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Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
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2
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El-Sayed A, Kamel M. Future threat from the past. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:1287-1291. [PMID: 33068243 PMCID: PMC7567650 DOI: 10.1007/s11356-020-11234-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/12/2020] [Indexed: 05/03/2023]
Abstract
Global warming is one of the major challenges facing humanity. The increase in the Earth's temperature and thawing of ancient ice release viable viruses, bacteria, fungi, and other microorganisms which were trapped for thousands and millions of years. Such microorganisms may belong to novel microbial species, unknown genotypes of present pathogens, already eradicated pathogens, or even known pathogens that gained extremely robust characteristics due to their subjection to long-term stress. These worries drew more attention following the death of a child by ancient anthrax spores in Siberian in 2016 and the reconstruction of smallpox and Spanish flu genomes from ancient frozen biological samples. The present review illustrates some examples of recently recovered pathogens after being buried for millions of years, including some identified viable ancient viruses, bacteria and even other forms of life. While some pathogens could be revived, genomes of other ancient pathogens which could not be revived were re-constructed. The present study aims to highlight and alarm the hidden aspect of global warming on the international public health, which represents future threats from the past for humanity.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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El-Sayed A, Kamel M. Climatic changes and their role in emergence and re-emergence of diseases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:22336-22352. [PMID: 32347486 PMCID: PMC7187803 DOI: 10.1007/s11356-020-08896-w] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/14/2020] [Indexed: 05/11/2023]
Abstract
Global warming and the associated climate changes are predictable. They are enhanced by burning of fossil fuels and the emission of huge amounts of CO2 gas which resulted in greenhouse effect. It is expected that the average global temperature will increase with 2-5 °C in the next decades. As a result, the earth will exhibit marked climatic changes characterized by extremer weather events in the coming decades, such as the increase in temperature, rainfall, summertime, droughts, more frequent and stronger tornadoes and hurricanes. Epidemiological disease cycle includes host, pathogen and in certain cases intermediate host/vector. A complex mixture of various environmental conditions (e.g. temperature and humidity) determines the suitable habitat/ecological niche for every vector host. The availability of suitable vectors is a precondition for the emergence of vector-borne pathogens. Climate changes and global warming will have catastrophic effects on human, animal and environmental ecosystems. Pathogens, especially neglected tropical disease agents, are expected to emerge and re-emerge in several countries including Europe and North America. The lives of millions of people especially in developing countries will be at risk in direct and indirect ways. In the present review, the role of climate changes in the spread of infectious agents and their vectors is discussed. Examples of the major emerging viral, bacterial and parasitic diseases are also summarized.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
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4
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Afouda P, Dubourg G, Raoult D. Archeomicrobiology applied to environmental samples. Microb Pathog 2020; 143:104140. [DOI: 10.1016/j.micpath.2020.104140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/10/2020] [Accepted: 03/10/2020] [Indexed: 10/24/2022]
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A Myanmar amber cockroach with protruding feces contains pollen and a rich microcenosis. Naturwissenschaften 2020; 107:13. [DOI: 10.1007/s00114-020-1669-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/04/2020] [Accepted: 02/11/2020] [Indexed: 01/14/2023]
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6
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Cubillos CF, Paredes A, Yáñez C, Palma J, Severino E, Vejar D, Grágeda M, Dorador C. Insights Into the Microbiology of the Chaotropic Brines of Salar de Atacama, Chile. Front Microbiol 2019; 10:1611. [PMID: 31354691 PMCID: PMC6637823 DOI: 10.3389/fmicb.2019.01611] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 02/02/2023] Open
Abstract
Microbial life inhabiting hypersaline environments belong to a limited group of extremophile or extremotolerant taxa. Natural or artificial hypersaline environments are not limited to high concentrations of NaCl, and under such conditions, specific adaptation mechanisms are necessary to permit microbial survival and growth. Argentina, Bolivia, and Chile include three large salars (salt flats) which globally, represent the largest lithium reserves, and are commonly referred to as the Lithium Triangle Zone. To date, a large amount of information has been generated regarding chemical, geological, meteorological and economical perspectives of these salars. However, there is a remarkable lack of information regarding the biology of these unique environments. Here, we report the presence of two bacterial strains (isolates LIBR002 and LIBR003) from one of the most hypersaline lithium-dominated man-made environments (total salinity 556 g/L; 11.7 M LiCl) reported to date. Both isolates were classified to the Bacillus genera, but displayed differences in 16S rRNA gene and fatty acid profiles. Our results also revealed that the isolates are lithium-tolerant and that they are phylogenetically differentiated from those Bacillus associated with high NaCl concentration environments, and form a new clade from the Lithium Triangle Zone. To determine osmoadaptation strategies in these microorganisms, both isolates were characterized using morphological, metabolic and physiological attributes. We suggest that our characterization of bacterial isolates from a highly lithium-enriched environment has revealed that even at such extreme salinities with high concentrations of chaotropic solutes, scope for microbial life exists. These conditions have previously been considered to limit the development of life, and our work extends the window of life beyond high concentrations of MgCl2, as previously reported, to LiCl. Our results can be used to further the understanding of salt tolerance, most especially for LiCl-dominated brines, and likely have value as models for the understanding of putative extra-terrestrial (e.g., Martian) life.
