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DeMichele E, Buret AG, Taylor CT. Hypoxia-inducible factor-driven glycolytic adaptations in host-microbe interactions. Pflugers Arch 2024; 476:1353-1368. [PMID: 38570355 PMCID: PMC11310250 DOI: 10.1007/s00424-024-02953-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/07/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
Mammalian cells utilize glucose as a primary carbon source to produce energy for most cellular functions. However, the bioenergetic homeostasis of cells can be perturbed by environmental alterations, such as changes in oxygen levels which can be associated with bacterial infection. Reduction in oxygen availability leads to a state of hypoxia, inducing numerous cellular responses that aim to combat this stress. Importantly, hypoxia strongly augments cellular glycolysis in most cell types to compensate for the loss of aerobic respiration. Understanding how this host cell metabolic adaptation to hypoxia impacts the course of bacterial infection will identify new anti-microbial targets. This review will highlight developments in our understanding of glycolytic substrate channeling and spatiotemporal enzymatic organization in response to hypoxia, shedding light on the integral role of the hypoxia-inducible factor (HIF) during host-pathogen interactions. Furthermore, the ability of intracellular and extracellular bacteria (pathogens and commensals alike) to modulate host cellular glucose metabolism will be discussed.
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Affiliation(s)
- Emily DeMichele
- School of Medicine and Systems Biology Ireland, The Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Andre G Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Cormac T Taylor
- School of Medicine and Systems Biology Ireland, The Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.
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2
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Wang Y, Zhu H, Zhang S, Yang K, Liu Y, Lai B, Yu F. Disruption and recovery of outdoor bioaerosols before, during, and after the COVID-19 outbreak at a campus in Central China: pathogen composition, particle size distribution, influencing factors, and exposure risk. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024; 26:421-435. [PMID: 38258910 DOI: 10.1039/d3em00496a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Before (2019), during (2020), and after (2021) the COVID-19 outbreak, different response methods and measures were taken on campuses to control the spread of COVID-19 within schools. These response methods may have changed the outdoor bioaerosol characteristics, which may affect staff and student health. Therefore, we analyzed the bacterial concentrations, particle size distribution, microbial populations, exposure risks, and environmental influences of bioaerosols at a campus before, during, and after the COVID-19 outbreak. This study used eight-stage Andersen samplers to collect and analyze culturable bacteria in bioaerosols from various locations, high-throughput sequencing to analyze microbial species, principal component analysis to compare differences in samples, RDA to investigate the effects of environmental factors on bioaerosols, and hazard quotient (HQ) and BugBase to evaluate human health risks. The study findings revealed that average bacterial concentrations before, during, and after COVID-19 were 75 CFU m-3, 136 CFU m-3, and 78 CFU m-3, respectively. Moreover, the average percentage of bacteria attached to PM2.5 was 49.2%, 42.7%, and 29.9%, respectively. High-throughput sequencing revealed that species composition changed significantly during the three years of COVID-19. The proportion of Pantoea and Bacillus increased with the development of COVID-19 and these became the dominant strains after COVID-19, whereas Pseudomonas had the maximum proportion during COVID-19. Both risk assessment and BugBase phenotype prediction results indicated that the potential pathogenic risk was the highest in the outdoor environment of the campus during COVID-19 and that bioaerosol contamination was the most severe compared to the outdoor bioaerosol characteristics of the campus recovered after COVID-19.
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Affiliation(s)
- Yanjie Wang
- School of Public Health, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Haoran Zhu
- School of Public Health, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Song Zhang
- School of Public Health, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Kai Yang
- School of Public Health, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Yang Liu
- School of Public Health, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Bisheng Lai
- School of Public Health, Zhengzhou University, Zhengzhou 450001, P. R. China.
| | - Fangfang Yu
- School of Public Health, Zhengzhou University, Zhengzhou 450001, P. R. China.
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Kimura S, Ishikawa S, Hayashi N, Fujita K, Inatomi Y, Suzuki S. Bacterial and fungal bioburden reduction on material surfaces using various sterilization techniques suitable for spacecraft decontamination. Front Microbiol 2023; 14:1253436. [PMID: 38152378 PMCID: PMC10751312 DOI: 10.3389/fmicb.2023.1253436] [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: 07/05/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Planetary protection is a guiding principle aiming to prevent microbial contamination of the solar system by spacecraft (forward contamination) and extraterrestrial contamination of the Earth (backward contamination). Bioburden reduction on spacecraft, including cruise and landing systems, is required to prevent microbial contamination from Earth during space exploration missions. Several sterilization methods are available; however, selecting appropriate methods is essential to eliminate a broad spectrum of microorganisms without damaging spacecraft components during manufacturing and assembly. Here, we compared the effects of different bioburden reduction techniques, including dry heat, UV light, isopropyl alcohol (IPA), hydrogen peroxide (H2O2), vaporized hydrogen peroxide (VHP), and oxygen and argon plasma on microorganisms with different resistance capacities. These microorganisms included Bacillus atrophaeus spores and Aspergillus niger spores, Deinococcus radiodurans, and Brevundimonas diminuta, all important microorganisms for considering planetary protection. Bacillus atrophaeus spores showed the highest resistance to dry heat but could be reliably sterilized (i.e., under detection limit) through extended time or increased temperature. Aspergillus niger spores and D. radiodurans were highly resistant to UV light. Seventy percent of IPA and 7.5% of H2O2 treatments effectively sterilized D. radiodurans and B. diminuta but showed no immediate bactericidal effect against B. atrophaeus spores. IPA immediately sterilized A. niger spores, but H2O2 did not. During VHP treatment under reduced pressure, viable B. atrophaeus spores and A. niger spores were quickly reduced by approximately two log orders. Oxygen plasma sterilized D. radiodurans but did not eliminate B. atrophaeus spores. In contrast, argon plasma sterilized B. atrophaeus but not D. radiodurans. Therefore, dry heat could be used for heat-resistant component bioburden reduction, and VHP or plasma for non-heat-resistant components in bulk bioburden reduction. Furthermore, IPA, H2O2, or UV could be used for additional surface bioburden reduction during assembly and testing. The systemic comparison of sterilization efficiencies under identical experimental conditions in this study provides basic criteria for determining which sterilization techniques should be selected during bioburden reduction for forward planetary protection.
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Affiliation(s)
- Shunta Kimura
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space Exploration Innovation Hub Center, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Sagamihara, Japan
| | - Shu Ishikawa
- Engineering Division, Kajima Corporation, Tokyo, Japan
| | - Nobuya Hayashi
- Interdisciplinary Graduate School of Engineering Sciences, Kyushu University, Fukuoka, Japan
| | - Kazuhisa Fujita
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Safety and Mission Assurance Department, Japan Aerospace Exploration Agency, Tsukuba, Japan
| | - Yuko Inatomi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space Exploration Innovation Hub Center, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Sagamihara, Japan
| | - Shino Suzuki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Space Exploration Innovation Hub Center, Japan Aerospace Exploration Agency, Sagamihara, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Sagamihara, Japan
- Geobiology and Astrobiology Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
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Aydinoglu F, Kahriman TY, Balci H. Seed bio-priming enhanced salt stress tolerance of maize ( Zea mays L.) seedlings by regulating the antioxidant system and miRNA expression. 3 Biotech 2023; 13:378. [PMID: 37900268 PMCID: PMC10600073 DOI: 10.1007/s13205-023-03802-w] [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: 04/26/2023] [Accepted: 10/03/2023] [Indexed: 10/31/2023] Open
Abstract
Maize (Zea mays) is moderately sensitive to salt stress. Therefore, increasing salinity in soil causes the arrestment of physiological processes and retention of growth and development, consequently leading to yield loss. Although many strategies have been launched to improve salt stress tolerance, plant growth-promoting rhizobacteria (PGPR) are considered the most promising approach due to being more environmentally friendly and agronomically sustainable than chemicals. Therefore, this study aims to investigate the potential of Bacillus spp. and the role of microRNA-mediated genetic regulation in maize subjected to seed bio-priming application to mitigate salt stress effects. To this end, maize seeds were bio-primed with the vegetative form of B. pumilus, B. licheniformis, and B. coagulans both individually or combined, subsequently treated to NaCl, and the seedlings were screened morphologically, physiologically, and transcriptionally. The study revealed that seed bio-priming with B. licheniformis reduced the stress effects of maize seedlings by increasing catalase (CAT) and ascorbate peroxidase (APX) activities by 2.5- and 3-fold, respectively, tolerating the decrease in chlorophyll content (CC), upregulating miR160d expression which led to a 36% increase in root fresh weight (RFW) and a 39% increase in shoot fresh weight (SFW). In conclusion, Bacillus spp. successfully alleviated salt stress effects on maize by modulating antioxidant enzymes and miRNA expression.
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Affiliation(s)
- Fatma Aydinoglu
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
| | - Taha Yunus Kahriman
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
| | - Huseyin Balci
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey
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Vrankar D, Verseux C, Heinicke C. An airlock concept to reduce contamination risks during the human exploration of Mars. NPJ Microgravity 2023; 9:81. [PMID: 37805607 PMCID: PMC10560228 DOI: 10.1038/s41526-023-00329-5] [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: 06/22/2022] [Accepted: 09/22/2023] [Indexed: 10/09/2023] Open
Abstract
Protecting the Martian environment from contamination with terrestrial microbes is generally seen as essential to the scientific exploration of Mars, especially when it comes to the search for indigenous life. However, while companies and space agencies aim at getting to Mars within ambitious timelines, the state-of-the-art planetary protection measures are only applicable to uncrewed spacecraft. With this paper, we attempt to reconcile these two conflicting goals: the human exploration of Mars and its protection from biological contamination. In our view, the one nominal mission activity that is most prone to introducing terrestrial microbes into the Martian environment is when humans leave their habitat to explore the Martian surface, if one were to use state-of-the-art airlocks. We therefore propose to adapt airlocks specifically to the goals of planetary protection. We suggest a concrete concept for such an adapted airlock, believing that only practical and implementable solutions will be followed by human explorers in the long run.
