Microorganisms

16 pages, 1376 KiB

Open AccessArticle

Enhancing the Rice Seedlings Growth Promotion Abilities of Azoarcus sp. CIB by Heterologous Expression of ACC Deaminase to Improve Performance of Plants Exposed to Cadmium Stress

by Helga Fernández-Llamosas, Juan Ibero, Sofie Thijs, Valeria Imperato, Jaco Vangronsveld, Eduardo Díaz and Manuel Carmona

Microorganisms 2020, 8(9), 1453; https://doi.org/10.3390/microorganisms8091453 - 22 Sep 2020

Cited by 18 | Viewed by 3386

Abstract

Environmental pollutants can generate stress in plants causing increased ethylene production that leads to the inhibition of plant growth. Ethylene production by the stressed plant may be lowered by Plant Growth-Promoting Bacteria (PGPB) that metabolizes the immediate precursor of ethylene 1-aminocyclopropane-1-carboxylate (ACC). Thus, [...] Read more.

Environmental pollutants can generate stress in plants causing increased ethylene production that leads to the inhibition of plant growth. Ethylene production by the stressed plant may be lowered by Plant Growth-Promoting Bacteria (PGPB) that metabolizes the immediate precursor of ethylene 1-aminocyclopropane-1-carboxylate (ACC). Thus, engineering PGPB with ACC deaminase activity can be a promising alternative to mitigate the harmful effects of pollutants and thus enhance plant production. Here we show that the aromatics-degrading and metal-resistant Azoarcus sp. CIB behaves as a PGP-bacterium when colonizing rice as an endophyte, showing a 30% increment in plant weight compared to non-inoculated plants. The cloning and expression of an acdS gene led to a recombinant strain, Azoarcus sp. CIB (pSEVA237acdS), possessing significant ACC deaminase activity (6716 nmol mg⁻¹ h⁻¹), constituting the first PGPB of the Rhodocyclaceae family equipped with this PGP trait. The recombinant CIB strain acquired the ability to protect inoculated rice plants from the stress induced by cadmium (Cd) exposure and to increase the Cd concentration in rice seedlings. The observed decrease of the levels of reactive oxygen species levels in rice roots confirms such a protective effect. The broad-host-range pSEVA237acdS plasmid paves the way to engineer PGPB with ACC deaminase activity to improve the growth of plants that might face stress conditions. Full article

(This article belongs to the Section Environmental Microbiology)

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17 pages, 2332 KiB

Open AccessArticle

Chlorine Disinfection of Legionella spp., L. pneumophila, and Acanthamoeba under Warm Water Premise Plumbing Conditions

by Rebekah L. Martin, Kara Harrison, Caitlin R. Proctor, Amanda Martin, Krista Williams, Amy Pruden and Marc A. Edwards

Microorganisms 2020, 8(9), 1452; https://doi.org/10.3390/microorganisms8091452 - 22 Sep 2020

Cited by 12 | Viewed by 3890

Abstract

Premise plumbing conditions can contribute to low chlorine or chloramine disinfectant residuals and reactions that encourage opportunistic pathogen growth and create risk of Legionnaires’ Disease outbreaks. This bench-scale study investigated the growth of Legionella spp. and Acanthamoeba in direct contact with premise plumbing [...] Read more.

Premise plumbing conditions can contribute to low chlorine or chloramine disinfectant residuals and reactions that encourage opportunistic pathogen growth and create risk of Legionnaires’ Disease outbreaks. This bench-scale study investigated the growth of Legionella spp. and Acanthamoeba in direct contact with premise plumbing materials—glass-only control, cross-linked polyethylene (PEX) pipe, magnesium anode rods, iron pipe, iron oxide, pH 10, or a combination of factors. Simulated glass water heaters (SGWHs) were colonized by Legionella pneumophila and exposed to a sequence of 0, 0.1, 0.25, and 0.5 mg/L chlorine or chloramine, at two levels of total organic carbon (TOC), over 8 weeks. Legionella pneumophila thrived in the presence of the magnesium anode by itself and or combination with other factors. In most cases, 0.5 mg/L Cl₂ caused a significant rapid reduction of L. pneumophila, Legionella spp., or total bacteria (16S rRNA) gene copy numbers, but at higher TOC (>1.0 mg C/L), a chlorine residual of 0.5 mg/L Cl₂ was not effective. Notably, Acanthamoeba was not significantly reduced by the 0.5 mg/L chlorine dose. Full article

(This article belongs to the Special Issue Legionella and Legionnaires’ Disease: Pathogenesis, Prevention, and Public Health)

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18 pages, 3328 KiB

Open AccessArticle

Syngas as Electron Donor for Sulfate and Thiosulfate Reducing Haloalkaliphilic Microorganisms in a Gas-Lift Bioreactor

by Caroline M. Plugge, João A. B. Sousa, Stephan Christel, Mark Dopson, Martijn F. M. Bijmans, Alfons J. M. Stams and Martijn Diender

Microorganisms 2020, 8(9), 1451; https://doi.org/10.3390/microorganisms8091451 - 22 Sep 2020

Cited by 2 | Viewed by 3139

Abstract

Biodesulfurization processes remove toxic and corrosive hydrogen sulfide from gas streams (e.g., natural gas, biogas, or syngas). To improve the efficiency of these processes under haloalkaline conditions, a sulfate and thiosulfate reduction step can be included. The use of H₂/CO mixtures [...] Read more.

Biodesulfurization processes remove toxic and corrosive hydrogen sulfide from gas streams (e.g., natural gas, biogas, or syngas). To improve the efficiency of these processes under haloalkaline conditions, a sulfate and thiosulfate reduction step can be included. The use of H₂/CO mixtures (as in syngas) instead of pure H₂ was tested to investigate the potential cost reduction of the electron donor required. Syngas is produced in the gas-reforming process and consists mainly of H₂, carbon monoxide (CO), and carbon dioxide (CO₂). Purification of syngas to obtain pure H₂ implies higher costs because of additional post-treatment. Therefore, the use of syngas has merit in the biodesulfurization process. Initially, CO inhibited hydrogen-dependent sulfate reduction. However, after 30 days the biomass was adapted and both H₂ and CO were used as electron donors. First, formate was produced, followed by sulfate and thiosulfate reduction, and later in the reactor run acetate and methane were detected. Sulfide production rates with sulfate and thiosulfate after adaptation were comparable with previously described rates with only hydrogen. The addition of CO marginally affected the microbial community in which Tindallia sp. was dominant. Over time, acetate production increased and acetogenesis became the dominant process in the bioreactor. Around 50% of H₂/CO was converted to acetate. Acetate supported biomass growth and higher biomass concentrations were reached compared to bioreactors without CO feed. Finally, CO addition resulted in the formation of small, compact microbial aggregates. This suggests that CO or syngas can be used to stimulate aggregation in haloalkaline biodesulfurization systems. Full article

(This article belongs to the Special Issue Extremophiles 2.0)

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16 pages, 535 KiB

Open AccessArticle

Multicenter Comparative Study of Six Cryptosporidium parvum DNA Extraction Protocols Including Mechanical Pretreatment from Stool Samples

by Nicolas Valeix, Damien Costa, Louise Basmaciyan, Stéphane Valot, Anne Vincent, Romy Razakandrainibe, Florence Robert-Gangneux, Céline Nourrisson, Bruno Pereira, Emilie Fréalle, Philippe Poirier, Loic Favennec and Frederic Dalle

Microorganisms 2020, 8(9), 1450; https://doi.org/10.3390/microorganisms8091450 - 22 Sep 2020

Cited by 21 | Viewed by 3870

Abstract

Background: Nowadays, many commercial kits allow the detection of Cryptosporidium sp. in stool samples after deoxyribonucleic acid (DNA) extraction. Protocols of stool pretreatment have been proposed to optimize oocysts’ DNA extraction. Among them, mechanical grinding was reported to improve the performance of Cryptosporidium [...] Read more.