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Affiliation(s)
- Carolina F. Cubillos
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Department of Chemical Engineering and Mineral Process, Center for Advanced Study of Lithium and Industrial Minerals, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Adrián Paredes
- Laboratorio Química Biológica, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Química, Facultad de Ciencias Básicas, Universidad de Antofagasta, Antofagasta, Chile
| | - Carolina Yáñez
- Laboratorio Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jenifer Palma
- Departamento de Ciencias de los Alimentos, Facultad de Ciencias de la Salud, Universidad de Antofagasta, Antofagasta, Chile
| | - Esteban Severino
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
| | - Drina Vejar
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| | - Mario Grágeda
- Department of Chemical Engineering and Mineral Process, Center for Advanced Study of Lithium and Industrial Minerals, Universidad de Antofagasta, Antofagasta, Chile
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Antofagasta, Chile
- Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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Abstract
Theory and direct observation indicate that micro-organisms exist in liquid veins in ice and permafrost, provided the temperature is above the eutectic for H2O and soluble impurities present. Microbes can exist and metabolize in glacial ice and permafrost on Earth, Mars, and Europa. One can search directly (with fluorescence microscopy at liquid veins in Vostok ice core samples) or with a biologging instrument (for microbial fluorescence in a borehole in terrestrial or martian permafrost or ice). The viability lifetime against DNA destruction of bacterial spores can be measured with analytical techniques that identify calcium dipicolinate, which is unique to spores.
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Kashuba E, Dmitriev AA, Kamal SM, Melefors O, Griva G, Römling U, Ernberg I, Kashuba V, Brouchkov A. Ancient permafrost staphylococci carry antibiotic resistance genes. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1345574. [PMID: 28959177 PMCID: PMC5614383 DOI: 10.1080/16512235.2017.1345574] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/14/2017] [Indexed: 10/26/2022]
Abstract
Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years. Objective: To cultivate bacterial strains from permafrost. Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40-60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences. Results: Genomic sequence analysis revealed the close relation of the isolated ancient bacteria to the modern bacteria of this species. Moreover, several genes associated with resistance to different groups of antibiotics were found in the S. hominis MMP2 genome. Conclusions: These findings supports a hypothesis that antibiotic resistance has an ancient origin. The enrichment of cultivated bacterial communities with ancient permafrost strains is essential for the analysis of bacterial evolution and antibiotic resistance.
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Affiliation(s)
- Elena Kashuba
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Laboratory of Cancer Genetics, R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, NASU, Kyiv, Ukraine
| | - Alexey A Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology and Immunology, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, New Cairo, Egypt
| | - Ojar Melefors
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Gennady Griva
- Siberian Branch of RAS, Institute of the Earth Cryosphere, Tyumen, Russia
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Vladimir Kashuba
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics, NASU, Kyiv, Ukraine
| | - Anatoli Brouchkov
- Faculty of Geology, Lomonosov Moscow State University, Moscow, Russia
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Abstract
The convergence of several disparate research programmes raises the possibility that the long-term evolutionary processes of innovation and radiation may become amenable to laboratory experimentation. Ancestors might be resurrected directly from naturally stored propagules or tissues, or indirectly from the expression of ancestral genes in contemporary genomes. New kinds of organisms might be evolved through artificial selection of major developmental genes. Adaptive radiation can be studied by mimicking major ecological transitions in the laboratory. All of these possibilities are subject to severe quantitative and qualitative limitations. In some cases, however, laboratory experiments may be capable of illuminating the processes responsible for the evolution of new kinds of organisms.
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Affiliation(s)
- Graham Bell
- Biology Department, McGill University, 1205 avenue docteur Penfield, Montreal, Quebec, Canada H3A 1B1
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10
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Jaakkola ST, Pfeiffer F, Ravantti JJ, Guo Q, Liu Y, Chen X, Ma H, Yang C, Oksanen HM, Bamford DH. The complete genome of a viable archaeum isolated from 123-million-year-old rock salt. Environ Microbiol 2016; 18:565-79. [DOI: 10.1111/1462-2920.13130] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/02/2015] [Accepted: 03/15/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Salla T. Jaakkola
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry; Max Planck Institute of Biochemistry; München Germany
| | - Janne J. Ravantti
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Qinggong Guo
- State Key Laboratory of Virology; College of Life Sciences; Wuhan University; Wuhan China
| | - Ying Liu
- State Key Laboratory of Virology; College of Life Sciences; Wuhan University; Wuhan China
| | - Xiangdong Chen
- State Key Laboratory of Virology; College of Life Sciences; Wuhan University; Wuhan China
| | - Hongling Ma
- State Key Laboratory of Geomechanics and Geotechnical Engineering; Institute of Rock and Soil Mechanics; The Chinese Academy of Science; Wuhan China
| | - Chunhe Yang
- State Key Laboratory of Geomechanics and Geotechnical Engineering; Institute of Rock and Soil Mechanics; The Chinese Academy of Science; Wuhan China
| | - Hanna M. Oksanen
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
| | - Dennis H. Bamford
- Department of Biosciences; Institute of Biotechnology; University of Helsinki; Helsinki Finland
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11
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Santiago-Rodriguez TM, Fornaciari G, Luciani S, Dowd SE, Toranzos GA, Marota I, Cano RJ. Gut Microbiome of an 11th Century A.D. Pre-Columbian Andean Mummy. PLoS One 2015; 10:e0138135. [PMID: 26422376 PMCID: PMC4589460 DOI: 10.1371/journal.pone.0138135] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/25/2015] [Indexed: 01/30/2023] Open
Abstract
The process of natural mummification is a rare and unique process from which little is known about the resulting microbial community structure. In the present study, we characterized the microbiome of paleofeces, and ascending, transverse and descending colon of an 11th century A.D. pre-Columbian Andean mummy by 16S rRNA gene high-throughput sequencing and metagenomics. Firmicutes were the most abundant bacterial group, with Clostridium spp. comprising up to 96.2% of the mummified gut, while Turicibacter spp. represented 89.2% of the bacteria identified in the paleofeces. Microbiome profile of the paleofeces was unique when compared to previously characterized coprolites that did not undergo natural mummification. We identified DNA sequences homologous to Clostridium botulinum, Trypanosoma cruzi and human papillomaviruses (HPVs). Unexpectedly, putative antibiotic-resistance genes including beta-lactamases, penicillin-binding proteins, resistance to fosfomycin, chloramphenicol, aminoglycosides, macrolides, sulfa, quinolones, tetracycline and vancomycin, and multi-drug transporters, were also identified. The presence of putative antibiotic-resistance genes suggests that resistance may not necessarily be associated with a selective pressure of antibiotics or contact with European cultures. Identification of pathogens and antibiotic-resistance genes in ancient human specimens will aid in the understanding of the evolution of pathogens as a way to treat and prevent diseases caused by bacteria, microbial eukaryotes and viruses.
