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Sun M, Shao W, Liu Z, Ma X, Chen H, Zheng N, Zhao Y. Microbial diversity in camel milk from Xinjiang, China as revealed by metataxonomic analysis. Front Microbiol 2024; 15:1367116. [PMID: 38533337 PMCID: PMC10964795 DOI: 10.3389/fmicb.2024.1367116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
The quality of raw camel milk is affected by its bacterial composition and diversity. However, few studies have investigated the bacterial composition and diversity of raw camel milk. In this study, we obtained 20 samples of camel milk during spring and summer in Urumqi and Hami, Xinjiang, China. Single-molecule real-time sequencing technology was used to analyze the bacterial community composition. The results revealed that there were significant seasonal differences in the bacterial composition and diversity of camel milk. Overall, Epilithonimonas was the most abundant bacterial genus in our samples. Through the annotated genes inferred by PICRUSt2 were mapped against KEGG database. Non-parametric analysis of the bacterial community prediction function revealed a strong bacterial interdependence with metabolic pathways (81.83%). There were clear regional and seasonal differences in level 3 metabolic pathways such as fat, vitamins, and amino acids in camel milk. In addition, we identified lactic acid bacteria in camel milk with antibacterial and anti-tumor activities. Our findings revealed that camel milk from Xinjiang had serious risk of contamination by psychrophilic and pathogenic bacteria. Our research established a crucial theoretical foundation for ensuring the quality and safety of camel milk, thereby contributing significantly to the robust growth of China's camel milk industry.
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Affiliation(s)
- Miao Sun
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Wei Shao
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Zhengyu Liu
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- College of Animal Science Xinjiang Agriculture University, Urumqi, China
| | - Xianlan Ma
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
| | - He Chen
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yankun Zhao
- Institute of Quality Standards and Testing Technology for Agro-Products, Xinjiang Academy of Agricultural Sciences, Laboratory of Quality and Safety Risk Assessment for Agro-products, Ministry of Agriculture, Urumqi, China
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Marietou A, Schmidt JS, Rasmussen MR, Scoma A, Rysgaard S, Vergeynst L. The effect of hydrostatic pressure on the activity and community composition of hydrocarbon-degrading bacteria in Arctic seawater. Appl Environ Microbiol 2023; 89:e0098723. [PMID: 37943057 PMCID: PMC10686064 DOI: 10.1128/aem.00987-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE Increased ship traffic in the Arctic region raises the risk of oil spills. With an average sea depth of 1,000 m, there is a growing concern over the potential release of oil sinking in the form of marine oil snow into deep Arctic waters. At increasing depth, the oil-degrading community is exposed to increasing hydrostatic pressure, which can reduce microbial activity. However, microbes thriving in polar regions may adapt to low temperature by modulation of membrane fluidity, which is also a well-known adaptation to high hydrostatic pressure. At mild hydrostatic pressures up to 8-12 MPa, we did not observe an altered microbial activity or community composition, whereas comparable studies using deep-sea or sub-Arctic microbial communities with in situ temperatures of 4-5°C showed pressure-induced effects at 10-15 MPa. Our results suggest that the psychrophilic nature of the underwater microbial communities in the Arctic may be featured by specific traits that enhance their fitness at increasing hydrostatic pressure.