Background: Nowadays, many commercial kits allow the detection of Cryptosporidium sp. in stool samples after deoxyribonucleic acid (DNA) extraction. Protocols of stool pretreatment have been proposed to optimize oocysts’ DNA extraction. Among them, mechanical grinding was reported to improve the performance of Cryptosporidium oocysts’ DNA extraction. Methods: A multicenter comparative study was conducted within the framework of the French National Reference Center-Expert Laboratory for Cryptosporidiosis. Six extraction systems (i.e., manual or automated) associated with various mechanical pretreatment protocols, were compared for the Cryptosporidium parvum oocyst’ DNA extraction, before amplification using the same real-time PCR method targeting. Results: The sensitivity of real-time PCR assay was unequally impacted by the pretreatment/extraction protocol. We observed significant differences for the lowest concentrations of C. parvum oocysts (i.e., 0–94.4% and 33.3–100% respectively for 10 and 50 oocysts/mL). All in all, the protocol using Quick DNA Fecal/Soil Microbe-Miniprep^® manual kit showed the best performances. In addition, optimal performances of mechanical pretreatment were obtained by combining a grinding duration of 60 s with a speed of 4 m/s using Fastprep24^® with Lysing Matrix E^®. Conclusions: Sample pretreatment, as well as the extraction method, needs to be properly adapted to improve the diagnostic performances of the C. parvum DNA amplification methods. Full article

(This article belongs to the Special Issue Diagnosis of Intestinal Parasites in Humans: Can Molecular Diagnosis Replace Microscopy)

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18 pages, 1598 KiB

Open AccessArticle

Population Dynamics between Erwinia amylovora, Pantoea agglomerans and Bacteriophages: Exploiting Synergy and Competition to Improve Phage Cocktail Efficacy

by Steven Gayder, Michael Parcey, Darlene Nesbitt, Alan J. Castle and Antonet M. Svircev

Microorganisms 2020, 8(9), 1449; https://doi.org/10.3390/microorganisms8091449 - 22 Sep 2020

Cited by 26 | Viewed by 4715

Abstract

Bacteriophages are viruses capable of recognizing with high specificity, propagating inside of, and destroying their bacterial hosts. The phage lytic life cycle makes phages attractive as tools to selectively kill pathogenic bacteria with minimal impact on the surrounding microbiome. To effectively harness the [...] Read more.

Bacteriophages are viruses capable of recognizing with high specificity, propagating inside of, and destroying their bacterial hosts. The phage lytic life cycle makes phages attractive as tools to selectively kill pathogenic bacteria with minimal impact on the surrounding microbiome. To effectively harness the potential of phages in therapy, it is critical to understand the phage–host dynamics and how these interactions can change in complex populations. Our model examined the interactions between the plant pathogen Erwinia amylovora, the antagonistic epiphyte Pantoea agglomerans, and the bacteriophages that infect and kill both species. P. agglomerans strains are used as a phage carrier; their role is to deliver and propagate the bacteriophages on the plant surface prior to the arrival of the pathogen. Using liquid cultures, the populations of the pathogen, carrier, and phages were tracked over time with quantitative real-time PCR. The jumbo Myoviridae phage ϕEa35-70 synergized with both the Myoviridae ϕEa21-4 and Podoviridae ϕEa46-1-A1 and was most effective in combination at reducing E. amylovora growth over 24 h. Phage ϕEa35-70, however, also reduced the growth of P. agglomerans. Phage cocktails of ϕEa21-4, ϕEa46-1-A1, and ϕEa35-70 at multiplicities of infections (MOIs) of 10, 1, and 0.01, respectively, no longer inhibited growth of P. agglomerans. When this cocktail was grown with P. agglomerans for 8 h prior to pathogen introduction, pathogen growth was reduced by over four log units over 24 h. These findings present a novel approach to study complex phage–host dynamics that can be exploited to create more effective phage-based therapies. Full article

(This article belongs to the Special Issue Understanding Phage Particles)

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14 pages, 2747 KiB

Open AccessReview

Francisella tularensis Subspecies holarctica and Tularemia in Germany

by Sandra Appelt, Mirko Faber, Kristin Köppen, Daniela Jacob, Roland Grunow and Klaus Heuner

Microorganisms 2020, 8(9), 1448; https://doi.org/10.3390/microorganisms8091448 - 22 Sep 2020

Cited by 25 | Viewed by 4693

Abstract

Tularemia is a zoonotic disease caused by Francisella tularensis a small, pleomorphic, facultative intracellular bacterium. In Europe, infections in animals and humans are caused mainly by Francisella tularensis subspecies holarctica. Humans can be exposed to the pathogen directly and indirectly through contact [...] Read more.

Tularemia is a zoonotic disease caused by Francisella tularensis a small, pleomorphic, facultative intracellular bacterium. In Europe, infections in animals and humans are caused mainly by Francisella tularensis subspecies holarctica. Humans can be exposed to the pathogen directly and indirectly through contact with sick animals, carcasses, mosquitoes and ticks, environmental sources such as contaminated water or soil, and food. So far, F. tularensis subsp. holarctica is the only Francisella species known to cause tularemia in Germany. On the basis of surveillance data, outbreak investigations, and literature, we review herein the epidemiological situation—noteworthy clinical cases next to genetic diversity of F. tularensis subsp. holarctica strains isolated from patients. In the last 15 years, the yearly number of notified cases of tularemia has increased steadily in Germany, suggesting that the disease is re-emerging. By sequencing F. tularensis subsp. holarctica genomes, knowledge has been added to recent findings, completing the picture of genotypic diversity and geographical segregation of Francisella clades in Germany. Here, we also shortly summarize the current knowledge about a new Francisella species (Francisella sp. strain W12-1067) that has been recently identified in Germany. This species is the second Francisella species discovered in Germany. Full article

(This article belongs to the Special Issue Epidemiology of Tularemia and Francisella tularensis)

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11 pages, 762 KiB

Open AccessArticle

Colistin and Isavuconazole Interact Synergistically In Vitro against Aspergillus nidulans and Aspergillus niger

by Patrick Schwarz, Elie Djenontin and Eric Dannaoui

Microorganisms 2020, 8(9), 1447; https://doi.org/10.3390/microorganisms8091447 - 21 Sep 2020

Cited by 10 | Viewed by 2412

Abstract

The in vitro interactions of isavuconazole in combination with colistin were evaluated against 55 clinical Aspergillus species isolates belonging to the five most important species (Aspergillus flavus, Aspergillus fumigatus, Aspergillus nidulans, Aspergillus niger, and Aspergillus terreus) responsible [...] Read more.