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Affiliation(s)
| | - Gino Fornaciari
- Department of Translational Research on New Technologies in Medicine and Surgery, Division of Paleopathology, University of Pisa, Pisa, Italy
- Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Stefania Luciani
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Scot E. Dowd
- Molecular Research LP (MR DNA), Shallowater, Texas, United States of America
| | | | - Isolina Marota
- Laboratory of Molecular Archaeo-Anthropology/ancient DNA, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Raul J. Cano
- Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, CA, United States of America
- * E-mail:
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Davies PJ, Gore DB, Khan SJ. Managing produced water from coal seam gas projects: implications for an emerging industry in Australia. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:10981-1000. [PMID: 25783163 DOI: 10.1007/s11356-015-4254-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/17/2015] [Indexed: 05/14/2023]
Abstract
This paper reviews the environmental problems, impacts and risks associated with the generation and disposal of produced water by the emerging coal seam gas (CSG) industry and how it may be relevant to Australia and similar physical settings. With only limited independent research on the potential environmental impacts of produced water, is it necessary for industry and government policy makers and regulators to draw upon the experiences of related endeavours such as mining and groundwater extraction accepting that the conclusions may not always be directly transferrable. CSG is widely touted in Australia as having the potential to provide significant economic and energy security benefits, yet the environmental and health policies and the planning and regulatory setting are yet to mature and are continuing to evolve amidst ongoing social and environmental concerns and political indecision. In this review, produced water has been defined as water that is brought to the land surface during the process of recovering methane gas from coal seams and includes water sourced from CSG wells as well as flowback water associated with drilling, hydraulic fracturing and gas extraction. A brief overview of produced water generation, its characteristics and environmental issues is provided. A review of past lessons and identification of potential risks, including disposal options, is included to assist in planning and management of this industry.
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Affiliation(s)
- Peter J Davies
- Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia,
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Santiago-Rodriguez TM, Patrício AR, Rivera JI, Coradin M, Gonzalez A, Tirado G, Cano RJ, Toranzos GA. luxS in bacteria isolated from 25- to 40-million-year-old amber. FEMS Microbiol Lett 2013; 350:117-24. [PMID: 24102660 DOI: 10.1111/1574-6968.12275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 12/31/2022] Open
Abstract
Interspecies bacterial communication is mediated by autoinducer-2, whose synthesis depends on luxS. Due to the apparent universality of luxS (present in more than 40 bacterial species), it may have an ancient origin; however, no direct evidence is currently available. We amplified luxS in bacteria isolated from 25- to 40-million-year-old amber. The phylogenies and molecular clocks of luxS and the 16S rRNA gene from ancient and extant bacteria were determined as well. Luminescence assays using Vibrio harveyi BB170 aimed to determine the activity of luxS. While the phylogeny of luxS was very similar to that of extant Bacillus spp., amber isolates exhibited unique 16S rRNA gene phylogenies. This suggests that luxS may have been acquired by horizontal transfer millions of years ago. Molecular clocks of luxS suggest slow evolutionary rates, similar to those of the 16S rRNA gene and consistent with a conserved gene. Dendograms of the 16S rRNA gene and luxS show two separate clusters for the extant and ancient bacteria, confirming the uniqueness of the latter group.
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Affiliation(s)
- Tasha M Santiago-Rodriguez
- Environmental Microbiology Laboratory, Department of Biology, University of Puerto Rico, Rico, San Juan, Puerto Rico; Department of Pathology, University of California, San Diego, CA, USA
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Zhang DC, Brouchkov A, Griva G, Schinner F, Margesin R. Isolation and characterization of bacteria from ancient siberian permafrost sediment. BIOLOGY 2013; 2:85-106. [PMID: 24832653 PMCID: PMC4009857 DOI: 10.3390/biology2010085] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 11/29/2022]
Abstract
In this study, we isolated and characterized bacterial strains from ancient (Neogene) permafrost sediment that was permanently frozen for 3.5 million years. The sampling site was located at Mammoth Mountain in the Aldan river valley in Central Yakutia in Eastern Siberia. Analysis of phospolipid fatty acids (PLFA) demonstrated the dominance of bacteria over fungi; the analysis of fatty acids specific for Gram-positive and Gram-negative bacteria revealed an approximately twofold higher amount of Gram-negative bacteria compared to Gram-positive bacteria. Direct microbial counts after natural permafrost enrichment showed the presence of (4.7 ± 1.5) × 108 cells g-1 sediment dry mass. Viable heterotrophic bacteria were found at 0 °C, 10 °C and 25 °C, but not at 37 °C. Spore-forming bacteria were not detected. Numbers of viable fungi were low and were only detected at 0 °C and 10 °C. Selected culturable bacterial isolates were identified as representatives of Arthrobacter phenanthrenivorans, Subtercola frigoramans and Glaciimonas immobilis. Representatives of each of these species were characterized with regard to their growth temperature range, their ability to grow on different media, to produce enzymes, to grow in the presence of NaCl, antibiotics, and heavy metals, and to degrade hydrocarbons. All strains could grow at -5 °C; the upper temperature limit for growth in liquid culture was 25 °C or 30 °C. Sensitivity to rich media, antibiotics, heavy metals, and salt increased when temperature decreased (20 °C > 10 °C > 1 °C). In spite of the ligninolytic activity of some strains, no biodegradation activity was detected.
