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Yang G, Lin C, Hou T, Wu X, Fang Y, Yao S, Zhuang L, Yuan Y. The survival strategy of direct interspecies electron transfer-capable coculture under electron donor-limited environments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168223. [PMID: 37926263 DOI: 10.1016/j.scitotenv.2023.168223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/08/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Direct interspecies electron transfer (DIET) has been considered as an effective mechanism for interspecies electron exchange in microbial syntrophy. Understanding DIET-capable syntrophic associations under energy-limited environments is important because these conditions more closely approximate those found in natural subsurface environments than in the batch cultures in the laboratory. This study, investigated the metabolic dynamics and electron transfer mechanisms in DIET-capable syntrophic coculture of Geobacter metallireducens and Geobacter sulfurreducens under electron donor-limited condition. The wild-coculture and the mutant-coculture with a citrate synthase-deficient G. sulfurreducens exhibited similar rates of syntrophic metabolism under ethanol-limited and ethanol-replete conditions. Transcriptomic analyses revealed that, in the mutant-coculture in which interspecies electron exchange was the sole electron source for G. sulfurreducens, the transcription of genes associated with uptake hydrogenase in G. sulfurreducens were significantly repressed and thus DIET tended to be the preferred mode of interspecies electron exchange under electron donor-limited condition. To overcome electron donor limitation, c-type cytochromes in the coculture actively moved from outer membrane to extracellular environment, potentially via increased secretion of outer-membrane vesicles. These results suggested a preferred electron transfer mechanism for DIET-capable syntrophic communities' survival in the electron donor-limited environments, providing valuable insights into the biogeochemical processes mediated by DIET in natural and engineered environments.
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Affiliation(s)
- Guiqin Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Canfen Lin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Tiqun Hou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Xian Wu
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Yanlun Fang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Sijie Yao
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China
| | - Li Zhuang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, China.
| | - Yong Yuan
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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2
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Wang Y, Ling N, Jiao R, Zhang X, Ren Y, Li H, Zhao W, Wu Q, Ye Y. Transcriptomic analysis reveals novel desiccation tolerance mechanism of Cronobacter based on type VI secretion system inhibition. Food Res Int 2023; 172:113143. [PMID: 37689845 DOI: 10.1016/j.foodres.2023.113143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 09/11/2023]
Abstract
Cronobacter malonaticus (C. malonaticus) is a food-borne pathogen inducing severe infections both in infants and adults, and it could survive in dry powdered infant formula (PIF) for a long time, implying its strong tolerance to desiccation. However, the thorough molecular mechanism of resistance to desiccation remains elusive. When C. malonaticus was exposed to desiccation conditions (7, 15, and 30 d), transcriptomic analysis provided a universal adaptation strategy to withstand desiccation with the increased compatible solutes accumulation, activated stress resistance-related regulators, suppressed protein export and bacterial secretion system, and reduced other unessential survival functions including adhesion, invasion, virulence, and flagellar motility. Importantly, type VI secretion system (T6SS) genes exhibited significantly downregulated expressions, as well as markedly increased survival and viability of their mutants after desiccation treatment, revealing the negative regulation of T6SS in desiccation tolerance. Meanwhile, the decreased expressions of T6SS structure genes in other six species further confirmed the vital role of T6SS in desiccation tolerance of Cronobacter spp. Thus, our studies present a novel hypothesis of desiccation resistance in Cronobacter based on type VI secretion system inhibition, causing the reduction of macromolecule secretion such as effectors and hyperosmolality development within the cytomembrane, which allow Cronobacter to survive in desiccation.
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Affiliation(s)
- Yang Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Na Ling
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Rui Jiao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Xiyan Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Yuwei Ren
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Hui Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Wenhua Zhao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangzhou, China
| | - Yingwang Ye
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China.
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3
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Górecki I, Kołodziejczyk A, Harasymczuk M, Młynarczyk G, Szymanek-Majchrzak K. The Impact of Harsh Stratospheric Conditions on Survival and Antibiotic Resistance Profile of Non-Spore Forming Multidrug Resistant Human Pathogenic Bacteria Causing Hospital-Associated Infections. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2787. [PMID: 36833485 PMCID: PMC9956888 DOI: 10.3390/ijerph20042787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Bacteria are constantly being lifted to the stratosphere due to air movements caused by weather phenomena, volcanic eruptions, or human activity. In the upper parts of the atmosphere, they are exposed to extremely harsh and mutagenic conditions such as UV and space radiation or ozone. Most bacteria cannot withstand that stress, but for a fraction of them, it can act as a trigger for selective pressure and rapid evolution. We assessed the impact of stratospheric conditions on the survival and antibiotic resistance profile of common non-spore-forming human pathogenic bacteria, both sensitive and extremely dangerous multidrug-resistant variants, with plasmid-mediated mechanisms of resistance. Pseudomonas aeruginosa did not survive the exposure. In the case of strains that were recovered alive, the survival was extremely low: From 0.00001% of Klebsiella pneumoniae carrying the ndm-1 gene and methicillin-resistant Staphylococcus aureus mecA-positive with reduced susceptibility to vancomycin (MRSA/VISA), to a maximum of 0.001% of K. pneumoniae sensitive to all common antibiotics and S. aureus sensitive to vancomycin (MRSA/VSSA). We noticed a tendency towards increased antibiotic susceptibility after the stratospheric flight. Antimicrobial resistance is a current real, global, and increasing problem, and our results can inform current understandings of antibiotic resistance mechanisms and development in bacteria.
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Affiliation(s)
- Ignacy Górecki
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Agata Kołodziejczyk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
- Space Technology Centre, AGH University of Technology, Czarnowiejska Str. 36, 30-054 Cracow, Poland
| | - Matt Harasymczuk
- Analog Astronaut Training Center, Morelowa Str. 1F/4, 30-222 Cracow, Poland
| | - Grażyna Młynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
| | - Ksenia Szymanek-Majchrzak
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego, Str. 5, 02-004 Warsaw, Poland
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4
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Ren S, Jin Y, Ma J, Zheng N, Zhang J, Peng X, Xie B. Isolation and characterization of algicidal bacteria from freshwater aquatic environments in China. Front Microbiol 2023; 14:1156291. [PMID: 36970679 PMCID: PMC10033687 DOI: 10.3389/fmicb.2023.1156291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Algicidal bacteria can inhibit the growth of algae or lyse algal cells, thus playing roles in shaping aquatic microbial communities and maintaining the functions of aquatic ecosystems. Nevertheless, our understanding of their diversities and distributions remains limited. In this study, we collected water samples from 17 freshwater sites in 14 cities in China and screened a total of 77 algicidal bacterial strains using several prokaryotic cyanobacteria and eukaryotic algae as target strains. According to their target-specificities, these strains were classified into three subgroups, cyanobacterial algicidal bacteria, algal algicidal bacteria, and broad-target algicidal bacteria, each displaying distinctive compositions and geographical distribution patterns. They are assigned to Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes bacterial phyla, of which Pseudomonas and Bacillus are the most abundant gram-negative and gram-positive genus, respectively. A number of bacterial strains, such as Inhella inkyongensis and Massilia eburnean, are suggested as new algicidal bacteria. The diverse taxonomies, algal-inhibiting abilities and distributions of these isolates have suggested that there are rich algicidal bacterial resources in these aquatic environments. Our results provide new microbial resources for algal-bacterial interaction studies, and shed new insights into how algicidal bacteria can be used in the control of harmful algal blooms, as well as in algal biotechnology.
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Haddad G, Takakura T, Bellali S, Fontanini A, Ominami Y, Khalil JB, Raoult D. A preliminary investigation into bacterial viability using scanning electron microscopy–energy-dispersive X-ray analysis: The case of antibiotics. Front Microbiol 2022; 13:967904. [PMID: 36003945 PMCID: PMC9393632 DOI: 10.3389/fmicb.2022.967904] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
The metabolic stages of bacterial development and viability under different stress conditions induced by disinfection, chemical treatments, temperature, or atmospheric changes have been thoroughly investigated. Here, we aim to evaluate early metabolic modifications in bacteria following induced stress, resulting in alterations to bacterial metabolism. A protocol was optimized for bacterial preparation using energy-dispersive X-ray (EDX) microanalysis coupled with scanning electron microscopy (SEM), followed by optimizing EDX data acquisition and analysis. We investigated different preparation methods aiming to detect modifications in the bacterial chemical composition at different states. We first investigated Escherichia coli, acquiring data from fresh bacteria, after heat shock, and after contact with 70% ethanol, in order to prove the feasibility of this new strategy. We then applied the new method to different bacterial species following 1 h of incubation with increasing doses of antibiotics used as a stress-inducing agent. Among the different materials tested aiming to avoiding interaction with bacterial metabolites, phosphorous-doped silicon wafers were selected for the slide preparation. The 15 kV acceleration voltage ensured all the chemical elements of interest were excited. A thick layer of bacterial culture was deposited on the silicon wafer providing information from multiple cells and intra-cellular composition. The EDX spectra of fresh, heat-killed, and alcohol-killed E. coli revealed important modifications in magnesium, potassium, and sodium. Those same alterations were detected when applying this strategy to bacteria exposed to antibiotics. Tests based on SEM–EDX acquisition systems would provide early predictions of the bacterial viability state in different conditions, yielding earlier results than culture.