The in vitro interactions of isavuconazole in combination with colistin were evaluated against 55 clinical Aspergillus species isolates belonging to the five most important species (Aspergillus flavus, Aspergillus fumigatus, Aspergillus nidulans, Aspergillus niger, and Aspergillus terreus) responsible for human aspergillosis by a microdilution checkerboard technique based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) reference method for antifungal susceptibility testing. Selected isolates (A. nidulans, n = 10; A. niger, n = 15) were additionally evaluated by an agar diffusion assay using isavuconazole gradient concentration strips with or without colistin incorporated Roswell Parc Memorial Institute (RPMI) agar. Interpretation of the checkerboard results was done by the fractional inhibitory concentration index. Using the checkerboard method, combination isavuconazole–colistin was synergistic for 100% of the 15 A. nidulans isolates and for 60% of the 20 A. niger isolates. No interactions were found for any of the other isolates. By agar diffusion assay, minimal inhibitory concentrations (MICs) in combination decreased compared to isavuconazole alone for 92% of the isolates. No interactions were found for any A. nidulans isolates, but synergy was observed for 40% of the A. niger isolates. A poor essential agreement of EUCAST and gradient concentration strip MICs at ± 2 log₂ dilutions with 0% was obtained. Antagonistic interactions were never observed regardless of the technique used. Full article

(This article belongs to the Special Issue Aspergillus and Health 1.0)

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19 pages, 2152 KiB

Open AccessArticle

Assessment of Multilocus Sequence Analysis (MLSA) for Identification of Candidatus Liberibacter Solanacearum from Different Host Plants in Spain

by Ana Ruiz-Padilla, Cristina Redondo, Adrián Asensio, Jerson Garita-Cambronero, Carmen Martínez, Verónica Pérez-Padilla, Raquel Marquínez, Jesús Collar, Eva García-Méndez, Ana Alfaro-Fernández, Carmen Asensio-S.-Manzanera, José Luis Palomo, Felipe Siverio, Leandro De León and Jaime Cubero

Microorganisms 2020, 8(9), 1446; https://doi.org/10.3390/microorganisms8091446 - 21 Sep 2020

Cited by 5 | Viewed by 3062

Abstract

Liberibacter is a bacterial group causing different diseases and disorders in plants. Among liberibacters, Candidatus Liberibacter solanaceraum (CLso) produces disorders in several species mainly within Apiaceae and Solanaceae families. CLso isolates are usually grouped in defined haplotypes according to single nucleotide polymorphisms in [...] Read more.

Liberibacter is a bacterial group causing different diseases and disorders in plants. Among liberibacters, Candidatus Liberibacter solanaceraum (CLso) produces disorders in several species mainly within Apiaceae and Solanaceae families. CLso isolates are usually grouped in defined haplotypes according to single nucleotide polymorphisms in genes associated with ribosomal elements. In order to characterize more precisely isolates of CLso identified in potato in Spain, a Multilocus Sequence Analysis (MLSA) was applied. This methodology was validated by a complete analysis of ten housekeeping genes that showed an absence of positive selection and a nearly neutral mechanism for their evolution. Most of the analysis performed with single housekeeping genes, as well as MLSA, grouped together isolates of CLso detected in potato crops in Spain within the haplotype E, undistinguishable from those infecting carrots, parsnips or celery. Moreover, the information from these housekeeping genes was used to estimate the evolutionary divergence among the different CLso by using the concatenated sequences of the genes assayed. Data obtained on the divergence among CLso haplotypes support the hypothesis of evolutionary events connected with different hosts, in different geographic areas, and possibly associated with different vectors. Our results demonstrate the absence in Spain of CLso isolates molecularly classified as haplotypes A and B, traditionally considered causal agents of zebra chip in potato, as well as the uncertain possibility of the present haplotype to produce major disease outbreaks in potato that may depend on many factors that should be further evaluated in future works. Full article

(This article belongs to the Section Plant Microbe Interactions)

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18 pages, 3749 KiB

Open AccessArticle

Development of a High-Resolution Single-Nucleotide Polymorphism Strain-Typing Assay Using Whole Genome-Based Analyses for the Lactobacillus acidophilus Probiotic Strain

by Chien-Hsun Huang, Chih-Chieh Chen, Shih-Hau Chiu, Jong-Shian Liou, Yu-Chun Lin, Jin-Seng Lin, Lina Huang and Koichi Watanabe

Microorganisms 2020, 8(9), 1445; https://doi.org/10.3390/microorganisms8091445 - 21 Sep 2020

Cited by 4 | Viewed by 3165

Abstract

Lactobacillus acidophilus is one of the most commonly used industrial products worldwide. Since its probiotic efficacy is strain-specific, the identification of probiotics at both the species and strain levels is necessary. However, neither phenotypic nor conventional genotypic methods have enabled the effective differentiation [...] Read more.

Lactobacillus acidophilus is one of the most commonly used industrial products worldwide. Since its probiotic efficacy is strain-specific, the identification of probiotics at both the species and strain levels is necessary. However, neither phenotypic nor conventional genotypic methods have enabled the effective differentiation of L. acidophilus strains. In this study, a whole-genome sequence-based analysis was carried out to establish high-resolution strain typing of 41 L. acidophilus strains (including commercial isolates and reference strains) using the cano-wgMLST_BacCompare analytics platform; consequently, a strain-specific discrimination method for the probiotic strain LA1063 was developed. Using a core-genome multilocus sequence-typing (cgMLST) scheme based on 1390 highly conserved genes, 41 strains could be assigned to 34 sequence types. Subsequently, we screened a set of 92 loci with a discriminatory power equal to that of the 1390 loci cgMLST scheme. A strain-specific polymerase chain reaction combined with a multiplex minisequencing method was developed based on four (phoU, secY, tilS, and uvrA_1) out of 21 loci, which could be discriminated between LA1063 and other L. acidophilus strains using the cgMLST data. We confirmed that the strain-specific single-nucleotide polymorphisms method could be used to quickly and accurately identify the L. acidophilus probiotic strain LA1063 in commercial products. Full article

(This article belongs to the Section Food Microbiology)

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8 pages, 5719 KiB

Open AccessCommunication

Plasmid DNA Production in Proteome-Reduced Escherichia coli

by Mitzi de la Cruz, Elisa A. Ramírez, Juan-Carlos Sigala, José Utrilla and Alvaro R. Lara

Microorganisms 2020, 8(9), 1444; https://doi.org/10.3390/microorganisms8091444 - 21 Sep 2020

Cited by 8 | Viewed by 4021

Abstract

The design of optimal cell factories requires engineering resource allocation for maximizing product synthesis. A recently developed method to maximize the saving in cell resources released 0.5% of the proteome of Escherichia coli by deleting only three transcription factors. We assessed the capacity [...] Read more.

The design of optimal cell factories requires engineering resource allocation for maximizing product synthesis. A recently developed method to maximize the saving in cell resources released 0.5% of the proteome of Escherichia coli by deleting only three transcription factors. We assessed the capacity for plasmid DNA (pDNA) production in the proteome-reduced strain in a mineral medium, lysogeny, and terrific broths. In all three cases, the pDNA yield from biomass was between 33 and 53% higher in the proteome-reduced than in its wild type strain. When cultured in fed-batch mode in shake-flask, the proteome-reduced strain produced 74.8 mg L⁻¹ pDNA, which was four times greater than its wild-type strain. Nevertheless, the pDNA supercoiled fraction was less than 60% in all cases. Deletion of recA increased the pDNA yields in the wild type, but not in the proteome-reduced strain. Furthermore, recA mutants produced a higher fraction of supercoiled pDNA, compared to their parents. These results show that the novel proteome reduction approach is a promising starting point for the design of improved pDNA production hosts. Full article

(This article belongs to the Section Microbial Biotechnology)

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17 pages, 6491 KiB

Open AccessArticle

Transcriptome Profiling of Potato (Solanum tuberosum L.) Responses to Root-Knot Nematode (Meloidogyne javanica) Infestation during A Compatible Interaction

by Teresia N. Macharia, Daniel Bellieny-Rabelo and Lucy N. Moleleki

Microorganisms 2020, 8(9), 1443; https://doi.org/10.3390/microorganisms8091443 - 21 Sep 2020

Cited by 9 | Viewed by 3719

Abstract

Root-knot nematode (RKN) Meloidogyne javanica presents a great challenge to Solanaceae crops, including potato. In this study, we investigated transcriptional responses of potato roots during a compatible interaction with M. javanica. In this respect, differential gene expression of Solanum tuberosum cultivar (cv.) [...] Read more.