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Affiliation(s)
- Angeliki Marietou
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | | | - Martin R. Rasmussen
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
| | - Alberto Scoma
- Department of Biology, Section for Microbiology, Aarhus University, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Søren Rysgaard
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Leendert Vergeynst
- Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
- Arctic Research Centre, Department of Biology, Aarhus University, Aarhus, Denmark
- Centre for Water Technology (WATEC), Aarhus University, Aarhus, Denmark
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Shaffer JMC, Giddings LA, Samples RM, Mikucki JA. Genomic and phenotypic characterization of a red-pigmented strain of Massilia frigida isolated from an Antarctic microbial mat. Front Microbiol 2023; 14:1156033. [PMID: 37250028 PMCID: PMC10213415 DOI: 10.3389/fmicb.2023.1156033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/31/2023] Open
Abstract
The McMurdo Dry Valleys of Antarctica experience a range of selective pressures, including extreme seasonal variation in temperature, water and nutrient availability, and UV radiation. Microbial mats in this ecosystem harbor dense concentrations of biomass in an otherwise desolate environment. Microbial inhabitants must mitigate these selective pressures via specialized enzymes, changes to the cellular envelope, and the production of secondary metabolites, such as pigments and osmoprotectants. Here, we describe the isolation and characterization of a Gram-negative, rod-shaped, motile, red-pigmented bacterium, strain DJPM01, from a microbial mat within the Don Juan Pond Basin of Wright Valley. Analysis of strain DJMP01's genome indicates it can be classified as a member of the Massilia frigida species. The genome contains several genes associated with cold and salt tolerance, including multiple RNA helicases, protein chaperones, and cation/proton antiporters. In addition, we identified 17 putative secondary metabolite gene clusters, including a number of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides (RiPPs), among others, and the biosynthesis pathway for the antimicrobial pigment prodigiosin. When cultivated on complex agar, multiple prodiginines, including the antibiotic prodigiosin, 2-methyl-3-propyl-prodiginine, 2-methyl-3-butyl-prodiginine, 2-methyl-3-heptyl-prodiginine, and cycloprodigiosin, were detected by LC-MS. Genome analyses of sequenced members of the Massilia genus indicates prodigiosin production is unique to Antarctic strains. UV-A radiation, an ecological stressor in the Antarctic, was found to significantly decrease the abundance of prodiginines produced by strain DJPM01. Genomic and phenotypic evidence indicates strain DJPM01 can respond to the ecological conditions of the DJP microbial mat, with prodiginines produced under a range of conditions, including extreme UV radiation.
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Affiliation(s)
- Jacob M. C. Shaffer
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
| | | | - Robert M. Samples
- Department of Chemistry, Smith College, Northampton, MA, United States
| | - Jill A. Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, United States
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Hwang J, Park SH, Lee CW, Do H, Shin SC, Kim HW, Lee SG, Park HH, Kwon S, Lee JH. Crystal structure of a MarR family protein from the psychrophilic bacterium Paenisporosarcina sp. TG-14 in complex with a lipid-like molecule. IUCrJ 2021; 8:842-852. [PMID: 34584745 PMCID: PMC8420766 DOI: 10.1107/s2052252521005704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
MarR family proteins regulate the transcription of multiple antibiotic-resistance genes and are widely found in bacteria and archaea. Recently, a new MarR family gene was identified by genome analysis of the psychrophilic bacterium Paenisporosarcina sp. TG-14, which was isolated from sediment-laden basal ice in Antarctica. In this study, the crystal structure of the MarR protein from Paenisporosarcina sp. TG-14 (PaMarR) was determined at 1.6 Å resolution. In the crystal structure, a novel lipid-type compound (palmitic acid) was found in a deep cavity, which was assumed to be an effector-binding site. Comparative structural analysis of homologous MarR family proteins from a mesophile and a hyperthermophile showed that the DNA-binding domain of PaMarR exhibited relatively high mobility, with a disordered region between the β1 and β2 strands. In addition, structural comparison with other homologous complex structures suggests that this structure constitutes a conformer transformed by palmitic acid. Biochemical analysis also demonstrated that PaMarR binds to cognate DNA, where PaMarR is known to recognize two putative binding sites depending on its molar concentration, indicating that PaMarR binds to its cognate DNA in a stoichiometric manner. The present study provides structural information on the cold-adaptive MarR protein with an aliphatic compound as its putative effector, extending the scope of MarR family protein research.
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Affiliation(s)
- Jisub Hwang
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Sun-Ha Park
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Chang Woo Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Seung Chul Shin
- Division of Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Han-Woo Kim
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Sung Gu Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Sunghark Kwon
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk 27478, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Republic of Korea
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Ali P, Fucich D, Shah AA, Hasan F, Chen F. Cryopreservation of Cyanobacteria and Eukaryotic Microalgae Using Exopolysaccharide Extracted from a Glacier Bacterium. Microorganisms 2021; 9:395. [PMID: 33671910 DOI: 10.3390/microorganisms9020395] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Abstract
Exopolysaccharide (EPS) has been known to be a good cryoprotective agent for bacteria, but it has not been tested for cyanobacteria and eukaryotic microalgae. In this study, we used EPS extracted from a glacier bacterium as a cryoprotective agent for the cryopreservation of three unicellular cyanobacteria and two eukaryotic microalgae. Different concentrations of EPS (10%, 15%, and 20%) were tested, and the highest concentration (20%) of EPS yielded the best growth recovery for the algal strains we tested. We also compared EPS with 5% dimethyl sulfoxide (DMSO) and 10% glycerol for the cryopreservation recovery. The growth recovery for the microalgal strains after nine months of cryopreservation was better than 5% DMSO, a well-known cryoprotectant for microalgae. A poor recovery was recorded for all the tested strains with 10% glycerol as a cryoprotective agent. The patterns of growth recovery for most of these strains were similar after 5 days, 15 days, and 9 months of cryopreservation. Unlike common cryopreservants such as DMSO or methanol, which are hazardous materials, EPS is safe to handle. We demonstrate that the EPS from a psychrotrophic bacterium helped in the long-term cryopreservation of cyanobacteria and microalgae, and it has the potential to be used as natural cryoprotective agent for other cells.