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Affiliation(s)
- Gabriel Haddad
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
| | | | - Sara Bellali
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | - Anthony Fontanini
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
| | | | - Jacques Bou Khalil
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Jacques Bou Khalil,
| | - Didier Raoult
- Institut Hospitalo-Universitaire Méditerranée Infection, Marseille, France
- Aix-Marseille Univ, IRD, APHM, MEPHI, Marseille, France
- *Correspondence: Didier Raoult,
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6
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Dawan J, Ahn J. Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance. Microorganisms 2022; 10:microorganisms10071385. [PMID: 35889104 PMCID: PMC9322497 DOI: 10.3390/microorganisms10071385] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/03/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria can be adapted to adverse and detrimental conditions that induce general and specific responses to DNA damage as well as acid, heat, cold, starvation, oxidative, envelope, and osmotic stresses. The stress-triggered regulatory systems are involved in bacterial survival processes, such as adaptation, physiological changes, virulence potential, and antibiotic resistance. Antibiotic susceptibility to several antibiotics is reduced due to the activation of stress responses in cellular physiology by the stimulation of resistance mechanisms, the promotion of a resistant lifestyle (biofilm or persistence), and/or the induction of resistance mutations. Hence, the activation of bacterial stress responses poses a serious threat to the efficacy and clinical success of antibiotic therapy. Bacterial stress responses can be potential targets for therapeutic alternatives to antibiotics. An understanding of the regulation of stress response in association with antibiotic resistance provides useful information for the discovery of novel antimicrobial adjuvants and the development of effective therapeutic strategies to control antibiotic resistance in bacteria. Therefore, this review discusses bacterial stress responses linked to antibiotic resistance in Gram-negative bacteria and also provides information on novel therapies targeting bacterial stress responses that have been identified as potential candidates for the effective control of Gram-negative antibiotic-resistant bacteria.
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Affiliation(s)
- Jirapat Dawan
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
| | - Juhee Ahn
- Department of Biomedical Science, Kangwon National University, Chuncheon 24341, Gangwon, Korea;
- Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon 24341, Gangwon, Korea
- Correspondence: ; Tel.: +82-33-250-6564
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7
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Maharajan AD, Hjerde E, Hansen H, Willassen NP. Quorum Sensing Controls the CRISPR and Type VI Secretion Systems in Aliivibrio wodanis 06/09/139. Front Vet Sci 2022; 9:799414. [PMID: 35211539 PMCID: PMC8861277 DOI: 10.3389/fvets.2022.799414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/12/2022] [Indexed: 12/26/2022] Open
Abstract
For bacteria to thrive in an environment with competitors, phages and environmental cues, they use different strategies, including Type VI Secretion Systems (T6SSs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to compete for space. Bacteria often use quorum sensing (QS), to coordinate their behavior as the cell density increases. Like other aliivibrios, Aliivibrio wodanis 06/09/139 harbors two QS systems, the main LuxS/LuxPQ system and an N-acyl homoserine lactone (AHL)-mediated AinS/AinR system and a master QS regulator, LitR. To explore the QS and survival strategies, we performed genome analysis and gene expression profiling on A. wodanis and two QS mutants (ΔainS and ΔlitR) at two cell densities (OD600 2.0 and 6.0) and temperatures (6 and 12°C). Genome analysis of A. wodanis revealed two CRISPR systems, one without a cas loci (CRISPR system 1) and a type I-F CRISPR system (CRISPR system 2). Our analysis also identified three main T6SS clusters (T6SS1, T6SS2, and T6SS3) and four auxiliary clusters, as well about 80 potential Type VI secretion effectors (T6SEs). When comparing the wildtype transcriptome data at different cell densities and temperatures, 13-18% of the genes were differentially expressed. The CRISPR system 2 was cell density and temperature-independent, whereas the CRISPR system 1 was temperature-dependent and cell density-independent. The primary and auxiliary clusters of T6SSs were both cell density and temperature-dependent. In the ΔlitR and ΔainS mutants, several CRISPR and T6SS related genes were differentially expressed. Deletion of litR resulted in decreased expression of CRISPR system 1 and increased expression of CRISPR system 2. The T6SS1 and T6SS2 gene clusters were less expressed while the T6SS3 cluster was highly expressed in ΔlitR. Moreover, in ΔlitR, the hcp1 gene was strongly activated at 6°C compared to 12°C. AinS positively affected the csy genes in the CRISPR system 2 but did not affect the CRISPR arrays. Although AinS did not significantly affect the expression of T6SSs, the hallmark genes of T6SS (hcp and vgrG) were AinS-dependent. The work demonstrates that T6SSs and CRISPR systems in A. wodanis are QS dependent and may play an essential role in survival in its natural environment.
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Affiliation(s)
- Amudha Deepalakshmi Maharajan
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Erik Hjerde
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for Bioinformatics, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Hilde Hansen
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Nils Peder Willassen
- Norwegian Structural Biology Center and Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for Bioinformatics, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
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8
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Topić Popović N, Kazazić SP, Bojanić K, Strunjak-Perović I, Čož-Rakovac R. Sample preparation and culture condition effects on MALDI-TOF MS identification of bacteria: A review. MASS SPECTROMETRY REVIEWS 2021. [PMID: 34642960 DOI: 10.1002/mas.21739] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an excellent tool for bacterial identification. It allows high throughput, sensitive and specific applications in clinical diagnostics and environmental research. Currently, there is no optimal standardized protocol for sample preparation and culture conditions to profile bacteria. The performance of MALDI-TOF MS is affected by several variables, such as sample preparation, culture media and culture conditions, incubation time/growth stage, incubation temperature, high salt content, blood in the culture media, and others. This review thus aims to clarify why a uniformed protocol is not plausible, to assess the effects these factors have on MALDI-TOF MS identification score, and discuss possible optimizations for its methodology, in relation to specific bacterial representatives and strain requirements.
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Affiliation(s)
- Natalija Topić Popović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Snježana P Kazazić
- Laboratory for Mass Spectrometry and Functional Proteomics, Ruđer Bošković Institute, Zagreb, Croatia
| | - Krunoslav Bojanić
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivančica Strunjak-Perović
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
| | - Rozelindra Čož-Rakovac
- Laboratory for Aquaculture Biotechnology, Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Centre of Excellence for Marine Bioprospecting-BioProCro, Ruđer Bošković Institute, Zagreb, Croatia
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9
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Owens TG, King BA, Radford DR, Strange P, Arvaj L, Guazzelli Pezzali J, Edwards AM, Ganesh D, DeVries TJ, McBride BW, Balamurugan S, Shoveller AK. Use of 2-hydroxy-4-(methylthio)-butanoic acid to inhibit Salmonella and Listeria in raw meat for feline diets and palatability in domestic cats. J Anim Sci 2021; 99:6358425. [PMID: 34448863 DOI: 10.1093/jas/skab253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 08/26/2021] [Indexed: 11/12/2022] Open
Abstract
While the raw pet food market continues to grow, the risk of bacterial contamination in these types of diets is a major concern, with Salmonella enterica and Listeria monocytogenes being the most frequently associated pathogens in raw pet food product recalls. dl-Methionine is included in some commercial feline kibble and canned diets to improve protein quality; however, an alternative to this is a liquid methionine supplement, 2-hydroxy-4-(methylthio)-butanoic acid (HMTBa), which is also an organic acid. 2-Hydroxy-4-(methylthio)-butanoic acid has previously demonstrated similar efficacy to formic acid against pathogens in a liquid environment and may be a good candidate to inhibit S. enterica and L. monocytogenes in raw ground meat. First, the minimum inhibitory concentration and minimum bactericidal concentration of HMTBa against these pathogens under laboratory growth conditions were determined by measuring growth of pathogens over 36 h when exposed to 10 concentrations of HMTBa (0.10% to 1.00%) mixed with tryptic soy broth. 2-Hydroxy-4-(methylthio)-butanoic acid included at ≥0.50% was bactericidal to S. enterica and L. monocytogenes (P < 0.05). Next, five levels of HMTBa (0.50% to 1.25%) were included in raw ground meat mixtures inoculated with cocktails of S. enterica or L. monocytogenes, and contamination levels were determined at four timepoints: immediately, and after refrigerated storage (4 °C) at 24, 48, and 72 h after removal from freezer (24 h at -20 °C). 2-Hydroxy-4-(methylthio)-butanoic acid included as 1.25% of the meat mixture reduced S. enterica and L. monocytogenes compared with the control (P < 0.05); however, it did not result in total kill of either of these pathogens. Following this, feeding behaviors of seven domestic cats were assessed when offered a raw chicken diet treated with or without 1.25% HMTBa for 5 d each, after which a 2-d 2-choice preference test was conducted. Cats demonstrated a preference for raw diets without HMTBa, but still readily consumed diets with 1.25% HMTBa, suggesting that such a diet was still palatable to them.
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Affiliation(s)
- Tiana G Owens
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Broghan A King
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Devon R Radford
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Philip Strange
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
| | - Laura Arvaj
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
| | | | | | - Daniel Ganesh
- Bos Nutrition Services Inc., Novus International (Canada) Inc , Guelph, ON N1G 4P1, Canada
| | - Trevor J DeVries
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.,Campbell Centre for the Study of Animal Welfare, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Brian W McBride
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Nutrition Modelling, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sampathkumar Balamurugan
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON N1G 5C9, Canada
| | - Anna K Shoveller
- Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada.,Campbell Centre for the Study of Animal Welfare, University of Guelph, Guelph, ON N1G 2W1, Canada.,Centre for Nutrition Modelling, University of Guelph, Guelph, ON N1G 2W1, Canada
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10
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Post-Transcriptional Control in the Regulation of Polyhydroxyalkanoates Synthesis. Life (Basel) 2021; 11:life11080853. [PMID: 34440597 PMCID: PMC8401924 DOI: 10.3390/life11080853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/08/2023] Open
Abstract
The large production of non-degradable petrol-based plastics has become a major global issue due to its environmental pollution. Biopolymers produced by microorganisms such as polyhydroxyalkanoates (PHAs) are gaining potential as a sustainable alternative, but the high cost associated with their industrial production has been a limiting factor. Post-transcriptional regulation is a key step to control gene expression in changing environments and has been reported to play a major role in numerous cellular processes. However, limited reports are available concerning the regulation of PHA accumulation in bacteria, and many essential regulatory factors still need to be identified. Here, we review studies where the synthesis of PHA has been reported to be regulated at the post-transcriptional level, and we analyze the RNA-mediated networks involved. Finally, we discuss the forthcoming research on riboregulation, synthetic, and metabolic engineering which could lead to improved strategies for PHAs synthesis in industrial production, thereby reducing the costs currently associated with this procedure.
