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Brück P, Wasser D, Soppa J. One Advantage of Being Polyploid: Prokaryotes of Various Phylogenetic Groups Can Grow in the Absence of an Environmental Phosphate Source at the Expense of Their High Genome Copy Numbers. Microorganisms 2023; 11:2267. [PMID: 37764113 PMCID: PMC10536925 DOI: 10.3390/microorganisms11092267] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Genomic DNA has high phosphate content; therefore, monoploid prokaryotes need an external phosphate source or an internal phosphate storage polymer for replication and cell division. For two polyploid prokaryotic species, the halophilic archaeon Haloferax volcanii and the cyanobacterium Synechocystis PCC 6803, it has been reported that they can grow in the absence of an external phosphate source by reducing the genome copy number per cell. To unravel whether this feature might be widespread in and typical for polyploid prokaryotes, three additional polyploid prokaryotic species were analyzed in the present study, i.e., the alphaproteobacterium Zymomonas mobilis, the gammaproteobacterium Azotobacter vinelandii, and the haloarchaeon Halobacterium salinarum. Polyploid cultures were incubated in the presence and in the absence of external phosphate, growth was recorded, and genome copy numbers per cell were quantified. Limited growth in the absence of phosphate was observed for all three species. Phosphate was added to phosphate-starved cultures to verify that the cells were still viable and growth-competent. Remarkably, stationary-phase cells grown in the absence or presence of phosphate did not become monoploid but stayed oligoploid with about five genome copies per cell. As a negative control, it was shown that monoploid Escherichia coli cultures did not exhibit any growth in the absence of phosphate. Taken together, all five polyploid prokaryotic species that have been characterized until now can grow in the absence of environmental phosphate by reducing their genome copy numbers, indicating that cell proliferation outperforms other evolutionary advantages of polyploidy.
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Affiliation(s)
| | | | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Goethe University, Max-von-Laue-Str. 9, D-60438 Frankfurt, Germany (D.W.)
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2
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Zhou S, Yang Z, Zhang S, Gao Y, Tang Z, Duan Y, Zhang Y, Wang Y. Metagenomic insights into the distribution, mobility, and hosts of extracellular antibiotic resistance genes in activated sludge under starvation stress. WATER RESEARCH 2023; 236:119953. [PMID: 37060877 DOI: 10.1016/j.watres.2023.119953] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 06/19/2023]
Abstract
Extracellular antibiotic resistance genes (eARGs) are important emerging environmental pollutants in wastewater treatment plants (WWTPs). Nutritional substrate deficiency (i.e., starvation) frequently occurs in WWTPs owing to annual maintenance, water quality fluctuation, and sludge storage; and it can greatly alter the antibiotic resistance and extracellular DNA content of bacteria. However, the fate and corresponding transmission risk of eARGs in activated sludge under starvation stress remain largely unknown. Herein, we used metagenomic sequencing to explore the effects of starvation scenarios (carbon, nitrogen, and/or phosphorus deficiency) and environmental conditions (alternating anaerobic-aerobic, anaerobic, anoxic, and aerobic) on the distribution, mobility, and hosts of eARGs in activated sludge. The results showed that 30 days of starvation reduced the absolute abundances of eARGs by 40.9%-88.2%, but high-risk dual and multidrug resistance genes persisted. Starvation, particularly the simultaneous lack of carbon, nitrogen, and phosphorus under aerobic conditions, effectively alleviated eARGs by reducing the abundance of extracellular mobile genetic elements (eMGEs). Starvation also altered the profile of bacterial hosts of eARGs and the bacterial community composition, the latter of which had an indirect positive effect on eARGs via changing eMGEs. Our findings shed light on the response patterns and mechanisms of eARGs in activated sludge under starvation conditions and highlight starvation as a potential strategy to mitigate the risk of previously neglected eARGs in WWTPs.
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Affiliation(s)
- Shuai Zhou
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, China; Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, School of Civil Engineering, University of South China, Hengyang 421001, China
| | - Zhengqing Yang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, School of Civil Engineering, University of South China, Hengyang 421001, China
| | - Siqi Zhang
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, School of Civil Engineering, University of South China, Hengyang 421001, China
| | - Yuanyuan Gao
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang 421001, China
| | - Zhenping Tang
- Hunan Province Key Laboratory of Rare Metal Minerals Exploitation and Geological Disposal of Wastes, University of South China, Hengyang 421001, China
| | - Yi Duan
- Hunan Province Key Laboratory of Pollution Control and Resources Reuse Technology, School of Civil Engineering, University of South China, Hengyang 421001, China
| | - Yalei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, China
| | - Yayi Wang
- State Key Laboratory of Pollution Control and Resources Reuse, College of Environmental Science and Engineering, Tongji University, Siping Road, Shanghai 200092, China.