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Affiliation(s)
- De-Chao Zhang
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria.
| | - Anatoli Brouchkov
- Faculty of Geology, Lomonosov Moscow State University, GSP-1,1 Leninskiye Gory, Moscow 119991, Russia.
| | - Gennady Griva
- Tyumen Scientific Center Siberian Branch of Russian Academy of Science, 86 Malygina, Tyumen 625000, Russia.
| | - Franz Schinner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria.
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria.
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Brouchkov AV, Melnikov VP, Sukhovei YG, Griva GI, Repin VE, Kalenova LF, Brenner EV, Subbotin AM, Trofimova YB, Tanaka M, Katayama T, Utsumi M. Relict microorganisms of cryolithozone as possible objects of gerontology. ADVANCES IN GERONTOLOGY 2011. [DOI: 10.1134/s207905701101005x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Koltunov V, Greenblatt CL, Goncharenko AV, Demina GR, Klein BY, Young M, Kaprelyants AS. Structural changes and cellular localization of resuscitation-promoting factor in environmental isolates of Micrococcus luteus. MICROBIAL ECOLOGY 2010; 59:296-310. [PMID: 19730766 DOI: 10.1007/s00248-009-9573-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 07/31/2009] [Indexed: 05/28/2023]
Abstract
Dormancy among nonsporulating actinobacteria is now a widely accepted phenomenon. In Micrococcus luteus, the resuscitation of dormant cells is caused by a small secreted protein (resuscitation-promoting factor, or Rpf) that is found in "spent culture medium." Rpf is encoded by a single essential gene in M. luteus. Homologs of Rpf are widespread among the high G + C Gram-positive bacteria, including mycobacteria and streptomycetes, and most organisms make several functionally redundant proteins. M. luteus Rpf comprises a lysozyme-like domain that is necessary and sufficient for activity connected through a short linker region to a LysM motif, which is present in a number of cell-wall-associated enzymes. Muralytic activity is responsible for resuscitation. In this report, we characterized a number of environmental isolates of M. luteus, including several recovered from amber. There was substantial variation in the predicted rpf gene product. While the lysozyme-like and LysM domains showed little variation, the linker region was elongated from ten amino acid residues in the laboratory strains to as many as 120 residues in one isolate. The genes encoding these Rpf proteins have been characterized, and a possible role for the Rpf linker in environmental adaptation is proposed. The environmental isolates show enhanced resistance to lysozyme as compared with the laboratory strains and this correlates with increased peptidoglycan acetylation. In strains that make a protein with an elongated linker, Rpf was bound to the cell wall, rather than being released to the growth medium, as occurs in reference strains. This rpf gene was introduced into a lysozyme-sensitive reference strain. Both rpf genes were expressed in transformants which showed a slight but statistically significant increase in lysozyme resistance.
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Affiliation(s)
- Viktoria Koltunov
- Kuvin Centre and Department of Microbiology and Molecular Genetics, Hebrew University, Jerusalem 91120, Israel
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Hahn MW, Kasalický V, Jezbera J, Brandt U, Šimek K. Limnohabitans australis sp. nov., isolated from a freshwater pond, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2010; 60:2946-2950. [PMID: 20118294 PMCID: PMC3031073 DOI: 10.1099/ijs.0.022384-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A chemo-organotrophic, aerobic, non-motile strain, MWH-BRAZ-DAM2DT, isolated from a freshwater pond in Brazil, was characterized phenotypically, phylogenetically and chemotaxonomically. Phylogenetic analysis of 16S rRNA gene sequences indicated affiliation of the strain with the genus Limnohabitans (Comamonadaceae, Betaproteobacteria). 16S rRNA gene sequence similarities between the isolate and Limnohabitanscurvus MWH-C5T, representing the type species of the genus, and the type strains of Limnohabitans parvus and Limnohabitans planktonicus were 98.2, 96.5 and 97.0 %, respectively. DNA–DNA reassociation analyses with DNA of the type strains of all three previously described Limnohabitans species revealed similarity values in the range 26.2–44.6 %. The predominant fatty acids of the isolate were C16 : 1ω7c/ω6c, C16 : 0, C12 : 0 and C8 : 0 3-OH, the major quinone was ubiquinone Q-8 and the DNA G+C content was 55.8 mol%. The isolate could be discriminated from the type strains of the three Limnohabitans species by several phenotypic traits including differences in the utilization of several carbon sources. Based on the phylogeny of the isolate and its differences from the three most closely related species, the isolate represents a novel species for which the name Limnohabitans australis sp. nov. is proposed. The type strain is MWH-BRAZ-DAM2DT (=DSM 21646T=CCUG 56719T).
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Affiliation(s)
- Martin W Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Vojtěch Kasalický
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Jan Jezbera
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic.,Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Brandt
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Karel Šimek
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
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Kasalický V, Jezbera J, Šimek K, Hahn MW. Limnohabitans planktonicus sp. nov. and Limnohabitans parvus sp. nov., planktonic betaproteobacteria isolated from a freshwater reservoir, and emended description of the genus Limnohabitans. Int J Syst Evol Microbiol 2010; 60:2710-2714. [PMID: 20061501 DOI: 10.1099/ijs.0.018952-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two bacterial strains, II-B4(T) and II-D5(T), isolated from the meso-eutrophic freshwater Římov reservoir (Czech Republic), were characterized phenotypically, phylogenetically and chemotaxonomically. Both strains were chemo-organotrophic, facultatively anaerobic, non-motile rods, with identical DNA G+C contents of 59.9 mol%. Their major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine and their major fatty acids were C(16 : 1)ω7c/C(16 : 1)ω6c, C(16 : 0), C(18 : 1)ω7c/C(18 : 1)ω6c and C(12 : 0). Both strains contained Q-8 as the only respiratory quinone component. The 16S rRNA gene sequences of the two strains possessed 99.1 % similarity; however, the level of DNA-DNA reassociation was only 26.7 %. The strains can also be discriminated from each other by several chemotaxonomic and biochemical traits. Phylogenetic analysis of the 16S rRNA gene sequences revealed the affiliation of both strains with the genus Limnohabitans within the family Comamonadaceae. The two investigated strains represent the first isolated members of a narrow phylogenetic cluster (the so-called R-BT065 cluster) formed by a large number of environmental sequences and abundant populations detected in the pelagic zones of various freshwater habitats. We propose to place the two strains in separate novel species within the genus Limnohabitans, Limnohabitans planktonicus sp. nov., with the type strain II-D5(T) (=DSM 21594(T) =CIP 109844(T)), and Limnohabitans parvus sp. nov., with the type strain II-B4(T) (=DSM 21592(T) =CIP 109845(T)). The description of the genus Limnohabitans is emended accordingly.
