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Microorganisms
Special Issues
Microbial Survival—Phenomenon, Forms and Mechanisms
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Microbial Survival—Phenomenon, Forms and Mechanisms

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 7709

Special Issue Editor

Dr. Yu A. Nikolaev

E-Mail Website
Guest Editor
Laboratory of Viability of Microorganisms, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
Interests: microbial physiology; viability survival; autoregulation; communication; resting forms; persisters; phase variation

Special Issue Information

Dear Colleagues,

This Special Issue will include research papers or reviews that cover all aspects of microbial survival, such as the forms and mechanisms of microbe survival at the molecular, sub-cellular, cellular, population, consortia and symbiotic levels.

Objects of research may be bacteria, archaea, fungi, microscopic algae and also their associations and symbiosis. Survival investigations under various unfavorable conditions and stressors will be welcomed (physical, chemical, biological and “natural stressors”, such as starvation, high population density, etc.).

Included papers may apply different methodologies, approaches and techniques (traditional microbiological, biochemical, chemical, physical, physicochemical, microscopical (of all kinds), molecular-biological, etc.).

Both fundamental and applied aspects (medicine, hygiene, food safety, environment, etc.) are welcomed.

Dr. Yu A. Nikolaev
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbial survival and viability
  • environmental and “natural“ stressors
  • phenomenology and mechanisms and forms of survival
  • genetics
  • autoregulation
  • intercellular communication
  • resting forms
  • persisters
  • phase variation

Published Papers (5 papers)