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3
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Robinson A, Ulrich SM. Haloferax volcanii Remains Viable and Shows Morphological Changes under Anoxic (CO 2-Enriched) and Hypobaric (2.4 kPa) Atmospheric Conditions. ASTROBIOLOGY 2022; 22:829-837. [PMID: 35325555 DOI: 10.1089/ast.2021.0076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Potentially habitable zones have been discovered on Mars today in underground areas containing perchlorate brines. Understanding the low-pressure adaptations of microorganisms is essential in learning more about what life could potentially be found on Mars today or could have existed in the distant past. Many studies have looked at low-pressure adaptations in bacteria; however, studies aimed at understanding these adaptations in archaea are scarcer. Haloferax volcanii is a species of halophilic archaea documented to tolerate high concentrations of oxidizing agents present on Mars (i.e., perchlorates and nitrates). In this study, we expose H. volcanii to a hypobaric (2.4 kPa) and an anoxic CO2-enriched atmosphere in the presence of perchlorate, chlorate, and nitrate. While no growth was observed during incubation in these conditions, survivability was increased in cultures incubated in low-pressure atmospheric conditions compared to ambient Earth atmospheric pressures. Scanning electron microscopy observations showed morphological changes in low-pressure conditions not observed at ambient Earth atmospheric pressures. Results suggest that previously undocumented low-pressure adaptations in H. volcanii increase survivability in simulated subsurface martian conditions. Future experiments to understand the changes in gene expression under these conditions may be valuable to understand more about low-pressure adaptations in archaea.
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Affiliation(s)
- Adam Robinson
- Department of Natural Science, St. Petersburg College, Clearwater, Florida, USA
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4
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Gophna U, Altman-Price N. Horizontal Gene Transfer in Archaea-From Mechanisms to Genome Evolution. Annu Rev Microbiol 2022; 76:481-502. [PMID: 35667126 DOI: 10.1146/annurev-micro-040820-124627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Archaea remains the least-studied and least-characterized domain of life despite its significance not just to the ecology of our planet but also to the evolution of eukaryotes. It is therefore unsurprising that research into horizontal gene transfer (HGT) in archaea has lagged behind that of bacteria. Indeed, several archaeal lineages may owe their very existence to large-scale HGT events, and thus understanding both the molecular mechanisms and the evolutionary impact of HGT in archaea is highly important. Furthermore, some mechanisms of gene exchange, such as plasmids that transmit themselves via membrane vesicles and the formation of cytoplasmic bridges that allows transfer of both chromosomal and plasmid DNA, may be archaea specific. This review summarizes what we know about HGT in archaea, and the barriers that restrict it, highlighting exciting recent discoveries and pointing out opportunities for future research. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; ,
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel; , .,Department of Natural and Life Sciences, The Open University of Israel, Raanana, Israel
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5
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Wang Y, Li T, Xue W, Zheng Y, Wang Y, Zhang N, Zhao Y, Wang J, Li Y, Wang C, Hu W. Physicochemical and Biological Insights Into the Molecular Interactions Between Extracellular DNA and Exopolysaccharides in Myxococcus xanthus Biofilms. Front Microbiol 2022; 13:861865. [PMID: 35531272 PMCID: PMC9073016 DOI: 10.3389/fmicb.2022.861865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular DNA (eDNA) is a critical component in the extracellular matrix (ECM) of bacterial biofilms, while little is known about the mechanisms underlying how eDNA integrates into the ECM through potential macromolecular interactions. Myxococcus xanthus biofilm was employed as a suitable model for the investigation due to the co-distribution of eDNA and exopolysaccharides (EPS) owing to their direct interactions in the ECM. DNA is able to combine with M. xanthus EPS to form a macromolecular conjugate, which is dominated by the electrostatic forces participating in the polymer-polymer interactions. Without intercalation binding, DNA-EPS interactions exhibit a certain degree of reversibility. Acting as a strong extracellular framework during biofilm formation process, the eDNA-EPS complex not only facilitates the initial cell adhesion and subsequent establishment of ECM architecture, but also renders cells within biofilms stress resistances that are relevant to the survival of M. xanthus in some hostile environments. Furthermore, the EPS protects the conjugated DNA from the degradation by nucleic acid hydrolases, which leads to the continuous and stable existence of eDNA in the native ECM of M. xanthus biofilms. These results will shed light on developing prevention and treatment strategies against biofilm-related risks.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Tingyi Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weiwei Xue
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yue Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yipeng Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Ning Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yue Zhao
- College of Pharmaceutical Science, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jing Wang
- College of Pharmaceutical Science, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Chuandong Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- *Correspondence: Chuandong Wang,
| | - Wei Hu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- Wei Hu,
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6
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Tellgren-Roth C, Couturier M. Detecting DNA Methylations in the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius Using SMRT Sequencing. Methods Mol Biol 2022; 2516:39-50. [PMID: 35922620 DOI: 10.1007/978-1-0716-2413-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA methylations are one of the most well-known epigenetic modifications along with histone modifications and noncoding RNAs. They are found at specific sites along the DNA in all domains of life, with 5-mC and 6-mA/4-mC being well-characterized in eukaryotes and bacteria respectively, and they have not only been described as contributing to the structure of the double helix itself but also as regulators of DNA-based processes such as replication, transcription, and recombination. Different methods have been developed to accurately identify and/or map methylated motifs to decipher the involvement of DNA methylations in regulatory networks that affect the cellular state.Although DNA methylations have been detected along archaeal genomes, their involvement as regulators of DNA-based processes remains the least known. To highlight the importance of DNA methylations in the control of key cellular mechanisms and their dynamics in archaea cells, we have used single-molecule real-time (SMRT) sequencing. This sequencing technology allows the identification and direct mapping of the methylated motifs along the genome of an organism. In this chapter, we present a step-by-step protocol for detecting DNA methylations in the hyperthermophilic crenarchaeon Sulfolobus acidocaldarius using SMRT sequencing. This protocol can easily be adapted to other prokaryotes.
