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Bajerski F, Nagel M, Overmann J. Is the occurrence of microorganism liquid nitrogen storage tanks a challenge for cryobanking? Cryobiology 2022. [DOI: 10.1016/j.cryobiol.2022.11.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Bajerski F, Bürger A, Glasmacher B, Keller EJ, Müller K, Mühldorfer K, Nagel M, Rüdel H, Müller T, Schenkel J, Overmann J. What Factors Affect The Presence of Microorganisms In Cryotanks? - A Culture-Independent Approach To Assess Potential Microbial Colonization of Liquid Nitrogen Storage Tanks. Cryobiology 2021. [DOI: 10.1016/j.cryobiol.2021.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Bajerski F, Nagel M, Overmann J. Microbial occurrence in liquid nitrogen storage tanks: a challenge for cryobanking? Appl Microbiol Biotechnol 2021; 105:7635-7650. [PMID: 34559283 PMCID: PMC8460408 DOI: 10.1007/s00253-021-11531-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/30/2022]
Abstract
Abstract Modern biobanks maintain valuable living materials for medical diagnostics, reproduction medicine, and conservation purposes. To guarantee high quality during long-term storage and to avoid metabolic activities, cryostorage is often conducted in the N2 vapour phase or in liquid nitrogen (LN) at temperatures below − 150 °C. One potential risk of cryostorage is microbial cross contamination in the LN storage tanks. The current review summarises data on the occurrence of microorganisms that may compromise the safety and quality of biological materials during long-term storage. We assess the potential for the microbial contamination of LN in storage tanks holding different biological materials based on the detection by culture-based and molecular approaches. The samples themselves, the LN, the human microbiome, and the surrounding environment are possible routes of contamination and can cause cross contaminations via the LN phase. In general, the results showed that LN is typically not the source of major contaminations and only a few studies provided evidence for a risk of microbial cross contamination. So far, culture-based and culture-independent techniques detected only low amounts of microbial cells, indicating that cross contamination may occur at a very low frequency. To further minimise the potential risk of microbial cross contaminations, we recommend reducing the formation of ice crystals in cryotanks that can entrap environmental microorganisms and using sealed or second sample packing. A short survey demonstrated the awareness for microbial contaminations of storage containers among different culture collections. Although most participants consider the risk of cross contaminations in LN storage tanks as low, they prevent potential contaminations by using sealed devices and − 150 °C freezers. It is concluded that the overall risk for cross contaminations in biobanks is relatively low when following standard operating procedures (SOPs). We evaluated the potential sources in detail and summarised our results in a risk assessment spreadsheet which can be used for the quality management of biobanks. Key points • Identification of potential contaminants and their sources in LN storage tanks. • Recommendations to reduce this risk of LN storage tank contamination. • Development of a risk assessment spreadsheet to support quality management. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11531-4.
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Affiliation(s)
- Felizitas Bajerski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany.
| | - Manuela Nagel
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Seeland OT Gatersleben, Germany
| | - Joerg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124, Brunswick, Germany.,Institute of Microbiology, Braunschweig University of Technology, 38106, Brunswick, Germany
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Vitale GA, Sciarretta M, Palma Esposito F, January GG, Giaccio M, Bunk B, Spröer C, Bajerski F, Power D, Festa C, Monti MC, D'Auria MV, de Pascale D. Genomics-Metabolomics Profiling Disclosed Marine Vibrio spartinae 3.6 as a Producer of a New Branched Side Chain Prodigiosin. J Nat Prod 2020; 83:1495-1504. [PMID: 32275146 DOI: 10.1021/acs.jnatprod.9b01159] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A wide range of prescreening tests for antimicrobial activity of 59 bacterial isolates from sediments of Ria Formosa Lagoon (Algarve, Portugal) disclosed Vibrio spartinae 3.6 as the most active antibacterial producing strain. This bacterial strain, which has not previously been submitted for chemical profiling, was subjected to de novo whole genome sequencing, which aided in the discovery and elucidation of a prodigiosin biosynthetic gene cluster that was predicted by the bioinformatic tool KEGG BlastKoala. Comparative genomics led to the identification of a new membrane di-iron oxygenase-like enzyme, annotated as Vspart_02107, which is likely to be involved in the biosynthesis of cycloprodigiosin and analogues. The combined genomics-metabolomics profiling of the strain led to the isolation and identification of one new branched-chain prodigiosin (5) and to the detection of two new cyclic forms. Furthermore, the evaluation of the minimum inhibitory concentrations disclosed the major prodigiosin as very effective against multi-drug-resistant pathogens including Stenotrophomonas maltophilia, a clinical isolate of Listeria monocytogenes, as well as some human pathogens reported by the World Health Organization as prioritized targets.
