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Vishnivetskaya TA, Mironov VA, Abramov AA, Shcherbakova VA, Rivkina EM. Biogeochemical Characteristics of Earth's Volcanic Permafrost: An Analog of Extraterrestrial Environments. ASTROBIOLOGY 2022; 22:812-828. [PMID: 35333595 DOI: 10.1089/ast.2021.0137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article describes a study of frozen volcanic deposits collected from volcanoes Tolbachik and Bezymianny on the Kamchatka Peninsula, Russia, and Deception Island volcano, Antarctica. In addition, we studied suprasnow ash layers deposited after the 2007 eruptions of volcanoes Shiveluch and Bezymianny on Kamchatka. The main objectives were to characterize the presence and survivability of thermophilic microorganisms in perennially frozen volcanic deposits. As opposed to permafrost from the polar regions, viable thermophiles were detected in volcanic permafrost by cultivation, microscopy, and sequencing. In the permafrost of Tolbachik volcano, we observed methane formation by both psychrophilic and thermophilic methanogenic archaea, while at 37°C, methane production was noticeably lower. Thermophilic bacteria isolated from volcanic permafrost from the Deception Island were 99.93% related to Geobacillus stearothermophilus. Our data showed biological sulfur reduction to sulfide at 85°C and even at 130°C, where hyperthermophilic archaea of the genus Thermoproteus were registered. Sequences of hyperthermophilic bacteria of the genus Caldicellulosiruptor were discovered in clone libraries from fresh volcanic ash deposited on snow. Microorganisms found in volcanic terrestrial permafrost may serve as a model for the alien inhabitants of Mars, a cryogenic planet with numerous volcanoes. Thermophiles and hyperthermophiles and their metabolic processes represent a guideline for the future exploration missions on Mars.
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Affiliation(s)
- Tatiana A Vishnivetskaya
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Vasiliy A Mironov
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Andrey A Abramov
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Viktoria A Shcherbakova
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
| | - Elizaveta M Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences," Pushchino, Russia
- Institute of Geography, Russian Academy of Sciences, Moscow, 119017, Russia
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Bakke M. A Comprehensive Analysis of ATP Tests: Practical Use and Recent Progress in the Total Adenylate Test for the Effective Monitoring of Hygiene. J Food Prot 2022; 85:1079-1095. [PMID: 35503956 DOI: 10.4315/jfp-21-384] [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: 10/15/2021] [Accepted: 04/26/2022] [Indexed: 11/11/2022]
Abstract
ABSTRACT Rapid hygiene monitoring tests based on the presence of ATP have been widely used in the food industry to ensure that adequate cleanliness is maintained. In this study, the practical applications and limitations of these tests and recent technological progress for facilitating more accurate control were evaluated. The presence of ATP on a surface indicates improper cleaning and the presence of contaminants, including organic debris and bacteria. Food residues are indicators of insufficient cleaning and are direct hazards because they may provide safe harbors for bacteria, provide sources of nutrients for bacterial growth, interfere with the antimicrobial activity of disinfectants, and support the formation of biofilms. Residues of allergenic foods on a surface may increase the risk of allergen cross-contact. However, ATP tests cannot detect bacteria or allergenic proteins directly. To ensure efficient use of commercially available ATP tests, in-depth knowledge is needed regarding their practical applications, methods for determining pass-fail limits, and differences in performance. Conventional ATP tests have limitations due to possible hydrolysis of ATP to ADP and AMP, which further hinders the identification of food residues. To overcome this problem, a total adenylate test was developed that could detect ATP+ADP+AMP (A3 test). The A3 test is suitable for the detection of adenylates from food residues and useful for verification of hygiene levels. The A3 test in conjunction with other methods, such as microorganism culture and food allergen tests, may be a useful strategy for identifying contamination sources and facilitating effective hygiene management. HIGHLIGHTS
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Affiliation(s)
- Mikio Bakke
- Kikkoman Biochemifa Company, Marketing & Planning Division, 2-1-1 Nishi-shinbashi, Minato-ku, Tokyo 105-0003, Japan
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Lebeuf M, Turgeon N, Faubert C, Robillard J, Paradis É, Duchaine C. Managing the bacterial contamination risk in an axenic mice animal facility. Can J Microbiol 2021; 67:657-666. [PMID: 33844954 DOI: 10.1139/cjm-2020-0519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A gap exists between good laboratory practices with axenic animals and the procedures applied. This work examined the efficacy of sodium dichloroisocyanurate (MB-10) and potassium peroxymonosulfate (Virkon™) disinfectants, as well as the appropriate soaking time for materials used with the ISOcage Biosafety Station™. We also compared the microbial load in cage systems hosting mice over 2 weeks in axenic rooms (ARs) and in typical specific-pathogen-free (SPF) non-axenic rooms (NARs) to identify resistant microorganisms, targeted for longer soaking disinfection, and evaluated the necessary procedures for reducing the microbial load in AR. Staphylococcus was the most frequently isolated genus (in both ARs and NARs). An average of three spore-forming microorganisms per cage were counted from AR. The disinfection time to reach 1 log reduction for Bacillus atrophaeus spores varied from 138 s (100 ppm MB-10) to 290 (Virkon™) to <20 s for S. epidermidis (100 ppm MB-10). AR management protocols lead to a microbial load that is 1000 times lower than that found in NARs. Data comparing the microbial load in SPF and axenic facilities can be used to improve the effectiveness of their microbial control procedures.