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Hassan N, Anesio AM, Rafiq M, Holtvoeth J, Bull I, Haleem A, Shah AA, Hasan F. Temperature Driven Membrane Lipid Adaptation in Glacial Psychrophilic Bacteria. Front Microbiol 2020; 11:824. [PMID: 32477293 PMCID: PMC7240044 DOI: 10.3389/fmicb.2020.00824] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/07/2020] [Indexed: 11/30/2022] Open
Abstract
Bacteria inhabiting non-polar glaciers are exposed to large variations in temperature, which significantly affects the fluidity of bacterial cell membranes. In order to maintain normal functions of the cell membranes, psychrophilic bacteria adapt by changing the composition of cell membrane fatty acids. However, information on the exact pattern of cell membrane adaptability in non-polar low-temperature habitats is scarce. In the present study, 42 bacterial strains were isolated from the Ghulmet, Ghulkin, and Hopar glaciers of the Hunza Valley in the Karakoram Mountain Range, Pakistan and their cell membrane fatty acid distributions studied, using gas chromatography/mass spectrometry (GC-MS) for the analysis of fatty acid methyl esters (FAMEs) liberated by acid-catalyzed methanolysis. Furthermore, Gram-negative and Gram-positive groups were grown under different temperature settings (5, 15, 25, and 35°C) in order to determine the effect of temperature on cell membrane (CM) fatty acid distribution. The analyses identified the major groups of cell membrane fatty acids (FA) as straight-chain monounsaturated fatty acids (n-MUFAs) and branched fatty acids (br-FAs), accounting for more than 70% of the fatty acids analyzed. The distribution of br-FAs and n-FAs in bacterial cell membranes was significantly affected by temperature, with the level of br-FAs decreasing relative to n-FAs with increasing temperature. Notably, the production of polyunsaturated fatty acids (PUFAs) was only seen at lower temperatures. This study contributes to understanding, for the first time, the role of br-FAs in the maintenance of cell membrane fluidity of bacteria inhabiting non-polar habitats.
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Affiliation(s)
- Noor Hassan
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
- Bristol Glaciology Centre, School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, United Kingdom
| | | | - Muhammad Rafiq
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
- Bristol Glaciology Centre, School of Geographical Sciences, Faculty of Science, University of Bristol, Bristol, United Kingdom
- Department of Microbiology, Balochistan University of Information Technology, Engineering and Management Sciences, Quetta, Pakistan
| | - Jens Holtvoeth
- Organic Geochemistry Unit, School of Chemistry, Cantock’s Close, University of Bristol, Bristol, United Kingdom
| | - Ian Bull
- Organic Geochemistry Unit, School of Chemistry, Cantock’s Close, University of Bristol, Bristol, United Kingdom
| | - Abdul Haleem
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Aamer Ali Shah
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fariha Hasan
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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Bazhenov SV, Khrulnova SA, Konopleva MN, Manukhov IV. Seasonal changes in luminescent intestinal microflora of the fish inhabiting the Bering and Okhotsk seas. FEMS Microbiol Lett 2019; 366:5322163. [PMID: 30772893 DOI: 10.1093/femsle/fnz040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/15/2019] [Indexed: 11/14/2022] Open
Abstract
Here, we present a study of luminescent intestinal microflora of the fish inhabiting Bering and Okhotsk seas in summer and winter seasons. Sampling of intestinal luminescent microflora was carried for several years, with all recovered species belonging to psychrophilic bacteria of either Aliivibrio logei or Photobacterium phosphoreum species. A seasonal change in fish intestinal luminescent microflora detected include an increase in prevalence of P. phosphoreum bacteria in summer and an increase in prevalence of A. logei bacteria in winter seasons. In fact, 90% of all luminescent bacteria isolated in winter period (January-March) were A. logei, while 88% of luminescent isolates recovered in summer period (July-September) were that of P. phosphoreum species. Seasonal changes were similar across all six sampling expeditions, three in winter and three in summer seasons, evenly spread through 2010-2018 period.