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11
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Pietrzyk-Brzezinska AJ, Cociurovscaia A. Structures of the TetR-like transcription regulator RcdA alone and in complexes with ligands. Proteins 2021; 90:33-44. [PMID: 34288132 DOI: 10.1002/prot.26183] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/20/2021] [Accepted: 07/11/2021] [Indexed: 01/25/2023]
Abstract
RcdA is a helix-turn-helix (HTH) transcriptional regulator belonging to the TetR family. The protein regulates the transcription of curlin subunit gene D, the master regulator of biofilm formation. Moreover, it was predicted that it might be involved in the regulation of up to 27 different genes. However, an effector of RcdA and the environmental conditions which trigger RcdA action remain unknown. Herein, we report the first crystal structures of RcdA in complexes with ligands, trimethylamine N-oxide (TMAO) and tris(hydroxymethyl)aminomethane (Tris), which might serve as RcdA effectors. Based on these structures, the ligand-binding pocket of RcdA was characterized in detail. The conservation of the amino acid residues forming the ligand-binding cavity was analyzed and the comprehensive search for RcdA structural homologs was performed. This analysis indicated that RcdA is structurally similar to multidrug-binding TetR family members, however, its ligand-binding cavity differs significantly from the pockets of its structural homologs. The interaction of RcdA with TMAO and Tris indicates that the protein might be involved in alkaline stress response.
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Affiliation(s)
- Agnieszka J Pietrzyk-Brzezinska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Anna Cociurovscaia
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
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Fan Y, Chen C, Zhang Y, Liu H, Liu H, Liu H. Early corrosion behavior of X80 pipeline steel in a simulated soil solution containing Desulfovibrio desulfuricans. Bioelectrochemistry 2021; 141:107880. [PMID: 34229181 DOI: 10.1016/j.bioelechem.2021.107880] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/31/2021] [Accepted: 06/22/2021] [Indexed: 01/24/2023]
Abstract
Microbiologically influenced corrosion (MIC) is one of the reasons leading to the service failure of pipelines buried in the soil. The effects of sulfate-reducing bacteria (SRB) on steel corrosion without organic carbon are not clear. In this work, SRB cells were enriched in the simulated soil solution, aiming to study SRB corrosion behavior without organic carbon source using weight loss, electrochemical measurements, and surface analysis. Effects of DO on SRB corrosion were also studied. Results indicate that SRB can survive after 14 days of incubation without organic carbon source, but approximately 90% SRB have died. SRB without organic carbon source could inhibit the uniform corrosion but enhance the pitting corrosion compared with the control specimen. The corrosion rate of the control calculated from weight loss is highest with a value of (0.081 ± 0.013) mm/y. The highest localized corrosion rate of (0.306 ± 0.006) mm/y is obtained with an initial SRB count of 107 cells/mL. The presence of DO influences the steel corrosion process. Oxygen corrosion dominates for the specimens in the absence and presence of SRB with an initial count of 103 cells/mL, while SRB MIC is primary for the specimens with high SRB counts.
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Affiliation(s)
- Yuxing Fan
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhu Hai 519082, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhu Hai 519082, PR China
| | - Cuiying Chen
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhu Hai 519082, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhu Hai 519082, PR China
| | - Yuxuan Zhang
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhu Hai 519082, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhu Hai 519082, PR China
| | - Haixian Liu
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhu Hai 519082, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhu Hai 519082, PR China
| | - Hongwei Liu
- School of Chemical Engineering and Technology, Sun Yat-sen University, Zhu Hai 519082, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhu Hai 519082, PR China.
| | - Hongfang Liu
- Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, Hubei Key Laboratory of Materials Chemistry and Service Failure, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, Hubei 430074, PR China
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13
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Craig K, Johnson BR, Grunden A. Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications. Front Microbiol 2021; 12:660134. [PMID: 34040596 PMCID: PMC8141521 DOI: 10.3389/fmicb.2021.660134] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/12/2021] [Indexed: 12/25/2022] Open
Abstract
Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.
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Affiliation(s)
- Kelly Craig
- AgBiome Inc., Research Triangle Park, NC, United States
| | | | - Amy Grunden
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
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Acinetobacter baumannii: An Ancient Commensal with Weapons of a Pathogen. Pathogens 2021; 10:pathogens10040387. [PMID: 33804894 PMCID: PMC8063835 DOI: 10.3390/pathogens10040387] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022] Open
Abstract
Acinetobacter baumannii is regarded as a life-threatening pathogen associated with community-acquired and nosocomial infections, mainly pneumonia. The rise in the number of A. baumannii antibiotic-resistant strains reduces effective therapies and increases mortality. Bacterial comparative genomic studies have unraveled the innate and acquired virulence factors of A. baumannii. These virulence factors are involved in antibiotic resistance, environmental persistence, host-pathogen interactions, and immune evasion. Studies on host–pathogen interactions revealed that A. baumannii evolved different mechanisms to adhere to in order to invade host respiratory cells as well as evade the host immune system. In this review, we discuss current data on A. baumannii genetic features and virulence factors. An emphasis is given to the players in host–pathogen interaction in the respiratory tract. In addition, we report recent investigations into host defense systems using in vitro and in vivo models, providing new insights into the innate immune response to A. baumannii infections. Increasing our knowledge of A. baumannii pathogenesis may help the development of novel therapeutic strategies based on anti-adhesive, anti-virulence, and anti-cell to cell signaling pathways drugs.
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15
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Liao J, Bergholz P, Wiedmann M. Adjacent Terrestrial Landscapes Impact the Biogeographical Pattern of Soil Escherichia coli Strains in Produce Fields by Modifying the Importance of Environmental Selection and Dispersal. Appl Environ Microbiol 2021; 87:e02516-20. [PMID: 33452036 PMCID: PMC8105029 DOI: 10.1128/aem.02516-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 11/20/2022] Open
Abstract
High-quality habitats for wildlife (e.g., forest) provide essential ecosystem services while increasing species diversity and habitat connectivity. Unfortunately, the presence of such habitats adjacent to produce fields may increase risk for contamination of fruits and vegetables by enteric bacteria, including Escherichia coliE. coli survives in extrahost environments (e.g., soil) and could be dispersed across landscapes by wildlife. Understanding how terrestrial landscapes impact the distribution of soil E. coli strains is of importance in assessing the contamination risk of agricultural products. Here, using multilocus sequence typing, we characterized 938 E. coli soil isolates collected from two watersheds with different landscape patterns in New York State, USA, and compared the distribution of E. coli and the influence that environmental selection and dispersal have on the distribution between these two watersheds. Results showed that for the watershed with widespread produce fields, sparse forests, and limited interaction between the two land use types, E. coli composition was significantly different between produce field sites and forest sites; this distribution appears to be shaped by relatively strong environmental selection, likely from soil phosphorus, and slight dispersal limitation. For the watershed with more forested areas and stronger interaction between produce field sites and forest sites, E. coli composition between these two land use types was relatively homogeneous; this distribution appeared to be a consequence of wildlife-driven dispersal, inferred by competing models. Collectively, our results suggest that terrestrial landscape attributes could impact the biogeographic pattern of enteric bacteria by adjusting the importance of environmental selection and dispersal.IMPORTANCE Understanding the ecology of enteric bacteria in extrahost environments is important for the development and implementation of strategies to minimize preharvest contamination of produce with enteric pathogens. Our findings suggest that watershed landscape is an important factor influencing the importance of ecological drivers and dispersal patterns of E. coli Agricultural areas in such watersheds may have a higher risk of produce contamination due to fewer environmental constraints and higher potential of dispersal of enteric bacteria between locations. Thus, there is a perceived trade-off between priorities of environmental conservation and public health in on-farm food safety, with limited ecological data supporting or refuting the role of wildlife in dispersing pathogens under normal operating conditions. By combining field sampling and spatial modeling, we explored ecological principles underlying the biogeographic pattern of enteric bacteria at the regional level, which can benefit agricultural, environmental, and public health scientists who aim to reduce the risk of food contamination by enteric bacteria while minimizing negative impacts on wildlife habitats.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, Cornell University, Ithaca, New York, USA
- Graduate Field of Microbiology, Cornell University, Ithaca, New York, USA
| | - Peter Bergholz
- Department of Microbiological Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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16
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Zarattini M, Farjad M, Launay A, Cannella D, Soulié MC, Bernacchia G, Fagard M. Every cloud has a silver lining: how abiotic stresses affect gene expression in plant-pathogen interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1020-1033. [PMID: 33188434 PMCID: PMC7904152 DOI: 10.1093/jxb/eraa531] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/10/2020] [Indexed: 05/03/2023]
Abstract
Current environmental and climate changes are having a pronounced influence on the outcome of plant-pathogen interactions, further highlighting the fact that abiotic stresses strongly affect biotic interactions at various levels. For instance, physiological parameters such as plant architecture and tissue organization together with primary and specialized metabolism are affected by environmental constraints, and these combine to make an individual plant either a more or less suitable host for a given pathogen. In addition, abiotic stresses can affect the timely expression of plant defense and pathogen virulence. Indeed, several studies have shown that variations in temperature, and in water and mineral nutrient availability affect the expression of plant defense genes. The expression of virulence genes, known to be crucial for disease outbreak, is also affected by environmental conditions, potentially modifying existing pathosystems and paving the way for emerging pathogens. In this review, we summarize our current knowledge on the impact of abiotic stress on biotic interactions at the transcriptional level in both the plant and the pathogen side of the interaction. We also perform a metadata analysis of four different combinations of abiotic and biotic stresses, which identifies 197 common modulated genes with strong enrichment in Gene Ontology terms related to defense . We also describe the multistress-specific responses of selected defense-related genes.