Root-knot nematode (RKN) Meloidogyne javanica presents a great challenge to Solanaceae crops, including potato. In this study, we investigated transcriptional responses of potato roots during a compatible interaction with M. javanica. In this respect, differential gene expression of Solanum tuberosum cultivar (cv.) Mondial challenged with M. javanica at 0, 3 and 7 days post-inoculation (dpi) was profiled. In total, 4948 and 4484 genes were detected, respectively, as differentially expressed genes (DEGs) at 3 and 7 dpi. Functional annotation revealed that genes associated with metabolic processes were enriched, suggesting they might have an important role in M. javanica disease development. MapMan analysis revealed down-regulation of genes associated with pathogen perception and signaling suggesting interference with plant immunity system. Notably, delayed activation of pathogenesis-related genes, down-regulation of disease resistance genes, and activation of host antioxidant system contributed to a susceptible response. Nematode infestation suppressed ethylene (ET) and jasmonic acid (JA) signaling pathway hindering JA/ET responsive genes associated with defense. Genes related to cell wall modification were differentially regulated while transport-related genes were up-regulated, facilitating the formation of nematode feeding sites (NFSs). Several families of transcription factors (TFs) were differentially regulated by M. javanica infestation. Suggesting that TFs play an indispensable role in physiological adaptation for successful M. javanica disease development. This genome-wide analysis reveals the molecular regulatory networks in potato roots which are potentially manipulated by M. javanica. Being the first study analyzing transcriptome profiling of M. javanica-diseased potato, it provides unparalleled insight into the mechanism underlying disease development. Full article

(This article belongs to the Section Plant Microbe Interactions)

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17 pages, 647 KiB

Open AccessReview

Microbial Nitrogen Cycling in Antarctic Soils

by Max Ortiz, Jason Bosch, Clément Coclet, Jenny Johnson, Pedro Lebre, Adeola Salawu-Rotimi, Surendra Vikram, Thulani Makhalanyane and Don Cowan

Microorganisms 2020, 8(9), 1442; https://doi.org/10.3390/microorganisms8091442 - 21 Sep 2020

Cited by 28 | Viewed by 9406

Abstract

The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of [...] Read more.

The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more “hospitable” maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change. Full article

(This article belongs to the Special Issue Polar Microbial Ecology: The Role of Microbes in the Functioning of Extremely Cold Ecosystems)

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15 pages, 2237 KiB

Open AccessArticle

Updated Taxonomy of Pectobacterium Genus in the CIRM-CFBP Bacterial Collection: When Newly Described Species Reveal “Old” Endemic Population

by Perrine Portier, Jacques Pédron, Géraldine Taghouti, Cécile Dutrieux and Marie-Anne Barny

Microorganisms 2020, 8(9), 1441; https://doi.org/10.3390/microorganisms8091441 - 20 Sep 2020

Cited by 33 | Viewed by 3961

Abstract

Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited [...] Read more.

Bacterial collections are invaluable tools for microbiologists. However, their practical use is compromised by imprecise taxonomical assignation of bacterial strains. This is particularly true for soft rotting plant pathogens of the Pectobacterium genus. We analysed the taxonomic status of 265 Pectobacterium strains deposited at CIRM-CFBP collection from 1944 to 2020. This collection gathered Pectobacterium strains isolated in 27 countries from 32 plant species representing 17 botanical families or from nonhost environments. The MLSA approach completed by genomic analysis of 15 strains was performed to update the taxonomic status of these 265 strains. The results showed that the CIRM-CFBP Pectobacterium collection harboured at least one strain of each species, with the exception of P. polonicum. Yet, seven strains could not be assigned to any of the described species and may represent at least two new species. Surprisingly, P. versatile, recently described in 2019, is the most prevalent species among CIRM-CFBP strains. An analysis of P. versatile strains revealed that this species is pandemic and isolated from various host plants and environments. At the opposite, other species gathered strains isolated from only one botanical family or exclusively from a freshwater environment. Our work also revealed new host plants for several Pectobacterium spp. Full article

(This article belongs to the Special Issue Dickeya and Pectobacterium: Ecology, Pathology and Plant Protection)

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20 pages, 4022 KiB

Open AccessArticle

Central Asian Rodents as Model Animals for Leishmania major and Leishmania donovani Research

by Barbora Vojtkova, Tatiana Spitzova, Jan Votypka, Tereza Lestinova, Iveta Kominkova, Michaela Hajkova, David Santos-Mateus, Michael A. Miles, Petr Volf and Jovana Sadlova

Microorganisms 2020, 8(9), 1440; https://doi.org/10.3390/microorganisms8091440 - 20 Sep 2020

Cited by 8 | Viewed by 3949

Abstract

The clinical manifestation of leishmaniases depends on parasite species, host genetic background, and immune response. Manifestations of human leishmaniases are highly variable, ranging from self-healing skin lesions to fatal visceral disease. The scope of standard model hosts is insufficient to mimic well the [...] Read more.

The clinical manifestation of leishmaniases depends on parasite species, host genetic background, and immune response. Manifestations of human leishmaniases are highly variable, ranging from self-healing skin lesions to fatal visceral disease. The scope of standard model hosts is insufficient to mimic well the wide disease spectrum, which compels the introduction of new model animals for leishmaniasis research. In this article, we study the susceptibility of three Asian rodent species (Cricetulus griseus, Lagurus lagurus, and Phodopus sungorus) to Leishmania major and L. donovani. The external manifestation of the disease, distribution, as well as load of parasites and infectiousness to natural sand fly vectors, were compared with standard models, BALB/c mice and Mesocricetus auratus. No significant differences were found in disease outcomes in animals inoculated with sand fly- or culture-derived parasites. All Asian rodent species were highly susceptible to L. major. Phodopus sungorus showed the non-healing phenotype with the progressive growth of ulcerative lesions and massive parasite loads. Lagurus lagurus and C. griseus represented the healing phenotype, the latter with high infectiousness to vectors, mimicking best the character of natural reservoir hosts. Both, L. lagurus and C. griseus were also highly susceptible to L. donovani, having wider parasite distribution and higher parasite loads and infectiousness than standard model animals. Full article

(This article belongs to the Special Issue Leishmania and Leishmaniasis)

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9 pages, 668 KiB

Open AccessArticle

Antibiotic-Resistant Escherichia coli and Sequence Type 131 in Fecal Colonization in Dogs in Taiwan

by Jenn-Wei Chen, Han Hsiang Huang, Szu-Min Chang, Joy Scaria, Yu-Lung Chiu, Chih-Ming Chen, Wen-Chien Ko and Jiun-Ling Wang

Microorganisms 2020, 8(9), 1439; https://doi.org/10.3390/microorganisms8091439 - 20 Sep 2020

Cited by 17 | Viewed by 3224

Abstract

Background: Most drug-resistant Escherichia coli isolates in dogs come from diseased dogs. Prior to this study, the prevalence and risk factors of fecal carriage drug-resistant E. coli and epidemic clone sequence type (ST) 131 (including subtypes) isolates in dogs were unknown. Methods: Rectal [...] Read more.