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Affiliation(s)
- Sergey V Bazhenov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation.,State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
| | - Svetlana A Khrulnova
- State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
| | - Maria N Konopleva
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - Ilya V Manukhov
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation.,State Research Institute of Genetics and Selection of Industrial Microorganisms of the National Research Center "Kurchatov Institute", 1st Dorozhnii pr., 1, Moscow 117545, Russian Federation
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Michalska M, Wąż P, Zorena K, Bartoszewicz M, Korzeniowska K, Krawczyk S, Beń-Skowronek I, Myśliwiec M. Potential effects of microbial air quality on the number of new cases of diabetes type 1 in children in two regions of Poland: a pilot study. Infect Drug Resist 2019; 12:2323-2334. [PMID: 31534351 PMCID: PMC6681153 DOI: 10.2147/idr.s207138] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/12/2019] [Indexed: 12/15/2022] Open
Abstract
Aim: The aim of the study was to investigate the relationship between the concentration of psychrophilic bacteria, mesophilic bacteria and mold fungi in bioaerosols, and the number of new cases of type 1 diabetes mellitus (T1DM) in children. Methods: Air samples from the Lubelskie and Pomeranian voivodeships in Poland were collected from January 2015 to December 2016 in winter, spring, summer and autumn. Thirty-three samples were collected in the Pomeranian and 27 in the Lubelskie voivodeship. The air samples were collected on the first day of each month at 1:00 pm for 10 mins at a height of 1.5 m above the ground. The number of mesophilic bacteria was detected after 24-48 hrs incubation at 37°C on tryptone soya agar (TSA; Merck, Darmstadt, Germany). The number of psychrophilic bacteria was detected after 72 hrs incubation at 22°C on TSA. The number of fungi was detected by a 5-day long incubation at 28°C on chloramphenicol yeast glucose agar. Results: In the Lubelskie voivodeship, the mean concentration of psychrophilic bacteria was significantly higher than in the Pomeranian voivodeship (2739 vs 608 CFU/m3, respectively), the mean concentration of mesophilic bacteria was significantly higher (2493 vs 778/m3, respectively) and the concentration of fungi was significantly higher (3840 vs 688 CFU/m3, respectively). We also showed a statistically significant relationship between the number of children with recently diagnosed T1DM and the mean concentration of psychrophilic and mesophilic bacteria in the Pomeranian and Lubelskie voivodeships (P<0.001). Moreover, we found a significant relationship between the number of new cases of T1DM in children and the mean concentration of fungi in bioaerosols in the Lubelskie voivodeship (P<0.001), but not in the Pomeranian voivodeship (P=NS). Conclusion: The results of our research showed that there is a higher concentration of microbial particles in the Lublin voivodeship. Therefore, we recommend changes in climate for children (trips to the sea, mountains, etc) as often as possible.