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Affiliation(s)
- Daniel Vrankar
- Faculty of Business and Economics, Technische Universität Dresden, Helmholtzstraße 10, 01069, Dresden, Germany
- Center of Applied Space Technology and Microgravity - ZARM, University of Bremen, Am Fallturm 2, 28359, Bremen, Germany
| | - Cyprien Verseux
- Center of Applied Space Technology and Microgravity - ZARM, University of Bremen, Am Fallturm 2, 28359, Bremen, Germany
| | - Christiane Heinicke
- Center of Applied Space Technology and Microgravity - ZARM, University of Bremen, Am Fallturm 2, 28359, Bremen, Germany.
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Sánchez-Díaz R, Molina-Garza ZJ, Cruz-Suárez LE, Selvin J, Kiran GS, Gómez-Gil B, Galaviz-Silva L, Ibarra-Gámez JC. Draft genome sequences of Bacillus pumilus 36R ATNSAL and B. safensis 13L LOBSAL, two potential candidate probiotic strains for shrimp aquaculture. J Glob Antimicrob Resist 2022; 31:304-308. [PMID: 36272706 DOI: 10.1016/j.jgar.2022.10.002] [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: 04/08/2020] [Revised: 09/21/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES This work aimed to isolate bacterial strains with antagonist activity against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (VPAHPND) that was isolated from outbreaks in Mexico. Here, we report the draft genome sequences of two antagonistic strains, isolated from saline sediment in Sonora, Mexico. METHODS Cross-streak and well diffusion tests were employed to find the bacterial strains with higher inhibitory activity against VPAHPND. The whole genomes of B. pumilus 36R ATNSAL and B. safensis 13L LOBSAL were sequenced using Ion TorrentTM (PGM) and Illumina MiseqTM platforms, respectively. Annotation was performed using the RAST server, and the genes involved in the biosynthesis of bacterial secondary metabolites were predicted using antiSMASH. RESULTS Two bacterial isolates, B. safensis 13L LOBSAL and B. pumilus 36R ATNSAL, were chosen based on their strong antagonistic profiles. The genome of 36R ATNSAL was 3.94 Mbp in length and contained 3824 genes and a total of 4116 coding sequences (CDSs); the genome of 13L LOBSAL was 3.68 Mbp and contained 3619 genes and 3688 CDSs. Twenty-eight and 32 biosynthetic gene clusters responsible for putative antimicrobial metabolite production were identified in 36R ATNSAL and 13L LOBSAL, respectively. CONCLUSIONS The two strains 13L LOBSAL and 36R ATNSAL showed excellent probiotic profiles in vitro. The genome sequences will help with the mining and reconstruction of metabolic pathways in Bacillus strains. Genome sequence-guided strain improvement could augment the probiotic potential of Bacillus strains for applications in shrimp aquaculture.
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Affiliation(s)
- Ricardo Sánchez-Díaz
- Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México
| | - Zinnia Judith Molina-Garza
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico
| | - Lucía Elizabeth Cruz-Suárez
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, India
| | - Bruno Gómez-Gil
- Research Center for Food and Development (CIAD), Mazatlan Unit, Av. Sábalo Cerritos S/N, Mazatlán, Sinaloa, C.P. 82112. Mexico
| | - Lucio Galaviz-Silva
- Autonomous University of Nuevo Leon (UANL), Ave. Universidad S/N, Cd. Universitaria, San Nicolás de los Garza, Nuevo León, CP 66455, Mexico.
| | - José Cuauhtémoc Ibarra-Gámez
- Technological Institute of Sonora (ITSON), 5 de Febrero 818 Sur, Col. Centro, Ciudad Obregón, Sonora,CP 85000, México.
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Vejar N, Gutiérrez S, Tareelap N, Alvarado C, Solís R, Guerra C, Pineda F, Sancy M, Páez M. Influence of Bacillus safensis and Bacillus pumilus on the electrochemical behavior of 2024-T3 aluminum alloy. Bioelectrochemistry 2022; 143:107950. [PMID: 34592630 DOI: 10.1016/j.bioelechem.2021.107950] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/18/2021] [Accepted: 09/15/2021] [Indexed: 11/20/2022]
Abstract
In this work, electrochemical techniques were employed to evaluate the contribution to the corrosion and corrosion inhibition of 2024-T3 aluminum alloy by two Gram-positive bacteria. In addition, polarized impedance was used to determine the microbial effect on the cathodic and anodic reactions. These microorganisms were collected from a tropical environment due to the favorable bacterial growth of this kind of climate. The alloy was exposed to the sterile medium and inoculated for up to 12 days evaluating the microbiological and electrochemical behavior. The results by linear scanning voltammetry showed that the B. safensis and B. pumilus caused a dual effect of increase and decrease currents, and through electrochemical impedance spectroscopy, showed in some cases, inductive loop, which could be associated with local corrosion and another case, an increasing impedance could be related to protection. In addition, a morphological characterization was performed by scanning electron microscopy before and after exposure, showing an increase in copper precipitation in the vicinity of the intermetallic phases by bacteria, attributed to local corrosion, but, in general, a significant effect of damages was not observed.
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Affiliation(s)
- Nelson Vejar
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile.
| | - Sebastián Gutiérrez
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile
| | - Napachat Tareelap
- School of Energy, Environment and Materials, King Mongkut's University of Technology Thonburi, 126 Pracha Uthit Road, Bangmod, Thungkru, Bangkok 10140, Thailand
| | - Claudia Alvarado
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile
| | - Roberto Solís
- Centro de Investigación y Desarrollo en Ciencias Aeroespaciales, Fuerza Aérea de Chile, Av. José Miguel Carrera 11087, Santiago, Chile
| | - Carolina Guerra
- Escuela de Construcción Civil, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Fabiola Pineda
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago, 8580745, Chile
| | - Mamié Sancy
- Escuela de Construcción Civil, Facultad de Ingeniería, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Maritza Páez
- Universidad de Santiago de Chile, Av. Libertador Bernardo ÓHiggins 3363, Santiago, Chile
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Abd-El-Kareem F, Elshahawy IE, Abd-Elgawad MMM. Application of Bacillus pumilus isolates for management of black rot disease in strawberry. EGYPTIAN JOURNAL OF BIOLOGICAL PEST CONTROL 2021; 31:25. [DOI: 10.1186/s41938-021-00371-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/28/2021] [Indexed: 09/01/2023]
Abstract
Abstract
Background
Black root rot of strawberry plants caused by Rhizoctonia solani, Fusarium solani, and Pythium sp. is a serious disease in Egypt. Biocontrol agents have frequently proved to possess paramount and safe tools against many diseases. The impact of soil treatments with 3 Bacillus pumilus isolates on black root rot disease of strawberry plants caused by R. solani, F., and Pythium sp. under laboratory and field conditions was examined herein on the commonly used ‘Festival’ strawberry cultivar. To increase the bacterial adhesion and distribution on the roots, each seedling was dipped in bacterial cell suspension at 1 × 108 colony-forming units/ml of each separate bacterial isolate for 30 min then mixed with 5% Arabic gum.
Results
The tested B. pumilus isolates significantly reduced the growth area of these 3 fungi. The two bacterial isolates Nos. 2 and 3 reduced the growth area by more than 85.2, 83.6, and 89.0% for R. solani, F. solani, and Pythium sp., respectively. Likewise, the 3 bacterial isolates significantly (P ≤ 0.05) inhibited the disease under field conditions. Isolates Nos. 2 and 3 suppressed the disease incidence by 64.4 and 68.9% and disease severity by 65.3 and 67.3%, respectively. The fungicide Actamyl had effect similar to that of the 2 isolates. B. pumilus isolates significantly enhanced growth parameters and yields of strawberry plants; isolates Nos. 2 and 3 raised the yield by 66.7 and 73.3%, respectively.
Conclusions
Bacillus pumilus isolates could effectively manage the black rot disease in strawberry herein. Due to the significant impact of the root rot disease on strawberry yield, B. pumilus should be further tested to manage the disease on strawberry on large scale in Egypt.
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Stanton CR, Rice DTF, Beer M, Batinovic S, Petrovski S. Isolation and Characterisation of the Bundooravirus Genus and Phylogenetic Investigation of the Salasmaviridae Bacteriophages. Viruses 2021; 13:1557. [PMID: 34452423 PMCID: PMC8402886 DOI: 10.3390/v13081557] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 01/21/2023] Open
Abstract
Bacillus is a highly diverse genus containing over 200 species that can be problematic in both industrial and medical settings. This is mainly attributed to Bacillus sp. being intrinsically resistant to an array of antimicrobial compounds, hence alternative treatment options are needed. In this study, two bacteriophages, PumA1 and PumA2 were isolated and characterized. Genome nucleotide analysis identified the two phages as novel at the DNA sequence level but contained proteins similar to phi29 and other related phages. Whole genome phylogenetic investigation of 34 phi29-like phages resulted in the formation of seven clusters that aligned with recent ICTV classifications. PumA1 and PumA2 share high genetic mosaicism and form a genus with another phage named WhyPhy, more recently isolated from the United States of America. The three phages within this cluster are the only candidates to infect B. pumilus. Sequence analysis of B. pumilus phage resistant mutants revealed that PumA1 and PumA2 require polymerized and peptidoglycan bound wall teichoic acid (WTA) for their infection. Bacteriophage classification is continuously evolving with the increasing phages' sequences in public databases. Understanding phage evolution by utilizing a combination of phylogenetic approaches provides invaluable information as phages become legitimate alternatives in both human health and industrial processes.
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Affiliation(s)
- Cassandra R. Stanton
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
| | - Daniel T. F. Rice
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
| | - Michael Beer
- Department of Defence Science and Technology, Port Melbourne, VIC 3207, Australia;
| | - Steven Batinovic
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
| | - Steve Petrovski
- Department of Physiology, Anatomy & Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (C.R.S.); (D.T.F.R.); (S.B.)