Background: Most drug-resistant Escherichia coli isolates in dogs come from diseased dogs. Prior to this study, the prevalence and risk factors of fecal carriage drug-resistant E. coli and epidemic clone sequence type (ST) 131 (including subtypes) isolates in dogs were unknown. Methods: Rectal swabs were used for E. coli isolation from 299 non-infectious dogs in a veterinary teaching hospital in Taiwan. Antibiotic resistance and multiplex PCR analyses of E. coli for major STs were performed. Result: There were 43.1% cefazolin-resistant, 22.1% fluoroquinolone-resistant, and 9.4% extended-spectrum beta-lactamase-producing E. coli in our cohort. In the phylogenetic study, B2 was the predominant group (30.1%). The cefazolin-resistant group and ciprofloxacin-resistant group had greater antibiotic exposure in the last 14 days (p < 0.05). The age, sex, and dietary habits of the antibiotic-resistant and -susceptible groups were similar. In the seven isolates of ST131 in fecal colonization, the most predominant subtypes were FimH41 and FimH22. Conclusion: Recent antibiotic exposure was related to the fecal carriage of antibiotic-resistant E. coli isolates. Three major subtypes (FimH41, H22, and H30) of ST131 can thus be found in fecal carriage in dogs in Taiwan. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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26 pages, 1790 KiB

Open AccessReview

The Role of Bacterial Symbionts in Triatomines: An Evolutionary Perspective

by Nicolas Salcedo-Porras, Claudia Umaña-Diaz, Ricardo de Oliveira Barbosa Bitencourt and Carl Lowenberger

Microorganisms 2020, 8(9), 1438; https://doi.org/10.3390/microorganisms8091438 - 19 Sep 2020

Cited by 32 | Viewed by 8908

Abstract

Insects have established mutualistic symbiotic interactions with microorganisms that are beneficial to both host and symbiont. Many insects have exploited these symbioses to diversify and expand their ecological ranges. In the Hemiptera (i.e., aphids, cicadas, and true bugs), symbioses have established and evolved [...] Read more.

Insects have established mutualistic symbiotic interactions with microorganisms that are beneficial to both host and symbiont. Many insects have exploited these symbioses to diversify and expand their ecological ranges. In the Hemiptera (i.e., aphids, cicadas, and true bugs), symbioses have established and evolved with obligatory essential microorganisms (primary symbionts) and with facultative beneficial symbionts (secondary symbionts). Primary symbionts are usually intracellular microorganisms found in insects with specialized diets such as obligate hematophagy or phytophagy. Most Heteroptera (true bugs), however, have gastrointestinal (GI) tract extracellular symbionts with functions analogous to primary endosymbionts. The triatomines, are vectors of the human parasite, Trypanosoma cruzi. A description of their small GI tract microbiota richness was based on a few culturable microorganisms first described almost a century ago. A growing literature describes more complex interactions between triatomines and bacteria with properties characteristic of both primary and secondary symbionts. In this review, we provide an evolutionary perspective of beneficial symbioses in the Hemiptera, illustrating the context that may drive the evolution of symbioses in triatomines. We highlight the diversity of the triatomine microbiota, bacterial taxa with potential to be beneficial symbionts, the unique characteristics of triatomine-bacteria symbioses, and the interactions among trypanosomes, microbiota, and triatomines. Full article

(This article belongs to the Special Issue Insect Gut Microbiology and Symbiosis)

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12 pages, 2108 KiB

Open AccessArticle

Development of Monoclonal Antibodies and Antigen-Capture ELISA for Human Parechovirus Type 3

by Keiko Goto, Yutaro Yamaoka, Hajera Khatun, Kei Miyakawa, Mayuko Nishi, Noriko Nagata, Toshikazu Yanaoka, Hirokazu Kimura and Akihide Ryo

Microorganisms 2020, 8(9), 1437; https://doi.org/10.3390/microorganisms8091437 - 19 Sep 2020

Cited by 4 | Viewed by 3625

Abstract

Human parechovirus type 3 (HPeV3) is an etiologic agent of respiratory diseases, meningitis, and sepsis-like illness in both infants and adults. Monoclonal antibodies (mAbs) can be a promising diagnostic tool for antigenic diseases such as virus infection, as they offer a high specificity [...] Read more.

Human parechovirus type 3 (HPeV3) is an etiologic agent of respiratory diseases, meningitis, and sepsis-like illness in both infants and adults. Monoclonal antibodies (mAbs) can be a promising diagnostic tool for antigenic diseases such as virus infection, as they offer a high specificity toward a specific viral antigen. However, to date, there is no specific mAb available for the diagnosis of HPeV3 infection. In this study, we developed and characterized mAbs specific for HPeV3 capsid protein VP0. We used cell-free, wheat germ-synthesized viral VP0 protein for immunizing BALB/c mice to generate hybridomas. From the resultant hybridoma clones, we selected nine clones producing mAbs reactive to the HPeV3-VP0 antigen, based on enzyme-linked immunosorbent assay (ELISA). Epitope mapping showed that these mAbs recognized three distinct domains in HPeV3 VP0. Six mAbs recognized HPeV3 specifically and the other three mAbs showed cross-reactivity with other HPeVs. Using the HPeV3-specific mAbs, we then developed an ELISA for viral antigen detection that could be reliably used for laboratory diagnosis of HPeV3. This ELISA system exhibited no cross-reactivity with other related viruses. Our newly developed mAbs would, thus, provide a useful set of tools for future research and ensure HPeV3-specific diagnosis. Full article

(This article belongs to the Special Issue Molecular Epidemiology, Diagnostics and Management of Respiratory Virus Infections)

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15 pages, 1976 KiB

Open AccessArticle

Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx

by Stephanie Serena Schäpe, Jannike Lea Krause, Rebecca Katharina Masanetz, Sarah Riesbeck, Robert Starke, Ulrike Rolle-Kampczyk, Christian Eberlein, Hermann-Josef Heipieper, Gunda Herberth, Martin von Bergen and Nico Jehmlich

Microorganisms 2020, 8(9), 1436; https://doi.org/10.3390/microorganisms8091436 - 19 Sep 2020

Cited by 13 | Viewed by 3758

Abstract

Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the [...] Read more.

Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS. By determining biomass, growth of SIHUMIx was followed but no differences during BPS exposure were observed. To validate if the membrane composition was affected, fatty acid methyl esters (FAMEs) profiles were compared. Changes in the individual membrane fatty acid composition could not been described; however, the saturation level of the membranes slightly increased during BPS exposure. By applying targeted metabolomics to quantify short-chain fatty acids (SCFA), it was shown that the activity of SIHUMIx was unaffected. Metaproteomics revealed temporal effect on the community structure and function, showing that BPS has minor effects on the structure or functionality of SIHUMIx. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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12 pages, 2071 KiB

Open AccessArticle

Isolation and Characterization of Facultative-Anaerobic Antimonate-Reducing Bacteria

by Ziran Yang, Hisaaki Hosokawa, Takuya Sadakane, Masashi Kuroda, Daisuke Inoue, Hiroshi Nishikawa and Michihiko Ike

Microorganisms 2020, 8(9), 1435; https://doi.org/10.3390/microorganisms8091435 - 18 Sep 2020

Cited by 12 | Viewed by 3924

Abstract

Microbial antimonate (Sb(V)) reduction is a promising approach to remove Sb(V) from wastewater. However, current knowledge regarding microbial Sb(V) reduction is limited to strictly anaerobic conditions. This study was the first to isolate three facultative-anaerobic Sb(V)-reducing bacterial strains from the sludge collected from [...] Read more.