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Research

14 pages, 4057 KiB  
Article
Distinct Effects of Moxifloxacin and Bedaquiline on Growing and ‘Non-Culturable’ Mycobacterium abscessus
by Andrey L. Mulyukin, Deborah Recchia, Nadezhda A. Kostrikina, Maria V. Artyukhina, Billy A. Martini, Alessandro Stamilla, Giulia Degiacomi and Elena G. Salina
Microorganisms 2023, 11(11), 2690; https://doi.org/10.3390/microorganisms11112690 - 2 Nov 2023
Cited by 1 | Viewed by 1490
Abstract
Mycobacterium abscessus has recently emerged as the cause of an increasing number of human infections worldwide. Unfortunately, it is highly resistant to existing drugs, and new specific agents to combat M. abscessus have not yet been found. The discovery of antibiotics that are [...] Read more.
Mycobacterium abscessus has recently emerged as the cause of an increasing number of human infections worldwide. Unfortunately, it is highly resistant to existing drugs, and new specific agents to combat M. abscessus have not yet been found. The discovery of antibiotics that are effective not only against replicating but also against dormant and often recalcitrant cells is a daunting challenge. In this study, we developed a model of non-replicating M. abscessus, which represents a valuable screening tool for antibacterial agents. Thus, we demonstrated that, under a deficiency of potassium ions in the growth media and prolonged incubation, M. abscessus entered a ‘non-culturable’ state with a significant loss of colony-forming ability, but it retained viability, as confirmed using the most-probable-number (MPN) assay. The ‘non-culturable’ mycobacteria possessed decelerated cellular metabolism and noticeable differences in cell morphology from actively growing mycobacteria. ‘Non-culturable’ cells were used in a comprehensive screening of the efficacy of antibiotics, along with actively growing cells. Both CFU and MPN tests confirmed the prominent bactericidal effect of moxifloxacin on actively growing and ‘non-culturable’ M. abscessus, as proven by less than 0.01% of cells surviving after antibiotic treatment and prolonged storage. Bedaquiline exhibited a comparable bactericidal effect only on metabolically inactive non-culturable cells aged for 44 days. There were reductions ranging from 1000 to 10,000-fold in CFU and MPN, but it was not so efficient with respect to active cells, resulting in a bacteriostatic effect. The demonstrated specificity of bedaquiline in relation to inert non-replicating M. abscessus offers a new and unexpected result. Based on the findings of this research, moxifloxacin and bedaquiline can be regarded as potential treatments for infections caused by M. abscessus. In addition, a key outcome is the proposal to include the combination of viability assays for comprehensive testing of drug candidates. Relying on CFU-based assays alone resulted in overestimates of antibacterial efficacy, as demonstrated in our experiments. Full article
(This article belongs to the Special Issue Microbial Survival—Phenomenon, Forms and Mechanisms)
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18 pages, 3808 KiB  
Article
Epinephrine Affects Ribosomes, Cell Division, and Catabolic Processes in Micrococcus luteus Skin Strain C01: Revelation of the Conditionally Extensive Hormone Effect Using Orbitrap Mass Spectrometry and Proteomic Analysis
by Andrei V. Gannesen, Rustam H. Ziganshin, Maria A. Ovcharova, Ekaterina D. Nevolina, Alena I. Klimko, Sergey V. Martyanov and Vladimir K. Plakunov
Microorganisms 2023, 11(9), 2181; https://doi.org/10.3390/microorganisms11092181 - 29 Aug 2023
Cited by 2 | Viewed by 1091
Abstract
In the current study, extensive Orbitrap mass spectrometry analysis was conducted for skin strain Micrococcus luteus C01 planktonic cultures and biofilms after 24 h and 72 h of incubation either in the presence of epinephrine or without any implementations. The investigation revealed the [...] Read more.
In the current study, extensive Orbitrap mass spectrometry analysis was conducted for skin strain Micrococcus luteus C01 planktonic cultures and biofilms after 24 h and 72 h of incubation either in the presence of epinephrine or without any implementations. The investigation revealed the complex and conditionally extensive effect of epinephrine at concentrations closer to normal blood plasma concentrations on both planktonic cultures and biofilms of skin strain M. luteus C01. The concentrations of hundreds of proteins changed during the shift from planktonic growth mode to biofilm and hundreds of proteins were downregulated or upregulated in the presence of epinephrine. Ribosomal, TCA, and cell division proteins appear to be the most altered in their amounts in the presence of the hormone. Potentially, the regulatory mechanism of this process is connected with c-di-GMP and histidine kinases, which were affected by epinephrine in different samples. The phenomenon of epinephrine-based biofilm regulation in M. luteus C01 has wide implications for microbial endocrinology and other research areas. Full article
(This article belongs to the Special Issue Microbial Survival—Phenomenon, Forms and Mechanisms)
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11 pages, 700 KiB  
Article
Aerotolerant Thiosulfate-Reducing Bacterium Fusibacter sp. Strain WBS Isolated from Littoral Bottom Sediments of the White Sea—Biochemical and Genome Analysis
by Andrei L. Brioukhanov, Vitaly V. Kadnikov, Alexey V. Beletsky and Alexander S. Savvichev
Microorganisms 2023, 11(7), 1642; https://doi.org/10.3390/microorganisms11071642 - 23 Jun 2023
Cited by 2 | Viewed by 1304
Abstract
The strain WBS, an anaerobic, psychro- and halotolerant bacterium belonging to the genus Fusibacter, was isolated from the littoral bottom sediments of the White Sea, Arctic, Russia. Fusibacter bizertensis WBS grew at temperatures between 8 and 32 °C (optimum growth at 18–20 °C), [...] Read more.
