focused on their effects against three fungal pathogens, Verticillium theobromae, Colletotrichum musae, and Aspergillus niger, which significantly impact banana crops, an essential agricultural commodity in Ecuador. The results have revealed that the application of 80% ethanol as an organic solvent led to increased soluble polyphenol content compared to 96% ethanol. Extraction time significantly influenced the phenolic content, with the highest values obtained at 90 min. Interestingly, despite substantial mycelial growth observed across all extract concentrations, the antifungal effect varied among the pathogens. Specifically, V. theobromae exhibited the highest sensitivity, while C. musae and A. niger were less affected. These results underscore the importance of considering both antioxidant and antimicrobial properties when evaluating natural extracts for potential applications in plant disease management. Full article

(This article belongs to the Special Issue Advanced Research on Biological Control of Plant Disease or Microbial Interactions (2nd Edition))

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17 pages, 3272 KiB

Open AccessArticle

AraC Functional Suppressors of Mutations in the C-Terminal Domain of the RpoA Subunit of the Escherichia coli RNA Polymerase

by Dominique Belin, Jordan Costafrolaz and Filo Silva

Microorganisms 2024, 12(9), 1928; https://doi.org/10.3390/microorganisms12091928 - 23 Sep 2024

Abstract

In E. coli, transcriptional activation is often mediated by the C-terminal domain of RpoA, the α subunit of RNA polymerase. Random mutations that prevent activation of the arabinose P_BAD promoter are clustered in the RpoA C-terminal domain (α-CTD). We have isolated [...] Read more.

In E. coli, transcriptional activation is often mediated by the C-terminal domain of RpoA, the α subunit of RNA polymerase. Random mutations that prevent activation of the arabinose P_BAD promoter are clustered in the RpoA C-terminal domain (α-CTD). We have isolated functional suppressors of rpoA α-CTD mutations that map to araC, the main transcriptional regulator of ara genes, or to the P_BAD promoter. No mutation was found in the DNA regulatory region between araC and P_BAD. Most suppressors that improve P_BAD transcription are localized to the N-terminal domain of AraC. One class of araC mutations generates substitutions in the core of the N-terminal domain, suggesting that they affect its conformation. Other suppressors localize to the flexible N-terminal arm of AraC. Some, but not all, suppressors confer an arabinose constitutive phenotype. Suppression by both classes of araC mutations requires the α-CTD to stimulate expression from P_BAD. Surprisingly, in rpoA⁺ strains lacking Crp, the cAMP receptor protein, these araC mutations largely restore arabinose gene expression and can essentially bypass Crp activation. Thus, the N-terminal domain of AraC exhibits at least three distinct activities: dimerization, arabinose binding, and transcriptional activation. Finally, one mutation maps to the AraC C-terminal domain and can synergize with AraC mutations in the N-terminal domain. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Bacteria)

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17 pages, 2832 KiB

Open AccessArticle

Root Endophytic Microorganisms Contribute to the Attribute of Full-Year Shooting in Woody Bamboo Cephalostachyum pingbianense

by Lushuang Li, Bin Li, Qing Li, Lianchun Wang and Hanqi Yang

Microorganisms 2024, 12(9), 1927; https://doi.org/10.3390/microorganisms12091927 - 22 Sep 2024

Abstract

Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang is unique among bamboo species for its ability to produce bamboo shoots in all seasons under natural conditions. Apart from the physiological mechanism, information regarding the effects of [...] Read more.

Cephalostachyum pingbianense (Hsueh & Y.M. Yang ex Yi et al.) D.Z. Li & H.Q. Yang is unique among bamboo species for its ability to produce bamboo shoots in all seasons under natural conditions. Apart from the physiological mechanism, information regarding the effects of endophytic microorganisms on this full-year shooting characteristic is limited. We hypothesize that root endophytic microorganisms will have a positive impact on the full-year bamboo shooting characteristic of C. pingbianense by increasing the availability or supply of nutrients. To identify the seasonal variations in the root endophytic bacterial and fungal communities of C. pingbianense, and to assess their correlation with bamboo shoot productivity, the roots of C. pingbianense were selected as research materials, and the 16S rRNA and ITS rDNA genes of root endophytic microorganisms were sequenced using the Illumina platform. Following this sequencing, raw sequencing reads were processed, and OTUs were annotated. Alpha and beta diversity, microbial composition, and functional predictions were analyzed, with correlations to bamboo shoot numbers assessed. The results showed that seasonal changes significantly affected the community diversity and structure of root endophytic microbes of C. pingbianense. Bacterial communities in root samples from all seasons contained more nitrogen-fixing microorganisms, with members of the Burkholderiales and Rhizobiales predominating. The relative abundances of ectomycorrhizal and arbuscular mycorrhizal fungi in the autumn sample were significantly higher than in other seasons. Correlation analysis revealed that the bamboo shoot productivity was significantly and positively correlated with bacterial functions of nitrogen fixation, arsenate detoxification, and ureolysis, as well as with symbiotrophic fungi, ectomycorrhizal fungi, and arbuscular mycorrhizal fungi. At the genus level, the bacterial genus Herbaspirillum and the fungal genera Russula, unclassified_f_Acaulosporaceae, and unclassified_f_Glomeraceae were found to have a significant positive correlation with bamboo shoot number. Our study provides an ecological perspective for understanding the highly productive attribute of C. pingbianense and offers new insights into the forest management of woody bamboos. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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