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Affiliation(s)
- Giovanni Andrea Vitale
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
| | - Martina Sciarretta
- Department of Pharmacy, University of Naples "Federico II" (UNINA), Via Domenico Montesanto, 49, I-80131 Naples, Italy
| | - Fortunato Palma Esposito
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
- Stazione Zoologica Anton Dohrn (SZN), Villa Comunale di Napoli, I-80121 Naples, Italy
| | - Grant Garren January
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
| | - Marianna Giaccio
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, German
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, German
| | - Felizitas Bajerski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, German
| | - Deborah Power
- Centro de Ciencias do Mar (CCMAR), Universidade do Algarve Campus de Gambelas, 8005-139 Faro, Portugal
| | - Carmen Festa
- Department of Pharmacy, University of Naples "Federico II" (UNINA), Via Domenico Montesanto, 49, I-80131 Naples, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno (UNISA), I-84084 Fisciano, SA, Italy
| | - Maria Valeria D'Auria
- Department of Pharmacy, University of Naples "Federico II" (UNINA), Via Domenico Montesanto, 49, I-80131 Naples, Italy
| | - Donatella de Pascale
- Institute of Biochemistry and Cellular Biology, National Research Council (IBBC-CNR), Via Pietro Castellino 111, I-80131 Naples, Italy
- Stazione Zoologica Anton Dohrn (SZN), Villa Comunale di Napoli, I-80121 Naples, Italy
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Petermann JS, Roberts AL, Hemmerling C, Bajerski F, Pascual J, Overmann J, Weisser WW, Ruess L, Gossner MM. Direct and indirect effects of forest management on tree-hole inhabiting aquatic organisms and their functional traits. Sci Total Environ 2020; 704:135418. [PMID: 31896218 DOI: 10.1016/j.scitotenv.2019.135418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/04/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Ecological communities in forests have been shown to be strongly affected by forest management but a detailed understanding of how different components of management affect insect communities directly and indirectly via environmental variables, how management influences functional trait diversity and composition, and whether these results can be transferred to other functional groups besides insects (e.g. bacteria or nematodes) is still missing. To address these questions we used water-filled tree holes, which provide habitats for insect larvae and other aquatic organisms in forests, as a model system. We mapped all water-filled tree holes in 75 forest plots (1 ha) under different management intensity in three regions of Germany. We measured structural and climatic conditions at different spatial scales, sampled insect communities in 123 tree holes and bacterial and nematode communities in a subset of these. We found that forest management in terms of harvesting intensity and the proportion of non-natural tree species (species not part of the natural vegetation at the sites) negatively affected tree-hole abundance. An increased proportion of non-natural tree species had a positive direct effect on insect richness and functional diversity in the tree holes. However, a structural equation model showed that increasing management intensity had negative indirect effects on insect abundance and richness, operating via environmental variables at stand and tree-hole scale. Functional diversity and trait composition of insect communities similarly responded to changes in management-related variables. In contrast to insects, bacterial and nematode richness were not directly impacted by forest management but by other environmental variables. Our results suggest that forest management may strongly alter insect communities of tree holes, while nematodes and bacteria seem less affected. Most effects in our study were indirect and negative, indicating that management has often complex consequences for forest communities that should be taken into account in forest management schemes.