Microbial antimonate (Sb(V)) reduction is a promising approach to remove Sb(V) from wastewater. However, current knowledge regarding microbial Sb(V) reduction is limited to strictly anaerobic conditions. This study was the first to isolate three facultative-anaerobic Sb(V)-reducing bacterial strains from the sludge collected from a wastewater treatment facility in an antimony products plant. Two of the isolated strains, designated Dechloromonas sp. AR-2 and Propionivibrio sp. AR-3, were characterized based on their Sb(V)-reducing abilities. When cultivated under anaerobic conditions with Sb(V) and acetate as the electron acceptor and donor, respectively, both strains could efficiently reduce 5.0 mM Sb(V), removing most of it from the water phase within 7 d. Along with Sb(V) reduction by the strains, white precipitates, which were likely amorphous Sb(OH)₃ solids, were formed with a minor generation of soluble antimonite. Additionally, respiratory Sb(V) reduction by both strains occurred not only under anaerobic but also microaerobic conditions. It was suggested that Sb(V) reduction and the growth abilities of the strains under microaerobic conditions presented a substantial advantage of the use of strains AR-2 and AR-3 for practical applications to Sb(V)-containing wastewater treatment. Full article

(This article belongs to the Section Environmental Microbiology)

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19 pages, 328 KiB

Open AccessArticle

Resistance Profiling and Molecular Characterization of Extended-Spectrum/Plasmid-Mediated AmpC β-Lactamase-Producing Escherichia coli Isolated from Healthy Broiler Chickens in South Korea

by Hyun-Ju Song, Dong Chan Moon, Abraham Fikru Mechesso, Hee Young Kang, Mi Hyun Kim, Ji-Hyun Choi, Su-Jeong Kim, Soon-Seek Yoon and Suk-Kyung Lim

Microorganisms 2020, 8(9), 1434; https://doi.org/10.3390/microorganisms8091434 - 18 Sep 2020

Cited by 11 | Viewed by 2789

Abstract

We aimed to identify and characterize extended-spectrum β-lactamase (ESBL)-and/or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli isolated from healthy broiler chickens slaughtered for human consumption in Korea. A total of 332 E. coli isolates were identified from 339 cloacal swabs in 2019. More than [...] Read more.

We aimed to identify and characterize extended-spectrum β-lactamase (ESBL)-and/or plasmid-mediated AmpC β-lactamase (pAmpC)-producing Escherichia coli isolated from healthy broiler chickens slaughtered for human consumption in Korea. A total of 332 E. coli isolates were identified from 339 cloacal swabs in 2019. More than 90% of the isolates were resistant to multiple antimicrobials. ESBL/pAmpC-production was noted in 14% (46/332) of the isolates. Six of the CTX-M-β-lactamase-producing isolates were found to co-harbor at least one plasmid-mediated quinolone resistance gene. We observed the co-existence of bla_CMY-2 and mcr-1 genes in the same isolate for the first time in Korea. Phylogenetic analysis demonstrated that the majority of bla_CMY-2-carrying isolates belonged to subgroup D. Conjugation confirmed the transferability of bla_CTX-M and bla_CMY-2 genes, as well as non-β-lactam resistance traits from 60.9% (28/46) of the ESBL/pAmpC-producing isolates to a recipient E. coli J53. The ISECP, IS903, and orf477 elements were detected in the upstream or downstream regions. The bla_CTX-M and bla_CMY-2 genes mainly belonged to the IncI1, IncHI2, and/or IncFII plasmids. Additionally, the majority of ESBL/pAmpC-producing isolates exhibited heterogeneous PFGE profiles. This study showed that healthy chickens act as reservoirs of ESBL/pAmpC-producing E. coli that can potentially be transmitted to humans. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Molecular Tracing of Foodborne Pathogens)

17 pages, 753 KiB

Open AccessReview

Fecal Microbiota Transplantation in the Treatment of Chronic Pouchitis: A Systematic Review

by Frederik Cold, Sabrina Just Kousgaard, Sofie Ingdam Halkjaer, Andreas Munk Petersen, Hans Linde Nielsen, Ole Thorlacius-Ussing and Lars Hestbjerg Hansen

Microorganisms 2020, 8(9), 1433; https://doi.org/10.3390/microorganisms8091433 - 18 Sep 2020

Cited by 21 | Viewed by 2935

Abstract

The objective was to evaluate available literature on treatment of chronic pouchitis with fecal microbiota transplantation (FMT) focusing on clinical outcomes, safety, and different approaches to FMT preparation and delivery. A systematic review of electronic databases was conducted using Medline, EMBASE, and the [...] Read more.

The objective was to evaluate available literature on treatment of chronic pouchitis with fecal microbiota transplantation (FMT) focusing on clinical outcomes, safety, and different approaches to FMT preparation and delivery. A systematic review of electronic databases was conducted using Medline, EMBASE, and the Cochrane Central Register of Controlled Trials Library from inception through April 2020. Human studies of all study types reporting results of FMT to treat chronic pouchitis were included. Nine studies, reporting FMT treatment of 69 patients with chronic pouchitis were found eligible for the review. Most studies were case series and cohort studies rated as having fair to poor quality due to high risk of bias and small sample size. Only one randomized controlled trial was included, finding no beneficial effect of FMT. In total clinical response after FMT was reported in 14 (31.8%) out of 44 evaluated patients at various timepoints after FMT, and clinical remission in ten (22.7%) patients. Only minor self-limiting adverse events were reported. FMT varied greatly regarding preparation, length of treatment, and route of delivery. The effects of FMT on symptoms of chronic pouchitis are not established, though some studies show promising results. Future controlled well-designed studies are warranted. Full article

(This article belongs to the Special Issue Therapeutic Potential of Fecal Microbiota Therapy (FMT))

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21 pages, 2060 KiB

Open AccessArticle

Oral Pathogen Porphyromonas gingivalis Can Escape Phagocytosis of Mammalian Macrophages

by Erik R. Werheim, Kevin G. Senior, Carly A. Shaffer and Giancarlo A. Cuadra

Microorganisms 2020, 8(9), 1432; https://doi.org/10.3390/microorganisms8091432 - 18 Sep 2020

Cited by 20 | Viewed by 4294

Abstract

Macrophages are phagocytic cells that play a key role in host immune response and clearance of microbial pathogens. Porphyromonas gingivalis is an oral pathogen associated with the development of periodontitis. Escape from macrophage phagocytosis was tested by infecting THP-1-derived human macrophages and RAW [...] Read more.