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Affiliation(s)
- Marco Zarattini
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- PhotoBioCatalysis Unit – Crop Production and Biostimulation Lab (CPBL), Interfaculty School of Bioengineers, Université Libre de Bruxelles (ULB), CP150, Avenue F.D. Roosevelt 50, Brussels, Belgium
| | - Mahsa Farjad
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - Alban Launay
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
| | - David Cannella
- PhotoBioCatalysis Unit – Crop Production and Biostimulation Lab (CPBL), Interfaculty School of Bioengineers, Université Libre de Bruxelles (ULB), CP150, Avenue F.D. Roosevelt 50, Brussels, Belgium
| | - Marie-Christine Soulié
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
- Sorbonne Universités, UPMC Univ. Paris 06, UFR 927, 4 place Jussieu, Paris, France
| | - Giovanni Bernacchia
- Department of Life Sciences and Biotechnology, University of Ferrara, Via Borsari 46, Ferrara, Italy
| | - Mathilde Fagard
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, Versailles, France
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17
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Pátek M, Grulich M, Nešvera J. Stress response in Rhodococcus strains. Biotechnol Adv 2021; 53:107698. [PMID: 33515672 DOI: 10.1016/j.biotechadv.2021.107698] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 12/13/2022]
Abstract
Rhodococci are bacteria which can survive under various extreme conditions, in the presence of toxic compounds, and in other hostile habitats. Their tolerance of unfavorable conditions is associated with the structure of their cell wall and their large array of enzymes, which degrade or detoxify harmful compounds. Their physiological and biotechnological properties, together with tools for their genetic manipulation, enable us to apply them in biotransformations, biodegradation and bioremediation. Many such biotechnological applications cause stresses that positively or negatively affect their efficiency. Whereas numerous reviews on rhodococci described their enzyme activities, the optimization of degradation or production processes, and corresponding technological solutions, only a few reviews discussed some specific effects of stresses on the physiology of rhodococci and biotechnological processes. This review aims to comprehensively describe individual stress responses in Rhodococcus strains, the interconnection of different types of stresses and their consequences for cell physiology. We examine here the responses to (1) environmental stresses (desiccation, heat, cold, osmotic and pH stress), (2) the presence of stress-inducing compounds (metals, organic compounds and antibiotics) in the environment (3) starvation and (4) stresses encountered during biotechnological applications. Adaptations of the cell envelope, the formation of multicellular structures and stresses induced by the interactions of hosts with pathogenic rhodococci are also included. The roles of sigma factors of RNA polymerase in the global regulation of stress responses in rhodococci are described as well. Although the review covers a large number of stressful conditions, our intention was to provide an overview of the selected stress responses and their possible connection to biotechnological processes, not an exhaustive survey of the scientific literature. The findings on stress responses summarized in this review and the demonstration of gaps in current knowledge may motivate researchers working to fill these gaps.
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Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Michal Grulich
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
| | - Jan Nešvera
- Institute of Microbiology of the CAS, v. v. i., Prague, Czech Republic.
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18
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Haan TJ, Drown DM. Unearthing Antibiotic Resistance Associated with Disturbance-Induced Permafrost Thaw in Interior Alaska. Microorganisms 2021; 9:116. [PMID: 33418967 PMCID: PMC7825290 DOI: 10.3390/microorganisms9010116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 01/02/2023] Open
Abstract
Monitoring antibiotic resistance genes (ARGs) across ecological niches is critical for assessing the impacts distinct microbial communities have on the global spread of resistance. In permafrost-associated soils, climate and human driven disturbances augment near-surface thaw shifting the predominant bacteria that shape the resistome in overlying active layer soils. This thaw is of concern in Alaska, because 85% of land is underlain by permafrost, making soils especially vulnerable to disturbances. The goal of this study is to assess how soil disturbance, and the subsequent shift in community composition, will affect the types, abundance, and mobility of ARGs that compose the active layer resistome. We address this goal through the following aims: (1) assess resistance phenotypes through antibiotic susceptibility testing, and (2) analyze types, abundance, and mobility of ARGs through whole genome analyses of bacteria isolated from a disturbance-induced thaw gradient in Interior Alaska. We found a high proportion of isolates resistant to at least one of the antibiotics tested with the highest prevalence of resistance to ampicillin. The abundance of ARGs and proportion of resistant isolates increased with disturbance; however, the number of ARGs per isolate was explained more by phylogeny than isolation site. When compared to a global database of soil bacteria, RefSoil+, our isolates from the same genera had distinct ARGs with a higher proportion on plasmids. These results emphasize the hypothesis that both phylogeny and ecology shape the resistome and suggest that a shift in community composition as a result of disturbance-induced thaw will be reflected in the predominant ARGs comprising the active layer resistome.
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Affiliation(s)
- Tracie J. Haan
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775, USA;
| | - Devin M. Drown
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775, USA;
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
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19
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Hayes RA, Rebolleda‐Gómez M, Butela K, Cabo LF, Cullen N, Kaufmann N, O'Neill S, Ashman T. Spatially explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals. Microbiologyopen 2021; 10:e1158. [PMID: 33650801 PMCID: PMC7859501 DOI: 10.1002/mbo3.1158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/04/2023] Open
Abstract
The microbiome of flowers (anthosphere) is an understudied compartment of the plant microbiome. Within the flower, petals represent a heterogeneous environment for microbes in terms of resources and environmental stress. Yet, little is known of drivers of structure and function of the epiphytic microbial community at the within-petal scale. We characterized the petal microbiome in two co-flowering plants that differ in the pattern of ultraviolet (UV) absorption along their petals. Bacterial communities were similar between plant hosts, with only rare phylogenetically distant species contributing to differences. The epiphyte community was highly culturable (75% of families) lending confidence in the spatially explicit isolation and characterization of bacteria. In one host, petals were heterogeneous in UV absorption along their length, and in these, there was a negative relationship between growth rate and position on the petal, as well as lower UV tolerance in strains isolated from the UV-absorbing base than from UV reflecting tip. A similar pattern was not seen in microbes isolated from a second host whose petals had uniform patterning along their length. Across strains, the variation in carbon usage and chemical tolerance followed common phylogenetic patterns. This work highlights the value of petals for spatially explicit explorations of bacteria of the anthosphere.
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Affiliation(s)
- Rebecca A. Hayes
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Maria Rebolleda‐Gómez
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Kristen Butela
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Leah F. Cabo
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Nevin Cullen
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Nancy Kaufmann
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Steffani O'Neill
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
| | - Tia‐Lynn Ashman
- Department of Biological SciencesUniversity of PittsburghPittsburghPAUSA
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Effect of Heat Stress and the Recovery Potential of Heterocystous Cyanobacterium, Anabaena iyengarii Bharadwaja 1935. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.4.24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria, the major photosynthetic organisms, cover a large surface area of this planet. These organisms, being photosynthetic, have the capacity for sequestration of atmospheric carbon dioxide, a significant greenhouse gas that causes global warming. In this work, we have collected, developed pure culture, and identified 25 cyanobacterial species from semi arid agricultural rice fields of western Odisha with the high-temperature environmental setting. The purpose was to screen the cyanobacteria that can survive and grow at high temperatures with high photosynthetic efficiency. Cyanobacteria belong to genera Nostoc, Anabaena, Calothrix, and Hapalosiphon are observed to survive at 45°C. Among the cyanobacterial species, Anabaena iyengarii 17-SKD-2014 was found to exhibit higher growth, protein content, photosynthetic pigments, and photosynthetic O2 evolution at 45°C in comparison to other cyanobacterial isolates. Further, this cyanobacterium was grown at 50°C to analyze the cellular viability, and only up to ninth day incubated culture could recover from high-temperature stress after transferring to 25°C. Even though this indigenous cyanobacterial species failed to survive at 50°C in the laboratory conditions beyond a time limit, but this could be biotechnologically manipulated for effective carbon dioxide sequestration contributing to minimization of global warming.
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21
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Mokrani S, Nabti EH. Heavy metal resistance and bioremediation capacity of rhizospheric strain BioRPaz-3 Pseudomonas azotoformans endowed with antifungal activities and multi-abiotic stress tolerance in in vitro trials. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03828-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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22
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Ghosh S, Mohapatra B, Satyanarayana T, Sar P. Molecular and taxonomic characterization of arsenic (As) transforming Bacillus sp. strain IIIJ3-1 isolated from As-contaminated groundwater of Brahmaputra river basin, India. BMC Microbiol 2020; 20:256. [PMID: 32807097 PMCID: PMC7430025 DOI: 10.1186/s12866-020-01893-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
Background Microbe-mediated redox transformation of arsenic (As) leading to its mobilization has become a serious environmental concern in various subsurface ecosystems especially within the alluvial aquifers. However, detailed taxonomic and eco-physiological attributes of indigenous bacteria from As impacted aquifer of Brahmaputra river basin has remained under-studied. Results A newly isolated As-resistant and -transforming facultative anaerobic bacterium IIIJ3–1 from As-contaminated groundwater of Jorhat, Assam was characterized. Near complete 16S rRNA gene sequence affiliated the strain IIIJ3–1 to the genus Bacillus and phylogenetically placed within members of B. cereus sensu lato group with B. cereus ATCC 14579(T) as its closest relative with a low DNA-DNA relatedness (49.9%). Presence of iC17:0, iC15:0 fatty acids and menaquinone 7 corroborated its affiliation with B. cereus group, but differential hydroxy-fatty acids, C18:2 and menaquinones 5 & 6 marked its distinctiveness. High As resistance [Maximum Tolerable Concentration = 10 mM As3+, 350 mM As5+], aerobic As3+ (5 mM) oxidation, and near complete dissimilatory reduction of As 5+ (1 mM) within 15 h of growth designated its physiological novelty. Besides O2, cells were found to reduce As5+, Fe3+, SO42−, NO3−, and Se6+ as alternate terminal electron acceptors (TEAs), sustaining its anaerobic growth. Lactate was the preferred carbon source for anaerobic growth of the bacterium with As5+ as TEA. Genes encoding As5+ respiratory reductase (arr A), As3+ oxidase (aioB), and As3+ efflux systems (ars B, acr3) were detected. All these As homeostasis genes showed their close phylogenetic lineages to Bacillus spp. Reduction in cell size following As exposure exhibited the strain’s morphological response to toxic As, while the formation of As-rich electron opaque dots as evident from SEM-EDX possibly indicated a sequestration based As resistance strategy of strain IIIJ3–1. Conclusion This is the first report on molecular, taxonomic, and ecophysiological characterization of a highly As resistant, As3+ oxidizing, and dissimilatory As5+ reducing Bacillus sp. IIIJ3–1 from As contaminated sites of Brahmaputra river basin. The strain’s ability to resist and transform As along with its capability to sequester As within the cells demonstrate its potential in designing bioremediation strategies for As contaminated groundwater and other ecosystems.