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Affiliation(s)
- Jana S Petermann
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria.
| | - Anastasia L Roberts
- Department of Biosciences, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria
| | - Christin Hemmerling
- Humboldt-Universität zu Berlin, Institute of Biology, Ecology Group, Philippstraße 13, 10115 Berlin, Germany
| | - Felizitas Bajerski
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Javier Pascual
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany; Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Wolfgang W Weisser
- Technical University of Munich, Hans-von-Carlowitz-Platz 2, D-85354 Freising, Germany
| | - Liliane Ruess
- Humboldt-Universität zu Berlin, Institute of Biology, Ecology Group, Philippstraße 13, 10115 Berlin, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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Bajerski F, Bürger A, Glasmacher B, Keller ERJ, Müller K, Mühldorfer K, Nagel M, Rüdel H, Müller T, Schenkel J, Overmann J. Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples. Appl Microbiol Biotechnol 2019; 104:131-144. [PMID: 31781817 PMCID: PMC6942587 DOI: 10.1007/s00253-019-10242-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 01/19/2023]
Abstract
The availability of bioresources is a precondition for life science research, medical applications, and diagnostics, but requires a dedicated quality management to guarantee reliable and safe storage. Anecdotal reports of bacterial isolates and sample contamination indicate that organisms may persist in liquid nitrogen (LN) storage tanks. To evaluate the safety status of cryocollections, we systematically screened organisms in the LN phase and in ice layers covering inner surfaces of storage tanks maintained in different biobanking facilities. We applied a culture-independent approach combining cell detection by epifluorescence microscopy with the amplification of group-specific marker genes and high-throughput sequencing of bacterial ribosomal genes. In the LN phase, neither cells nor bacterial 16S rRNA gene copy numbers were detectable (detection limit, 102 cells per ml, 103 gene copies per ml). In several cases, small numbers of bacteria of up to 104 cells per ml and up to 106 gene copies per ml, as well as Mycoplasma, or fungi were detected in the ice phase formed underneath the lids or accumulated at the bottom. The bacteria most likely originated from the stored materials themselves (Elizabethingia, Janthibacterium), the technical environment (Pseudomonas, Acinetobacter, Methylobacterium), or the human microbiome (Bacteroides, Streptococcus, Staphylococcus). In single cases, bacteria, Mycoplasma, fungi, and human cells were detected in the debris at the bottom of the storage tanks. In conclusion, the limited microbial load of the ice phase and in the debris of storage tanks can be effectively avoided by minimizing ice formation and by employing hermetically sealed sample containers.
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Affiliation(s)
- F Bajerski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
| | - A Bürger
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, München, Germany
| | - B Glasmacher
- Institute for Multiphase Processes, Leibniz University Hannover, Hannover, Germany
| | - E R J Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - K Müller
- Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany
| | - K Mühldorfer
- Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany
| | - M Nagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - H Rüdel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | | | - J Schenkel
- German Cancer Research Centre, Heidelberg, Germany
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - J Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
- Microbiology, Braunschweig University of Technology, Braunschweig, Germany
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Bajerski F, Stock J, Hanf B, Darienko T, Heine-Dobbernack E, Lorenz M, Naujox L, Keller ERJ, Schumacher HM, Friedl T, Eberth S, Mock HP, Kniemeyer O, Overmann J. ATP Content and Cell Viability as Indicators for Cryostress Across the Diversity of Life. Front Physiol 2018; 9:921. [PMID: 30065659 PMCID: PMC6056685 DOI: 10.3389/fphys.2018.00921] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 06/25/2018] [Indexed: 11/30/2022] Open
Abstract
In many natural environments, organisms get exposed to low temperature and/or to strong temperature shifts. Also, standard preservation protocols for live cells or tissues involve ultradeep freezing in or above liquid nitrogen (-196°C or -150°C, respectively). To which extent these conditions cause cold- or cryostress has rarely been investigated systematically. Using ATP content as an indicator of the physiological state of cells, we found that representatives of bacteria, fungi, algae, plant tissue, as well as plant and human cell lines exhibited similar responses during freezing and thawing. Compared to optimum growth conditions, the cellular ATP content of most model organisms decreased significantly upon treatment with cryoprotectant and cooling to up to -196°C. After thawing and a longer period of regeneration, the initial ATP content was restored or even exceeded the initial ATP levels. To assess the implications of cellular ATP concentration for the physiology of cryostress, cell viability was determined in parallel using independent approaches. A significantly positive correlation of ATP content and viability was detected only in the cryosensitive algae Chlamydomonas reinhardtii SAG 11-32b and Chlorella variabilis NC64A, and in plant cell lines of Solanum tuberosum. When comparing mesophilic with psychrophilic bacteria of the same genera, and cryosensitive with cryotolerant algae, ATP levels of actively growing cells were generally higher in the psychrophilic and cryotolerant representatives. During exposure to ultralow temperatures, however, psychrophilic and cryotolerant species showed a decline in ATP content similar to their mesophilic or cryosensitive counterparts. Nevertheless, psychrophilic and cryotolerant species attained better culturability after freezing. Cellular ATP concentrations and viability measurements thus monitor different features of live cells during their exposure to ultralow temperatures and cryostress.