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Paenibacillus albiflavus sp. nov., a bacterium isolated from soil. Arch Microbiol 2021; 203:4973-4979. [PMID: 34269834 DOI: 10.1007/s00203-021-02476-3] [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: 08/29/2020] [Revised: 06/19/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
Strain 18JY21-1T, a Gram-positive, endospore-forming, motile, and rod-shaped bacterium, was isolated from soil in South Korea and was characterised to determine its taxonomic position. Phylogenetic analysis based on the 16S rRNA gene sequence of strain 18JY21-1T revealed that the strain 18JY21-1T belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain 18JY21-1T was found with Paenibacillus doosanensis CAU 1055T (97.7%) and Paenibacillus protaetiae KACC 19327T (94.4%). In genome analysis, the calculated average nucleotide identity (ANI) and the digital DNA-DNA hybridization (DDH) values between strain 18JY21-1T and Paenibacillus protaetiae KACC 19327T were 66.3% and 22.8%, respectively. Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C15:0 (38.7%) and C16:0 (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG). The cell wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-7. Based on the phylogenetic, chemotaxonomic, and phenotypic data, strain 18JY21-1T (= KCTC 3396T = JCM 33183T) should be classified as a type strain of a novel species, for which the name Paenibacillus albiflavus sp. nov. is proposed.
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Karpov DS, Osipova PG, Domashin AI, Polyakov NB, Solovyev AI, Zubasheva MV, Zhukhovitsky VG, Karpov VL, Poddubko SV, Novikova ND. Hyper-Resistance of the Bacillus licheniformis 24 Strain to Oxidative Stress Is Associated with Overexpression of Enzymatic Antioxidant System Genes. Mol Biol 2020. [DOI: 10.1134/s0026893320050040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Shen L, Griffith TM, Nyangaresi PO, Qin Y, Pang X, Chen G, Li M, Lu Y, Zhang B. Efficacy of UVC-LED in water disinfection on Bacillus species with consideration of antibiotic resistance issue. JOURNAL OF HAZARDOUS MATERIALS 2020; 386:121968. [PMID: 31896007 DOI: 10.1016/j.jhazmat.2019.121968] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/05/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
Ultraviolet light emitting diode (UV-LED) has attracted extensive attention as a new technology to replace traditional mercury lamp for water disinfection. This study reported for the first time the application of UVC-LEDs in range of 200-280 nm for the treatment of two Gram-positive tetracycline resistant bacteria (TRB) from Bacillus species and their tetracycline resistant gene (TRG). The results showed that UVC-LEDs can inactivate TRB up to 5.7-log and inhibit TRG expression, especially at 268 nm. The required fluence was approximate to that of the referential non-resistant bacteria using the same UVC-LED, but far less than that of TRB using mercury lamp. After UVC-LED irradiation, photoreactivation was the dominant mechanism to repair TRB, just like non-resistant bacteria. But contrary to non-resistant bacteria, the regrowth ratio of TRB was remarkably high at 24 h since the end of the irradition, nevertheless the number of the regrown bacteria in the irradiated water was still less than that in the non-irradiated water. Whereas TRB restored resistance after repair even applying 268 nm at a fluence up to 46.08 mJ/cm2 (maximum in this study). This study highlights the merits of UVC-LED to effectively inactivate TRB in a prompt, energy-efficient and resistance-reducing way, while future study on TRB regrowth and resistance resilience is needed.
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Affiliation(s)
- Liang Shen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China.
| | - Tiffany Maria Griffith
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Paul Onkundi Nyangaresi
- Department of Electronic Engineering, Laboratory of Micro/Nano-Optoelectronics, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yi Qin
- Department of Electronic Engineering, Laboratory of Micro/Nano-Optoelectronics, Xiamen University, Xiamen, Fujian, 361005, China
| | - Xin Pang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Guolong Chen
- Department of Electronic Science, Fujian Engineering Research Center for Solid-State Lighting, Xiamen University, Xiamen, 361005, China
| | - Minglun Li
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yinghua Lu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian, 361005, China
| | - Baoping Zhang
- Department of Electronic Engineering, Laboratory of Micro/Nano-Optoelectronics, Xiamen University, Xiamen, Fujian, 361005, China.
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13
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Habitability of Mars: How Welcoming Are the Surface and Subsurface to Life on the Red Planet? GEOSCIENCES 2019. [DOI: 10.3390/geosciences9090361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mars is a planet of great interest in the search for signatures of past or present life beyond Earth. The years of research, and more advanced instrumentation, have yielded a lot of evidence which may be considered by the scientific community as proof of past or present habitability of Mars. Recent discoveries including seasonal methane releases and a subglacial lake are exciting, yet challenging findings. Concurrently, laboratory and environmental studies on the limits of microbial life in extreme environments on Earth broaden our knowledge of the possibility of Mars habitability. In this review, we aim to: (1) Discuss the characteristics of the Martian surface and subsurface that may be conducive to habitability either in the past or at present; (2) discuss laboratory-based studies on Earth that provide us with discoveries on the limits of life; and (3) summarize the current state of knowledge in terms of direction for future research.
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14
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Rettberg P, Antunes A, Brucato J, Cabezas P, Collins G, Haddaji A, Kminek G, Leuko S, McKenna-Lawlor S, Moissl-Eichinger C, Fellous JL, Olsson-Francis K, Pearce D, Rabbow E, Royle S, Saunders M, Sephton M, Spry A, Walter N, Wimmer Schweingruber R, Treuet JC. Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know? ASTROBIOLOGY 2019; 19:951-974. [PMID: 30762429 PMCID: PMC6767865 DOI: 10.1089/ast.2018.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.
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Affiliation(s)
- Petra Rettberg
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
- Address correspondence to: Petra Rettberg, German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Research Group Astrobiology, Linder Höhe, 51147 Köln, Germany
| | - André Antunes
- GEMM—Group for Extreme and Marine Microbiology, Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - John Brucato
- Department of Physics and Astronomy, Astrophysical Observatory of Arcetri, National Institute for Astrophysics (INAF), Florence, Italy
| | - Patricia Cabezas
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Geoffrey Collins
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Alissa Haddaji
- Committee on Space Research (COSPAR), Montpellier, France
| | - Gerhard Kminek
- Committee on Space Research (COSPAR), Montpellier, France
| | - Stefan Leuko
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | | | | | - Jean-Louis Fellous
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering & Mathematics, School of Environment, Earth & Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | - David Pearce
- Department of Applied Sciences, Northumbria University, Newcastle, United Kingdom
| | - Elke Rabbow
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Samuel Royle
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Mark Saunders
- Independent Consultant for the US National Academies of Sciences (NAS), Washington, District of Columbia
| | - Mark Sephton
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Andy Spry
- Carl Sagan Center, SETI, Mountain View, California
| | - Nicolas Walter
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Robert Wimmer Schweingruber
- Institut für Experimentelle und Angewandte Physik, Abteilung Extraterrestrische Physik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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15
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Zammuto V, Fuchs FM, Fiebrandt M, Stapelmann K, Ulrich NJ, Maugeri TL, Pukall R, Gugliandolo C, Moeller R. Comparing Spore Resistance of Bacillus Strains Isolated from Hydrothermal Vents and Spacecraft Assembly Facilities to Environmental Stressors and Decontamination Treatments. ASTROBIOLOGY 2018; 18:1425-1434. [PMID: 30289268 DOI: 10.1089/ast.2017.1715] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Submarine hydrothermal vents are inhabited by a variety of microorganisms capable of tolerating environmental extremes, making them ideal candidates to further expand our knowledge of the limitations for terrestrial life, including their ability to survive the exposure of spaceflight-relevant conditions. The spore resistance of two Bacillus spp. strains, APA and SBP3, isolated from two shallow vents off Panarea Island (Aeolian Islands, Italy), to artificial and environmental stressors (i.e., UVC radiation, X-rays, heat, space vacuum, hydrogen peroxide [H2O2], and low-pressure plasma), was compared with that of two close phylogenetic relatives (Bacillus horneckiae and Bacillus oceanisediminis). Additional comparisons were made with Bacillus sp. isolated from spacecraft assembly facilities (B. horneckiae, Bacillus pumilus SAFR-032, and Bacillus nealsonii) and the biodosimetry strain and space microbiology model organism Bacillus subtilis. Overall, a high degree of spore resistance to stressors was observed for the strains isolated from spacecraft assembly facilities, with an exceptional level of resistance seen by B. pumilus SAFR-032. The environmental isolate SBP3 showed a more robust spore resistance to UVC, X-rays, H2O2, dry heat, and space vacuum than the closely related B. horneckiae. Both strains (SBP3 and APA) were more thermotolerant than their relatives, B. horneckiae and B. oceanisediminis, respectively. SBP3 may have a novel use as a bacterial model organism for future interrogations into the potential of forward contamination in extraterrestrial environments (e.g., icy moons of Jupiter or Saturn), spacecraft sterilization and, broadly, microbial responses to spaceflight-relevant environmental stressors.
