51
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Kashif A, Tran LH, Jang SH, Lee C. Roles of Active-Site Aromatic Residues in Cold Adaptation of Sphingomonas glacialis Esterase EstSP1. ACS OMEGA 2017; 2:8760-8769. [PMID: 31457406 PMCID: PMC6645578 DOI: 10.1021/acsomega.7b01435] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/23/2017] [Indexed: 06/10/2023]
Abstract
The aromatic amino acids, Tyr or Trp, which line the active-site walls of esterases, stabilize the catalytic His loop via hydrogen bonding. A Tyr residue is preferred in extremophilic esterases (psychrophilic or hyperthermophilic esterases), whereas a Trp residue is preferred in moderate-temperature esterases. Here, we provide evidence that Tyr and Trp play distinct roles in cold adaptation of the psychrophilic esterase EstSP1 isolated from an Arctic bacterium Sphingomonas glacialis PAMC 26605. Stern-Volmer plots showed that the mutation of Tyr191 to Ala, Phe, Trp, and His resulted in reduced conformational flexibility of the overall protein structure. Interestingly, the Y191W and Y191H mutants showed increased thermal stability at moderate temperatures. All Tyr191 mutants showed reduced catalytic activity relative to wild-type EstSP1. Our results indicate that Tyr with its phenyl hydroxyl group is favored for increased conformational flexibility and high catalytic activity of EstSP1 at low temperatures at the expense of thermal stability. The results of this study suggest that, in the permanently cold Arctic zone, enzyme activity has been selected for psychrophilic enzymes over thermal stability. The results presented herein provide novel insight into the roles of Tyr and Trp residues for temperature adaptation of enzymes that function at low, moderate, and high temperatures.
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Affiliation(s)
| | | | | | - ChangWoo Lee
- E-mail: . Tel: +82-53-850-6464. Fax: +82-53-850-6469
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52
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Aben RCH, Barros N, van Donk E, Frenken T, Hilt S, Kazanjian G, Lamers LPM, Peeters ETHM, Roelofs JGM, de Senerpont Domis LN, Stephan S, Velthuis M, Van de Waal DB, Wik M, Thornton BF, Wilkinson J, DelSontro T, Kosten S. Cross continental increase in methane ebullition under climate change. Nat Commun 2017; 8:1682. [PMID: 29167452 PMCID: PMC5700168 DOI: 10.1038/s41467-017-01535-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 09/22/2017] [Indexed: 11/29/2022] Open
Abstract
Methane (CH4) strongly contributes to observed global warming. As natural CH4 emissions mainly originate from wet ecosystems, it is important to unravel how climate change may affect these emissions. This is especially true for ebullition (bubble flux from sediments), a pathway that has long been underestimated but generally dominates emissions. Here we show a remarkably strong relationship between CH4 ebullition and temperature across a wide range of freshwater ecosystems on different continents using multi-seasonal CH4 ebullition data from the literature. As these temperature-ebullition relationships may have been affected by seasonal variation in organic matter availability, we also conducted a controlled year-round mesocosm experiment. Here 4 °C warming led to 51% higher total annual CH4 ebullition, while diffusion was not affected. Our combined findings suggest that global warming will strongly enhance freshwater CH4 emissions through a disproportional increase in ebullition (6-20% per 1 °C increase), contributing to global warming.
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Affiliation(s)
- Ralf C H Aben
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Nathan Barros
- Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Ellen van Donk
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Department of Ecology and Biodiversity, University of Utrecht, P.O. Box 80.056, 3508 TB, Utrecht, The Netherlands
| | - Thijs Frenken
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Sabine Hilt
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587, Berlin, Germany
| | - Garabet Kazanjian
- Department of Ecosystem Research, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587, Berlin, Germany
| | - Leon P M Lamers
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
- B-WARE Research Centre, P.O. Box 6558, 6503 GB, Nijmegen, The Netherlands
| | - Edwin T H M Peeters
- Department of Aquatic Ecology and Water Quality Management, Wageningen University, P.O. Box 47, 6708 PB, Wageningen, The Netherlands
| | - Jan G M Roelofs
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands
- B-WARE Research Centre, P.O. Box 6558, 6503 GB, Nijmegen, The Netherlands
| | - Lisette N de Senerpont Domis
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
- Department of Aquatic Ecology and Water Quality Management, Wageningen University, P.O. Box 47, 6708 PB, Wageningen, The Netherlands
| | - Susanne Stephan
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, OT Neuglobsow, 16775, Stechlin, Germany
| | - Mandy Velthuis
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Dedmer B Van de Waal
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands
| | - Martin Wik
- Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm University, Stockholm, SE-10691, Sweden
| | - Brett F Thornton
- Department of Geological Sciences and Bolin Centre for Climate Research, Stockholm University, Stockholm, SE-10691, Sweden
| | - Jeremy Wilkinson
- University of Koblenz-Landau, Institute for Environmental Sciences, Fortstr. 7, 76829, Landau, Germany
| | - Tonya DelSontro
- Groupe de Recherche Interuniversitaire en Limnologie (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Canada, H3C 3P8, QC
| | - Sarian Kosten
- Department of Aquatic Ecology and Environmental Biology, Institute for Water and Wetland Research, Radboud University, P.O. Box 9010, 6500 GL, Nijmegen, The Netherlands.