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Affiliation(s)
- Soma Ghosh
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.,Present address: CSIR- National Environmental Engineering Research Institute, Kolkata Zonal Centre, Kolkata, 700107, India
| | - Balaram Mohapatra
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.,Present address: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Tulasi Satyanarayana
- Department of Microbiology, University of Delhi South Campus (UDSC), New Delhi, 110021, India.,Presently affiliated to Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Sector 3 Dwarka, New Delhi, 110078, India
| | - Pinaki Sar
- Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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Zhang L, Chen W, Jiang Q, Fei Z, Xiao M. Genome analysis of plant growth-promoting rhizobacterium Pseudomonas chlororaphis subsp. aurantiaca JD37 and insights from comparasion of genomics with three Pseudomonas strains. Microbiol Res 2020; 237:126483. [PMID: 32402945 DOI: 10.1016/j.micres.2020.126483] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/14/2020] [Accepted: 04/16/2020] [Indexed: 11/19/2022]
Abstract
Pseudomonas chlororaphis subsp. aurantiaca strain JD37 is a plant growth-promoting rhizobacterium (PGPR), which has important biotechnological features such as plant growth promotion, rhizosphere colonization and biocontrol activities. In present study, the genome sequence of JD37 was obtained and comparative genomic analysis were performed to explore unique features of the JD37 genome and its relationship with other Pseudomonas PGPR: P. chlororaphis PA23, P. protegens Pf-5 and P. aeruginosa M18. JD37 possessed a single circular chromosome of 6,702,062 bp in length with an average GC content of 62.75 %. No plasmid was detected in JD37. A total of 5003 functional proteins of JD37 were predicted according to the clusters of orthologous groups (COGs) database. The JD37 genome consisted of various genes involved in plant growth promotion, biocontrol activities and defense responses. Genes involved in the rhizosphere colonization and motility were also found in the genome of JD37, suggesting the common plant growth-promoting traits in PGPR. The identified resistance genes (e.g. those related to metal resistance, antibiotics, and osmotic and temperature-shock) and secondary metabolite biosynthesis revealed the pathways for metabolites it produced. Data presented in present study further provided valuable information on its molecular genetics and adaptive capacity in the rhizosphere niche.
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Affiliation(s)
- Lei Zhang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Wenbo Chen
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Qiuyue Jiang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Ming Xiao
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
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Abstract
Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.
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25
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Wu D, Forghani F, Daliri EBM, Li J, Liao X, Liu D, Ye X, Chen S, Ding T. Microbial response to some nonthermal physical technologies. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.11.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Life in High Salt Concentrations with Changing Environmental Conditions: Insights from Genomic and Phenotypic Analysis of Salinivibrio sp. Microorganisms 2019; 7:microorganisms7110577. [PMID: 31752335 PMCID: PMC6920786 DOI: 10.3390/microorganisms7110577] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/15/2019] [Indexed: 12/17/2022] Open
Abstract
Life in salt pans with varying chemical compositions require special adaptation strategies at both the physiological and molecular level. The Marakkanam salt pan in South India is characterized with a high fluctuation in salinity (19–490 ppt), Ultravioletradiation, and heavy metal concentrations. Several bacterial species have been isolated and identified in the view of phylogenetic analysis and for the subsequent production of industrially important enzymes. However, limited information exists on the genomic basis of their survival under variable environmental conditions. To this extent, we sequenced the whole genome of the Salinivibrio sp. HTSP, a moderately halophilic bacterium. We analysed the physiological and genomic attributes of Salinivibrio sp. HTSP to elucidate the strategies of adaptation under various abiotic stresses. The genome size is estimated to be 3.39 Mbp with a mean G + C content of 50.6%, including 3150 coding sequences. The genome possessed osmotic stress-related coding sequences, and genes involved in different pathways of DNA repair mechanisms and genes related to the resistance to toxic metals were identified. The periplasmic stress response genes and genes of different oxidative stress mechanisms were also identified. The tolerance capacity of the bacterial isolates to heavy metals, UV-radiation, and salinity was also confirmed through appropriate laboratory experiments under controlled conditions.
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Tang T, Sun X, Dong Y, Liu Q. Erythrobacter aureus sp. nov., a plant growth-promoting bacterium isolated from sediment in the Yellow Sea, China. 3 Biotech 2019; 9:430. [PMID: 31696035 PMCID: PMC6823416 DOI: 10.1007/s13205-019-1958-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/14/2019] [Indexed: 01/03/2023] Open
Abstract
The application of plant growth-promoting (PGP) bacterium in agriculture is expanding rapidly in recent years. With the development of microbial technology, new bacterial species effective in promoting plant growth have been identified. In this study, a PGP bacterium was isolated from marine sediments of the Yellow Sea in China. The confrontation culture test and pot experiments showed that strain YH-07T inhibited the growth of Fusarium oxysporum f. sp. lycopersici (a plant pathogenic fungus), benefiting plant growth and reducing disease incidence of tomato wilt. We used polyphasic approaches including phenotypic, chemotaxonomic and phylogenetic information to determine its taxonomic status. In addition to profiling general features of the YH-07T genome, we identified genes related to PGP traits and genes involved in environmental stress tolerance. Metabolic assays showed that strain YH-07T could produce siderophores, solubilize phosphate, resist to salinity, and grow well within a wide range of temperature and pH, which is a promising PGP bacterium for future agricultural applications. These results provide evidence that strain YH-07T is a novel species of the genus Erythrobacter, for which the name Erythrobacter aureus sp. nov. is proposed. The type strain is YH-07T (= CGMCC 1.16784T = DSM 107319T).
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Affiliation(s)
- Tongtong Tang
- Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 Jiangsu Province China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xing Sun
- School of Biological Science and Food Engineering, Chuzhou University, Chuzhou, 239000 China
| | - Yuanhua Dong
- Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 Jiangsu Province China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qin Liu
- Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 Jiangsu Province China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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Hu J, Ben Maamar S, Glawe AJ, Gottel N, Gilbert JA, Hartmann EM. Impacts of indoor surface finishes on bacterial viability. INDOOR AIR 2019; 29:551-562. [PMID: 30980566 PMCID: PMC6851865 DOI: 10.1111/ina.12558] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 04/08/2019] [Accepted: 04/09/2019] [Indexed: 05/21/2023]
Abstract
Microbes in indoor environments are constantly being exposed to antimicrobial surface finishes. Many are rendered non-viable after spending extended periods of time under low-moisture, low-nutrient surface conditions, regardless of whether those surfaces have been amended with antimicrobial chemicals. However, some microorganisms remain viable even after prolonged exposure to these hostile conditions. Work with specific model pathogens makes it difficult to draw general conclusions about how chemical and physical properties of surfaces affect microbes. Here, we explore the survival of a synthetic community of non-model microorganisms isolated from built environments following exposure to three chemically and physically distinct surface finishes. Our findings demonstrated the differences in bacterial survival associated with three chemically and physically distinct materials. Alkaline clay surfaces select for an alkaliphilic bacterium, Kocuria rosea, whereas acidic mold-resistant paint favors Bacillus timonensis, a Gram-negative spore-forming bacterium that also survives on antimicrobial surfaces after 24 hours of exposure. Additionally, antibiotic-resistant Pantoea allii did not exhibit prolonged retention on antimicrobial surfaces. Our controlled microcosm experiment integrates measurement of indoor chemistry and microbiology to elucidate the complex biochemical interactions that influence the indoor microbiome.
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Affiliation(s)
- Jinglin Hu
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
| | - Sarah Ben Maamar
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
| | - Adam J. Glawe
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
| | - Neil Gottel
- Department of SurgeryThe University of ChicagoChicagoIllinois
| | - Jack A. Gilbert
- Department of SurgeryThe University of ChicagoChicagoIllinois
| | - Erica M. Hartmann
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIllinois
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Zeidler S, Müller V. Coping with low water activities and osmotic stress in Acinetobacter baumannii: significance, current status and perspectives. Environ Microbiol 2019; 21:2212-2230. [PMID: 30773801 DOI: 10.1111/1462-2920.14565] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 01/26/2023]
Abstract
Multidrug resistant (MDR) pathogens are one of the most pressing challenges of contemporary health care. Acinetobacter baumannii takes a predominant position, emphasized in 2017 by the World Health Organization. The increasing emergence of MDR strains strengthens the demand for new antimicrobials. Possible targets for such compounds might be proteins involved in resistance against low water activity environments, since A. baumannii is known for its pronounced resistance against desiccation stress. Despite the importance of desiccation resistance for persistence of this pathogen in hospitals, comparable studies and precise data on this topic are rare and the mechanisms involved are largely unknown. This review aims to give an overview of the studies performed so far and the current knowledge on genes and proteins important for desiccation survival. 'Osmotic stress' is not identical to 'desiccation stress', but the two share the response of bacteria to low water activities. Osmotic stress resistance is in general studied much better, and in recent years it turned out that accumulation of compatible solutes in A. baumannii comprises some special features such as the bifunctional enzyme MtlD synthesizing the unusual solute mannitol. Furthermore, the regulatory pathways, as understood today, will be discussed.
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Affiliation(s)
- Sabine Zeidler
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt am Main, Germany
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Atieno M, Lesueur D. Opportunities for improved legume inoculants: enhanced stress tolerance of rhizobia and benefits to agroecosystems. Symbiosis 2018. [DOI: 10.1007/s13199-018-0585-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Zeidler S, Müller V. The role of compatible solutes in desiccation resistance of Acinetobacter baumannii. Microbiologyopen 2018; 8:e00740. [PMID: 30277310 PMCID: PMC6528591 DOI: 10.1002/mbo3.740] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 01/03/2023] Open
Abstract
Acinetobacter baumannii is a nosocomial pathogen which can persist in the hospital environment not only due to the acquirement of multiple antibiotic resistances, but also because of its exceptional resistance against disinfectants and desiccation. A suitable desiccation assay was established in which A. baumannii ATCC 19606T survived for ca. 1 month. The growth medium slightly influenced survival after subsequent desiccation. A significant effect could be attributed to the growth phase in which bacteria were dried: In exponential phase, cells were much more desiccation sensitive. The main focus of the present study was the elucidation of the role of compatible solutes, which are known to protect many bacteria under low water activity conditions, in desiccation survival of A. baumannii. Exogenous trehalose was shown to efficiently protect A. baumannii on dry surfaces, in contrast to other compatible solutes tested such as mannitol or glycine betaine. To analyze the importance of intracellularly accumulated solutes, a double mutant lacking biosynthesis pathways for mannitol and trehalose was generated. This mutant accumulated glutamate as sole solute in the presence of high NaCl concentrations and showed severe growth defects under osmotic stress conditions. However, no effect on desiccation tolerance could be seen, neither when cells were dried in water nor in the presence of NaCl.