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Affiliation(s)
- Felizitas Bajerski
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Johanna Stock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Benjamin Hanf
- Leibniz Institute for Natural Product Research and Infection Biology e.V. - Hans-Knöll-Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Tatyana Darienko
- Experimental Phycology and Culture Collection of Algae, University of Göttingen (EPSAG), Göttingen, Germany
| | - Elke Heine-Dobbernack
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Maike Lorenz
- Experimental Phycology and Culture Collection of Algae, University of Göttingen (EPSAG), Göttingen, Germany
| | - Lisa Naujox
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - E R J Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - H M Schumacher
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas Friedl
- Experimental Phycology and Culture Collection of Algae, University of Göttingen (EPSAG), Göttingen, Germany
| | - Sonja Eberth
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Olaf Kniemeyer
- Leibniz Institute for Natural Product Research and Infection Biology e.V. - Hans-Knöll-Institute (HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Bajerski F, Wagner D, Mangelsdorf K. Cell Membrane Fatty Acid Composition of Chryseobacterium frigidisoli PB4 T, Isolated from Antarctic Glacier Forefield Soils, in Response to Changing Temperature and pH Conditions. Front Microbiol 2017; 8:677. [PMID: 28469614 PMCID: PMC5395617 DOI: 10.3389/fmicb.2017.00677] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 04/03/2017] [Indexed: 11/30/2022] Open
Abstract
Microorganisms in Antarctic glacier forefields are directly exposed to the hostile environment of their habitat characterized by extremely low temperatures and changing geochemical conditions. To survive under those stress conditions microorganisms adapt, among others, their cell membrane fatty acid inventory. However, only little is known about the adaptation potential of microorganisms from Antarctic soil environments. In this study, we examined the adaptation of the cell membrane polar lipid fatty acid inventory of Chryseobacterium frigidisoli PB4T in response to changing temperature (0°C to 20°C) and pH (5.5 to 8.5) regimes, because this new strain isolated from an Antarctic glacier forefield showed specific adaptation mechanisms during its detailed physiological characterization. Flavobacteriaceae including Chryseobacterium species occur frequently in extreme habitats such as ice-free oases in Antarctica. C. frigidisoli shows a complex restructuring of membrane derived fatty acids in response to different stress levels. Thus, from 20°C to 10°C a change from less iso-C15:0 to more iso-C17:1ω7 is observed. Below 10°C temperature adaptation is regulated by a constant increase of anteiso-FAs and decrease of iso-FAs. An anteiso- and bis-unsaturated fatty acid, anteiso-heptadeca-9,13-dienoic acid, shows a continuous increase with decreasing cultivation temperatures underlining the particular importance of this fatty acid for temperature adaptation in C. frigidisoli. Concerning adaptation to changing pH conditions, most of the dominant fatty acids reveal constant relative proportions around neutral pH (pH 6–8). Strong variations are mainly observed at the pH extremes (pH 5.5 and 8.5). At high pH short chain saturated iso- and anteiso-FAs increase while longer chain unsaturated iso- and anteiso-FAs decrease. At low pH the opposite trend is observed. The study shows a complex interplay of different membrane components and provides, therefore, deep insights into adaptation strategies of microorganisms from extreme habitats to changing environmental conditions.