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Affiliation(s)
- Maria Lebeuf
- Département de biochimie, microbiologie et bioinformatique, Université Laval, Quebec city, Quebec, Canada
| | - Nathalie Turgeon
- Research center, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Cynthia Faubert
- Research animal facility, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Justin Robillard
- Research animal facility, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Éric Paradis
- Research center, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Caroline Duchaine
- Département de biochimie, microbiologie et bioinformatique, Université Laval, Quebec city, Quebec, Canada; Tier-1, Canada Research Chair on Bioaerosols, Institutuniversitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
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Liu P, Fang X, Cao H, Gu M, Kong J, Deng A. Magnetic-bioluminescent-nanoliposomes for ultrasensitive and portable detection of protein biomarkers in blood. Anal Chim Acta 2018; 1039:98-107. [DOI: 10.1016/j.aca.2018.07.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 12/26/2022]
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Mohapatra BR, La Duc MT. Detecting the dormant: a review of recent advances in molecular techniques for assessing the viability of bacterial endospores. Appl Microbiol Biotechnol 2013; 97:7963-75. [PMID: 23912118 DOI: 10.1007/s00253-013-5115-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
Abstract
Due to their contribution to gastrointestinal and pulmonary disease, their ability to produce various deadly exotoxins, and their resistance to extreme temperature, pressure, radiation, and common chemical disinfecting agents, bacterial endospores of the Firmicutes phylum are a major concern for public and environmental health. In addition, the hardy and dormant nature of endospores renders them a particularly significant threat to the integrity of robotic extraterrestrial life-detection investigations. To prevent the contamination of critical surfaces with seemingly ubiquitous bacterial endospores, clean rooms maintained at exceedingly stringent cleanliness levels (i.e., fewer than 100,000 airborne particles per ft(3)) are used for surgical procedures, pharmaceutical processing and packaging, and fabrication and assembly of medical devices and spacecraft components. However, numerous spore-forming bacterial species have been reported to withstand typical clean room bioreduction strategies (e.g., UV lights, maintained humidity, paucity of available nutrients), which highlights the need for rapid and reliable molecular methods for detecting, enumerating, and monitoring the incidence of viable endospores. Robust means of evaluating and tracking spore burden not only provide much needed information pertaining to endospore ecophysiology in different environmental niches but also empower decontamination and bioreduction strategies aimed at sustaining the reliability and integrity of clean room environments. An overview of recent molecular advances in detecting and enumerating viable endospores, as well as the expanding phylogenetic diversity of pathogenic and clean room-associated spore-forming bacteria, ensues.
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Affiliation(s)
- Bidyut R Mohapatra
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA 91109, USA.
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Holwerda EK, Ellis LD, Lynd LR. Development and evaluation of methods to infer biosynthesis and substrate consumption in cultures of cellulolytic microorganisms. Biotechnol Bioeng 2013; 110:2380-8. [PMID: 23568345 DOI: 10.1002/bit.24915] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 03/01/2013] [Accepted: 03/18/2013] [Indexed: 11/06/2022]
Abstract
Concentrations of biosynthate (microbial biomass plus extracellular proteins) and residual substrate were inferred using elemental analysis for batch cultures of Clostridium thermocellum. Inferring residual substrate based on elemental analysis for a cellulose (Avicel)-grown culture shows similar results to residual substrate determined by quantitative saccharification using acid hydrolysis. Inference based on elemental analysis is also compared to different on-line measurements: base addition, CO2 production, and Near Infra Red optical density (OD850 ). Of these three on-line techniques, NIR OD850 has the best correlation with residual substrate concentration and is the most practical to use. Both biosynthate and residual substrate concentration demonstrate typical sigmoidal trends that can easily be fitted with a five-parameter Richards curve. The sigmoidal character of the inferred concentrations and on-line data, especially the CO2 production rate, suggest that there is a maximum in cell-specific rates of growth and substrate utilization during batch fermentations of crystalline cellulose, which is not observed during grown on cellobiose. Using a sigmoidal fit curve, the instantaneous specific growth rate was determined. While soluble substrate grown cultures show a constant growth rate, cultures grown on solid substrate do not. Features of various approaches are compared, with some more appropriate for rapid general indication of metabolic activity and some more appropriate for quantitative physiological studies.