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Affiliation(s)
- Sabine Zeidler
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
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32
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Multivariate optimization of a method for the determination of fatty acids in dental biofilm by GC-MS. Bioanalysis 2018; 10:1319-1333. [PMID: 30141343 DOI: 10.4155/bio-2018-0106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
AIM Phospholipid fatty acid methyl ester (FAME) analysis offers a simple option additionally to 16S rRNA sequencing to characterize microbial communities and to monitor changes. A method was established for the characterization of dental plaque via FAME profiles. METHODOLOGY Fatty acids were determined as FAMEs (direct, acidic transesterification) and analyzed by GC-MS using an optimized temperature gradient. The transesterification reaction was optimized using a fractional factorial central composite face-centered design. RESULTS Optimal conditions for the transesterification in methanol/toluene: hydrochloric acid concentration 2% (w/v), reaction time 40 min, temperature 110 °C. Method validation showed satisfactory accuracy, precision and linearity. CONCLUSION The method provides a useful tool to characterize plaque via FAME profiles and was successfully applied to samples from ten subjects demonstrating its applicability.
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Chen B, Feder ME, Kang L. Evolution of heat-shock protein expression underlying adaptive responses to environmental stress. Mol Ecol 2018; 27:3040-3054. [PMID: 29920826 DOI: 10.1111/mec.14769] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/03/2018] [Accepted: 06/07/2018] [Indexed: 12/27/2022]
Abstract
Heat-shock proteins (Hsps) and their cognates are primary mitigators of cell stress. With increasingly severe impacts of climate change and other human modifications of the biosphere, the ability of the heat-shock system to affect evolutionary fitness in environments outside the laboratory and to evolve in response is topic of growing importance. Since the last major reviews, several advances have occurred. First, demonstrations of the heat-shock response outside the laboratory now include many additional taxa and environments. Many of these demonstrations are only correlative, however. More importantly, technical advances in "omic" quantification of nucleic acids and proteins, genomewide association analysis, and manipulation of genes and their expression have enabled the field to move beyond correlation. Several consequent advances are already evident: The pathway from heat-shock gene expression to stress tolerance in nature can be extremely complex, mediated through multiple biological processes and systems, and even multiple species. The underlying genes are more numerous, diverse and variable than previously appreciated, especially with respect to their regulatory variation and epigenetic changes. The impacts and limitations (e.g., due to trade-offs) of natural selection on these genes have become more obvious and better established. At last, as evolutionary capacitors, Hsps may have distinctive impacts on the evolution of other genes and ecological consequences.
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Affiliation(s)
- Bing Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Martin E Feder
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Ricke SC, Dawoud TM, Kim SA, Park SH, Kwon YM. Salmonella Cold Stress Response: Mechanisms and Occurrence in Foods. ADVANCES IN APPLIED MICROBIOLOGY 2018; 104:1-38. [PMID: 30143250 DOI: 10.1016/bs.aambs.2018.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Since bacteria in foods often encounter various cold environments during food processing, such as chilling, cold chain distribution, and cold storage, lower temperatures can become a major stress environment for foodborne pathogens. Bacterial responses in stressful environments have been considered in the past, but now the importance of stress responses at the molecular level is becoming recognized. Documenting how bacterial changes occur at the molecular level may help to achieve the in-depth understanding of stress responses, to predict microbial fate when they encounter cold temperatures, and to design and develop more effective strategies to control pathogens in food for ensuring food safety. Microorganisms differ in responding to a sudden downshift in temperature and this, in turn, impacts their metabolic processes and can cause various structural modifications. In this review, the fundamental aspects of bacterial cold stress responses focused on cell membrane modification, DNA supercoiling modification, transcriptional and translational responses, cold-induced protein synthesis including CspA, CsdA, NusA, DnaA, RecA, RbfA, PNPase, KsgA, SrmB, trigger factors, and initiation factors are discussed. In this context, specific Salmonella responses to cold temperature including growth, injury, and survival and their physiological and genetic responses to cold environments with a focus on cross-protection, different gene expression levels, and virulence factors will be discussed.
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Affiliation(s)
- Steven C Ricke
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States.
| | - Turki M Dawoud
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Sun Ae Kim
- Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
| | - Si Hong Park
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Young Min Kwon
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States; Center for Food Safety, University of Arkansas, Fayetteville, AR, United States; Department of Poultry Science, University of Arkansas, Fayetteville, AR, United States
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Madueño L, Coppotelli B, Festa S, Alvarez H, Morelli I. Insights into the mechanisms of desiccation resistance of the Patagonian PAH-degrading strainSphingobiumsp. 22B. J Appl Microbiol 2018; 124:1532-1543. [DOI: 10.1111/jam.13742] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 02/09/2018] [Accepted: 02/16/2018] [Indexed: 01/05/2023]
Affiliation(s)
- L. Madueño
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
| | - B.M. Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
| | - S. Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
| | - H.M. Alvarez
- INBIOP (Instituto de Biociencias de la Patagonia); Consejo Nacional de Investigaciones Científicas y Técnicas; Facultad de Ciencias Naturales; Universidad Nacional de la Patagonia San Juan Bosco; Comodoro Rivadavia Chubut Argentina
| | - I.S. Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales; CINDEFI, (UNLP-CCT-La Plata, CONICET); La Plata Buenos Aires Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CIC-PBA); Buenos Aires Argentina
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Berninger T, González López Ó, Bejarano A, Preininger C, Sessitsch A. Maintenance and assessment of cell viability in formulation of non-sporulating bacterial inoculants. Microb Biotechnol 2018; 11:277-301. [PMID: 29205959 PMCID: PMC5812248 DOI: 10.1111/1751-7915.12880] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 09/11/2017] [Accepted: 10/08/2017] [Indexed: 01/20/2023] Open
Abstract
The application of beneficial, plant-associated microorganisms is a sustainable approach to improving crop performance in agriculture. However, microbial inoculants are often susceptible to prolonged periods of storage and deleterious environmental factors, which negatively impact their viability and ultimately limit efficacy in the field. This particularly concerns non-sporulating bacteria. To overcome this challenge, the availability of protective formulations is crucial. Numerous parameters influence the viability of microbial cells, with drying procedures generally being among the most critical ones. Thus, technological advances to attenuate the desiccation stress imposed on living cells are key to successful formulation development. In this review, we discuss the core aspects important to consider when aiming at high cell viability of non-sporulating bacteria to be applied as microbial inoculants in agriculture. We elaborate the suitability of commonly applied drying methods (freeze-drying, vacuum-drying, spray-drying, fluidized bed-drying, air-drying) and potential measures to prevent cell damage from desiccation (externally applied protectants, stress pre-conditioning, triggering of exopolysaccharide secretion, 'helper' strains). Furthermore, we point out methods for assessing bacterial viability, such as colony counting, spectrophotometry, microcalorimetry, flow cytometry and viability qPCR. Choosing appropriate technologies for maintenance of cell viability and evaluation thereof will render formulation development more efficient. This in turn will aid in utilizing the vast potential of promising, plant beneficial bacteria as sustainable alternatives to standard agrochemicals.
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Affiliation(s)
- Teresa Berninger
- AIT Austrian Institute of Technology GmbHCenter for Health and BioresourcesBioresources UnitKonrad‐Lorenz‐Straße 243430TullnAustria
| | - Óscar González López
- AIT Austrian Institute of Technology GmbHCenter for Health and BioresourcesBioresources UnitKonrad‐Lorenz‐Straße 243430TullnAustria
| | - Ana Bejarano
- AIT Austrian Institute of Technology GmbHCenter for Health and BioresourcesBioresources UnitKonrad‐Lorenz‐Straße 243430TullnAustria
| | - Claudia Preininger
- AIT Austrian Institute of Technology GmbHCenter for Health and BioresourcesBioresources UnitKonrad‐Lorenz‐Straße 243430TullnAustria
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbHCenter for Health and BioresourcesBioresources UnitKonrad‐Lorenz‐Straße 243430TullnAustria
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Immediate response mechanisms of Gram-negative solvent-tolerant bacteria to cope with environmental stress: cis-trans isomerization of unsaturated fatty acids and outer membrane vesicle secretion. Appl Microbiol Biotechnol 2018; 102:2583-2593. [PMID: 29450619 PMCID: PMC5847196 DOI: 10.1007/s00253-018-8832-9] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 11/03/2022]
Abstract
Bacteria have evolved an array of adaptive mechanisms enabling them to survive and grow in the presence of different environmental stresses. These mechanisms include either modifications of the membrane or changes in the overall energy status, cell morphology, and cell surface properties. Long-term adaptations are dependent on transcriptional regulation, the induction of anabolic pathways, and cell growth. However, to survive sudden environmental changes, bacterial short-term responses are essential to keep the cells alive after the occurrence of an environmental stress factor such as heat shock or the presence of toxic organic solvents. Thus far, two main short-term responses are known. On the one hand, a fast isomerization of cis into trans unsaturated fatty leads to a quick rigidification of the cell membrane, a mechanism known in some genera of Gram-negative bacteria. On the other hand, a fast, effective, and ubiquitously present countermeasure is the release of outer membrane vesicles (OMVs) from the cell surface leading to a rapid increase in cell surface hydrophobicity and finally to the formation of cell aggregates and biofilms. These immediate response mechanisms just allow the bacteria to stay physiologically active and to employ long-term responses to assure viability upon changing environmental conditions. Here, we provide insight into the two aforementioned rapid adaptive mechanisms affecting ultimately the cell envelope of Gram-negative bacteria.