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Affiliation(s)
- Christian Tellgren-Roth
- Department of Immunology, Genetics and Pathology, National Genomics Infrastructure, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mohea Couturier
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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7
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Hua Z, Ouellette M, Makkay AM, Papke RT, Zhaxybayeva O. Nutrient supplementation experiments with saltern microbial communities implicate utilization of DNA as a source of phosphorus. THE ISME JOURNAL 2021; 15:2853-2864. [PMID: 33846564 PMCID: PMC8443641 DOI: 10.1038/s41396-021-00960-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 02/01/2023]
Abstract
All environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities used DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. The preferential eDNA consumption and differential growth under various nutrient availability regimes were associated with substantial shifts in the taxonomic composition and diversity of microcosm communities. Therefore, we conjecture that in salterns the microbial community assembly is driven by the available resources, including eDNA.
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Affiliation(s)
- Zhengshuang Hua
- grid.254880.30000 0001 2179 2404Department of Biological Sciences, Dartmouth College, Hanover, NH USA ,grid.59053.3a0000000121679639Present Address: Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei, PR China
| | - Matthew Ouellette
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA ,grid.38142.3c000000041936754XPresent Address: The Forsyth Institute, Cambridge, MA USA ,grid.38142.3c000000041936754XPresent Address: Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA USA
| | - Andrea M. Makkay
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA
| | - R. Thane Papke
- grid.63054.340000 0001 0860 4915Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT USA
| | - Olga Zhaxybayeva
- grid.254880.30000 0001 2179 2404Department of Biological Sciences, Dartmouth College, Hanover, NH USA ,grid.254880.30000 0001 2179 2404Department of Computer Science, Dartmouth College, Hanover, NH USA
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8
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Prokaryotic Communities in the Thalassohaline Tuz Lake, Deep Zone, and Kayacik, Kaldirim and Yavsan Salterns (Turkey) Assessed by 16S rRNA Amplicon Sequencing. Microorganisms 2021; 9:microorganisms9071525. [PMID: 34361960 PMCID: PMC8304926 DOI: 10.3390/microorganisms9071525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 01/31/2023] Open
Abstract
Prokaryotic communities and physico-chemical characteristics of 30 brine samples from the thalassohaline Tuz Lake (Salt Lake), Deep Zone, Kayacik, Kaldirim, and Yavsan salterns (Turkey) were analyzed using 16S rRNA amplicon sequencing and standard methods, respectively. Archaea (98.41% of reads) was found to dominate in these habitats in contrast to the domain Bacteria (1.38% of reads). Representatives of the phylum Euryarchaeota were detected as the most predominant, while 59.48% and 1.32% of reads, respectively, were assigned to 18 archaeal genera, 19 bacterial genera, 10 archaeal genera, and one bacterial genus that were determined to be present, with more than 1% sequences in the samples. They were the archaeal genera Haloquadratum, Haloarcula, Halorhabdus, Natronomonas, Halosimplex, Halomicrobium, Halorubrum, Halonotius, Halolamina, Halobacterium, and Salinibacter within the domain Bacteria. The genera Haloquadratum and Halorhabdus were found in all sampling sites. While Haloquadratum, Haloarcula, and Halorhabdus were the most abundant genera, two uncultured Tuz Lake Halobacteria (TLHs) 1 and 2 were detected in high abundance, and an additional uncultured haloarchaeal TLH-3 was found as a minor abundant uncultured taxon. Their future isolation in pure culture would permit us to expand our knowledge on hypersaline thalassohaline habitats, as well as their ecological role and biomedical and biotechnological potential applications.
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9
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Huby TJC, Clark DR, McKew BA, McGenity TJ. Extremely halophilic archaeal communities are resilient to short-term entombment in halite. Environ Microbiol 2021; 23:3370-3383. [PMID: 31919959 PMCID: PMC8359394 DOI: 10.1111/1462-2920.14913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite-entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory-grown halite over 21 weeks, using high-throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite-entombed communities. These results show that halite-entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of 'halite specialists' observed in ancient halite must occur over periods of years, rather than months, hinting at long-term successional dynamics in this environment.
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Affiliation(s)
- Tom J. C. Huby
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Dave R. Clark
- School of Life SciencesUniversity of EssexColchesterEssexUK
| | - Boyd A. McKew
- School of Life SciencesUniversity of EssexColchesterEssexUK
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10
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Aldeguer-Riquelme B, Ramos-Barbero MD, Santos F, Antón J. Environmental dissolved DNA harbours meaningful biological information on microbial community structure. Environ Microbiol 2021; 23:2669-2682. [PMID: 33817941 DOI: 10.1111/1462-2920.15510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/03/2021] [Indexed: 01/21/2023]
Abstract
Extracellular DNA (eDNA) comprises all the DNA molecules outside cells. This component of microbial ecosystems may serve as a source of nutrients and genetic information. Hypersaline environments harbour one of the highest concentrations of eDNA reported for natural systems, which has been attributed to the physicochemical preservative effect of salts and to high viral abundance. Here, we compared centrifugation and filtration protocols for the extraction of dissolved DNA (dDNA, as opposed to eDNA that also includes DNA from free viral particles) from a solar saltern crystallizer pond (CR30) water sample. The crystallizer dDNA fraction has been characterized, for the first time, and compared with cellular and viral metagenomes from the same location. High-speed centrifugation affected CR30 dDNA concentration and composition due to cell lysis, highlighting that protocol optimization should be the first step in dDNA studies. Crystallizer dDNA, which accounted for lower concentrations than those previously reported for hypersaline anoxic sediments, had a mixed viral and cellular origin, was enriched in archaeal DNA and had a distinctive taxonomic composition compared to that from the cellular assemblage of the same sample. Bioinformatic analyses indicated that nanohaloarchaeal viruses could be a cause for these differences.