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Affiliation(s)
- Felizitas Bajerski
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine ResearchPotsdam, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 5.3 GeomicrobiologyPotsdam, Germany
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.2 Organic GeochemistryPotsdam, Germany
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Bajerski F, Senula A, Keller J, Overmann J. Novel insights into cellular processes affecting the cryopreservation of bacterial and eukaryotic cells. Cryobiology 2015. [DOI: 10.1016/j.cryobiol.2015.10.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ganzert L, Bajerski F, Wagner D. Bacterial community composition and diversity of five different permafrost-affected soils of Northeast Greenland. FEMS Microbiol Ecol 2014; 89:426-41. [DOI: 10.1111/1574-6941.12352] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 03/05/2014] [Accepted: 05/07/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lars Ganzert
- Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | - Felizitas Bajerski
- Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; Potsdam Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences; Section 4.5 Geomicrobiology; Potsdam Germany
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Bajerski F, Wagner D. Bacterial succession in Antarctic soils of two glacier forefields on Larsemann Hills, East Antarctica. FEMS Microbiol Ecol 2013; 85:128-42. [PMID: 23480659 DOI: 10.1111/1574-6941.12105] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 02/28/2013] [Accepted: 02/28/2013] [Indexed: 11/29/2022] Open
Abstract
Antarctic glacier forefields are extreme environments and pioneer sites for ecological succession. Increasing temperatures due to global warming lead to enhanced deglaciation processes in cold-affected habitats, and new terrain is becoming exposed to soil formation and microbial colonization. However, only little is known about the impact of environmental changes on microbial communities and how they develop in connection to shifting habitat characteristics. In this study, using a combination of molecular and geochemical analysis, we determine the structure and development of bacterial communities depending on soil parameters in two different glacier forefields on Larsemann Hills, East Antarctica. Our results demonstrate that deglaciation-dependent habitat formation, resulting in a gradient in soil moisture, pH and conductivity, leads to an orderly bacterial succession for some groups, for example Cyanobacteria, Bacteroidetes and Deltaproteobacteria in a transect representing 'classical' glacier forefields. A variable bacterial distribution and different composed communities were revealed according to soil heterogeneity in a slightly 'matured' glacier forefield transect, where Gemmatimonadetes, Flavobacteria, Gamma- and Deltaproteobacteria occur depending on water availability and soil depth. Actinobacteria are dominant in both sites with dominance connected to certain trace elements in the glacier forefields.
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Affiliation(s)
- Felizitas Bajerski
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Potsdam, Germany.
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Bajerski F, Ganzert L, Mangelsdorf K, Lipski A, Busse HJ, Padur L, Wagner D. Herbaspirillum psychrotolerans sp. nov., a member of the family Oxalobacteraceae from a glacier forefield. Int J Syst Evol Microbiol 2013; 63:3197-3203. [PMID: 23456802 DOI: 10.1099/ijs.0.046920-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel psychrotolerant, Gram-negative, shiny white, curved-rod-shaped, facultatively anaerobic bacterium PB1(T) was isolated from a soil sample collected from a glacier forefield of the Larsemann Hills, East Antarctica. Isolate PB1(T) has catalase and low urease activity and hydrolyses gelatin and starch. Strain PB1(T) is able to grow between -5 °C and 30 °C with optimum growth at 14-20 °C. Glycerol, dl-arabinose, d-xylose, d-galactose, d-fructose, d-lyxose, d-fucose and potassium gluconate are used as sole carbon sources. The major quinone is ubiquinone Q-8. The major fatty acids (>10%) for PB1(T) are C(16:0) (19.1%), C(16:1)ω7cis (44.6%) and C(18:1)ω7cis (16.2%). The major polyamines are putrescine [54.9 µmol (g dry weight)(-1)] and 2-hydroxy putrescine [18.5 µmol (g dry weight)(-1)]. DNA G+C content is 62.5 mol%. Strain PB1(T) is phylogenetically related to species of the genus Herbaspirillum, with highest 16S rRNA gene sequence similarities to Herbaspirillum canariense (97.3%), Herbaspirillum aurantiacum (97.2%), Herbaspirillum soli (97.2%) and Herbaspirillum frisingense (97.0%). The DNA-DNA relatedness values were below 30% between PB1(T) and the type strains of Herbaspirillum canariense, Herbaspirillum aurantiacum and Herbaspirillum soli. The different geographical origin of strain PB1(T) from its closest phylogenetic relatives resulted in different phenotypic and genotypic specifications, whereby strain PB(T) represents a novel species of the genus Herbaspirillum, for which the name Herbaspirillum psychrotolerans is proposed. The type strain is PB1(T) (DSM 26001(T) =LMG 27282(T)).