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Affiliation(s)
- Małgorzata Michalska
- Department of Immunobiology and Environment Microbiology, Faculty of Health Sciences, Medical University of Gdańsk, Gdańsk, Poland
| | - Piotr Wąż
- Department of Nuclear Medicine, Faculty of Health Sciences, Medical University of Gdańsk, Gdańsk, Poland
| | - Katarzyna Zorena
- Department of Immunobiology and Environment Microbiology, Faculty of Health Sciences, Medical University of Gdańsk, Gdańsk, Poland
| | - Maria Bartoszewicz
- Department of Immunobiology and Environment Microbiology, Faculty of Health Sciences, Medical University of Gdańsk, Gdańsk, Poland
| | - Katarzyna Korzeniowska
- Clinic of Pediatrics, Diabetology and Endocrinology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Sylwia Krawczyk
- Department of Pediatric Endocrinology and Diabetology, Faculty of Medicine, Medical University of Lublin, Lublin, Poland
| | - Iwona Beń-Skowronek
- Department of Pediatric Endocrinology and Diabetology, Faculty of Medicine, Medical University of Lublin, Lublin, Poland
| | - Małgorzata Myśliwiec
- Clinic of Pediatrics, Diabetology and Endocrinology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
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Hilgarth M, Fuertes-Pèrez S, Ehrmann M, Vogel RF. An adapted isolation procedure reveals Photobacterium spp. as common spoilers on modified atmosphere packaged meats. Lett Appl Microbiol 2018; 66:262-267. [PMID: 29419881 DOI: 10.1111/lam.12860] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 11/27/2022]
Abstract
The genus Photobacterium comprises species of marine bacteria, commonly found in open-ocean and deep-sea environments. Some species (e.g. Photobacterium phosphoreum) are associated with fish spoilage. Recently, culture-independent studies have drawn attention to the presence of photobacteria on meat. This study employed a comparative isolation approach of Photobacterium spp. and aimed to develop an adapted isolation procedure for recovery from food samples, as demonstrated for different meats: Marine broth is used for resuspending and dilution of food samples, followed by aerobic cultivation on marine broth agar supplemented with meat extract and vancomycin at 15°C for 72 h. Identification of spoilage-associated microbiota was carried out via Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry using a database supplemented with additional mass spectrometry profiles of Photobacterium spp. This study provides evidence for the common abundance of multiple Photobacterium species in relevant quantities on various modified atmosphere packaged meats. Photobacterium carnosum was predominant on beef and chicken, while Photobacterium iliopiscarium represented the major species on pork and Photobacterium phosphoreum on salmon, respectively. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates highly frequent isolation of multiple photobacteria (Photobacterium carnosum, Photobacterium phosphoreum, and Photobacterium iliopiscarium) from different modified-atmosphere packaged spoiled and unspoiled meats using an adapted isolation procedure. The abundance of photobacteria in high numbers provides evidence for the hitherto neglected importance and relevance of Photobacterium spp. to meat spoilage.
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Affiliation(s)
- M Hilgarth
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - S Fuertes-Pèrez
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - M Ehrmann
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
| | - R F Vogel
- Lehrstuhl Technische Mikrobiologie, Technische Universität München, Freising, Germany
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10
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Rondón J, Gómez W, Ball MM, Melfo A, Rengifo M, Balcázar W, Dávila-Vera D, Balza-Quintero A, Mendoza-Briceño RV, Yarzábal LA. Diversity of culturable bacteria recovered from Pico Bolívar's glacial and subglacial environments, at 4950 m, in Venezuelan tropical Andes. Can J Microbiol 2016; 62:904-917. [PMID: 27564086 DOI: 10.1139/cjm-2016-0172] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Even though tropical glaciers are retreating rapidly and many will disappear in the next few years, their microbial diversity remains to be studied in depth. In this paper we report on the biodiversity of the culturable fraction of bacteria colonizing Pico Bolívar's glacier ice and subglacial meltwaters, at ∼4950 m in the Venezuelan Andean Mountains. Microbial cells of diverse morphologies and exhibiting uncompromised membranes were present at densities ranging from 1.5 × 104 to 4.7 × 104 cells/mL in glacier ice and from 4.1 × 105 to 9.6 × 105 cells/mL in subglacial meltwater. Of 89 pure isolates recovered from the samples, the majority were eurypsychrophilic or stenopsychrophilic, according to their temperature range of growth. Following analysis of their 16S rDNA nucleotidic sequence, 54 pure isolates were assigned to 23 phylotypes distributed within 4 different phyla or classes: Beta- and Gammaproteobacteria, Actinobacteria, and Bacteroidetes. Actinobacteria dominated the culturable fraction of glacier ice samples, whereas Proteobacteria were dominant in subglacial meltwater samples. Chloramphenicol and ampicillin resistance was exhibited by 73.07% and 65.38%, respectively, of the subglacial isolates, and nearly 35% of them were multiresistant. Considering the fast rate at which tropical glaciers are melting, this study confirms the urgent need to study the microbial communities immured in such environments.