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Affiliation(s)
- Borja Aldeguer-Riquelme
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain
| | | | - Fernando Santos
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain
| | - Josefa Antón
- Department of Physiology, Genetics, and Microbiology, University of Alicante, Alicante, 03080, Spain.,Multidisciplinary Institute of Environmental Studies Ramón Margalef, University of Alicante, Alicante, 03080, Spain
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11
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Guo L, Wang J, Gou Y, Tan L, Liu H, Pan Y, Zhao Y. Comparative proteomics reveals stress responses of Vibrio parahaemolyticus biofilm on different surfaces: Internal adaptation and external adjustment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:138386. [PMID: 32417469 DOI: 10.1016/j.scitotenv.2020.138386] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Vibrio parahaemolyticus is a kind of gram-negative marine pathogen, which usually adheres to stainless steel (SS), glass (GS) and other abiotic surfaces in aquaculture and food processing in the form of biofilm and causes the spread of gastrointestinal illness. However, the deeply survival adaptation mechanism of V. parahaemolyticus biofilm cells on these contact surface remained unclear. Here, proteomics was used to investigated the physiological response of the V. parahaemolyticus biofilms cells to different abiotic surfaces (SS, GS and polystyrene (PS)). In addition, the effect of contact materials on the physical-chemical properties of biofilms are also characterized. Results showed that the expression of proteins of biofilm cells established on the SS surface were mainly related to the alleviation of metal ion stress and toxicity. The up-regulated proteins in the biofilm cells formed on the GS surface were mainly involved in the biological processes of sugar uptake, protein synthesis and bacterial chemotaxis. Meanwhile, the significantly expressed proteins in the biofilm cells formed on the PS surface were mainly involved in the cellular physiological activity of aromatic compound metabolism, osmotic stress and nutrient transport. All functional proteins mentioned above were closely related to the interaction characteristics of the contact surface and biofilm. This study provided an in-depth comparison of V. parahaemolyticus biofilm formation on these three abiotic surfaces, and presented a model in first time for the adaptation behavior of biofilm cells on different surfaces as affected by metal ion stress, nutrition, osmotic stress, and sugar utilization, which could facilitate an efficient control strategy for biofilm formation in industrial field.
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Affiliation(s)
- Linxia Guo
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Jingjing Wang
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China; Department of Food Science, Foshan University, Foshan, 528000, China
| | - Yi Gou
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Ling Tan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China; Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingjie Pan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China.
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12
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Dombrowski N, Williams TA, Sun J, Woodcroft BJ, Lee JH, Minh BQ, Rinke C, Spang A. Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nat Commun 2020; 11:3939. [PMID: 32770105 PMCID: PMC7414124 DOI: 10.1038/s41467-020-17408-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/25/2020] [Indexed: 01/08/2023] Open
Abstract
The recently discovered DPANN archaea are a potentially deep-branching, monophyletic radiation of organisms with small cells and genomes. However, the monophyly and early emergence of the various DPANN clades and their role in life's evolution are debated. Here, we reconstructed and analysed genomes of an uncharacterized archaeal phylum (Candidatus Undinarchaeota), revealing that its members have small genomes and, while potentially being able to conserve energy through fermentation, likely depend on partner organisms for the acquisition of certain metabolites. Our phylogenomic analyses robustly place Undinarchaeota as an independent lineage between two highly supported 'DPANN' clans. Further, our analyses suggest that DPANN have exchanged core genes with their hosts, adding to the difficulty of placing DPANN in the tree of life. This pattern can be sufficiently dominant to allow identifying known symbiont-host clades based on routes of gene transfer. Together, our work provides insights into the origins and evolution of DPANN and their hosts.
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Affiliation(s)
- Nina Dombrowski
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Benjamin J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jun-Hoe Lee
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden
| | - Bui Quang Minh
- Research School of Computer Science and Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, NL-1790 AB, Den Burg, The Netherlands.
- Department of Cell- and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-75123, Uppsala, Sweden.
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13
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Li W, Wang JJ, Qian H, Tan L, Zhang Z, Liu H, Pan Y, Zhao Y. Insights Into the Role of Extracellular DNA and Extracellular Proteins in Biofilm Formation of Vibrio parahaemolyticus. Front Microbiol 2020; 11:813. [PMID: 32508761 PMCID: PMC7248202 DOI: 10.3389/fmicb.2020.00813] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/06/2020] [Indexed: 12/26/2022] Open
Abstract
The extracellular polymeric substances (EPS) construct the three-dimensional (3-D) structure of biofilms, but their respective roles are still not clear. Therefore, this study aimed to illuminate the role of key chemical components [extracellular DNA (eDNA), extracellular proteins, and carbohydrates] of EPS in biofilm formation of Vibrio parahaemolyticus. The correlations between each key chemical component and biofilm formation were first determined, showing that the biofilm formation of V. parahaemolyticus was strongly positively correlated with both eDNA and protein content (P < 0.01), but not with carbohydrates. Subsequently, individual DNase I or protease K treatment markedly reduced the initial adhesion and structural stability of the formed biofilms by hydrolyzing the eDNA or extracellular proteins, but did not induce significant dispersion of mature biofilms. However, the combination of DNase I and protease K treatment induced the obvious dispersion of the mature biofilms through the concurrent destruction of eDNA and extracellular proteins. The analysis at a structural level showed that the collapse of biofilms was mainly attributed to the great damage of the loop configuration of eDNA and the secondary structure of proteins caused by the enzyme treatment. Therefore, this study provides a deep understanding of the role of key chemical components of EPS in biofilm development of V. parahaemolyticus, which may give a new strategy to develop environmentally friendly methods to eradicate the biofilms in food industry.