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Affiliation(s)
- Vincenzo Zammuto
- 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Center for Extreme Environments and Extremophiles, University of Messina , Messina, Italy
| | - Felix M Fuchs
- 2 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Marcel Fiebrandt
- 3 Biomedical Applications of Plasma Technology, Institute for Electrical Engineering and Plasma Technology, Faculty of Electrical Engineering and Information Technology, Ruhr University Bochum , Bochum, Germany
| | - Katharina Stapelmann
- 3 Biomedical Applications of Plasma Technology, Institute for Electrical Engineering and Plasma Technology, Faculty of Electrical Engineering and Information Technology, Ruhr University Bochum , Bochum, Germany
| | - Nikea J Ulrich
- 2 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR e.V.), Cologne, Germany
| | - Teresa L Maugeri
- 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Center for Extreme Environments and Extremophiles, University of Messina , Messina, Italy
| | - Rüdiger Pukall
- 4 Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures , Braunschweig, Germany
| | - Concetta Gugliandolo
- 1 Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Research Center for Extreme Environments and Extremophiles, University of Messina , Messina, Italy
| | - Ralf Moeller
- 2 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR e.V.), Cologne, Germany
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16
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Draft genome sequence of Bacillus pumilus strain EZ-C07 isolated from digested agricultural wastes. BMC Res Notes 2018; 11:606. [PMID: 30134972 PMCID: PMC6106879 DOI: 10.1186/s13104-018-3710-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/14/2018] [Indexed: 11/10/2022] Open
Abstract
Objectives Bacillus species, belonging to the family Bacillaceae, are rod-shaped aerobic or facultative anaerobic Gram-positive bacteria that can be isolated from various environmental niches. Bacillus pumilus strains are resistant to unfavorable conditions such as UV, H2O2 and chemical disinfection. Furthermore, B. pumilus strains synthesize multifarious important enzymes and can be used in the production of some fermented foods, bioremediation of wastewater systems and biodegradation of environmental contaminants. Hence, investigation at the genomic level is required to understand their ecology, genetics and potential applications. Data description In this research, we provide the genomic insights into one Bacillus species (EZ-C07) isolated from digested agricultural waste materials. The draft genome of the strain EZ-C07 consists of 3,724,869 bp with 3890 coding sequences and 41.5% G + C content. Based on 16S rRNA gene sequence analysis followed by in silico DNA–DNA hybridization studies, the strain EZ-C07 was identified as Bacillus pumilus belonging to the family Bacillaceae within the phylum Firmicutes. The whole genome shotgun project of B. pumilus strain EZ-C07 can be accessed at DDBJ/ENA/GenBank under the Accession QLVI00000000.
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17
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Müller J, Beckers M, Mußmann N, Bongaerts J, Büchs J. Elucidation of auxotrophic deficiencies of Bacillus pumilus DSM 18097 to develop a defined minimal medium. Microb Cell Fact 2018; 17:106. [PMID: 29986716 PMCID: PMC6036677 DOI: 10.1186/s12934-018-0956-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/02/2018] [Indexed: 11/27/2022] Open
Abstract
Background Culture media containing complex compounds like yeast extract or peptone show numerous disadvantages. The chemical composition of the complex compounds is prone to significant variations from batch to batch and quality control is difficult. Therefore, the use of chemically defined media receives more and more attention in commercial fermentations. This concept results in better reproducibility, it simplifies downstream processing of secreted products and enable rapid scale-up. Culturing bacteria with unknown auxotrophies in chemically defined media is challenging and often not possible without an extensive trial-and-error approach. In this study, a respiration activity monitoring system for shake flasks and its recent version for microtiter plates were used to clarify unknown auxotrophic deficiencies in the model organism Bacillus pumilus DSM 18097. Results Bacillus pumilus DSM 18097 was unable to grow in a mineral medium without the addition of complex compounds. Therefore, a rich chemically defined minimal medium was tested containing basically all vitamins, amino acids and nucleobases, which are essential ingredients of complex components. The strain was successfully cultivated in this medium. By monitoring of the respiration activity, nutrients were supplemented to and omitted from the rich chemically defined medium in a rational way, thus enabling a systematic and fast determination of the auxotrophic deficiencies. Experiments have shown that the investigated strain requires amino acids, especially cysteine or histidine and the vitamin biotin for growth. Conclusions The introduced method allows an efficient and rapid identification of unknown auxotrophic deficiencies and can be used to develop a simple chemically defined tailor-made medium. B. pumilus DSM 18097 was chosen as a model organism to demonstrate the method. However, the method is generally suitable for a wide range of microorganisms. By combining a systematic combinatorial approach based on monitoring the respiration activity with cultivation in microtiter plates, high throughput experiments with high information content can be conducted. This approach facilitates media development, strain characterization and cultivation of fastidious microorganisms in chemically defined minimal media while simultaneously reducing the experimental effort. Electronic supplementary material The online version of this article (10.1186/s12934-018-0956-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Janina Müller
- AVT‑Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Mario Beckers
- AVT‑Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Nina Mußmann
- International R&D Laundry and Homecare, Henkel AG & Co KGaA, Henkelstr. 67, 40589, Düsseldorf, Germany
| | - Johannes Bongaerts
- Faculty of Chemistry and Biotechnology, FH Aachen-University of Applied Sciences, Heinrich-Mußmannstr. 1, 52428, Jülich, Germany
| | - Jochen Büchs
- AVT‑Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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18
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Johnson SS, Anslyn EV, Graham HV, Mahaffy PR, Ellington AD. Fingerprinting Non-Terran Biosignatures. ASTROBIOLOGY 2018; 18:915-922. [PMID: 29634318 PMCID: PMC6067094 DOI: 10.1089/ast.2017.1712] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 12/31/2017] [Indexed: 05/05/2023]
Abstract
Most strategies for life detection rely upon finding features known to be associated with terran life, such as particular classes of molecules. But life may be vastly different on other planets and moons, particularly as we expand our efforts to explore ocean worlds like Europa and Enceladus. We propose a new concept for life detection that harnesses the power of DNA sequencing to yield intricate informatics fingerprints, even for life that is not nucleic acid-based. The concept is based on the fact that folded nucleic acid structures (aptamers) have been shown to be capable of binding a wide variety of compounds, whether inorganic, organic, or polymeric, and irrespective of being from a biotic or abiotic source. Each nucleic acid sequence can be thought of as a code, and a combination of codes as a "fingerprint." Over multiple analytes, the "fingerprint" of a non-terran sample can be analyzed by chemometric protocols to provide a classifier of molecular patterns and complexity. Ultimately the chemometric fingerprints of living systems, which may differ significantly from nonliving systems, could provide an empirical, agnostic means of detecting life. Because nucleic acids are exponentially amplified by the polymerase chain reaction, even very small input signals could be translated into a robust readable output. The derived sequences could be identified by a small, portable sequencing device or by capture and optical imaging on a DNA microarray. Without presupposing any particular molecular framework, this agnostic approach to life detection could be used from Mars to the far reaches of the Solar System, all within the framework of an instrument drawing little heat and power. Key Words: Agnostic biosignatures-Astrobiology-Chemometrics-DNA sequencing-Life detection-Proximity ligation assay. Astrobiology 18, 915-922.
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Affiliation(s)
- Sarah S. Johnson
- Department of Biology, Georgetown University, Washington, DC
- Science, Technology, and International Affairs Program, Georgetown University, Washington, DC
| | - Eric V. Anslyn
- Department of Chemistry, The University of Texas at Austin, Austin, Texas
| | - Heather V. Graham
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, Maryland
| | - Paul R. Mahaffy
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, Maryland
| | - Andrew D. Ellington
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas
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19
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Tirumalai MR, Stepanov VG, Wünsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GE. Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates. BMC Microbiol 2018; 18:57. [PMID: 29884123 PMCID: PMC5994023 DOI: 10.1186/s12866-018-1191-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. Results The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. Conclusions It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group. Electronic supplementary material The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madhan R Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Racquel O Gonzalez
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Kasturi Venkateswaran
- Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, 91109, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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20
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Nicholson WL, Schuerger AC, Douki T. The Photochemistry of Unprotected DNA and DNA inside Bacillus subtilis Spores Exposed to Simulated Martian Surface Conditions of Atmospheric Composition, Temperature, Pressure, and Solar Radiation. ASTROBIOLOGY 2018; 18:393-402. [PMID: 29589975 DOI: 10.1089/ast.2017.1721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA is considered a potential biomarker for life-detection experiments destined for Mars. Experiments were conducted to examine the photochemistry of bacterial DNA, either unprotected or within Bacillus subtilis spores, in response to exposure to simulated martian surface conditions consisting of the following: temperature (-10°C), pressure (0.7 kPa), atmospheric composition [CO2 (95.54%), N2 (2.7%), Ar (1.6%), O2 (0.13%), and H2O (0.03%)], and UV-visible-near IR solar radiation spectrum (200-1100 nm) calibrated to 4 W/m2 of UVC (200-280 nm). While the majority (99.9%) of viable spores deposited in multiple layers on spacecraft-qualified aluminum coupons were inactivated within 5 min, a detectable fraction survived for up to the equivalent of ∼115 martian sols. Spore photoproduct (SP) was the major lesion detected in spore DNA, with minor amounts of cyclobutane pyrimidine dimers (CPD), in the order TT CPD > TC CPD >> CT CPD. In addition, the (6-4)TC, but not the (6-4)TT, photoproduct was detected in spore DNA. When unprotected DNA was exposed to simulated martian conditions, all photoproducts were detected. Surprisingly, the (6-4)TC photoproduct was the major photoproduct, followed by SP ∼ TT CPD > TC CPD > (6-4)TT > CT CPD > CC CPD. Differences in the photochemistry of unprotected DNA and spore DNA in response to simulated martian surface conditions versus laboratory conditions are reviewed and discussed. The results have implications for the planning of future life-detection experiments that use DNA as the target, and for the long-term persistence on Mars of forward contaminants or their DNA. Key Words: Bacillus subtilis-DNA-Mars-Photochemistry-Spore-Ultraviolet. Astrobiology 18, 393-402.
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Affiliation(s)
- Wayne L Nicholson
- 1 Department of Microbiology and Cell Science, University of Florida , Merritt Island, Florida, USA
| | - Andrew C Schuerger
- 2 Department of Plant Pathology, University of Florida , Merritt Island, Florida, USA
| | - Thierry Douki
- 3 Univ. Grenoble Alpes , CEA, CNRS, INAC, SyMMES/CIBEST, Grenoble, France
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21
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Lentibacillus alimentarius sp. nov., isolated from Myeolchi-jeotgal, a traditional Korean high-salt fermented anchovy. Antonie van Leeuwenhoek 2018; 111:1065-1071. [DOI: 10.1007/s10482-017-1006-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 12/15/2017] [Indexed: 10/18/2022]
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22
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Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments. Appl Microbiol Biotechnol 2018; 102:1869-1887. [DOI: 10.1007/s00253-017-8712-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/09/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
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23
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Zhang L, Lou J, Zhang W, Wu C, Jin Z. Bacteria killing in ICU associated infections: antibacterial nanosheets as disinfectant. RSC Adv 2018. [DOI: 10.1039/c7ra12148b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Here we propose Zn–CuO@GO nanosheets that induce rapid bacterial lysis via physically penetrating and wrapping into the cell wall. Such an irreversible damage make them promising as ICU disinfectants to combat ICU-associated multidrug resistant bacteria.