The strain WBS, an anaerobic, psychro- and halotolerant bacterium belonging to the genus Fusibacter, was isolated from the littoral bottom sediments of the White Sea, Arctic, Russia. Fusibacter bizertensis WBS grew at temperatures between 8 and 32 °C (optimum growth at 18–20 °C), pH between 5.2 and 8.3 (optimum growth at pH 7.2), and at NaCl concentrations between 0 and 70 g L−1 (optimum growth at 32 g L−1). It reduced sulfate, thiosulfate, and elemental sulfur into sulfide, and, probably, the strain is able to disproportionate thiosulfate. The strain also utilized a wide range of substrates as it is a chemoorganotrophic bacterium. Analysis of the sequenced genome revealed genes for all enzymes involved in the Embden–Meyerhof glycolytic pathway as well as genes for the non-oxidative stage of the pentose phosphate pathway. The presence of genes encoding aldehyde dehydrogenases and alcohol dehydrogenases also suggests that, in addition to acetate, alcohols can also be the fermentation products. The strain possessed superoxide dismutase and peroxidase activities and the ability to consume O2, which is in full accordance with the presence of corresponding genes of antioxidant defense in the genome. The phylogenetic analysis suggested that the strain WBS is the closest relative of Fusibacter bizertensis LTF Kr01T (16S rRNA gene sequence similarity 98.78%). Based on biochemical and genomic characteristics, the strain WBS is proposed to represent a novel aero-, halo- and psychrotolerant strain from the genus Fusibacter, isolated for the first time among its members from cold oxygenated marine bottom sediments. Full article
(This article belongs to the Special Issue Microbial Survival—Phenomenon, Forms and Mechanisms)
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16 pages, 2774 KiB  
Article
Oxidative Stress Response and E. coli Biofilm Formation under the Effect of Pristine and Modified Carbon Nanotubes
by Yuliya Maksimova, Anastasiya Zorina and Larisa Nesterova
Microorganisms 2023, 11(5), 1221; https://doi.org/10.3390/microorganisms11051221 - 6 May 2023
Cited by 5 | Viewed by 1828
Abstract
The article investigates the expression of oxyR and soxS oxidative stress genes in E. coli under the effect of pristine multi-walled carbon nanotubes (MWCNTs) and pristine single-walled carbon nanotubes (SWCNTs), MWCNTs and SWCNTs functionalized with carboxyl groups (MWCNTs-COOH and SWCNTs-COOH, respectively), SWCNTs functionalized [...] Read more.
The article investigates the expression of oxyR and soxS oxidative stress genes in E. coli under the effect of pristine multi-walled carbon nanotubes (MWCNTs) and pristine single-walled carbon nanotubes (SWCNTs), MWCNTs and SWCNTs functionalized with carboxyl groups (MWCNTs-COOH and SWCNTs-COOH, respectively), SWCNTs functionalized with amino groups (SWCNTs-NH2) and SWCNTs functionalized with octadecylamine (SWCNTs-ODA). Significant differences were found in the expression of the soxS gene, while no changes were observed in the expression level of the oxyR gene. The pro-oxidant effect of SWCNTs, SWCNTs-COOH, SWCNTs-NH2, and SWCNTs-ODA is presented, and the contrary antioxidant effect of pristine MWCNTs and MWCNTs-COOH in the presence of methyl viologen hydrate (paraquat) is shown. The article shows that SWCNTs-COOH, SWCNTs-NH2, and SWCNTs-ODA added to the medium generate the production of reactive oxygen species (ROS) in bacterial cells. SWCNTs-COOH intensified the E. coli biofilm formation, and the biofilm biomass exceeded the control by 25 times. Additionally, it is shown that the rpoS expression increased in response to MWCNTs-COOH and SWCNTs-COOH, and the effect of SWCNTs-COOH was more significant. SWCNTs-COOH and SWCNTs-NH2 initiated an increase in ATP concentration in the planktonic cells and a decrease in the biofilm cells. The atomic force microscopy (AFM) method showed that the volume of E. coli planktonic cells after the exposure to carbon nanotubes (CNTs) decreased compared to that without exposure, mainly due to a decrease in cell height. The absence of a strong damaging effect of functionalized SWCNTs on E. coli K12 cells, both in suspension and in biofilms, is shown. Contact with functionalized SWCNTs initiated the aggregation of the polymeric substances of the biofilms; however, the cells did not lyse. Among the studied CNTs, SWCNTs-COOH caused an increased expression of the soxS and rpoS, the formation of ROS, and stimulation of the biofilm formation. Full article
(This article belongs to the Special Issue Microbial Survival—Phenomenon, Forms and Mechanisms)
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19 pages, 5435 KiB  
Article
Ways of Long-Term Survival of Hydrocarbon-Oxidizing Bacteria in a New Biocomposite Material—Silanol-Humate Gel
by Yury A. Nikolaev, Elena V. Demkina, Ekaterina A. Ilicheva, Timur A. Kanapatskiy, Igor A. Borzenkov, Anna E. Ivanova, Ekaterina N. Tikhonova, Diyana S. Sokolova, Alexander O. Ruzhitsky and Galina I. El-Registan
Microorganisms 2023, 11(5), 1133; https://doi.org/10.3390/microorganisms11051133 - 27 Apr 2023
Viewed by 1439
Abstract
Immobilized bacterial cells are presently widely used in the development of bacterial preparations for the bioremediation of contaminated environmental objects. Oil hydrocarbons are among the most abundant pollutants. We have previously described a new biocomposite material containing hydrocarbon-oxidizing bacteria (HOB) embedded in silanol-humate [...] Read more.
Immobilized bacterial cells are presently widely used in the development of bacterial preparations for the bioremediation of contaminated environmental objects. Oil hydrocarbons are among the most abundant pollutants. We have previously described a new biocomposite material containing hydrocarbon-oxidizing bacteria (HOB) embedded in silanol-humate gels (SHG) based on humates and aminopropyltriethoxysilane (APTES); high viable cell titer was maintained in this material for at least 12 months. The goal of the work was to describe the ways of long-term HOB survival in SHG and the relevant morphotypes using the techniques of microbiology, instrumental analytical chemistry and biochemistry, and electron microscopy. Bacteria surviving in SHG were characterized by: (1) capacity for rapid reactivation (growth and hydrocarbon oxidation) in fresh medium; (2) ability to synthesize surface-active compounds, which was not observed in the cultures stored without SHG); (3) elevated stress resistance (ability to grow at high Cu2+ and NaCl concentrations); (4) physiological heterogeneity of the populations, which contained the stationary hypometabolic cells, cystlike anabiotic dormant forms (DF), and ultrasmall cells; (5) occurrence of piles in many cells, which were probably used to exchange genetic material; (6) modification of the phase variants spectrum in the population growing after long-term storage in SHG; and (7) oxidation of ethanol and acetate by HOB populations stored in SHG. The combination of the physiological and cytomorphological properties of the cells surviving in SHG for long periods may indicate a new type of long-term bacterial survival, i.e., in a hypometabolic state. Full article
(This article belongs to the Special Issue Microbial Survival—Phenomenon, Forms and Mechanisms)
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