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Affiliation(s)
- Wei Li
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jing Jing Wang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
| | - Hui Qian
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Ling Tan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China.,Engineering Research Center of Food Thermal-Processing Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation, Ministry of Agriculture, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing and Preservation, Shanghai, China
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14
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Chalmers TJ, Wu LE. Transposable Elements Cross Kingdom Boundaries and Contribute to Inflammation and Ageing: Somatic Acquisition of Foreign Transposable Elements as a Catalyst of Genome Instability, Epigenetic Dysregulation, Inflammation, Senescence, and Ageing. Bioessays 2020; 42:e1900197. [PMID: 31994769 DOI: 10.1002/bies.201900197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/23/2019] [Indexed: 01/07/2023]
Abstract
The de-repression of transposable elements (TEs) in mammalian genomes is thought to contribute to genome instability, inflammation, and ageing, yet is viewed as a cell-autonomous event. In contrast to mammalian cells, prokaryotes constantly exchange genetic material through TEs, crossing both cell and species barriers, contributing to rapid microbial evolution and diversity in complex communities such as the mammalian gut. Here, it is proposed that TEs released from prokaryotes in the microbiome or from pathogenic infections regularly cross the kingdom barrier to the somatic cells of their eukaryotic hosts. It is proposed this horizontal transfer of TEs from microbe to host is a stochastic, ongoing catalyst of genome destabilization, resulting in structural and epigenetic variations, and activation of well-evolved host defense mechanisms contributing to inflammation, senescence, and biological ageing. It is proposed that innate immunity pathways defend against the horizontal acquisition of microbial TEs, and that activation of this pathway during horizontal transposon transfer promotes chronic inflammation during ageing. Finally, it is suggested that horizontal acquisition of prokaryotic TEs into mammalian genomes has been masked and subsequently under-reported due to flaws in current sequencing pipelines, and new strategies to uncover these events are proposed.
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Affiliation(s)
| | - Lindsay E Wu
- School of Medical Sciences, UNSW, Sydney, NSW, 2052, Australia
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15
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Abstract
Biofilms are structured and organized communities of microorganisms that represent one of the most successful forms of life on Earth. Bacterial biofilms have been studied in great detail, and many molecular details are known about the processes that govern bacterial biofilm formation, however, archaea are ubiquitous in almost all habitats on Earth and can also form biofilms. In recent years, insights have been gained into the development of archaeal biofilms, how archaea communicate to form biofilms and how the switch from a free-living lifestyle to a sessile lifestyle is regulated. In this Review, we explore the different stages of archaeal biofilm development and highlight similarities and differences between archaea and bacteria on a molecular level. We also consider the role of archaeal biofilms in industry and their use in different industrial processes.
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Affiliation(s)
- Marleen van Wolferen
- Molecular Biology of Archaea, Institute of Biology II, Microbiology, University of Freiburg, Freiburg, Germany
| | - Alvaro Orell
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Microbiology, University of Freiburg, Freiburg, Germany.
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16
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The Patchy Distribution of Restriction⁻Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. Genes (Basel) 2019; 10:genes10030233. [PMID: 30893937 PMCID: PMC6471742 DOI: 10.3390/genes10030233] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 12/26/2022] Open
Abstract
Restriction⁻modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase.
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17
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Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nat Microbiol 2018; 4:177-186. [PMID: 30478289 PMCID: PMC6298592 DOI: 10.1038/s41564-018-0302-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/23/2018] [Indexed: 02/06/2023]
Abstract
CRISPR-Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids, based on DNA acquired from these invaders, known as spacers. Surprisingly, many archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that inter-species spacers are common. We show experimentally by mating Haloferax volcanii and Haloferax mediterranei, that spacers are indeed acquired chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be targeted by the other's CRISPR-Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role for CRISPR-Cas systems in microbial speciation.
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18
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Bader M, Rossberg A, Steudtner R, Drobot B, Großmann K, Schmidt M, Musat N, Stumpf T, Ikeda-Ohno A, Cherkouk A. Impact of Haloarchaea on Speciation of Uranium-A Multispectroscopic Approach. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12895-12904. [PMID: 30125086 DOI: 10.1021/acs.est.8b02667] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Haloarchaea represent a predominant part of the microbial community in rock salt, which can serve as host rock for the disposal of high level radioactive waste. However, knowledge is missing about how Haloarchaea interact with radionuclides. Here, we used a combination of spectroscopic and microscopic methods to study the interactions of an extremely halophilic archaeon with uranium, one of the major radionuclides in high level radioactive waste, on a molecular level. The obtained results show that Halobacterium noricense DSM 15987T influences uranium speciation as a function of uranium concentration and incubation time. X-ray absorption spectroscopy reveals the formation of U(VI) phosphate minerals, such as meta-autunite, as the major species at a lower uranium concentration of 30 μM, while U(VI) is mostly associated with carboxylate groups of the cell wall and extracellular polymeric substances at a higher uranium concentration of 85 μM. For the first time, we identified uranium biomineralization in the presence of Halobacterium noricense DSM 15987T cells. These findings highlight the potential importance of Archaea in geochemical cycling of uranium and their role in biomineralization in hypersaline environments, offering new insights into the microbe-actinide interactions in highly saline conditions relevant to the disposal of high-level radioactive waste as well as bioremediation.