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Affiliation(s)
- Li Zhang
- Department of Critical Care Medicine Unit
- The Affiliated People's Hospital of Jiangsu University
- Zhenjiang
- China
| | - Jiaming Lou
- Department of Emergency Medicine
- The Affiliated People's Hospital of Jiangsu University
- Zhenjiang
- China
| | - Wei Zhang
- Department of Pain Medicine
- The Affiliated People's Hospital of Jiangsu University
- Zhenjiang
- China
| | - Chaoyang Wu
- Department of Oncology
- The Affiliated People's Hospital of Jiangsu University
- Zhenjiang
- China
| | - Zhaocheng Jin
- Department of Critical Care Medicine Unit
- The Affiliated People's Hospital of Jiangsu University
- Zhenjiang
- China
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24
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Handtke S, Albrecht D, Zühlke D, Otto A, Becher D, Schweder T, Riedel K, Hecker M, Voigt B. Bacillus pumilus KatX2 confers enhanced hydrogen peroxide resistance to a Bacillus subtilis PkatA::katX2 mutant strain. Microb Cell Fact 2017; 16:72. [PMID: 28446175 PMCID: PMC5406934 DOI: 10.1186/s12934-017-0684-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/19/2017] [Indexed: 11/27/2022] Open
Abstract
Background Bacillus pumilus cells exhibit a significantly higher resistance to hydrogen peroxide compared to closely related Bacilli like Bacillus subtilis. Results In this study we analyzed features of the catalase KatX2 of B. pumilus as one of the most important parts of the cellular response to hydrogen peroxide. KatX2, the vegetative catalase expressed in B. pumilus, was compared to the vegetative catalase KatA of B. subtilis. Data of our study demonstrate that B. pumilus can degrade toxic concentrations of hydrogen peroxide faster than B. subtilis. By replacing B. subtiliskatA gene by katX2 we could significantly enhance its resistance to H2O2 and its potential to eliminate this toxic compound. Mutant cells showed a 1.5- to 2-fold higher survival to toxic concentrations of hydrogen peroxide compared to wild type cells. Furthermore, we found reversible but also irreversible oxidations of the KatX2 protein which, in contrast to KatA, contains several cysteine residues. Conclusions Our study indicates that the catalase KatX2 plays a major role in the increased resistance of B. pumilus to oxidative stress caused by hydrogen peroxide. Resistance to hydrogen peroxide of other Bacilli can be enhanced by exchanging the native catalase in the cells with katX2. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0684-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Daniela Zühlke
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Andreas Otto
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Kathrin Riedel
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany.,Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology, University of Greifswald, 17489, Greifswald, Germany. .,Institute of Marine Biotechnology, 17489, Greifswald, Germany. .,Research Institute for Leather and Plastic Sheeting, Meißner-Ring 1-5, 09599, Freiberg, Germany.
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25
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Khodadad CL, Wong GM, James LM, Thakrar PJ, Lane MA, Catechis JA, Smith DJ. Stratosphere Conditions Inactivate Bacterial Endospores from a Mars Spacecraft Assembly Facility. ASTROBIOLOGY 2017; 17:337-350. [PMID: 28323456 PMCID: PMC5399745 DOI: 10.1089/ast.2016.1549] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
Every spacecraft sent to Mars is allowed to land viable microbial bioburden, including hardy endospore-forming bacteria resistant to environmental extremes. Earth's stratosphere is severely cold, dry, irradiated, and oligotrophic; it can be used as a stand-in location for predicting how stowaway microbes might respond to the martian surface. We launched E-MIST, a high-altitude NASA balloon payload on 10 October 2015 carrying known quantities of viable Bacillus pumilus SAFR-032 (4.07 × 107 spores per sample), a radiation-tolerant strain collected from a spacecraft assembly facility. The payload spent 8 h at ∼31 km above sea level, exposing bacterial spores to the stratosphere. We found that within 120 and 240 min, spore viability was significantly reduced by 2 and 4 orders of magnitude, respectively. By 480 min, <0.001% of spores carried to the stratosphere remained viable. Our balloon flight results predict that most terrestrial bacteria would be inactivated within the first sol on Mars if contaminated spacecraft surfaces receive direct sunlight. Unfortunately, an instrument malfunction prevented the acquisition of UV light measurements during our balloon mission. To make up for the absence of radiometer data, we calculated a stratosphere UV model and conducted ground tests with a 271.1 nm UVC light source (0.5 W/m2), observing a similarly rapid inactivation rate when using a lower number of contaminants (640 spores per sample). The starting concentration of spores and microconfiguration on hardware surfaces appeared to influence survivability outcomes in both experiments. With the relatively few spores that survived the stratosphere, we performed a resequencing analysis and identified three single nucleotide polymorphisms compared to unexposed controls. It is therefore plausible that bacteria enduring radiation-rich environments (e.g., Earth's upper atmosphere, interplanetary space, or the surface of Mars) may be pushed in evolutionarily consequential directions. Key Words: Planetary protection-Stratosphere-Balloon-Mars analog environment-E-MIST payload-Bacillus pumilus SAFR-032. Astrobiology 17, 337-350.
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Affiliation(s)
| | - Gregory M. Wong
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania
| | | | | | - Michael A. Lane
- NASA, Engineering Directorate, Kennedy Space Center, Florida
| | | | - David J. Smith
- NASA, Space Biosciences Division, Ames Research Center, Moffett Field, California
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26
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Smith SA, Benardini JN, Anderl D, Ford M, Wear E, Schrader M, Schubert W, DeVeaux L, Paszczynski A, Childers SE. Identification and Characterization of Early Mission Phase Microorganisms Residing on the Mars Science Laboratory and Assessment of Their Potential to Survive Mars-like Conditions. ASTROBIOLOGY 2017; 17:253-265. [PMID: 28282220 PMCID: PMC5373329 DOI: 10.1089/ast.2015.1417] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/04/2016] [Indexed: 05/23/2023]
Abstract
Planetary protection is governed by the Outer Space Treaty and includes the practice of protecting planetary bodies from contamination by Earth life. Although studies are constantly expanding our knowledge about life in extreme environments, it is still unclear what the probability is for terrestrial organisms to survive and grow on Mars. Having this knowledge is paramount to addressing whether microorganisms transported from Earth could negatively impact future space exploration. The objectives of this study were to identify cultivable microorganisms collected from the surface of the Mars Science Laboratory, to distinguish which of the cultivable microorganisms can utilize energy sources potentially available on Mars, and to determine the survival of the cultivable microorganisms upon exposure to physiological stresses present on the martian surface. Approximately 66% (237) of the 358 microorganisms identified are related to members of the Bacillus genus, although surprisingly, 22% of all isolates belong to non-spore-forming genera. A small number could grow by reduction of potential growth substrates found on Mars, such as perchlorate and sulfate, and many were resistant to desiccation and ultraviolet radiation (UVC). While most isolates either grew in media containing ≥10% NaCl or at 4°C, many grew when multiple physiological stresses were applied. The study yields details about the microorganisms that inhabit the surfaces of spacecraft after microbial reduction measures, information that will help gauge whether microorganisms from Earth pose a forward contamination risk that could impact future planetary protection policy. Key Words: Planetary protection-Spore-Bioburden-MSL-Curiosity-Contamination-Mars. Astrobiology 17, 253-265.
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Affiliation(s)
| | - James N Benardini
- 2 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - David Anderl
- 1 School of Food Science, University of Idaho , Moscow, Idaho
| | - Matt Ford
- 3 Department of Biological Sciences, Idaho State University , Pocatello, Idaho
| | - Emmaleen Wear
- 1 School of Food Science, University of Idaho , Moscow, Idaho
| | | | - Wayne Schubert
- 2 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Linda DeVeaux
- 4 Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology , Rapid City, South Dakota
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27
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Hanano A, Shaban M, Almousally I. Biochemical, Molecular, and Transcriptional Highlights of the Biosynthesis of an Effective Biosurfactant Produced by Bacillus safensis PHA3, a Petroleum-Dwelling Bacteria. Front Microbiol 2017; 8:77. [PMID: 28179901 PMCID: PMC5263155 DOI: 10.3389/fmicb.2017.00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/11/2017] [Indexed: 11/13/2022] Open
Abstract
Petroleum crude oil (PCO)-dwelling microorganisms have exceptional biological capabilities to tolerate the toxicity of petroleum contaminants and are therefore promising emulsifier and/or degraders of PCO. This study describes a set of PCO-inhabiting bacterial species, one of which, identified as Bacillus safensis PHA3, produces an efficient biosurfactant which was characterized as a glycolipid. Fourier transform infrared spectrometer, nuclear magnetic resonance, Thin layer chromatography, HPLC, and GC-MS analysis of the purified biosurfactant revealed that the extracted molecule under investigation is likely a mannolipid molecule with a hydrophilic part as mannose and a hydrophobic part as hexadecanoic acid (C16:0). The data reveal that: (i) PHA3 is a potential producer of biosurfactant (9.8 ± 0.5 mg mL-1); (ii) pre-adding 0.15% of the purified glycolipid enhanced the degradation of PCO by approximately 2.5-fold; (iii) the highest emulsifying activity of biosurfactant was found against the PCO and the lowest was against the naphthalene; (iv) the optimal PCO-emulsifying activity was found at 30-60°C, pH 8 and a high salinity. An orthologous gene encodes a putative β-diglucosyldiacylglycerol synthase (β-DGS) was identified in PHA3 and its transcripts were significantly up-regulated by exogenous PAHs, i.e., pyrene and benzo(e)pyrene but much less by mid-chain n-alkanes (ALKs) and fatty acids. Subsequently, the accumulation of β-DGS transcripts coincided with an optimal growth of bacteria and a maximal accumulation of the biosurfactant. Of particular interest, we found that PHA3 actively catalyzed the degradation of PAHs notably the pyrene and benzo(e)pyrene but was much less effective in the mono-terminal oxidation of ALKs. Such characteristics make Bacillus safensis PHA3 a promising model for enhanced microbial oil recovery and environmental remediation.