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Affiliation(s)
- Felizitas Bajerski
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Germany
| | - Lars Ganzert
- University of Tromsø, Department for Arctic and Marine Biology, Tromsø, Norway
| | - Kai Mangelsdorf
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Section 4.3, Organic Geochemistry, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, Bonn, Germany
| | - Hans-Jürgen Busse
- University of Veterinary Medicine Vienna, Division for Clinical Microbiology and Infectious Biology, Vienna, Austria
| | - Lisa Padur
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Germany
| | - Dirk Wagner
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Section 4.5 Geomicrobiology, Potsdam, Germany.,Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Germany
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Bajerski F, Ganzert L, Mangelsdorf K, Padur L, Lipski A, Wagner D. Chryseobacterium frigidisoli sp. nov., a psychrotolerant species of the family Flavobacteriaceae isolated from sandy permafrost from a glacier forefield. Int J Syst Evol Microbiol 2013; 63:2666-2671. [PMID: 23291884 DOI: 10.1099/ijs.0.046904-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During diversity studies of the glacier forefields of the Larsemann Hills, East Antarctica, a novel psychrotolerant, non-motile Gram-negative, shiny yellow, rod-shaped, aerobic bacterium, designated strain PB4(T) was isolated from a soil sample. Strain PB4(T) produces indole from tryptophan and hydrolyses casein. It grows between 0 and 25 °C with an optimum growth temperature of 20 °C. A wide range of substrates are used as sole carbon sources and acid is produced from numerous carbohydrates. The major menaquinone is MK-6. Identified polar lipids are ethanolamines and ornithine lipids. Major fatty acids (>10 %) are iso-C15 : 0 (13.0 %) and iso-2OH-C15 : 0 (51.2 %). G+C content is 33.7 mol%. The polyamine pattern is composed of sym-homospermidine (25.1 µmol g(-1) dry weight), minor amounts of cadaverine (0.2 µmol g(-1) dry weight) and spermidine (0.4 µmol g(-1) dry weight) and traces of putrescine and spermine (<0.1 µmol g(-1) dry weight). Strain PB4(T) had highest 16S rRNA gene similarities with the type strains of Chryseobacterium humi (97.0 %) and Chryseobacterium marinum (96.5 %). Considering phenotypic and genotypic characterization, strain PB4(T) represents a novel species in the genus Chryseobacterium (family Flavobacteriaceae), for which the name Chryseobacterium frigidisoli sp. nov. is proposed. The type strain is PB4(T) ( = DSM 26000(T) = LMG 27025(T)).
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Affiliation(s)
- Felizitas Bajerski
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Germany
| | - Lars Ganzert
- University of Tromsø, Department for Arctic and Marine Biology, Tromsø, Norway
| | - Kai Mangelsdorf
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Section 4.3, Organic Geochemistry, Germany
| | - Lisa Padur
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, Bonn, Germany
| | - Dirk Wagner
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Germany
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Bajerski F, Ganzert L, Mangelsdorf K, Lipski A, Wagner D. Cryobacterium arcticum sp. nov., a psychrotolerant bacterium from an Arctic soil. Int J Syst Evol Microbiol 2011; 61:1849-1853. [DOI: 10.1099/ijs.0.027128-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
A psychrotolerant, Gram-stain-positive, yellow-pigmented, aerobic rod, designated SK1T, was isolated from a soil sample collected from Store Koldewey, north-east Greenland. Cells were catalase- and methyl red-positive, produced H2S and produced acid from glucose, mannitol and salicin. Strain SK1T was able to grow between −6 and 28 °C, with an optimum at 20 °C. The isolate contained 2,4-diaminobutyrate, glycine, alanine and glutamic acid in the cell wall and the major menaquinones were MK-10 and MK-11. Identified polar lipids were phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were anteiso-C15 : 0 (53.5 %), anteiso-C17 : 0 (17.0 %) and C18 : 0 (12.1 %). The genomic DNA G+C content was 67.8 mol%. Strain SK1T showed the highest 16S rRNA gene sequence similarity with Cryobacterium psychrotolerans 0549T (97.6 %) and Cryobacterium roopkundense RuGl7T (96.8 %). Considering morphological, physiological, biochemical and chemotaxonomic characters and phylogenetic analysis, strain SK1T represents a novel species in the genus Cryobacterium, for which the name Cryobacterium arcticum sp. nov. is proposed. The type strain is SK1T ( = DSM 22823T = NCCB 100316T).