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Affiliation(s)
- Miriam Bader
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - André Rossberg
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Robin Steudtner
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Björn Drobot
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
- Technische Universität Dresden , Central Radionuclide Laboratory , Zellescher Weg 19 , 01062 Dresden , Germany
| | - Kay Großmann
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Matthias Schmidt
- Helmholtz Centre for Environmental Research , Department of Isotope Biogeochemistry , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Niculina Musat
- Helmholtz Centre for Environmental Research , Department of Isotope Biogeochemistry , Permoserstraße 15 , 04318 Leipzig , Germany
| | - Thorsten Stumpf
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Atsushi Ikeda-Ohno
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
| | - Andrea Cherkouk
- Helmholtz-Zentrum Dresden-Rossendorf , Institute of Resource Ecology , Bautzner Landstraße 400 , 01328 Dresden , Germany
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19
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Ibáñez de Aldecoa AL, Zafra O, González-Pastor JE. Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities. Front Microbiol 2017; 8:1390. [PMID: 28798731 PMCID: PMC5527159 DOI: 10.3389/fmicb.2017.01390] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/10/2017] [Indexed: 12/14/2022] Open
Abstract
The capacity to release genetic material into the extracellular medium has been reported in cultures of numerous species of bacteria, archaea, and fungi, and also in the context of multicellular microbial communities such as biofilms. Moreover, extracellular DNA (eDNA) of microbial origin is widespread in natural aquatic and terrestrial environments. Different specific mechanisms are involved in eDNA release, such as autolysis and active secretion, as well as through its association with membrane vesicles. It is noteworthy that in microorganisms, in which DNA release has been studied in detail, the production of eDNA is coordinated by the population when it reaches a certain cell density, and is induced in a subpopulation in response to the accumulation of quorum sensing signals. Interestingly, in several bacteria there is also a relationship between eDNA release and the development of natural competence (the ability to take up DNA from the environment), which is also controlled by quorum sensing. Then, what is the biological function of eDNA? A common biological role has not been proposed, since different functions have been reported depending on the microorganism. However, it seems to be important in biofilm formation, can be used as a nutrient source, and could be involved in DNA damage repair and gene transfer. This review covers several aspects of eDNA research: (i) its occurrence and distribution in natural environments, (ii) the mechanisms and regulation of its release in cultured microorganisms, and (iii) its biological roles. In addition, we propose that eDNA release could be considered a social behavior, based on its quorum sensing-dependent regulation and on the described functions of eDNA in the context of microbial communities.
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Affiliation(s)
- Alejandra L Ibáñez de Aldecoa
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (Consejo Superior de Investigaciones Científicas/Instituto Nacional de Técnica Aeroespacial)Madrid, Spain
| | - Olga Zafra
- Experimental Sciences Faculty, Francisco de Vitoria UniversityMadrid, Spain
| | - José E González-Pastor
- Laboratory of Molecular Adaptation, Department of Molecular Evolution, Centro de Astrobiología (Consejo Superior de Investigaciones Científicas/Instituto Nacional de Técnica Aeroespacial)Madrid, Spain
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20
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Williams TJ, Liao Y, Ye J, Kuchel RP, Poljak A, Raftery MJ, Cavicchioli R. Cold adaptation of the Antarctic haloarchaea
Halohasta litchfieldiae
and
Halorubrum lacusprofundi. Environ Microbiol 2017; 19:2210-2227. [DOI: 10.1111/1462-2920.13705] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/17/2017] [Accepted: 02/08/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
| | - Yan Liao
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
| | - Jun Ye
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
- Centre for Marine Bio‐InnovationThe University of New South WalesSydney New South Wales2052 Australia
| | - Rhiannon P. Kuchel
- Electron Microscopy UnitThe University of New South WalesSydney New South Wales2052 Australia
| | - Anne Poljak
- Bioanalytical Mass Spectrometry FacilityThe University of New South WalesSydney New South Wales2052 Australia
| | - Mark J. Raftery
- Bioanalytical Mass Spectrometry FacilityThe University of New South WalesSydney New South Wales2052 Australia
| | - Ricardo Cavicchioli
- School of Biotechnology and Biomolecular SciencesThe University of New South WalesSydney New South Wales2052 Australia
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21
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Liao Y, Williams TJ, Ye J, Charlesworth J, Burns BP, Poljak A, Raftery MJ, Cavicchioli R. Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi. Sci Rep 2016; 6:37454. [PMID: 27874045 PMCID: PMC5118699 DOI: 10.1038/srep37454] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/26/2016] [Indexed: 12/21/2022] Open
Abstract
Biofilms enhance rates of gene exchange, access to specific nutrients, and cell survivability. Haloarchaea in Deep Lake, Antarctica, are characterized by high rates of intergenera gene exchange, metabolic specialization that promotes niche adaptation, and are exposed to high levels of UV-irradiation in summer. Halorubrum lacusprofundi from Deep Lake has previously been reported to form biofilms. Here we defined growth conditions that promoted the formation of biofilms and used microscopy and enzymatic digestion of extracellular material to characterize biofilm structures. Extracellular DNA was found to be critical to biofilms, with cell surface proteins and quorum sensing also implicated in biofilm formation. Quantitative proteomics was used to define pathways and cellular processes involved in forming biofilms; these included enhanced purine synthesis and specific cell surface proteins involved in DNA metabolism; post-translational modification of cell surface proteins; specific pathways of carbon metabolism involving acetyl-CoA; and specific responses to oxidative stress. The study provides a new level of understanding about the molecular mechanisms involved in biofilm formation of this important member of the Deep Lake community.