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Affiliation(s)
- Abdulsamie Hanano
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria Damascus, Syria
| | - Mouhnad Shaban
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria Damascus, Syria
| | - Ibrahem Almousally
- Department of Molecular Biology and Biotechnology, Atomic Energy Commission of Syria Damascus, Syria
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Sundararaman A, Srinivasan S, Lee JH, Lee SS. Virgibacillus jeotgali sp. nov., isolated from Myeolchi-jeotgal, a traditional Korean high-salt-fermented anchovy. Int J Syst Evol Microbiol 2017; 67:158-163. [DOI: 10.1099/ijsem.0.001596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aravind Sundararaman
- Department of Life Science, Kyonggi University, Suwon 433-760, Republic of Korea
| | | | - Jong-Hoon Lee
- Department of Food Science and Biotechnology, Kyonggi University, Suwon 443-760, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, Kyonggi University, Suwon 433-760, Republic of Korea
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Fulbright SP, Chisholm S, Reardon KF. Growth inhibition of Nannochloropsis species by Bacillus pumilus. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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30
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Lee JB, Jeon SH, Choi SG, Jung HY, Kim MK, Srinivasan S. Bacillus piscis sp. nov., a novel bacterium isolated from the muscle of the antarctic fish Dissostichus mawsoni. J Microbiol 2016; 54:809-813. [DOI: 10.1007/s12275-016-6473-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/11/2016] [Accepted: 11/11/2016] [Indexed: 10/20/2022]
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31
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Stepanov VG, Tirumalai MR, Montazari S, Checinska A, Venkateswaran K, Fox GE. Bacillus pumilus SAFR-032 Genome Revisited: Sequence Update and Re-Annotation. PLoS One 2016; 11:e0157331. [PMID: 27351589 PMCID: PMC4924849 DOI: 10.1371/journal.pone.0157331] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
Bacillus pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. pumilus strains revealed indications of misassembly in the B. pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
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Affiliation(s)
- Victor G. Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Aleksandra Checinska
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- * E-mail:
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32
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Pham VHT, Jeong S, Chung S, Kim J. Brevundimonas albigilva sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:1144-1150. [DOI: 10.1099/ijsem.0.000848] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- V. H. T. Pham
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 443-760, Republic of Korea
| | - S. Jeong
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 443-760, Republic of Korea
| | - S. Chung
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 443-760, Republic of Korea
| | - J. Kim
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, Gyeonggi-Do 443-760, Republic of Korea
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33
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Alekhova TA, Zakharchuk LM, Tatarinova NY, Kadnikov VV, Mardanov AV, Ravin NV, Skryabin KG. Diversity of bacteria of the genus Bacillus on board of international space station. DOKL BIOCHEM BIOPHYS 2016; 465:347-50. [PMID: 26728721 DOI: 10.1134/s1607672915060010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Indexed: 11/23/2022]
Abstract
From swabs of surfaces of equipment and air samples of the Russian segment of the International Space Station, nine strains of spore-forming bacteria of the genus Bacillus belonging to the species B. pumilus, B. licheniformis, B. subtilis, B. megaterium, and B. amyloliquefaciens were isolated. The last species of bacilli on the equipment of RS ISS was detected for the first time. For these species of bacilli, there are known strains that can be opportunistic to humans, and their metabolites can cause biodegradation of equipment and materials. B. pumilus found on ISS belongs to the group of bacteria that exhibits a particularly high resistance to adverse environmental conditions, such as dehydration, ultraviolet and gamma radiation, and chemical disinfection.
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Affiliation(s)
- T A Alekhova
- Faculty of Biology Moscow State University, Moscow, 119991, Russia.
| | - L M Zakharchuk
- Faculty of Biology Moscow State University, Moscow, 119991, Russia
| | - N Yu Tatarinova
- Faculty of Biology Moscow State University, Moscow, 119991, Russia
| | - V V Kadnikov
- Bioengineering Center, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7/1, Moscow, 117312, Russia
| | - A V Mardanov
- Bioengineering Center, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7/1, Moscow, 117312, Russia
| | - N V Ravin
- Faculty of Biology Moscow State University, Moscow, 119991, Russia.,Bioengineering Center, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7/1, Moscow, 117312, Russia
| | - K G Skryabin
- Faculty of Biology Moscow State University, Moscow, 119991, Russia.,Bioengineering Center, Russian Academy of Sciences, pr. 60-letiya Oktyabrya 7/1, Moscow, 117312, Russia
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Salas EC, Bhartia R, Anderson L, Hug WF, Reid RD, Iturrino G, Edwards KJ. In situ Detection of Microbial Life in the Deep Biosphere in Igneous Ocean Crust. Front Microbiol 2015; 6:1260. [PMID: 26617595 PMCID: PMC4641887 DOI: 10.3389/fmicb.2015.01260] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 10/29/2015] [Indexed: 11/13/2022] Open
Abstract
The deep biosphere is a major frontier to science. Recent studies have shown the presence and activity of cells in deep marine sediments and in the continental deep biosphere. Volcanic lavas in the deep ocean subsurface, through which substantial fluid flow occurs, present another potentially massive deep biosphere. We present results from the deployment of a novel in situ logging tool designed to detect microbial life harbored in a deep, native, borehole environment within igneous oceanic crust, using deep ultraviolet native fluorescence spectroscopy. Results demonstrate the predominance of microbial-like signatures within the borehole environment, with densities in the range of 105 cells/mL. Based on transport and flux models, we estimate that such a concentration of microbial cells could not be supported by transport through the crust, suggesting in situ growth of these communities.
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Affiliation(s)
- Everett C Salas
- Jet Propulsion Laboratory, Planetary Chemistry and Astrobiology, California Insitute of Technology Pasadena, CA, USA ; Photon Systems, Inc. Covina, CA, USA
| | - Rohit Bhartia
- Jet Propulsion Laboratory, Planetary Chemistry and Astrobiology, California Insitute of Technology Pasadena, CA, USA
| | - Louise Anderson
- Department of Geology, University of Leicester Leicester, UK
| | | | | | - Gerardo Iturrino
- Lamont-Doherty Earth Observatory, Marine Geology and Geophysics Palisades, NY, USA
| | - Katrina J Edwards
- Department of Biological Sciences and Earth Sciences, University of Southern California Los Angeles, CA, USA
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35
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Spirosoma pulveris sp. nov., a bacterium isolated from a dust sample collected at Chungnam province, South Korea. J Microbiol 2015; 53:750-5. [DOI: 10.1007/s12275-015-5263-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/31/2015] [Accepted: 09/26/2015] [Indexed: 10/22/2022]
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36
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Aquabacterium olei sp. nov., an oil-degrading bacterium isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3597-3602. [DOI: 10.1099/ijsem.0.000458] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain NHI-1T is a Gram-negative, motile, non-spore-forming bacterium isolated from oil-contaminated soil in South Korea. The strain was able to grow by using gasoline, diesel and kerosene as energy and carbon sources. After incubation for 14 days, cells (1 g l− 1) degraded approximately 58 % of oil present at concentration of 1500 p.p.m. at pH 8 and 28 °C. Strain NHI-1T grew well under aerobic conditions, with optimal growth at pH 7–9 and 28 °C–37 °C but grew poorly in the presence of ≥ 0.5 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest relatives of strain NHI-1T were Aquabacterium fontiphilum CS-6T (97.96 % sequence similarity), Aquabacterium parvum B6T (96.39 %), Aquabacterium commune B8T (95.76 %), Aquabacterium limnoticum ABP-4T (95.72 %) and Aquabacterium citratiphilum B4T (95.25 %). DNA–DNA relatedness was 41–53 % between strain NHI-1T and its closest type strains. The major fatty acids present in strain NHI-1T were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c, 44.5 %), summed feature 8 (C18 : 1ω7c/C18 : 1ω6c, 21.5 %) and C16 : 0 (16.2 %), and the predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, diphosphatidylglycerol and uncharacterized aminophospholipids. Strain NHI-1T was distinguishable from other members of genus Aquabacterium based on phenotypic, chemotaxonomic and genotypic characteristics. Therefore, strain NHI-1T represents a novel species of the genus Aquabacterium for which the name Aquabacterium olei sp. nov. is proposed. The type strain is NHI-1T ( = KEMB 9005-082T = KACC 18244T = NBRC 110486T).
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Her J, Srinivasan S, Lee SS. Tumebacillus luteolus sp. nov., isolated from soil. Int J Syst Evol Microbiol 2015; 65:4107-4112. [PMID: 26303322 DOI: 10.1099/ijsem.0.000549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Gram-stain-positive, aerobic, spore-forming and rod-shaped bacteria, designated U13T and U14, were isolated from soil of the Ukraine. Comparative analysis of the 16S rRNA gene sequences indicated that these strains belong to the genus Tumebacillus, with the highest 16S rRNA gene sequence similarity with Tumebacillus ginsengisoli Gsoil 1105T (95.48% and 95.49%, respectively). Strains U13T and U14 had iso-C15:0 and summed features 1 and 4 as the main fatty acids, and were able to grow at pH ranging from pH 5.0 to 9.0 (optimum pH 6.0-7.0), temperatures ranging from 25 to 42 °C (optimum 28-37 °C) and with 0-1% (w/v) NaCl (optimum 0%, w/v) on R2A agar medium. Chemotaxonomic data revealed that the cell-wall peptidoglycan type of the two strains was type A1γ (meso-diaminopimelic acid). On the basis of the evidence from this study, strains U13T and U14 represent a novel species of the genus Tumebacillus, for which the name Tumebacillus luteolus sp. nov. is proposed. The type strain is U13T ( = KEMB 7305-100T = JCM 19866T) and a second strain is U14 ( = KEMB 7305-101 = JCM 19867).