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Affiliation(s)
- Johnma Rondón
- a Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias, Núcleo de La Hechicera, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida 5101, Estado Mérida, Venezuela
| | - Wileidy Gómez
- a Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias, Núcleo de La Hechicera, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida 5101, Estado Mérida, Venezuela
| | - María M Ball
- a Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias, Núcleo de La Hechicera, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida 5101, Estado Mérida, Venezuela
| | - Alejandra Melfo
- b Centro de Física Fundamental, Facultad de Ciencias, Núcleo de La Hechicera, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida 5101, Estado Mérida, Venezuela
| | - Marcos Rengifo
- a Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias, Núcleo de La Hechicera, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida 5101, Estado Mérida, Venezuela
| | - Wilvis Balcázar
- a Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias, Núcleo de La Hechicera, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida 5101, Estado Mérida, Venezuela
| | - Delsy Dávila-Vera
- c Centro de Microscopía Electrónica Dr. Ernesto Palacios Prü, Vicerrectorado Académico, Universidad de Los Andes, Av. Tulio Febres Cordero, Mérida 5101, Estado Mérida, Venezuela
| | - Alirio Balza-Quintero
- c Centro de Microscopía Electrónica Dr. Ernesto Palacios Prü, Vicerrectorado Académico, Universidad de Los Andes, Av. Tulio Febres Cordero, Mérida 5101, Estado Mérida, Venezuela
| | - Rosa Virginia Mendoza-Briceño
- c Centro de Microscopía Electrónica Dr. Ernesto Palacios Prü, Vicerrectorado Académico, Universidad de Los Andes, Av. Tulio Febres Cordero, Mérida 5101, Estado Mérida, Venezuela
| | - Luis Andrés Yarzábal
- a Laboratorio de Microbiología Molecular y Biotecnología, Facultad de Ciencias, Núcleo de La Hechicera, Universidad de Los Andes, Av. Alberto Carnevalli, Mérida 5101, Estado Mérida, Venezuela.,d Laboratorio de Biología Molecular, Carrera de Ingeniería Agronómica, Facultad de Ciencias Agropecuarias, Universidad de Cuenca, Av. 12 de Octubre, Cuenca, Ecuador
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11
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Cid FP, Rilling JI, Graether SP, Bravo LA, Mora MDLL, Jorquera MA. Properties and biotechnological applications of ice-binding proteins in bacteria. FEMS Microbiol Lett 2016; 363:fnw099. [PMID: 27190285 DOI: 10.1093/femsle/fnw099] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2016] [Indexed: 01/04/2023] Open
Abstract
Ice-binding proteins (IBPs), such as antifreeze proteins (AFPs) and ice-nucleating proteins (INPs), have been described in diverse cold-adapted organisms, and their potential applications in biotechnology have been recognized in various fields. Currently, both IBPs are being applied to biotechnological processes, primarily in medicine and the food industry. However, our knowledge regarding the diversity of bacterial IBPs is limited; few studies have purified and characterized AFPs and INPs from bacteria. Phenotypically verified IBPs have been described in members belonging to Gammaproteobacteria, Actinobacteria and Flavobacteriia classes, whereas putative IBPs have been found in Gammaproteobacteria, Alphaproteobacteria and Bacilli classes. Thus, the main goal of this minireview is to summarize the current information on bacterial IBPs and their application in biotechnology, emphasizing the potential application in less explored fields such as agriculture. Investigations have suggested the use of INP-producing bacteria antagonists and AFPs-producing bacteria (or their AFPs) as a very attractive strategy to prevent frost damages in crops. UniProt database analyses of reported IBPs (phenotypically verified) and putative IBPs also show the limited information available on bacterial IBPs and indicate that major studies are required.
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Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile
| | - Joaquín I Rilling
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco 4811230, Chile
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Leon A Bravo
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco 4811230, Chile
| | - María de La Luz Mora
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Milko A Jorquera
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
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12
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Li J, Hu Q, Li Y, Xu Y. Purification and characterization of cold-adapted beta-agarase from an Antarctic psychrophilic strain. Braz J Microbiol 2015; 46:683-90. [PMID: 26413048 PMCID: PMC4568857 DOI: 10.1590/s1517-838246320131289] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 11/28/2014] [Indexed: 11/22/2022] Open
Abstract
An extracellular β-agarase was purified from Pseudoalteromonas sp. NJ21, a Psychrophilic agar-degrading bacterium isolated from Antarctic Prydz Bay sediments. The purified agarase (Aga21) revealed a single band on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, with an apparent molecular weight of 80 kDa. The optimum pH and temperature of the agarase were 8.0 and 30 °C, respectively. However, it maintained as much as 85% of the maximum activities at 10 °C. Significant activation of the agarase was observed in the presence of Mg(2+), Mn(2+), K(+); Ca(2+), Na(+), Ba(2+), Zn(2+), Cu(2+), Co(2+), Fe(2+), Sr(2+) and EDTA inhibited the enzyme activity. The enzymatic hydrolyzed product of agar was characterized as neoagarobiose. Furthermore, this work is the first evidence of cold-adapted agarase in Antarctic psychrophilic bacteria and these results indicate the potential for the Antarctic agarase as a catalyst in medicine, food and cosmetic industries.