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Affiliation(s)
- Vojtěch Kasalický
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Biology Centre of the Academy of Sciences CR, v.v.i. Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Jan Jezbera
- Biology Centre of the Academy of Sciences CR, v.v.i. Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Karel Šimek
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Biology Centre of the Academy of Sciences CR, v.v.i. Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Martin W Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
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Dib JR, Wagenknecht M, Hill RT, Farías ME, Meinhardt F. First report of linear megaplasmids in the genus Micrococcus. Plasmid 2010; 63:40-5. [DOI: 10.1016/j.plasmid.2009.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 10/05/2009] [Accepted: 10/12/2009] [Indexed: 11/26/2022]
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Hahn MW, Kasalický V, Jezbera J, Brandt U, Jezberová J, Šimek K. Limnohabitans curvus gen. nov., sp. nov., a planktonic bacterium isolated from a freshwater lake. Int J Syst Evol Microbiol 2009; 60:1358-1365. [PMID: 19671731 DOI: 10.1099/ijs.0.013292-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
A chemo-organotrophic, aerobic, facultatively anaerobic, non-motile strain, MWH-C5(T), isolated from the water column of the oligomesotrophic Lake Mondsee (Austria), was characterized phenotypically, phylogenetically and chemotaxonomically. The predominant fatty acids of the strain were C(16 : 1)omega7c/omega6c, C(16 : 0), C(12 : 1) and C(8 : 0)-3OH, the major quinone was ubiquinone Q-8 and the G+C content of the DNA of the strain was 55.5 mol%. 16S rRNA gene similarity to the closest related type strains was 96.6 % (Curvibacter delicatus LMG 4328(T)) and 95.7 % (Rhodoferax fermentans FR3(T)). Phylogenetic analysis of 16S rRNA gene sequences revealed the affiliation of the strain with the family Comamonadaceae (Betaproteobacteria); however, the phylogenetic position of the strain did not support an affiliation to any previously described genus within this family. A family-wide comparison of traits revealed that the strain possesses a unique combination of DNA G+C content, major fatty acids and major 3-hydroxy fatty acid. Furthermore, the strain differs in several traits from the closest related genera. Based on the phylogeny of the strain and differences from closely related genera, we propose to establish the new genus and species Limnohabitans curvus gen. nov., sp. nov. to accommodate this strain. The type strain of Limnohabitans curvus is MWH-C5(T) (=DSM 21645(T) =CCUG 56720(T)). The type strain is closely related to a large number of uncultured bacteria detected by cultivation-independent methods in various freshwater systems.
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Affiliation(s)
- Martin W Hahn
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Vojtěch Kasalický
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
| | - Jan Jezbera
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic.,Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Ulrike Brandt
- Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Jitka Jezberová
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic.,Institute for Limnology, Austrian Academy of Sciences, Mondseestrasse 9, A-5310 Mondsee, Austria
| | - Karel Šimek
- Biology Centre of the Academy of Sciences ČR, v.v.i., Institute of Hydrobiology, Na Sádkách 7, 37005 České Budějovice, Czech Republic
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23
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Microbial Cretaceous park: biodiversity of microbial fossils entrapped in amber. Naturwissenschaften 2009; 96:551-64. [DOI: 10.1007/s00114-009-0508-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 01/12/2009] [Accepted: 01/22/2009] [Indexed: 11/25/2022]
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24
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Griffith JD, Willcox S, Powers DW, Nelson R, Baxter BK. Discovery of abundant cellulose microfibers encased in 250 Ma Permian halite: a macromolecular target in the search for life on other planets. ASTROBIOLOGY 2008; 8:215-228. [PMID: 18366344 DOI: 10.1089/ast.2007.0196] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this study, we utilized transmission electron microscopy to examine the contents of fluid inclusions in halite (NaCl) and solid halite crystals collected 650 m below the surface from the Late Permian Salado Formation in southeastern New Mexico (USA). The halite has been isolated from contaminating groundwater since deposition approximately 250 Ma ago. We show that abundant cellulose microfibers are present in the halite and appear remarkably intact. The cellulose is in the form of 5 nm microfibers as well as composite ropes and mats, and was identified by resistance to 0.5 N NaOH treatment and susceptibility to cellulase enzyme treatment. These cellulose microfibers represent the oldest native biological macromolecules to have been directly isolated, examined biochemically, and visualized (without growth or replication) to date. This discovery points to cellulose as an ideal macromolecular target in the search for life on other planets in our Solar System.
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Affiliation(s)
- Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.