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Affiliation(s)
- Felizitas Bajerski
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
| | - Lars Ganzert
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
| | - Kai Mangelsdorf
- Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Sektion 4.3, Organic Geochemistry, Telegrafenberg, B 423, 14473 Potsdam, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Dirk Wagner
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
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Ganzert L, Bajerski F, Mangelsdorf K, Lipski A, Wagner D. Arthrobacter livingstonensis sp. nov. and Arthrobacter cryotolerans sp. nov., salt-tolerant and psychrotolerant species from Antarctic soil. Int J Syst Evol Microbiol 2011; 61:979-984. [DOI: 10.1099/ijs.0.021022-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel cold-tolerant, Gram-stain-positive, motile, facultatively anaerobic bacterial strains, LI2T and LI3T, were isolated from moss-covered soil from Livingston Island, Antarctica, near the Bulgarian station St Kliment Ohridski. A rod–coccus cycle was observed for both strains. 16S rRNA gene sequence analysis revealed an affiliation to the genus Arthrobacter, with the highest similarity to Arthrobacter stackebrandtii and Arthrobacter psychrochitiniphilus for strain LI2T (97.8 and 97.7 % similarity to the respective type strains) and to Arthrobacter kerguelensis and Arthrobacter psychrophenolicus for strain LI3T (97.4 and 97.3 % similarity to the respective type strains). The growth temperature range was −6 to 28 °C for LI2T and −6 to 24 °C for LI3T, with an optimum at 16 °C for both strains. Growth occurred at 0–10 % (w/v) NaCl, with optimum growth at 0–1 % (w/v) for LI2T and 0.5–3 % (w/v) for LI3T. The pH range for growth was pH 4–9.5 with an optimum of pH 8 for LI2T and pH 6.5 for LI3T. The predominant fatty acids were anteiso-C15 : 0, C18 : 0 and anteiso-C17 : 0 for LI2T and anteiso-C15 : 0 and C18 : 0 for LI3T. Physiological and biochemical tests clearly differentiated strain LI2T from A. stackebrandtii and A. psychrochitiniphilus and strain LI3T from A. kerguelensis and A. psychrophenolicus. Therefore, two novel species within the genus Arthrobacter are proposed: Arthrobacter livingstonensis sp. nov. (type strain LI2T = DSM 22825T = NCCB 100314T) and Arthrobacter cryotolerans sp. nov. (type strain LI3T = DSM 22826T = NCCB 100315T).
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Affiliation(s)
- Lars Ganzert
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
| | - Felizitas Bajerski
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
| | - Kai Mangelsdorf
- Helmholtz Centre Potsdam GFZ German Research Centre for Geosciences, Section 4.3, Organic Geochemistry, Telegrafenberg B 423, 14473 Potsdam, Germany
| | - André Lipski
- Rheinische Friedrich-Wilhelms-Universität Bonn, Institute of Nutrition and Food Sciences, Department of Food Microbiology and Hygiene, Meckenheimer Allee 168, 53115 Bonn, Germany
| | - Dirk Wagner
- Alfred Wegener Institute for Polar and Marine Research, Research Department Potsdam, Telegrafenberg A45, 14473 Potsdam, Germany
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