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Affiliation(s)
- Jiang Li
- Key Laboratory of Marine Bioactive Substances, The First Institute of
Oceanography, Qingdao, China
| | - Qiushi Hu
- College of Chemical Engineering, Qingdao University of Science &
Technology, Qingdao, China
| | - Yuquan Li
- Marine Science and Engineering College, Qingdao Agriculture University,
Qingdao, China
| | - Yuan Xu
- Marine Science and Engineering College, Qingdao Agriculture University,
Qingdao, China
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13
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Feng S, Powell SM, Wilson R, Bowman JP. Extensive gene acquisition in the extremely psychrophilic bacterial species Psychroflexus torquis and the link to sea-ice ecosystem specialism. Genome Biol Evol 2014; 6:133-48. [PMID: 24391155 PMCID: PMC3914696 DOI: 10.1093/gbe/evt209] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Sea ice is a highly dynamic and productive environment that includes a diverse array of psychrophilic prokaryotic and eukaryotic taxa distinct from the underlying water column. Because sea ice has only been extensive on Earth since the mid-Eocene, it has been hypothesized that bacteria highly adapted to inhabit sea ice have traits that have been acquired through horizontal gene transfer (HGT). Here we compared the genomes of the psychrophilic bacterium Psychroflexus torquis ATCC 700755T, associated with both Antarctic and Arctic sea ice, and its closely related nonpsychrophilic sister species, P. gondwanensis ACAM 44T. Results show that HGT has occurred much more extensively in P. torquis in comparison to P. gondwanensis. Genetic features that can be linked to the psychrophilic and sea ice-specific lifestyle of P. torquis include genes for exopolysaccharide (EPS) and polyunsaturated fatty acid (PUFA) biosynthesis, numerous specific modes of nutrient acquisition, and proteins putatively associated with ice-binding, light-sensing (bacteriophytochromes), and programmed cell death (metacaspases). Proteomic analysis showed that several genes associated with these traits are highly translated, especially those involved with EPS and PUFA production. Because most of the genes relating to the ability of P. torquis to dwell in sea-ice ecosystems occur on genomic islands that are absent in closely related P. gondwanensis, its adaptation to the sea-ice environment appears driven mainly by HGT. The genomic islands are rich in pseudogenes, insertional elements, and addiction modules, suggesting that gene acquisition is being followed by a process of genome reduction potentially indicative of evolving ecosystem specialism.
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Affiliation(s)
- Shi Feng
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Australia
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14
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Malecki PH, Raczynska JE, Vorgias CE, Rypniewski W. Structure of a complete four-domain chitinase from Moritella marina, a marine psychrophilic bacterium. Acta Crystallogr D Biol Crystallogr 2013; 69:821-9. [PMID: 23633591 DOI: 10.1107/s0907444913002011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022]
Abstract
X-ray crystallography reveals chitinase from the psychrophilic bacterium Moritella marina to be an elongated molecule which in addition to the catalytic β/α-barrel domain contains two Ig-like domains and a chitin-binding domain, all linked in a chain. A ligand-binding study using NAG oligomers showed the enzyme to be active in the crystal lattice and resulted in complexes of the protein with oxazolinium ion (the reaction intermediate) and with NAG2, a reaction product. The characteristic motif DXDXE, containing three acidic amino-acid residues, which is a signature of type 18 chitinases, is conserved in the enzyme. Further analysis of the unliganded enzyme with the two protein-ligand complexes and a comparison with other known chitinases elucidated the roles of other conserved residues near the active site. Several features have been identified that are probably important for the reaction mechanism, substrate binding and the efficiency of the enzyme at low temperatures. The chitin-binding domain and the tryptophan patch on the catalytic domain provide general affinity for chitin, in addition to the affinity of the binding site; the two Ig-like domains give the protein a long reach over the chitin surface, and the flexible region between the chitin-binding domain and the adjacent Ig-like domain suggests an ability of the enzyme to probe the surface of the substrate, while the open shallow substrate-binding groove allows easy access to the active site.