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25
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Gilichinsky DA, Wilson GS, Friedmann EI, McKay CP, Sletten RS, Rivkina EM, Vishnivetskaya TA, Erokhina LG, Ivanushkina NE, Kochkina GA, Shcherbakova VA, Soina VS, Spirina EV, Vorobyova EA, Fyodorov-Davydov DG, Hallet B, Ozerskaya SM, Sorokovikov VA, Laurinavichyus KS, Shatilovich AV, Chanton JP, Ostroumov VE, Tiedje JM. Microbial populations in Antarctic permafrost: biodiversity, state, age, and implication for astrobiology. ASTROBIOLOGY 2007; 7:275-311. [PMID: 17480161 DOI: 10.1089/ast.2006.0012] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Antarctic permafrost soils have not received as much geocryological and biological study as has been devoted to the ice sheet, though the permafrost is more stable and older and inhabited by more microbes. This makes these soils potentially more informative and a more significant microbial repository than ice sheets. Due to the stability of the subsurface physicochemical regime, Antarctic permafrost is not an extreme environment but a balanced natural one. Up to 10(4) viable cells/g, whose age presumably corresponds to the longevity of the permanently frozen state of the sediments, have been isolated from Antarctic permafrost. Along with the microbes, metabolic by-products are preserved. This presumed natural cryopreservation makes it possible to observe what may be the oldest microbial communities on Earth. Here, we describe the Antarctic permafrost habitat and biodiversity and provide a model for martian ecosystems.
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Affiliation(s)
- D A Gilichinsky
- Institutes of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia. gilichin@online stack.net
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26
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Elhottová D, Kristůfek V, Frouz J, Nováková A, Chronáková A. Screening for microbial markers in Miocene sediment exposed during open-cast brown coal mining. Antonie van Leeuwenhoek 2006; 89:459-63. [PMID: 16622790 DOI: 10.1007/s10482-005-9044-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/21/2005] [Indexed: 10/24/2022]
Abstract
Viable microorganisms were found in Miocene lacustrine clays of the cypris formation excavated from 200-m below the surface as spoil during open-cast brown coal mining (Sokolov Brown Coal Basin, North-Western Bohemia, Czech Republic). Both saprotrophic microfungi of the genera Penicillium, Verticillium, Cladosporium and Aspergillus as well as heterotrophic bacteria were isolated from an intact sediment cores. Heterotrophic bacteria were classified by the MIS Sherlock System as representatives of genera Nocardiopsis, Arthrobacter, Micrococcus, Kocuria, Rothia, Clavibacter, Bacillus, Paenibacillus, Brevibacillus, Microbacterium, Acinetobacter and Pseudomonas. A bacterium found among the strains had an atypical fatty acids profile enriched by branched fatty acids and polyunsaturated fatty acid (18:3 omega 6) and gave no MIS Sherlock match. Phospholipid fatty acids analysis indicates a relatively high (535 pmol g(-1)) but inhomogeneously distributed viable microbial biomass. Fatty acids analyses of non-fractioned lipids (representing viable, storage and dead biomass; 8390 pmol g(-1)) detected rich and homogenous profiles with fungal, bacterial and actinomycetal markers but no protozoan and algal fatty acids markers.
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Affiliation(s)
- Dana Elhottová
- Institute of Soil Biology, Academy of Sciences of the Czech Republic, Na Sádkách 7, 370 05, Ceské Budejovice, Czech Republic.
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Affiliation(s)
- Ronald L Crawford
- Environmental Biotechnology Institute, University of Idaho, P.O. Box 441052, Moscow, Idaho 83844-1052, USA
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Pokorný R, Olejníková P, Balog M, Zifcák P, Hölker U, Janssen M, Bend J, Höfer M, Holiencin R, Hudecová D, Varecka L. Characterization of microorganisms isolated from lignite excavated from the Záhorie coal mine (southwestern Slovakia). Res Microbiol 2005; 156:932-43. [PMID: 16085397 DOI: 10.1016/j.resmic.2005.04.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Revised: 04/26/2005] [Accepted: 04/27/2005] [Indexed: 11/29/2022]
Abstract
Microorganisms were isolated from lignite freshly excavated in the Záhorie coal mine (southwestern Slovakia) under conditions excluding contamination with either soil or air-borne microorganisms. The isolates represented both Prokarya and Eukarya (fungi). All were able to grow on standard media, although some microorganisms were unstable and became extinct during storage of coal samples. Bacteria belonged to the genera Bacillus, Staphylococcus, and Rhodococcus, according to both morphological criteria and ITS sequences. Several bacterial isolates were resistant to antibiotics. The presence of anaerobic bacteria was also documented, although they have not yet been identified. Fungal isolates were typified by using their ITS sequences. They belonged to the genera Trichoderma (Hypocrea), Penicillium, Epicoccum, Metarhizium (Cordyceps), and Cladosporium. Several fungi produced compounds with antibiotic action against standard bacterial strains. The evidence for the presence of microorganisms in native lignite was obtained by means of fluorescence microscopy, scanning electron microscopy, and electron microprobe analysis. Results demonstrated that microorganisms were able to survive in the low-rank coal over a long time period.
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MESH Headings
- Anti-Bacterial Agents/biosynthesis
- Anti-Bacterial Agents/pharmacology
- Antibiosis
- Bacillus/classification
- Bacillus/isolation & purification
- Bacteria/classification
- Bacteria/isolation & purification
- Bacteria, Anaerobic/isolation & purification
- Coal/microbiology
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Drug Resistance, Microbial
- Electron Probe Microanalysis
- Fungi/classification
- Fungi/isolation & purification
- Microscopy, Electron, Scanning
- Microscopy, Fluorescence
- Mining
- Molecular Sequence Data
- Rhodococcus/classification
- Rhodococcus/isolation & purification
- Sequence Analysis, DNA
- Slovakia
- Staphylococcus/classification
- Staphylococcus/isolation & purification
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Affiliation(s)
- Richard Pokorný
- Department of Biochemistry and Microbiology, Slovak University of Technology, Radlinského 9, 81237 Bratislava, Slovakia
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Wang G, Skipper HD. Identification of denitrifying rhizobacteria from bentgrass and bermudagrass golf greens. J Appl Microbiol 2004; 97:827-37. [PMID: 15357733 DOI: 10.1111/j.1365-2672.2004.02368.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS As high rates of nitrogen fertilization are used in turfgrass management, there is a great potential for nitrogen loss. Research on identification of denitrifiers in turfgrass has been limited. Therefore, the aim was to identify denitrifier species and genes from turfgrass roots. METHODS AND RESULTS Rhizobacteria were isolated from roots of bentgrass and bermudagrass in sand-based United States Golf Association (USGA) golf greens and used for denitrification biochemical analysis. Seventeen per cent (34 isolates) were identified as denitrifiers, 47% were classified as nitrate-reducers and 36% were nondenitrifiers. Identification of species of the denitrifiers was performed by chromatography fatty acid methyl ester (GC-FAME) and16S rDNA analyses. Bacillus and Pseudomonas were the major turfgrass denitrifiers. The two methods showed a 60% agreement at the genus level. Nitrite reductase genes nirK and nirS were detected in 74 and 15% of the denitrifiers, respectively, but not in nondenitrifiers. The nosZ gene encoding nitrous oxide reductase was detected in all the denitrifiers, but also in some nondenitrifiers. CONCLUSIONS To our knowledge, this is the first report for identification of denitrifiers and denitrification-related genes associated with turfgrass roots. SIGNIFICANCE AND IMPACT OF THE STUDY These results provide valuable data for future denitrification studies that seek to improve turfgrass nitrogen management for maximum efficiency.