Macrophages are phagocytic cells that play a key role in host immune response and clearance of microbial pathogens. Porphyromonas gingivalis is an oral pathogen associated with the development of periodontitis. Escape from macrophage phagocytosis was tested by infecting THP-1-derived human macrophages and RAW 264.7 mouse macrophages with strains of P. gingivalis W83 and 33277 as well as Streptococcus gordonii DL1 and Escherichia coli OP50 at MOI = 100. CFU counts for all intracellular bacteria were determined. Then, infected macrophages were cultured in media without antibiotics to allow for escape and escaping bacteria were quantified by CFU counting. P. gingivalis W83 displayed over 60% of the bacterial escape from the total amount of intracellular CFUs, significantly higher compared to all other bacteria strains. In addition, bacterial escape and re-entry were also tested and P. gingivalis W83, once again, showed the highest numbers of CFUs able to exit and re-enter macrophages. Lastly, the function of the PG0717 gene of P. gingivalis W83 was tested on escape but found not related to this activity. Altogether, our results suggest that P. gingivalis W83 is able to significantly avoid macrophage phagocytosis. We propose this ability is likely linked to the chronic nature of periodontitis. Full article

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

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34 pages, 4103 KiB

Open AccessReview

Fungicide Resistance in Powdery Mildew Fungi

by Alejandra Vielba-Fernández, Álvaro Polonio, Laura Ruiz-Jiménez, Antonio de Vicente, Alejandro Pérez-García and Dolores Fernández-Ortuño

Microorganisms 2020, 8(9), 1431; https://doi.org/10.3390/microorganisms8091431 - 17 Sep 2020

Cited by 82 | Viewed by 16464

Abstract

Powdery mildew fungi (Erysiphales) are among the most common and important plant fungal pathogens. These fungi are obligate biotrophic parasites that attack nearly 10,000 species of angiosperms, including major crops, such as cereals and grapes. Although cultural and biological practices may reduce the [...] Read more.

Powdery mildew fungi (Erysiphales) are among the most common and important plant fungal pathogens. These fungi are obligate biotrophic parasites that attack nearly 10,000 species of angiosperms, including major crops, such as cereals and grapes. Although cultural and biological practices may reduce the risk of infection by powdery mildew, they do not provide sufficient protection. Therefore, in practice, chemical control, including the use of fungicides from multiple chemical groups, is the most effective tool for managing powdery mildew. Unfortunately, the risk of resistance development is high because typical spray programs include multiple applications per season. In addition, some of the most economically destructive species of powdery mildew fungi are considered to be high-risk pathogens and are able to develop resistance to several chemical classes within a few years. This situation has decreased the efficacy of the major fungicide classes, such as sterol demethylation inhibitors, quinone outside inhibitors and succinate dehydrogenase inhibitors, that are employed against powdery mildews. In this review, we present cases of reduction in sensitivity, development of resistance and failure of control by fungicides that have been or are being used to manage powdery mildew. In addition, the molecular mechanisms underlying resistance to fungicides are also outlined. Finally, a number of recommendations are provided to decrease the probability of resistance development when fungicides are employed. Full article

(This article belongs to the Special Issue Fungicide Resistance in Plant Pathogens)

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39 pages, 56781 KiB

Open AccessArticle

Re-Evaluation of the Order Sordariales: Delimitation of Lasiosphaeriaceae s. str., and Introduction of the New Families Diplogelasinosporaceae, Naviculisporaceae, and Schizotheciaceae

by Yasmina Marin-Felix, Andrew N. Miller, José F. Cano-Lira, Josep Guarro, D. García, Marc Stadler, Sabine M. Huhndorf and Alberto M. Stchigel

Microorganisms 2020, 8(9), 1430; https://doi.org/10.3390/microorganisms8091430 - 17 Sep 2020

Cited by 22 | Viewed by 6421

Abstract

The order Sordariales includes the polyphyletic family Lasiosphaeriaceae, which comprises approximately 30 genera characterized by its paraphysate ascomata, asci with apical apparati, and mostly two-celled ascospores, which have a dark apical cell and a hyaline lower cell, frequently ornamented with mucilaginous appendages. To [...] Read more.

The order Sordariales includes the polyphyletic family Lasiosphaeriaceae, which comprises approximately 30 genera characterized by its paraphysate ascomata, asci with apical apparati, and mostly two-celled ascospores, which have a dark apical cell and a hyaline lower cell, frequently ornamented with mucilaginous appendages. To produce a more natural classification of this family, we carried out a phylogenetic analysis based on sequences of the internal transcribed spacer region (ITS), the nuclear rDNA large subunit (LSU), and fragments of ribosomal polymerase II subunit 2 (rpb2) and β-tubulin (tub2) genes of several isolates from soil and of reference strains of the Sordariales. As a result, Lasiosphaeriaceae s. str. has been circumscribed for the clade including the type species of the genus Lasiosphaeria and, consequently, its description emended. In addition, the new families Diplogelasinosporaceae, Naviculisporaceae, and Schizotheciaceae are introduced to accommodate those taxa located far from the Lasiosphaeriaceae s. str. Moreover, we propose the erection of the new genera Areotheca, Lundqvistomyces, Naviculispora, Pseudoechria, Pseudoschizothecium, and Rhypophila based on morphological and sequence data. New combinations for several species of the genera Cladorrhinum, Jugulospora, Podospora, Schizothecium, and Triangularia are proposed, their descriptions are emended, and dichotomous keys are provided to discriminate among their species. Full article

(This article belongs to the Special Issue Hotspots of Fungal Diversity)

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15 pages, 3853 KiB

Open AccessArticle

Viral Abundance and Diversity of Production Fluids in Oil Reservoirs

by Liangcan Zheng, Xiaolong Liang, Rongjiu Shi, Ping Li, Jinyi Zhao, Guoqiao Li, Shuang Wang, Siqin Han, Mark Radosevich and Ying Zhang

Microorganisms 2020, 8(9), 1429; https://doi.org/10.3390/microorganisms8091429 - 17 Sep 2020

Cited by 3 | Viewed by 4165

Abstract

Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated [...] Read more.

Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 10⁸ mL⁻¹ and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 10⁸ mL⁻¹) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir’s ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment. Full article

(This article belongs to the Section Environmental Microbiology)

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21 pages, 3171 KiB

Open AccessArticle

An Assessment of the Molecular Diversity of Ticks and Tick-Borne Microorganisms of Small Ruminants in Pakistan

by Abdul Ghafar, Adil Khan, Alejandro Cabezas-Cruz, Charles G. Gauci, Sadaf Niaz, Sultan Ayaz, Lourdes Mateos-Hernández, Clemence Galon, Nasreen Nasreen, Sara Moutailler, Robin B. Gasser and Abdul Jabbar

Microorganisms 2020, 8(9), 1428; https://doi.org/10.3390/microorganisms8091428 - 17 Sep 2020

Cited by 27 | Viewed by 5483

Abstract

This study investigated ticks and tick-borne microorganisms of small ruminants from five districts of the Federally Administered Tribal Area (FATA) of Pakistan. Morphological (n = 104) and molecular (n = 54) characterization of the ticks revealed the presence of six ixodid [...] Read more.