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Affiliation(s)
- Piotr H Malecki
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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15
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Do H, Lee JH, Lee SG, Kim HJ. Crystallization and preliminary X-ray crystallographic analysis of an ice-binding protein (FfIBP) from Flavobacterium frigoris PS1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:806-9. [PMID: 22750870 PMCID: PMC3388927 DOI: 10.1107/s1744309112020465] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 05/07/2012] [Indexed: 11/10/2022]
Abstract
Ice growth in a cold environment is fatal for polar organisms, not only because of the physical destruction of inner cell organelles but also because of the resulting chemical damage owing to processes such as osmotic shock. The properties of ice-binding proteins (IBPs), which include antifreeze proteins (AFPs), have been characterized and IBPs exhibit the ability to inhibit ice growth by binding to specific ice planes and lowering the freezing point. An ice-binding protein (FfIBP) from the Gram-negative bacterium Flavobacterium frigoris PS1, which was isolated from the Antarctic, has recently been overexpressed. Interestingly, the thermal hysteresis activity of FfIBP was approximately 2.5 K at 50 µM, which is ten times higher than that of the moderately active IBP from Arctic yeast (LeIBP). Although FfIBP closely resembles LeIBP in its amino-acid sequence, the antifreeze activity of FfIBP appears to be much greater than that of LeIBP. In an effort to understand the reason for this difference, an attempt was made to solve the crystal structure of FfIBP. Here, the crystallization and X-ray diffraction data of FfIBP are reported. FfIBP was crystallized using the hanging-drop vapour-diffusion method with 0.1 M sodium acetate pH 4.4 and 3 M sodium chloride as precipitant. A complete diffraction data set was collected to a resolution of 2.9 Å. The crystal belonged to space group P4(1)22, with unit-cell parameters a = b = 69.4, c = 178.2 Å. The asymmetric unit contained one monomer.
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Affiliation(s)
- Hackwon Do
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea
| | - Jun Hyuck Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea
| | - Sung Gu Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea
| | - Hak Jun Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 406-840, Republic of Korea
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16
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Chin JP, Megaw J, Magill CL, Nowotarski K, Williams JP, Bhaganna P, Linton M, Patterson MF, Underwood GJC, Mswaka AY, Hallsworth JE. Solutes determine the temperature windows for microbial survival and growth. Proc Natl Acad Sci U S A 2010; 107:7835-40. [PMID: 20404182 PMCID: PMC2867857 DOI: 10.1073/pnas.1000557107] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbial cells, and ultimately the Earth's biosphere, function within a narrow range of physicochemical conditions. For the majority of ecosystems, productivity is cold-limited, and it is microbes that represent the failure point. This study was carried out to determine if naturally occurring solutes can extend the temperature windows for activity of microorganisms. We found that substances known to disorder cellular macromolecules (chaotropes) did expand microbial growth windows, fungi preferentially accumulated chaotropic metabolites at low temperature, and chemical activities of solutes determined microbial survival at extremes of temperature as well as pressure. This information can enhance the precision of models used to predict if extraterrestrial and other hostile environments are able to support life; furthermore, chaotropes may be used to extend the growth windows for key microbes, such as saprotrophs, in cold ecosystems and man-made biomes.
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Affiliation(s)
- Jason P. Chin
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
| | - Julianne Megaw
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
| | - Caroline L. Magill
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
| | - Krzysztof Nowotarski
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
| | - Jim P. Williams
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
| | - Prashanth Bhaganna
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
| | - Mark Linton
- Food Microbiology Branch, Agri-Food and Biosciences Institute, Belfast BT9 5PX, Northern Ireland; and
| | - Margaret F. Patterson
- Food Microbiology Branch, Agri-Food and Biosciences Institute, Belfast BT9 5PX, Northern Ireland; and
| | - Graham J. C. Underwood
- Department of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
| | - Allen Y. Mswaka
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
| | - John E. Hallsworth
- School of Biological Sciences, Medical Biology Centre, Queen's University, Belfast BT9 7BL, Northern Ireland
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