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Affiliation(s)
- Jihee Her
- Department of Life Science, Graduate School of Kyonggi University, , 94-6 Iui-dong Yeongtong-gu, Suwon 433-760, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Life Science, College of Natural Science, Kyonggi university, 94-6 Iui-dong Yeongtong-gu, Suwon 433-760, Republic of Korea
| | - Sang-Seob Lee
- Department of Life Science, College of Natural Science, Kyonggi university, 94-6 Iui-dong Yeongtong-gu, Suwon 433-760, Republic of Korea
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Pham VHT, Jeong SW, Kim J. Psychrobacillus soli sp. nov., capable of degrading oil, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3046-3052. [PMID: 26065735 DOI: 10.1099/ijs.0.000375] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel, aerobic, psychrotolerant, Gram-stain-positive, endospore-forming strain, NHI-2(T), was isolated from oil-contaminated soil near a gas station in Mongolia. This strain was characterized by motile rods and grew over a wide range of temperatures ( -2 to 40 °C) with optimal growth at 28-30 °C. It tolerated salt concentrations of up to 7% over a five-day incubation period. Analysis of 16S rRNA gene sequence indicated that strain NHI-2(T) belongs to the genus Psychrobacillus. Sequence similarity between NHI-2(T) and members of the genus Psychrobacillus with validly published names ranged from 97.83 to 98.18%. DNA-DNA hybridization indicated less than 70% relatedness to reference strains within the genus. The G+C content of the genomic DNA was 36 mol%. This strain contained MK-8 as a predominant isoprenoid menaquinone. NHI-2(T) had ornithine in the cell wall similar to reference strains of the genus Psychrobacillus. The major fatty acids present in NHI-2(T )were anteiso-C15 : 0 (51.0%), iso-C15 : 0 (9.1%) and anteiso-C17 : 0 (8.0%). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. These data highlight that the phenotype of strain NHI-2(T) differs from that of related species in terms of chemotaxonomic properties and genotype characteristics. Therefore, this strain is proposed as a representative of a novel species, named Psychrobacillus soli. The type strain is NHI-2(T) ( = KEMB 9005-135(T) = KACC 18243(T) = NBRC 110600(T)).
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Affiliation(s)
- Van Hong Thi Pham
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon 443-760, Republic of Korea
| | - Seung-Woo Jeong
- Department of Environmental Engineering, Kunsan National University, Kunsan 573-701, Republic of Korea
| | - Jaisoo Kim
- Ecology Laboratory, Department of Life Science, Kyonggi University, Suwon 443-760, Republic of Korea
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Draft Genome Sequences of Five Spore-Forming Food Isolates of Bacillus pumilus. GENOME ANNOUNCEMENTS 2015; 3:3/2/e01539-14. [PMID: 25767247 PMCID: PMC4357769 DOI: 10.1128/genomea.01539-14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Here, we report the draft genome sequences of five food isolates of
Bacillus pumilus
, a spore-forming Gram-positive bacterium.
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40
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Checinska A, Paszczynski A, Burbank M. Bacillusand Other Spore-Forming Genera: Variations in Responses and Mechanisms for Survival. Annu Rev Food Sci Technol 2015; 6:351-69. [DOI: 10.1146/annurev-food-030713-092332] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aleksandra Checinska
- School of Food Science, University of Idaho, Moscow, Idaho 83844-1052 and Washington State University, Pullman, Washington 99164-6376; ,
- Present address: Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109;
| | - Andrzej Paszczynski
- School of Food Science, University of Idaho, Moscow, Idaho 83844-1052 and Washington State University, Pullman, Washington 99164-6376; ,
| | - Malcolm Burbank
- School of Food Science, University of Idaho, Moscow, Idaho 83844-1052 and Washington State University, Pullman, Washington 99164-6376; ,
- Present address: BioCement Technologies Inc., Seattle, Washington 98101
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Handtke S, Volland S, Methling K, Albrecht D, Becher D, Nehls J, Bongaerts J, Maurer KH, Lalk M, Liesegang H, Voigt B, Daniel R, Hecker M. Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach. J Biotechnol 2014; 192 Pt A:204-14. [PMID: 25281541 DOI: 10.1016/j.jbiotec.2014.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 12/18/2022]
Abstract
Members of the species Bacillus pumilus get more and more in focus of the biotechnological industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182 cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS, IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed metabolic pathways. In the genome sequence a functional secretion system including the components of the Sec- and Tat-secretion machinery was found. Analysis of the exoproteome revealed secretion of about 70 proteins with predicted secretion signals. In addition, selected production-relevant genome features such as restriction modification systems and NRPS clusters of B. pumilus Jo2 are discussed.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Sonja Volland
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Karen Methling
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Jenny Nehls
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Heinrich-Mußmannstr. 1, 52428 Jülich, Germany.
| | | | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Birgit Voigt
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
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Derecho I, McCoy KB, Vaishampayan P, Venkateswaran K, Mogul R. Characterization of hydrogen peroxide-resistant Acinetobacter species isolated during the Mars Phoenix spacecraft assembly. ASTROBIOLOGY 2014; 14:837-847. [PMID: 25243569 DOI: 10.1089/ast.2014.1193] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The microbiological inventory of spacecraft and the associated assembly facility surfaces represent the primary pool of forward contaminants that may impact the integrity of life-detection missions. Herein, we report on the characterization of several strains of hydrogen peroxide-resistant Acinetobacter, which were isolated during the Mars Phoenix lander assembly. All Phoenix-associated Acinetobacter strains possessed very high catalase specific activities, and the specific strain, A. gyllenbergii 2P01AA, displayed a survival against hydrogen peroxide (no loss in 100 mM H2O2 for 1 h) that is perhaps the highest known among Gram-negative and non-spore-forming bacteria. Proteomic characterizations reveal a survival mechanism inclusive of proteins coupled to peroxide degradation (catalase and alkyl hydroperoxide reductase), energy/redox management (dihydrolipoamide dehydrogenase), protein synthesis/folding (EF-G, EF-Ts, peptidyl-tRNA hydrolase, DnaK), membrane functions (OmpA-like protein and ABC transporter-related protein), and nucleotide metabolism (HIT family hydrolase). Together, these survivability and biochemical parameters support the hypothesis that oxidative tolerance and the related biochemical features are the measurable phenotypes or outcomes for microbial survival in the spacecraft assembly facilities, where the low-humidity (desiccation) and clean (low-nutrient) conditions may serve as selective pressures. Hence, the spacecraft-associated Acinetobacter, due to the conferred oxidative tolerances, may ultimately hinder efforts to reduce spacecraft bioburden when using chemical sterilants, thus suggesting that non-spore-forming bacteria may need to be included in the bioburden accounting for future life-detection missions.
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Affiliation(s)
- I Derecho
- 1 California State Polytechnic University , Pomona, California
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Vaishampayan P, Roberts AH, Augustus A, Pukall R, Schumann P, Schwendner P, Mayilraj S, Salmassi T, Venkateswaran K. Deinococcus phoenicis sp. nov., an extreme ionizing-radiation-resistant bacterium isolated from the Phoenix Lander assembly facility. Int J Syst Evol Microbiol 2014; 64:3441-3446. [PMID: 25030518 DOI: 10.1099/ijs.0.063107-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, designated 1P10ME(T), which was resistant to extreme doses of ionizing radiation, pale-pink, non-motile, and a tetrad-forming coccoid was isolated from a cleanroom at the Kennedy Space Center, where the Phoenix spacecraft was assembled. Strain 1P10ME(T) showed optimum growth at 30 °C, with a pH range for growth of 6.5-9.0 and was highly sensitive to sodium chloride, growing only in medium with no added NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1P10ME(T) represents a novel member of the genus Deinococcus, with low sequence similarities (<93.5%) to recognized species of the genus Deinococcus. The predominant cellular fatty acid was C15:1ω6c. This novel strain exhibits extreme resistance to gamma radiation (D10 >8 kGy) and UV (D10 >1000 Jm(-2)). The results of our polyphasic taxonomic analyses suggest that strain 1P10ME(T) represents a novel species of the genus Deinococcus, for which the name Deinococcus phoenicis sp. nov. is proposed. The type strain is 1P10ME(T) ( = NRRL B-59546(T) = DSM 27173(T)).
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Affiliation(s)
- Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California, Institute of Technology, Pasadena, CA 91109, USA
| | - Anne Hayden Roberts
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Angela Augustus
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Peter Schumann
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstr. 7B, D-38124 Braunschweig, Germany
| | - Petra Schwendner
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Shanmugam Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - Tina Salmassi
- Department of Biological Sciences, California State University Los Angeles, Los Angeles, CA 90032, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California, Institute of Technology, Pasadena, CA 91109, USA
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Draft Genome Sequence of Bacillus pumilus Fairview, an Isolate Recovered from a Microbial Methanogenic Enrichment of Coal Seam Gas Formation Water from Queensland, Australia. GENOME ANNOUNCEMENTS 2014; 2:2/2/e00279-14. [PMID: 24744330 PMCID: PMC3990746 DOI: 10.1128/genomea.00279-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Despite its global abundance, Bacillus pumilus is poorly studied. The Fairview strain was obtained from a methanogenic anaerobic coal digester. The draft genome sequence was 3.8 Mbp long and contained 3,890 protein-coding genes. Like the SAFR-032 strain, it includes B. pumilus-specific proteins that likely confer enhanced resistance to environmental stresses.