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Affiliation(s)
- Y Liao
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - T J Williams
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Ye
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - J Charlesworth
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - B P Burns
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - A Poljak
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - M J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales, Australia
| | - R Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, 2052, Australia
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22
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Torti A, Lever MA, Jørgensen BB. Origin, dynamics, and implications of extracellular DNA pools in marine sediments. Mar Genomics 2015; 24 Pt 3:185-96. [DOI: 10.1016/j.margen.2015.08.007] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 08/29/2015] [Indexed: 12/17/2022]
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23
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Abstract
Horizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a parent-offspring relationship. HGT is a widely recognized mechanism for adaptation in bacteria and archaea. Microbial antibiotic resistance and pathogenicity are often associated with HGT, but the scope of HGT extends far beyond disease-causing organisms. In this Review, we describe how HGT has shaped the web of life using examples of HGT among prokaryotes, between prokaryotes and eukaryotes, and even between multicellular eukaryotes. We discuss replacement and additive HGT, the proposed mechanisms of HGT, selective forces that influence HGT, and the evolutionary impact of HGT on ancestral populations and existing populations such as the human microbiome.
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24
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Papke RT. Preface to the proceedings of Halophiles 2013. Front Microbiol 2015; 6:341. [PMID: 25954264 PMCID: PMC4406061 DOI: 10.3389/fmicb.2015.00341] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022] Open
Affiliation(s)
- R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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25
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Ouellette M, Jackson L, Chimileski S, Papke RT. Genome-wide DNA methylation analysis of Haloferax volcanii H26 and identification of DNA methyltransferase related PD-(D/E)XK nuclease family protein HVO_A0006. Front Microbiol 2015; 6:251. [PMID: 25904898 PMCID: PMC4389544 DOI: 10.3389/fmicb.2015.00251] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Accepted: 03/13/2015] [Indexed: 01/16/2023] Open
Abstract
Restriction-modification (RM) systems have evolved to protect the cell from invading DNAs and are composed of two enzymes: a DNA methyltransferase and a restriction endonuclease. Although RM systems are present in both archaeal and bacterial genomes, DNA methylation in archaea has not been well defined. In order to characterize the function of RM systems in archaeal species, we have made use of the model haloarchaeon Haloferax volcanii. A genomic DNA methylation analysis of H. volcanii strain H26 was performed using PacBio single molecule real-time (SMRT) sequencing. This analysis was also performed on a strain of H. volcanii in which an annotated DNA methyltransferase gene HVO_A0006 was deleted from the genome. Sequence analysis of H26 revealed two motifs which are modified in the genome: C(m4)TAG and GCA(m6)BN6VTGC. Analysis of the ΔHVO_A0006 strain indicated that it exhibited reduced adenine methylation compared to the parental strain and altered the detected adenine motif. However, protein domain architecture analysis and amino acid alignments revealed that HVO_A0006 is homologous only to the N-terminal endonuclease region of Type IIG RM proteins and contains a PD-(D/E)XK nuclease motif, suggesting that HVO_A0006 is a PD-(D/E)XK nuclease family protein. Further bioinformatic analysis of the HVO_A0006 gene demonstrated that the gene is rare among the Halobacteria. It is surrounded by two transposition genes suggesting that HVO_A0006 is a fragment of a Type IIG RM gene, which has likely been acquired through gene transfer, and affects restriction-modification activity by interacting with another RM system component(s). Here, we present the first genome-wide characterization of DNA methylation in an archaeal species and examine the function of a DNA methyltransferase related gene HVO_A0006.
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Affiliation(s)
- Matthew Ouellette
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Laura Jackson
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Scott Chimileski
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
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26
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Oren A. DNA as genetic material and as a nutrient in halophilic Archaea. Front Microbiol 2014; 5:539. [PMID: 25352841 PMCID: PMC4196559 DOI: 10.3389/fmicb.2014.00539] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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27
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Chimileski S, Franklin MJ, Papke RT. Biofilms formed by the archaeon Haloferax volcanii exhibit cellular differentiation and social motility, and facilitate horizontal gene transfer. BMC Biol 2014; 12:65. [PMID: 25124934 PMCID: PMC4180959 DOI: 10.1186/s12915-014-0065-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/31/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Archaea share a similar microbial lifestyle with bacteria, and not surprisingly then, also exist within matrix-enclosed communities known as biofilms. Advances in biofilm biology have been made over decades for model bacterial species, and include characterizations of social behaviors and cellular differentiation during biofilm development. Like bacteria, archaea impact ecological and biogeochemical systems. However, the biology of archaeal biofilms is only now being explored. Here, we investigated the development, composition and dynamics of biofilms formed by the haloarchaeon Haloferax volcanii DS2. RESULTS Biofilms were cultured in static liquid and visualized with fluorescent cell membrane dyes and by engineering cells to express green fluorescent protein (GFP). Analysis by confocal scanning laser microscopy showed that H. volcanii cells formed microcolonies within 24 h, which developed into larger clusters by 48 h and matured into flake-like towers often greater than 100 μm in height after 7 days. To visualize the extracellular matrix, biofilms formed by GFP-expressing cells were stained with concanavalin A, DAPI, Congo red and thioflavin T. Stains colocalized with larger cellular structures and indicated that the extracellular matrix may contain a combination of polysaccharides, extracellular DNA and amyloid protein. Following a switch to biofilm growth conditions, a sub-population of cells differentiated into chains of long rods sometimes exceeding 25 μm in length, compared to their planktonic disk-shaped morphology. Time-lapse photography of static liquid biofilms also revealed wave-like social motility. Finally, we quantified gene exchange between biofilm cells, and found that it was equivalent to the mating frequency of a classic filter-based experimental method. CONCLUSIONS The developmental processes, functional properties and dynamics of H. volcanii biofilms provide insight on how haloarchaeal species might persist, interact and exchange DNA in natural communities. H. volcanii demonstrates some biofilm phenotypes similar to bacterial biofilms, but also has interesting phenotypes that may be unique to this organism or to this class of organisms, including changes in cellular morphology and an unusual form of social motility. Because H. volcanii has one of the most advanced genetic systems for any archaeon, the phenotypes reported here may promote the study of genetic and developmental processes in archaeal biofilms.