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Affiliation(s)
- Evert K Holwerda
- Thayer School of Engineering at Dartmouth College, 14 Engineering Drive, Hanover, NH 03755, USA
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Ratphitagsanti W, Park E, Lee CS, Amos Wu RY, Lee J. High-throughput detection of spore contamination in food packages and food powders using tiered approach of ATP bioluminescence and real-time PCR. Lebensm Wiss Technol 2012. [DOI: 10.1016/j.lwt.2011.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Seto Y. Research and Development of On-site Decontamination System for Biological and Chemical Warfare Agents. ACTA ACUST UNITED AC 2011. [DOI: 10.1248/jhs.57.311] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yasuo Seto
- Third Department of Forensic Science, National Research Institute of Police Science
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Detection of saxitoxin in counterterrorism using a commercial lateral flow immunoassay kit. Forensic Toxicol 2010. [DOI: 10.1007/s11419-010-0102-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Semi-automated bacterial spore detection system with micro-fluidic chips for aerosol collection, spore treatment and ICAN DNA detection. Biosens Bioelectron 2009; 24:3299-305. [DOI: 10.1016/j.bios.2009.04.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2009] [Revised: 03/27/2009] [Accepted: 04/17/2009] [Indexed: 11/18/2022]
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Affiliation(s)
- Yasuo SETO
- National Research Institute of Police Science
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Seto Y, Kanamori-Kataoka M, Tsuge K, Ohsawa I, Maruko H, Sekiguchi H, Sano Y, Yamashiro S, Matsushita K, Sekiguchi H, Itoi T, Iura K. DEVELOPMENT OF AN ON-SITE DETECTION METHOD FOR CHEMICAL AND BIOLOGICAL WARFARE AGENTS. TOXIN REV 2008. [DOI: 10.1080/15569540701506756] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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SETO Y, KANAMORI-KATAOKA M, TSUGE K. Mass Spectrometric Technologies for Countering Chemical and Biological Terrorism Incidents. ACTA ACUST UNITED AC 2008. [DOI: 10.5702/massspec.56.91] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Detection of proteinous toxins using the Bio-Threat Alert system, part 3: effects of heat pretreatment and interfering substances. Forensic Toxicol 2007. [DOI: 10.1007/s11419-007-0029-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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SEKIOKA R, TAKAYAMA Y, SETO Y, URASAKI Y, SHINZAWA H. Detection Performance of Portable Colona Discharge Ionization Type Ion Mobility Spectrometer for Chemical Warfare Agents. BUNSEKI KAGAKU 2007. [DOI: 10.2116/bunsekikagaku.56.117] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | - Yasuo SETO
- National Research Institute of Police Science
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TAKAYAMA Y, SEKIOKA R, SEKIGUCHI H, MARUKO H, OHMORI T, SETO Y. Detection Performance of Draeger Safety Gas Detection Tube for Chemical Warfare Agents. BUNSEKI KAGAKU 2007. [DOI: 10.2116/bunsekikagaku.56.355] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yasuo TAKAYAMA
- National Research Institute of Police Science
- Tokyo Metropolitan Police Depaertment
| | - Ryoji SEKIOKA
- National Research Institute of Police Science
- Tokyo Metropolitan Police Depaertment
| | | | | | | | - Yasuo SETO
- National Research Institute of Police Science
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MARUKO H, SEKIGUCHI H, SETO Y, SATO A. Detection Performance of Chemical Warfare Agent with Portable Aspiration-Type Ion Mobility Spectrometer. BUNSEKI KAGAKU 2006. [DOI: 10.2116/bunsekikagaku.55.191] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | - Yasuo SETO
- National Research Institute of Police Science
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Gfeller KY, Nugaeva N, Hegner M. Micromechanical oscillators as rapid biosensor for the detection of active growth of Escherichia coli. Biosens Bioelectron 2005; 21:528-33. [PMID: 16076445 DOI: 10.1016/j.bios.2004.11.018] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 11/19/2004] [Accepted: 11/23/2004] [Indexed: 11/18/2022]
Abstract
A rapid biosensor for the detection of bacterial growth was developed using micromechanical oscillators coated by common nutritive layers. The change in resonance frequency as a function of the increasing mass on a cantilever array forms the basis of the detection scheme. The sensor is able to detect active growth of Escherichia coli cells within 1 h which is significantly faster than any conventional plating method which requires at least 24 h. The growth of E. coli was confirmed by scanning electron microscopy. This new sensing method for the detection of active bacterial growth allows future applications in, e.g., rapid antibiotic susceptibility testing by adding antibiotics to the nutritive layer.
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Affiliation(s)
- Karin Y Gfeller
- Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland
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