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Moon J, Kim J. Isolation of Paenibacillus pinesoli sp. nov. from forest soil in Gyeonggi-Do, Korea. J Microbiol 2014; 52:273-7. [PMID: 24682991 DOI: 10.1007/s12275-014-3622-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/21/2014] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
Abstract
Using a new culture method for unculturable soil bacteria, strain NB5(T) was isolated from forest soil at Kyonggi University, and characterized taxonomically on the basis of 16S rRNA gene sequence as well as phenotypic and chemotaxonomic characteristics. The novel strain was a Gram- and catalase-positive, rod-shaped bacterium, which grew in the pH range 6.0-9.5 (optimum, 6.5-9.5) and at temperatures between 15°C and 45°C (optimum, 25-40°C). Growth was possible at 0-5% NaCl (optimum, 0% to 3%) in nutrient, Luria-Bertani, and trypticase soy broths (TSB), as well as R2A medium (with optimal growth in TSB). A phylogenetic analysis of the 16S rRNA gene sequence showed that the novel strain was affiliated with the genus Paenibacillus and had 96.8% and 96.5% similarity to P. nanensis MX2-3(T) and P. agaridevorans DSM 1355(T), respectively. The predominant menaquinone in NB5(T) was MK-7; the major fatty acids were anteiso-C15:0 and iso-C16:0; and the DNA G+C content was 54.5 mol%. We propose this strain as a novel species of the genus Paenibacillus, and suggest the name Paenibacillus pinesoli sp. nov. (type strain, KACC 17472(T)=KEMB 9005-025(T)=JCM 19203(T)).
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Affiliation(s)
- Jeongsuk Moon
- Department of Life Science, College of Natural Sciences, Kyonggi University, Suwon, 443-760, Republic of Korea
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Lee JJ, Yang DH, Ko YS, Park JK, Im EY, Kim JY, Kwon KY, Lee YJ, Kim HM, Kim MK. Paenibacillus swuensis sp. nov., a bacterium isolated from soil. J Microbiol 2014; 52:106-10. [PMID: 24500474 DOI: 10.1007/s12275-014-3546-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/09/2013] [Accepted: 12/11/2013] [Indexed: 11/28/2022]
Abstract
Strain DY6(T), a Gram-positive endospore-forming motile rod-shaped bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence of strain DY6(T) revealed that strain DY6(T) belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain DY6(T) were found with Paenibacillus gansuensis B518(T) (97.9%), P. chitinolyticus IFO 15660(T) (95.3%), P. chinjuensis WN9T (94.7%), and P. rigui WPCB173(T) (94.7%). Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C(15:0) (38.7%) and C(16:0) (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The predominant respiratory quinone was MK-7. Based on these phylogenetic, chemotaxonomic, and phenotypic data, strain DY6(T) (=KCTC 33026(T) =JCM 18491(T)) should be classified as a type strain of a novel species, for which the name Paenibacillus swuensis sp. nov. is proposed.
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Affiliation(s)
- Jae-Jin Lee
- Department of Bio & Environmental Technology, Seoul Women's University, Seoul, 139-774, Republic of Korea
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Handtke S, Schroeter R, Jürgen B, Methling K, Schlüter R, Albrecht D, van Hijum SAFT, Bongaerts J, Maurer KH, Lalk M, Schweder T, Hecker M, Voigt B. Bacillus pumilus reveals a remarkably high resistance to hydrogen peroxide provoked oxidative stress. PLoS One 2014; 9:e85625. [PMID: 24465625 PMCID: PMC3896406 DOI: 10.1371/journal.pone.0085625] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 12/05/2013] [Indexed: 12/16/2022] Open
Abstract
Bacillus pumilus is characterized by a higher oxidative stress resistance than other comparable industrially relevant Bacilli such as B. subtilis or B. licheniformis. In this study the response of B. pumilus to oxidative stress was investigated during a treatment with high concentrations of hydrogen peroxide at the proteome, transcriptome and metabolome level. Genes/proteins belonging to regulons, which are known to have important functions in the oxidative stress response of other organisms, were found to be upregulated, such as the Fur, Spx, SOS or CtsR regulon. Strikingly, parts of the fundamental PerR regulon responding to peroxide stress in B. subtilis are not encoded in the B. pumilus genome. Thus, B. pumilus misses the catalase KatA, the DNA-protection protein MrgA or the alkyl hydroperoxide reductase AhpCF. Data of this study suggests that the catalase KatX2 takes over the function of the missing KatA in the oxidative stress response of B. pumilus. The genome-wide expression analysis revealed an induction of bacillithiol (Cys-GlcN-malate, BSH) relevant genes. An analysis of the intracellular metabolites detected high intracellular levels of this protective metabolite, which indicates the importance of bacillithiol in the peroxide stress resistance of B. pumilus.
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Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Rebecca Schroeter
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Britta Jürgen
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
| | - Sacha A. F. T. van Hijum
- Centre for Molecular and Biomolecular Informatics (CMBI), Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands; and Division Processing and Safety, NIZO Food Research B.V., Ede, The Netherlands
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Jülich, Germany
| | | | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
| | - Birgit Voigt
- Institute for Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology, Greifswald, Germany
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Kilmer BR, Eberl TC, Cunderla B, Chen F, Clark BC, Schneegurt MA. Molecular and Phenetic Characterization of the Bacterial Assemblage of Hot Lake, WA, an Environment with High Concentrations of Magnesium Sulfate, and Its Relevance to Mars. INTERNATIONAL JOURNAL OF ASTROBIOLOGY 2014; 13:69-80. [PMID: 24748851 PMCID: PMC3989109 DOI: 10.1017/s1473550413000268] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Hot Lake (Oroville, WA) is an athalassohaline epsomite lake that can have precipitating concentrations of MgSO4 salts, mainly epsomite. Little biotic study has been done on epsomite lakes and it was unclear whether microbes isolated from epsomite lakes and their margins would fall within recognized halotolerant genera, common soil genera, or novel phyla. Our initial study cultivated and characterized epsotolerant bacteria from the lake and its margins. Approximately 100 aerobic heterotrophic microbial isolates were obtained by repetitive streak-plating in high-salt media including either 10% NaCl or 2 M MgSO4. The collected isolates were all bacteria, nearly evenly divided between Gram-positive and Gram-negative clades, the most abundant genera being Halomonas, Idiomarina, Marinobacter, Marinococcus, Nesterenkonia, Nocardiopsis, and Planococcus. Bacillus, Corynebacterium, Exiguobacterium, Kocuria, and Staphylococcus also were cultured. This initial study included culture-independent community analysis of direct DNA extracts of lake margin soil using PCR-based clone libraries and 16S rRNA gene phylogeny. Clones assigned Gram-positive bacterial clades (70% of total clones) were dominated by sequences related to uncultured actinobacteria. There were abundant Deltaproteobacteria clones related to bacterial sulfur metabolisms and clones of Legionella and Coxiella. These epsomite lake microbial communities seem to be divided between bacteria primarily associated with hyperhaline environments rich in NaCl and salinotolerant relatives of common soil organisms. Archaea appear to be in low abundance and none were isolated, despite near-saturated salinities. Growth of microbes at very high concentrations of magnesium and other sulfates has relevance to planetary protection and life-detection missions to Mars, where scant liquid water may form as deliquescent brines and appear as eutectic liquids.
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Affiliation(s)
- Brian R. Kilmer
- Department of Biological Sciences, Wichita State University, Wichita, KS
| | - Timothy C. Eberl
- Department of Biological Sciences, Wichita State University, Wichita, KS
| | | | - Fei Chen
- Planetary Protection Group, Jet Propulsion Laboratory, NASA, Pasadena, CA
| | | | - Mark A. Schneegurt
- Department of Biological Sciences, Wichita State University, Wichita, KS
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Bacillus thaonhiensis sp. nov., a new species, was isolated from the forest soil of Kyonggi University by using a modified culture method. Curr Microbiol 2013; 68:88-95. [PMID: 23995763 DOI: 10.1007/s00284-013-0443-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 07/15/2013] [Indexed: 10/26/2022]
Abstract
Using a new culture method for unculturable soil bacteria, we discovered a novel species, NHI-38(T), from the forest soil of Kyonggi University campus, South Korea. It was a Gram-positive, rod-shaped, and endospore-forming bacterial strain. It grew over a wide pH range (6.5-9.5), with an optimum range of pH 7-9, and in a wide range of temperatures (15-60 °C), with an optimum range of 35-45 °C. Growth was possible at 0-2 % NaCl concentration, and the optimal range was between 0.5 and 1.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that this new species clustered within the genus Bacillus; it was closely related to "Bacillus abyssalis" SCSIO 15042(T) (98.86 %), B. methanolicus NCIMB 13113(T) (95.97 %), B. vietnamensis 15-1(T) (95.8 %), B. seohaeanensis BH724(T) (95.5 %), B. timonensis MM10403188(T) (95.33 %), and B. subtilis subsp. subtilis NCIB 3610(T) (94.87 %). The main fatty acid components of this bacterium were iso-C15:0 (35.92 %), summed feature 3 (C16:1ω7c/C16:1ω6c; 16.92 %), and anteiso-C15:0 (14.19 %). The predominant quinone in this bacterial strain was MK-7. The polar lipid profile primarily comprised phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol. The genomic DNA G+C composition of the isolate was 40.7 mol%. The DNA-DNA hybridization results indicated that this strain was distinct from other Bacillus species, the degree of similarity being 50 % with "B. abyssalis", 56 % with B. methanolicus, 47 % with B. vietnamensis, 43 % with B. seohaeanensis, 46 % with B. timonensis, and 32 % with B. subtilis. Based on our results, we regard strain NHI-38(T) as a novel member of the Bacillus genus, and we propose the name Bacillus thaonhiensis (=KACC 17216(T) = KEMB 9005-019(T) = JCM 18863(T)).
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50
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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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