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28
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Taxonomy of halophilic Archaea: current status and future challenges. Extremophiles 2014; 18:825-34. [DOI: 10.1007/s00792-014-0654-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 05/09/2014] [Indexed: 10/24/2022]
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29
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Zerulla K, Soppa J. Polyploidy in haloarchaea: advantages for growth and survival. Front Microbiol 2014; 5:274. [PMID: 24982654 PMCID: PMC4056108 DOI: 10.3389/fmicb.2014.00274] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 05/19/2014] [Indexed: 02/02/2023] Open
Abstract
The investigated haloarchaeal species, Halobacterium salinarum, Haloferax mediterranei, and H. volcanii, have all been shown to be polyploid. They contain several replicons that have independent copy number regulation, and most have a higher copy number during exponential growth phase than in stationary phase. The possible evolutionary advantages of polyploidy for haloarchaea, most of which have experimental support for at least one species, are discussed. These advantages include a low mutation rate and high resistance toward X-ray irradiation and desiccation, which depend on homologous recombination. For H. volcanii, it has been shown that gene conversion operates in the absence of selection, which leads to the equalization of genome copies. On the other hand, selective forces might lead to heterozygous cells, which have been verified in the laboratory. Additional advantages of polyploidy are survival over geological times in halite deposits as well as at extreme conditions on earth and at simulated Mars conditions. Recently, it was found that H. volcanii uses genomic DNA as genetic material and as a storage polymer for phosphate. In the absence of phosphate, H. volcanii dramatically decreases its genome copy number, thereby enabling cell multiplication, but diminishing the genetic advantages of polyploidy. Stable storage of phosphate is proposed as an alternative driving force for the emergence of DNA in early evolution. Several additional potential advantages of polyploidy are discussed that have not been addressed experimentally for haloarchaea. An outlook summarizes selected current trends and possible future developments.
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Affiliation(s)
- Karolin Zerulla
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
| | - Jörg Soppa
- Biocentre, Institute for Molecular Biosciences, Department of Biological Sciences, Goethe University Frankfurt Frankfurt, Germany
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Fernández AB, Vera-Gargallo B, Sánchez-Porro C, Ghai R, Papke RT, Rodriguez-Valera F, Ventosa A. Comparison of prokaryotic community structure from Mediterranean and Atlantic saltern concentrator ponds by a metagenomic approach. Front Microbiol 2014; 5:196. [PMID: 24847316 PMCID: PMC4021199 DOI: 10.3389/fmicb.2014.00196] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/12/2014] [Indexed: 12/02/2022] Open
Abstract
We analyzed the prokaryotic community structure of a saltern pond with 21% total salts located in Isla Cristina, Huelva, Southwest Spain, close to the Atlantic ocean coast. For this purpose, we constructed a metagenome (designated as IC21) obtained by pyrosequencing consisting of 486 Mb with an average read length of 397 bp and compared it with other metagenomic datasets obtained from ponds with 19, 33, and 37% total salts acquired from Santa Pola marine saltern, located in Alicante, East Spain, on the Mediterranean coast. Although the salinity in IC21 is closer to the pond with 19% total salts from Santa Pola saltern (designated as SS19), IC21 is more similar at higher taxonomic levels to the pond with 33% total salts from Santa Pola saltern (designated as SS33), since both are predominated by the phylum Euryarchaeota. However, there are significant differences at lower taxonomic levels where most sequences were related to the genus Halorubrum in IC21 and to Haloquadratum in SS33. Within the Bacteroidetes, the genus Psychroflexus is the most abundant in IC21 while Salinibacter dominates in SS33. Sequences related to bacteriorhodopsins and halorhodopsins correlate with the abundance of Haloquadratum in Santa Pola SS19 to SS33 and of Halorubrum in Isla Cristina IC21 dataset, respectively. Differences in composition might be attributed to local ecological conditions since IC21 showed a decrease in the number of sequences related to the synthesis of compatible solutes and in the utilization of phosphonate.
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Affiliation(s)
- Ana B Fernández
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
| | - Rohit Ghai
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante Alicante, Spain
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut Storrs, CT, USA
| | - Francisco Rodriguez-Valera
- Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante Alicante, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla Sevilla, Spain
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