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Affiliation(s)
- G Wang
- Department of Crop and Soil Environmental Science, Clemson University, Clemson, SC, USA
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Greenblatt CL, Baum J, Klein BY, Nachshon S, Koltunov V, Cano RJ. Micrococcus luteus -- survival in amber. MICROBIAL ECOLOGY 2004; 48:120-127. [PMID: 15164240 DOI: 10.1007/s00248-003-2016-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Accepted: 08/27/2003] [Indexed: 05/24/2023]
Abstract
A growing body of evidence now supports the isolation of microorganisms from ancient materials. However, questions about the stringency of extraction methods and the genetic relatedness of isolated organisms to their closest living relatives continue to challenge the authenticity of these ancient life forms. Previous studies have successfully isolated a number of spore-forming bacteria from organic and inorganic deposits of considerable age whose survival is explained by their ability to enter suspended animation for extended periods of time. However, despite a number of putative reports, the isolation of non-spore-forming bacteria and an explanation for their survival have remained enigmatic. Here we describe the isolation of non-spore-forming cocci from a 120-million-year-old block of amber, which by genetic, morphological, and biochemical analyses are identified as belonging to the bacterial species Micrococcus luteus. Although comparison of 16S rRNA sequences from the ancient isolates with their modern counterparts is unable to confirm the precise age of these bacteria, we demonstrate, using complementary molecular and cell biological techniques, evidence supporting the view that these (and related modern members of the genus) have numerous adaptations for survival in extreme, nutrient-poor environments, traits that will assist in this bacteria's persistence and dispersal in the environment. The bacteria's ability to utilize succinic acid and process terpine-related compounds, both major components of natural amber, support its survival in this oligotrophic environment.
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Affiliation(s)
- C L Greenblatt
- Kuvin Centre for the Study of Infectious and Tropical Disease, The Hebrew University-Hadassah School of Medicine, P.O. Box 12272, 91120 Jerusalem, Israel.
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Wickramasinghe C. The universe: a cryogenic habitat for microbial life. Cryobiology 2004; 48:113-25. [PMID: 15094088 DOI: 10.1016/j.cryobiol.2004.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2003] [Accepted: 03/04/2004] [Indexed: 11/20/2022]
Abstract
Panspermia, an ancient idea, posits that microbial life is ubiquitous in the Universe. After several decades of almost irrational rejection, panspermia is at last coming to be regarded as a serious contender for the beginnings of life on our planet. Astronomical data is shown to be consistent with the widespread distribution of complex organic molecules and dust particles that may have a biological provenance. A minuscule (10(-21)) survival rate of freeze-dried bacteria in space is all that is needed to ensure the continual re-cycling of cosmic microbial life in the galaxy. Evidence that terrestrial life may have come from elsewhere in the solar system has accumulated over the past decade. Mars is seen by some as a possible source of terrestrial life, but some hundreds of billions of comets that enveloped the entire solar system, are a far more likely primordial reservoir of life. Comets would then have seeded Earth, Mars, and indeed all other habitable planetary bodies in the inner regions of the solar system. The implications of this point of view, which was developed in conjunction with the late Sir Fred Hoyle since the 1970s, are now becoming amenable to direct empirical test by studies of pristine organic material in the stratosphere. The ancient theory of panspermia may be on the verge of vindication, in which case the entire universe would be a grand crucible of cryomicrobiology.
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Affiliation(s)
- Chandra Wickramasinghe
- Cardiff Centre for Astrobiology, Cardiff University, 2 North Road, Cardiff CF10 3DY, UK.
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Baker GC, Tow LA, Cowan DA. PCR-based detection of non-indigenous microorganisms in 'pristine' environments. J Microbiol Methods 2003; 53:157-64. [PMID: 12654487 DOI: 10.1016/s0167-7012(03)00021-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
PCR-based technologies are widely employed for the detection of specific microorganisms, and may be applied to the identification of non-indigenous microorganisms in 'pristine' environments. For 'pristine' environments such as those found on the Antarctic continent, the application of these methods to the assessment of environmental contamination from human activities must be treated with caution. Issues such as the possibility of non-human dispersal of organisms, stability and survival of non-indigenous organisms in vivo, the sensitivity, reproducibility and specificity of the PCR process (and particularly primer design) and the sampling regime employed must all be considered in detail. We conclude that despite these limitations, PCR and related technologies offer enormous scope for assessment of both natural and non-indigenous microbial distributions.
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Affiliation(s)
- Gillian C Baker
- Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town, South Africa.