This study investigated ticks and tick-borne microorganisms of small ruminants from five districts of the Federally Administered Tribal Area (FATA) of Pakistan. Morphological (n = 104) and molecular (n = 54) characterization of the ticks revealed the presence of six ixodid ticks: Rhipicephalus (Rh.) haemaphysaloides, Rh. microplus, Rh. turanicus, Haemaphysalis (Hs.) punctata, Hs. sulcata and Hyalomma anatolicum. Phylogenetic analyses of nucleotide sequence data for two mitochondrial (16S and cytochrome c oxidase 1) and one nuclear (second internal transcribed spacer) DNA regions provided strong support for the grouping of the six tick species identified in this study. Microfluidic real-time PCR, employing multiple pre-validated nuclear and mitochondrial genetic markers, detected 11 potential pathogens and endosymbionts in 72.2% of the ticks (n = 54) tested. Rickettsia (R.) massiliae was the most common pathogen found (42.6% of ticks) followed by Theileria spp. (33.3%), Anaplasma (A.) ovis and R. slovaca (25.9% each). Anaplasma centrale, A. marginale, Ehrlichia spp., R. aeschlimannii, R. conorii and endosymbionts (Francisella- and Coxiella-like) were detected at much lower rates (1.9–22.2%) in ticks. Ticks from goats (83.9%) carried significantly higher microorganisms than those from sheep (56.5%). This study demonstrates that ticks of small ruminants from the FATA are carrying multiple microorganisms of veterinary and medical health significance and provides the basis for future investigations of ticks and tick-borne diseases of animals and humans in this and neighboring regions. Full article

(This article belongs to the Special Issue Advance in Tick-Borne Diseases Research)

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18 pages, 3850 KiB

Open AccessArticle

A Protective Vaccine against Johne’s Disease in Cattle

by Yashdeep Phanse, Chia-Wei Wu, Amanda J. Venturino, Chungyi Hansen, Kathryn Nelson, Scott R Broderick, Howard Steinberg and Adel M. Talaat

Microorganisms 2020, 8(9), 1427; https://doi.org/10.3390/microorganisms8091427 - 17 Sep 2020

Cited by 13 | Viewed by 4357

Abstract

Johne’s disease (JD) caused by Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) is a chronic infection characterized by the development of granulomatous enteritis in wild and domesticated ruminants. It is one of the most significant livestock diseases not only in the USA [...] Read more.

Johne’s disease (JD) caused by Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) is a chronic infection characterized by the development of granulomatous enteritis in wild and domesticated ruminants. It is one of the most significant livestock diseases not only in the USA but also globally, accounting for USD 200–500 million losses annually for the USA alone with potential link to cases of Crohn’s disease in humans. Developing safe and protective vaccines is of a paramount importance for JD control in dairy cows. The current study evaluated the safety, immunity and protective efficacy of a novel live attenuated vaccine (LAV) candidate with and without an adjuvant in comparison to an inactivated vaccine. Results indicated that the LAV, irrespective of the adjuvant presence, induced robust T cell immune responses indicated by proinflammatory cytokine production such as IFN-γ, IFN-α, TNF-α and IL-17 as well as strong response to intradermal skin test against M. paratuberculosis antigens. Furthermore, the LAV was safe with minimal tissue pathology. Finally, calves vaccinated with adjuvanted LAV did not shed M. paratuberculosis post-challenge, a much-desired characteristic of an effective vaccine against JD. Together, this data suggests a strong potential of testing LAV in field trials to curb JD in dairy herds. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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4 pages, 162 KiB

Open AccessCorrection

Correction: Saarinen, N.V.V., et al. Multiplexed High-Throughput Serological Assay for Human Enteroviruses. Microorganismis 2020, 8, 963

by Niila V. V. Saarinen, Jussi Lehtonen, Riitta Veijola, Johanna Lempainen, Mikael Knip, Heikki Hyöty, Olli H. Laitinen and Vesa P. Hytönen

Microorganisms 2020, 8(9), 1426; https://doi.org/10.3390/microorganisms8091426 - 17 Sep 2020

Cited by 1 | Viewed by 1947

Abstract

The authors wish to make the following corrections to this paper [...] Full article

(This article belongs to the Special Issue Enterovirus and Type 1 Diabetes)

26 pages, 2357 KiB

Open AccessArticle

Multidrug-Resistant Bacteria Isolated from Different Aquatic Environments in the North of Spain and South of France

by Lara Pérez-Etayo, David González, José Leiva and Ana Isabel Vitas

Microorganisms 2020, 8(9), 1425; https://doi.org/10.3390/microorganisms8091425 - 16 Sep 2020

Cited by 15 | Viewed by 5212

Abstract

Due to the global progress of antimicrobial resistance, the World Health Organization (WHO) published the list of the antibiotic-resistant “priority pathogens” in order to promote research and development of new antibiotics to the families of bacteria that cause severe and often deadly infections. [...] Read more.

Due to the global progress of antimicrobial resistance, the World Health Organization (WHO) published the list of the antibiotic-resistant “priority pathogens” in order to promote research and development of new antibiotics to the families of bacteria that cause severe and often deadly infections. In the framework of the One Health approach, the surveillance of these pathogens in different environments should be implemented in order to analyze their spread and the potential risk of transmission of antibiotic resistances by food and water. Therefore, the objective of this work was to determine the presence of high and critical priority pathogens included in the aforementioned list in different aquatic environments in the POCTEFA area (North Spain–South France). In addition to these pathogens, detection of colistin-resistant Enterobacteriaceae was included due its relevance as being the antibiotic of choice to treat infections caused by multidrug resistant bacteria (MDR). From the total of 80 analyzed samples, 100% of the wastewater treatment plants (WWTPs) and collectors (from hospitals and slaughterhouses) and 96.4% of the rivers, carried antibiotic resistant bacteria (ARB) against the tested antibiotics. Fifty-five (17.7%) of the isolates were identified as target microorganisms (high and critical priority pathogens of WHO list) and 58.2% (n = 32) of them came from WWTPs and collectors. Phenotypic and genotypic characterization showed that 96.4% were MDR and resistance to penicillins/cephalosporins was the most widespread. The presence of bla genes, KPC-type carbapenemases, mcr-1 and vanB genes has been confirmed. In summary, the presence of clinically relevant MDR bacteria in the studied aquatic environments demonstrates the need to improve surveillance and treatments of wastewaters from slaughterhouses, hospitals and WWTPs, in order to minimize the dispersion of resistance through the effluents of these areas. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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13 pages, 1762 KiB

Open AccessReview

TRIM Proteins and Their Roles in the Influenza Virus Life Cycle

by Hye-Ra Lee, Myoung Kyu Lee, Chan Woo Kim and Meehyein Kim

Microorganisms 2020, 8(9), 1424; https://doi.org/10.3390/microorganisms8091424 - 16 Sep 2020

Cited by 11 | Viewed by 4520

Abstract

The ubiquitin-proteasome system (UPS) has been recognized for regulating fundamental cellular processes, followed by induction of proteasomal degradation of target proteins, and triggers multiple signaling pathways that are crucial for numerous aspects of cellular physiology. Especially tripartite motif (TRIM) proteins, well-known E3 ubiquitin [...] Read more.

The ubiquitin-proteasome system (UPS) has been recognized for regulating fundamental cellular processes, followed by induction of proteasomal degradation of target proteins, and triggers multiple signaling pathways that are crucial for numerous aspects of cellular physiology. Especially tripartite motif (TRIM) proteins, well-known E3 ubiquitin ligases, emerge as having critical roles in several antiviral signaling pathways against varying viral infections. Here we highlight recent advances in the study of antiviral roles of TRIM proteins toward influenza virus infection in terms of the modulation of pathogen recognition receptor (PRR)-mediated innate immune sensing, direct obstruction of influenza viral propagation, and participation in virus-induced autophagy. Full article

(This article belongs to the Special Issue The Biology of Influenza Viruses)

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Microorganisms, Volume 8, Issue 9 (September 2020) – 199 articles

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