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Esbelin J, Santos T, Hébraud M. Desiccation: An environmental and food industry stress that bacteria commonly face. Food Microbiol 2018; 69:82-88. [DOI: 10.1016/j.fm.2017.07.017] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 06/09/2017] [Accepted: 07/24/2017] [Indexed: 02/07/2023]
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Liang X, Yu X, Pan X, Wu J, Duan Y, Wang J, Zhou M. A thiadiazole reduces the virulence of Xanthomonas oryzae pv. oryzae by inhibiting the histidine utilization pathway and quorum sensing. MOLECULAR PLANT PATHOLOGY 2018; 19:116-128. [PMID: 27756112 PMCID: PMC6638098 DOI: 10.1111/mpp.12503] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 05/08/2023]
Abstract
Thiazole, isothiazole, thiadiazole and their derivatives are widely thought to induce host defences against plant pathogens. In this article, we report that bismerthiazol, a thiadiazole molecule, reduces disease by inhibiting the histidine utilization (Hut) pathway and quorum sensing (QS). Bismerthiazol provides excellent control of bacterial rice leaf blight (BLB) caused by Xanthomonas oryzae pv. oryzae (Xoo), but does not greatly inhibit Xoo growth in vitro. According to RNA-sequencing analysis, the transcription of the Hut pathway genes of Xoo ZJ173 was inhibited after 4.5 and 9.0 h of bismerthiazol treatment. Functional studies of hutG and hutU indicated that the Hut pathway had little effect on the growth and bismerthiazol sensitivity of Xoo in vitro, but significantly reduced the aggregation of Xoo cells. Deletion mutants of hutG or hutU were more motile, produced less biofilm and were less virulent than the wild-type, indicating that the Hut pathway is involved in QS and contributes to virulence. The overexpression of the hutG-U operons in ZJ173 reduced Xoo control by bismerthiazol. Bismerthiazol did not inhibit the transcription of Hut pathway genes, QS or virulence of the bismerthiazol-resistant strain 2-1-1. The results indicate that bismerthiazol reduces Xoo virulence by inhibiting the Hut pathway and QS.
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Affiliation(s)
- Xiaoyu Liang
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of PesticideJiangsu ProvinceNanjing210095China
| | - Xiaoyue Yu
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of PesticideJiangsu ProvinceNanjing210095China
| | - Xiayan Pan
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of PesticideJiangsu ProvinceNanjing210095China
| | - Jian Wu
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of PesticideJiangsu ProvinceNanjing210095China
| | - Yabing Duan
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of PesticideJiangsu ProvinceNanjing210095China
| | - Jianxin Wang
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of PesticideJiangsu ProvinceNanjing210095China
| | - Mingguo Zhou
- College of Plant Protection, Nanjing Agricultural University, Key Laboratory of PesticideJiangsu ProvinceNanjing210095China
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Zeidler S, Hubloher J, Schabacker K, Lamosa P, Santos H, Müller V. Trehalose, a temperature- and salt-induced solute with implications in pathobiology of Acinetobacter baumannii. Environ Microbiol 2017; 19:5088-5099. [PMID: 29124876 DOI: 10.1111/1462-2920.13987] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/03/2017] [Indexed: 01/01/2023]
Abstract
Acinetobacter baumannii is an opportunistic human pathogen that has become a global threat to healthcare institutions worldwide. A major factor contributing to success of this bacterium is its outstanding ability to survive on dry surfaces. The molecular basis for desiccation resistance is not completely understood. This study focused on growth under osmotic stress and aimed to identify the pool of compatible solutes synthesized in response to these low water activity conditions. A. baumannii produced mannitol as compatible solute, but in contrast to Acinetobacter baylyi, also trehalose was accumulated in response to increasing NaCl concentrations. The genome of A. baumannii encodes a trehalose-6-phosphate phosphatase (OtsB) and a trehalose-6-phosphate synthase (OtsA). Deletion of otsB abolished trehalose formation, demonstrating that otsB is essential for trehalose biosynthesis. Growth of the mutant was neither impaired at low salt nor at 500 mM NaCl, but it did not grow at high temperatures, indicating a dual function of trehalose in osmo- and thermoprotection. This led us to analyse temperature dependence of trehalose formation. Indeed, expression of otsB was not only induced by high osmolarity but also by high temperature. Concurrently, trehalose was accumulated in cells grown at high temperature. Taken together, these data point to an important role of trehalose in A. baumannii beyond osmoprotection.
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Affiliation(s)
- Sabine Zeidler
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Josephine Hubloher
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Kim Schabacker
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
| | - Pedro Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Germany
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Liu R, Chen C, Cheng L, Lu R, Fu G, Shi S, Chen H, Wan C, Lin J, Fu Q, Huang Y. Ducks as a potential reservoir for Pasteurella multocida infection detected using a new rOmpH-based ELISA. J Vet Med Sci 2017. [PMID: 28626158 PMCID: PMC5559375 DOI: 10.1292/jvms.17-0124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Pasteurella multocida is an important pathogen of numerous domestic poultry and wild animals and is associated with a variety of diseases including fowl cholera. The aim of this study was to develop an indirect
enzyme-linked immunosorbent assay (ELISA) based on recombinant outer-membrane protein H (rOmpH) for detection of anti-P. multocida antibodies in serum to determine their prevalence in Chinese ducks. The P.
multocida ompH gene was cloned into pET32a, and rOmpH was expressed in Escherichia coli BL21 (DE3). Western blotting revealed that purified rOmpH was recognized by duck antisera against P.
multocida, and an indirect ELISA was established. During analysis of serum samples (n=115) from ducks, the rOmpH ELISA showed 95.0% specificity, 100% sensitivity and a 92.0% κ coefficient (95%
confidence interval 0.844–0.997) as compared with a microtiter agglutination test. Among 165 randomly selected serum samples, which were collected in 2015 and originated from six duck farms across Fujian Province, China,
anti-P. multocida antibodies were detected in 22.42% of apparently healthy ducks, including 25 of 90 sheldrakes (27.8%), eight of 50 Peking ducks (16.0%) and four of 25 Muscovy ducks (16%). Overall, the data
suggest that rOmpH is a suitable candidate antigen for the development of an indirect ELISA for detection of P. multocida in ducks; moreover, our results showed that ducks could serve as a potential reservoir for
P. multocida infection.
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Affiliation(s)
- Rongchang Liu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Cuiteng Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Longfei Cheng
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Ronghui Lu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Guanghua Fu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Shaohua Shi
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Hongmei Chen
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Chunhe Wan
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Jiansheng Lin
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Qiuling Fu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
| | - Yu Huang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fujian Animal Diseases Control Technology Center, Fujian Provincial Key Laboratory for Avian Diseases Control and Prevention, Fuzhou 350013, China
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Zdarta A, Tracz J, Luczak M, Guzik U, Kaczorek E. Hydrocarbon-induced changes in proteins and fatty acids profiles of Raoultella ornithinolytica M03. J Proteomics 2017; 164:43-51. [DOI: 10.1016/j.jprot.2017.05.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/25/2017] [Accepted: 05/31/2017] [Indexed: 01/04/2023]
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Impact of Membrane Phospholipid Alterations in Escherichia coli on Cellular Function and Bacterial Stress Adaptation. J Bacteriol 2017; 199:JB.00849-16. [PMID: 28439040 DOI: 10.1128/jb.00849-16] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/20/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria have evolved multiple strategies to sense and rapidly adapt to challenging and ever-changing environmental conditions. The ability to alter membrane lipid composition, a key component of the cellular envelope, is crucial for bacterial survival and adaptation in response to environmental stress. However, the precise roles played by membrane phospholipids in bacterial physiology and stress adaptation are not fully elucidated. The goal of this study was to define the role of membrane phospholipids in adaptation to stress and maintenance of bacterial cell fitness. By using genetically modified strains in which the membrane phospholipid composition can be systematically manipulated, we show that alterations in major Escherichia coli phospholipids transform these cells globally. We found that alterations in phospholipids impair the cellular envelope structure and function, the ability to form biofilms, and bacterial fitness and cause phospholipid-dependent susceptibility to environmental stresses. This study provides an unprecedented view of the structural, signaling, and metabolic pathways in which bacterial phospholipids participate, allowing the design of new approaches in the investigation of lipid-dependent processes involved in bacterial physiology and adaptation.IMPORTANCE In order to cope with and adapt to a wide range of environmental conditions, bacteria have to sense and quickly respond to fluctuating conditions. In this study, we investigated the effects of systematic and controlled alterations in bacterial phospholipids on cell shape, physiology, and stress adaptation. We provide new evidence that alterations of specific phospholipids in Escherichia coli have detrimental effects on cellular shape, envelope integrity, and cell physiology that impair biofilm formation, cellular envelope remodeling, and adaptability to environmental stresses. These findings hold promise for future antibacterial therapies that target bacterial lipid biosynthesis.
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Orruño M, Kaberdin VR, Arana I. Survival strategies of Escherichia coli and Vibrio spp.: contribution of the viable but nonculturable phenotype to their stress-resistance and persistence in adverse environments. World J Microbiol Biotechnol 2017; 33:45. [PMID: 28161849 DOI: 10.1007/s11274-017-2218-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
In their natural ecosystems, bacteria are continuously exposed to changing environmental factors including physicochemical parameters (e.g. temperature, pH, etc.), availability of nutrients as well as interaction(s) with other organisms. To increase their tolerance and survival under adverse conditions, bacteria trigger a number of adaptation mechanisms. One of the well-known adaptation responses of the non-spore-forming bacteria is the acquisition of the viable but non-culturable (VBNC) state. This phenotype is induced by different stress factors (e.g. low temperature) and is characterized by the temporal loss of culturability, which can potentially be restored. Moreover, this response can be combined with the bust and boom strategy, which implies the death of the main population of the stressed cells (or their entry into the VBNC state) upon stress, thus enabling the remaining cells (i.e. residual culturable population) to subsist at the expense of the dead or/and VBNC cells. In this review, we discuss the characteristics of the VBNC state, its biological significance and contribution to bacterial survival.
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Affiliation(s)
- M Orruño
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/n, 48940, Leioa, Spain
| | - V R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/n, 48940, Leioa, Spain.,IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013, Bilbao, Spain
| | - I Arana
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country (UPV/EHU), Barrio Sarriena S/n, 48940, Leioa, Spain.