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Crawford RL, Paszczynski A, Allenbach L. Potassium ferrate [Fe(VI)] does not mediate self-sterilization of a surrogate Mars soil. BMC Microbiol 2003; 3:4. [PMID: 12694634 PMCID: PMC153549 DOI: 10.1186/1471-2180-3-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2002] [Accepted: 03/06/2003] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Martian soil is thought to be enriched with strong oxidants such as peroxides and/or iron in high oxidation states that might destroy biological materials. There is also a high flux of ultraviolet radiation at the surface of Mars. Thus, Mars may be inhospitable to life as we know it on Earth. We examined the hypothesis that if the soil of Mars contains ferrates [Fe(VI)], the strongest of the proposed oxidizing species, and also is exposed to high fluxes of UV radiation, it will be self-sterilizing. RESULTS Under ambient conditions (25 degrees C, oxygen and water present) K2FeO4 mixed into sand mineralized some reactive organic molecules to CO2, while less reactive compounds were not degraded. Dried endospores of Bacillus subtilis incubated in a Mars surrogate soil comprised of dry silica sand containing 20% by weight K2FeO4 and under conditions similar to those now on Mars (extreme desiccation, cold, and a CO2-dominated atmosphere) were resistant to killing by the ferrate-enriched sand. Similar results were observed with permanganate. Spores in oxidant-enriched sand exposed to high fluxes of UV light were protected from the sporocidal activity of the radiation below about 5 mm depths. CONCLUSION Based on our data and previously published descriptions of ancient but dormant life forms on Earth, we suggest that if entities resembling bacterial endospores were produced at some point by life forms on Mars, they might still be present and viable, given appropriate germination conditions. Endospores delivered to Mars on spacecraft would possibly survive and potentially compromise life detection experiments.
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Affiliation(s)
- Ronald L Crawford
- Environmental Research Institute, University of Idaho, Moscow, ID 83.844-1052, USA
- Department of Microbiology, Molecular Biology & Biochemistry, University of Idaho, Moscow, ID 83844-1052, USA
| | - Andrzej Paszczynski
- Environmental Research Institute, University of Idaho, Moscow, ID 83.844-1052, USA
- Department of Microbiology, Molecular Biology & Biochemistry, University of Idaho, Moscow, ID 83844-1052, USA
| | - Lisa Allenbach
- Environmental Research Institute, University of Idaho, Moscow, ID 83.844-1052, USA
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Hill JE, Seipp RP, Betts M, Hawkins L, Van Kessel AG, Crosby WL, Hemmingsen SM. Extensive profiling of a complex microbial community by high-throughput sequencing. Appl Environ Microbiol 2002; 68:3055-66. [PMID: 12039767 PMCID: PMC123911 DOI: 10.1128/aem.68.6.3055-3066.2002] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Complex microbial communities remain poorly characterized despite their ubiquity and importance to human and animal health, agriculture, and industry. Attempts to describe microbial communities by either traditional microbiological methods or molecular methods have been limited in both scale and precision. The availability of genomics technologies offers an unprecedented opportunity to conduct more comprehensive characterizations of microbial communities. Here we describe the application of an established molecular diagnostic method based on the chaperonin-60 sequence, in combination with high-throughput sequencing, to the profiling of a microbial community: the pig intestinal microbial community. Four libraries of cloned cpn60 sequences were generated by two genomic DNA extraction procedures in combination with two PCR protocols. A total of 1,125 cloned cpn60 sequences from the four libraries were sequenced. Among the 1,125 cloned cpn60 sequences, we identified 398 different nucleotide sequences encoding 280 unique peptide sequences. Pairwise comparisons of the 398 unique nucleotide sequences revealed a high degree of sequence diversity within the library. Identification of the likely taxonomic origins of cloned sequences ranged from imprecise, with clones assigned to a taxonomic subclass, to precise, for cloned sequences with 100% DNA sequence identity with a species in our reference database. The compositions of the four libraries were compared and differences related to library construction parameters were observed. Our results indicate that this method is an alternative to 16S rRNA sequence-based studies which can be scaled up for the purpose of performing a potentially comprehensive assessment of a given microbial community or for comparative studies.
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Affiliation(s)
- Janet E Hill
- National Research Council Plant Biotechnology Institute, University of Saskatchewan, Saskatoon, Canada
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Affiliation(s)
- Martin A Line
- School of Agricultural Science, University of Tasmania, Hobart, Tasmania 7001, Australia1
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Vreeland RH, Rosenzweig WD, Powers DW. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 2000; 407:897-900. [PMID: 11057666 DOI: 10.1038/35038060] [Citation(s) in RCA: 301] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Bacteria have been found associated with a variety of ancient samples, however few studies are generally accepted due to questions about sample quality and contamination. When Cano and Borucki isolated a strain of Bacillus sphaericus from an extinct bee trapped in 25-30 million-year-old amber, careful sample selection and stringent sterilization techniques were the keys to acceptance. Here we report the isolation and growth of a previously unrecognized spore-forming bacterium (Bacillus species, designated 2-9-3) from a brine inclusion within a 250 million-year-old salt crystal from the Permian Salado Formation. Complete gene sequences of the 16S ribosomal DNA show that the organism is part of the lineage of Bacillus marismortui and Virgibacillus pantothenticus. Delicate crystal structures and sedimentary features indicate the salt has not recrystallized since formation. Samples were rejected if brine inclusions showed physical signs of possible contamination. Surfaces of salt crystal samples were sterilized with strong alkali and acid before extracting brines from inclusions. Sterilization procedures reduce the probability of contamination to less than 1 in 10(9).
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Affiliation(s)
- R H Vreeland
- Department of Biology, West Chester University, Pennsylvania 19383, USA.
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McGenity TJ, Gemmell RT, Grant WD, Stan-Lotter H. Origins of halophilic microorganisms in ancient salt deposits. Environ Microbiol 2000; 2:243-50. [PMID: 11200425 DOI: 10.1046/j.1462-2920.2000.00105.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- T J McGenity
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, UK.
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