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Liu Z, Gao X, Wang H, Fang H, Yan Y, Liu L, Chen R, Zhou D, Yang R, Han Y. Plasmid pPCP1-derived sRNA HmsA promotes biofilm formation of Yersinia pestis. BMC Microbiol 2016; 16:176. [PMID: 27492011 PMCID: PMC4973556 DOI: 10.1186/s12866-016-0793-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/29/2016] [Indexed: 11/24/2022] Open
Abstract
Background The ability of Yersinia pestis to form a biofilm is an important characteristic in flea transmission of this pathogen. Y. pestis laterally acquired two plasmids (pPCP1and pMT1) and the ability to form biofilms when it evolved from Yersinia pseudotuberculosis. Small regulatory RNAs (sRNAs) are thought to play a crucial role in the processes of biofilm formation and pathogenesis. Results A pPCP1-derived sRNA HmsA (also known as sR084) was found to contribute to the enhanced biofilm formation phenotype of Y. pestis. The concentration of c-di-GMP was significantly reduced upon deletion of the hmsA gene in Y. pestis. The abundance of mRNA transcripts determining exopolysaccharide production, crucial for biofilm formation, was measured by primer extension, RT-PCR and lacZ transcriptional fusion assays in the wild-type and hmsA mutant strains. HmsA positively regulated biofilm synthesis-associated genes (hmsHFRS, hmsT and hmsCDE), but had no regulatory effect on the biofilm degradation-associated gene hmsP. Interestingly, the recently identified biofilm activator sRNA, HmsB, was rapidly degraded in the hmsA deletion mutant. Two genes (rovM and rovA) functioning as biofilm regulators were also found to be regulated by HmsA, whose regulatory effects were consistent with the HmsA-mediated biofilm phenotype. Conclusion HmsA potentially functions as an activator of biofilm formation in Y. pestis, implying that sRNAs encoded on the laterally acquired plasmids might be involved in the chromosome-based regulatory networks implicated in Y. pestis-specific physiological processes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0793-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zizhong Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,State Key Lab of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Xiaofang Gao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,Anhui Medical University, Hefei, Anhui, 230032, China
| | - Hongduo Wang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,College of Life Sciences, Anhui University, Hefei, Anhui, 230601, China
| | - Haihong Fang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Yanfeng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Lei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Rong Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.,The General Hospital of PLA, Beijing, 100853, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.
| | - Yanping Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, No. 20, Dongdajie, Fengtai, Beijing, 100071, China.
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Sundararaman N, Ash C, Guo W, Button R, Singh J, Feng X. iTAP: integrated transcriptomics and phenotype database for stress response of Escherichia coli and Saccharomyces cerevisiae. BMC Res Notes 2015; 8:771. [PMID: 26653323 PMCID: PMC4676837 DOI: 10.1186/s13104-015-1759-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 11/26/2015] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Organisms are subject to various stress conditions, which affect both the organism's gene expression and phenotype. It is critical to understand microbial responses to stress conditions and uncover the underlying molecular mechanisms. To this end, it is necessary to build a database that collects transcriptomics and phenotypic data of microbes growing under various stress factors for in-depth systems biology analysis. Despite of numerous databases that collect gene expression profiles, to our best knowledge, there are few, if any, databases that collect both transcriptomics and phenotype data simultaneously. In light of this, we have developed an open source, web-based database, namely integrated transcriptomics and phenotype (iTAP) database, that records and links the transcriptomics and phenotype data for two model microorganisms, Escherichia coli and Saccharomyces cerevisiae in response to exposure of various stress conditions. RESULTS To collect the data, we chose relevant research papers from the PubMed database containing all the necessary information for data curation including experimental conditions, transcriptomics data, and phenotype data. The transcriptomics data, including the p value and fold change, were obtained through the comparison of test strains against control strains using Gene Expression Omnibus's GEO2R analyzer. The phenotype data, including the cell growth rate and the productivity, volumetric rate, and mass-based yield of byproducts, were calculated independently from charts or graphs within the reference papers. Since the phenotype data was never reported in a standardized format, the curation of correlated transcriptomics-phenotype datasets became extremely tedious and time-consuming. Despite the challenges, till now, we successfully correlated 57 and 143 datasets of transcriptomics and phenotype for E. coli and S. cerevisiae, respectively, and applied a regression model within the iTAP database to accurately predict over 93 and 73 % of the growth rates of E. coli and S. cerevisiae, respectively, directly from the transcriptomics data. CONCLUSION This is the first time that transcriptomics and phenotype data are categorized and correlated in an open-source database. This allows biologists to access the database and utilize it to predict the phenotype of microorganisms from their transcriptomics data. The iTAP database is freely available at https://sites.google.com/a/vt.edu/biomolecular-engineering-lab/software .
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Affiliation(s)
- Niveda Sundararaman
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Christine Ash
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Weihua Guo
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Rebecca Button
- Commonwealth Governor's School, Fredericksburg, VA, 22407, USA.
| | - Jugroop Singh
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, 24061, USA.
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Ma H, Irudayanathan FJ, Jiang W, Nangia S. Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model. J Phys Chem B 2015; 119:14668-82. [DOI: 10.1021/acs.jpcb.5b07122] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Huilin Ma
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | | | - Wenjuan Jiang
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
| | - Shikha Nangia
- Department of Biomedical
and Chemical Engineering, Syracuse University, Syracuse, New York 13244, United States
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Maestre FT, Escolar C, Bardgett RD, Dungait JAJ, Gozalo B, Ochoa V. Warming reduces the cover and diversity of biocrust-forming mosses and lichens, and increases the physiological stress of soil microbial communities in a semi-arid Pinus halepensis plantation. Front Microbiol 2015; 6:865. [PMID: 26379642 PMCID: PMC4548238 DOI: 10.3389/fmicb.2015.00865] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/07/2015] [Indexed: 11/16/2022] Open
Abstract
Soil communities dominated by lichens and mosses (biocrusts) play key roles in maintaining ecosystem structure and functioning in drylands worldwide. However, few studies have explicitly evaluated how climate change-induced impacts on biocrusts affect associated soil microbial communities. We report results from a field experiment conducted in a semiarid Pinus halepensis plantation, where we setup an experiment with two factors: cover of biocrusts (low [<15%] versus high [>50%]), and warming (control versus a ∼2°C temperature increase). Warming reduced the richness and cover (∼45%) of high biocrust cover areas 53 months after the onset of the experiment. This treatment did not change the ratios between the major microbial groups, as measured by phospholipid fatty acid analysis. Warming increased the physiological stress of the Gram negative bacterial community, as indicated by the cy17:0/16:1ω7 ratio. This response was modulated by the initial biocrust cover, as the increase in this ratio with warming was higher in areas with low cover. Our findings suggest that biocrusts can slow down the negative effects of warming on the physiological status of the Gram negative bacterial community. However, as warming will likely reduce the cover and diversity of biocrusts, these positive effects will be reduced under climate change.
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Affiliation(s)
- Fernando T Maestre
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos Móstoles, Spain
| | - Cristina Escolar
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos Móstoles, Spain
| | | | - Jennifer A J Dungait
- Sustainable Soils and Grassland Systems Department, Rothamsted Research, North Wyke Okehampton, UK
| | - Beatriz Gozalo
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos Móstoles, Spain
| | - Victoria Ochoa
- Área de Biodiversidad y Conservación, Departamento de Biología y Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos Móstoles, Spain
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StressMicrobesInfo: Database of Microorganisms Responsive to Stress Conditions. Interdiscip Sci 2015; 8:203-8. [PMID: 26264053 DOI: 10.1007/s12539-015-0102-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 05/12/2015] [Accepted: 06/19/2015] [Indexed: 10/23/2022]
Abstract
Microorganisms are continuously exposed to numerous stress conditions and had evolved with numerous evolutionary adaptations and physiological acclimation mechanisms against stress effects. Any information related to the microbes responsive to stress conditions will help scientists working in the area of stress biology. Currently, there is lack of information resource on this aspect and for getting information about microbes susceptible or tolerant to different environmental changes, literature searching is the only option. Here, we present a database StressMicrobesInfo that was developed with a mandate to provide information about microbes responding to various biotic and abiotic stress conditions. This database currently contains information about 183 microbes along with a brief detail for each. StressMicrobesInfo will facilitate researchers working on stress-related microbes as a starting point and will facilitate them with the microbes which are susceptible or resistant towards particular stress conditions.
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Diomandé SE, Nguyen-The C, Guinebretière MH, Broussolle V, Brillard J. Role of fatty acids in Bacillus environmental adaptation. Front Microbiol 2015; 6:813. [PMID: 26300876 PMCID: PMC4525379 DOI: 10.3389/fmicb.2015.00813] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 07/23/2015] [Indexed: 11/23/2022] Open
Abstract
The large bacterial genus Bacillus is widely distributed in the environment and is able to colonize highly diverse niches. Some Bacillus species harbor pathogenic characteristics. The fatty acid (FA) composition is among the essential criteria used to define Bacillus species. Some elements of the FA pattern composition are common to Bacillus species, whereas others are specific and can be categorized in relation to the ecological niches of the species. Bacillus species are able to modify their FA patterns to adapt to a wide range of environmental changes, including changes in the growth medium, temperature, food processing conditions, and pH. Like many other Gram-positive bacteria, Bacillus strains display a well-defined FA synthesis II system that is equilibrated with a FA degradation pathway and regulated to efficiently respond to the needs of the cell. Like endogenous FAs, exogenous FAs may positively or negatively affect the survival of Bacillus vegetative cells and the spore germination ability in a given environment. Some of these exogenous FAs may provide a powerful strategy for preserving food against contamination by the Bacillus pathogenic strains responsible for foodborne illness.
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Affiliation(s)
- Sara E Diomandé
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Christophe Nguyen-The
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Marie-Hélène Guinebretière
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Véronique Broussolle
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France
| | - Julien Brillard
- INRA, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; Université d'Avignon, UMR408 Sécurité et Qualité des Produits d'Origine Végétale Avignon, France ; UMR 1333 DGIMI, INRA, Université de Montpellier Montpellier, France
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