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6708 PB, Wageningen, The Netherlands.
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53
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Dunn CD. Some Liked It Hot: A Hypothesis Regarding Establishment of the Proto-Mitochondrial Endosymbiont During Eukaryogenesis. J Mol Evol 2017; 85:99-106. [PMID: 28916841 PMCID: PMC5682861 DOI: 10.1007/s00239-017-9809-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/11/2017] [Indexed: 01/17/2023]
Abstract
Eukaryotic cells are characterized by a considerable increase in subcellular compartmentalization when compared to prokaryotes. Most evidence suggests that the earliest eukaryotes consisted of mitochondria derived from an α-proteobacterial ancestor enclosed within an archaeal host cell. However, what benefits the archaeal host and the proto-mitochondrial endosymbiont might have obtained at the beginning of this endosymbiotic relationship remains unclear. In this work, I argue that heat generated by the proto-mitochondrion initially permitted an archaeon living at high temperatures to colonize a cooler environment, thereby removing apparent limitations on cellular complexity. Furthermore, heat generation by the endosymbiont would have provided phenotypic flexibility not available through fixed alleles selected for fitness at specific temperatures. Finally, a role for heat production by the proto-mitochondrion bridges a conceptual gap between initial endosymbiont entry to the archaeal host and a later role for mitochondrial ATP production in permitting increased cellular complexity.
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Affiliation(s)
- Cory D Dunn
- Institute of Biotechnology, Helsinki Institute of Life Science, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland. .,College of Sciences, Koç University, 34450, Sarıyer, İstanbul, Turkey.
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54
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McHugh TA, Compson Z, van Gestel N, Hayer M, Ballard L, Haverty M, Hines J, Irvine N, Krassner D, Lyons T, Musta EJ, Schiff M, Zint P, Schwartz E. Climate controls prokaryotic community composition in desert soils of the southwestern United States. FEMS Microbiol Ecol 2017; 93:4111145. [DOI: 10.1093/femsec/fix116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Theresa A. McHugh
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO 81501, USA
| | - Zacchaeus Compson
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Canadian Rivers Institute, University of New Brunswick, Fredericton, New Brunswick, E3B 5A3, Canada
| | - Natasja van Gestel
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Texas Tech University Climate Science Center, Lubbock, TX 79409, USA
| | - Michaela Hayer
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
| | | | | | - Jeffrey Hines
- Northland Preparatory Academy, Flagstaff, AZ 86004, USA
| | - Nick Irvine
- Northland Preparatory Academy, Flagstaff, AZ 86004, USA
| | | | - Ted Lyons
- Coconino High School, Flagstaff, AZ 86004, USA
| | | | | | | | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ 86011-5620, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ 86011-5640, USA
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55
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Ahn E, Choi KY, Kang BS, Zylstra GJ, Kim D, Kim E. Salicylate degradation by a cold-adapted Pseudomonas sp. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1273-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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56
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Wagner A, Whitaker RJ, Krause DJ, Heilers JH, van Wolferen M, van der Does C, Albers SV. Mechanisms of gene flow in archaea. Nat Rev Microbiol 2017; 15:492-501. [DOI: 10.1038/nrmicro.2017.41] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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57
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Di Lorenzo F, Billod JM, Martín-Santamaría S, Silipo A, Molinaro A. Gram-Negative Extremophile Lipopolysaccharides: Promising Source of Inspiration for a New Generation of Endotoxin Antagonists. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Flaviana Di Lorenzo
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
| | - Jean-Marc Billod
- Department of Chemical and Physical Biology; CIB Centro de Investigaciones Biológicas; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Sonsoles Martín-Santamaría
- Department of Chemical and Physical Biology; CIB Centro de Investigaciones Biológicas; Ramiro de Maeztu 9 28040 Madrid Spain
| | - Alba Silipo
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
| | - Antonio Molinaro
- Department of Chemical Sciences; University of Naples Federico II; via Cinthia 480126 80126 Naples Italy
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58
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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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59
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Aguayo P, González P, Campos V, Maugeri TL, Papale M, Gugliandolo C, Martinez MA. Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia. Curr Microbiol 2017; 74:598-613. [PMID: 28265709 DOI: 10.1007/s00284-017-1209-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/31/2017] [Indexed: 11/26/2022]
Abstract
The prokaryotic abundance and diversity in three cold, oligotrophic Patagonian lakes (Témpanos, Las Torres and Mercedes) in the northern region Aysén (Chile) were compared in winter and summer using 16S rRNA fluorescence in situ hybridization and PCR-denaturing gradient gel electrophoresis technique. Prokaryotic abundances, numerically dominated by Bacteria, were quite similar in the three lakes, but higher in sediments than in waters, and they were also higher in summer than in winter. The relative contribution of Archaea was greater in waters than in sediments, and in winter rather than in summer. Despite the phylogenetic analysis indicated that most sequences were affiliated to a few taxonomic groups, mainly referred to Proteobacteria (consisting of Beta-, Alpha- and Gammaproteobacteria) and Euryarchaeota (mainly related to uncultured methanogens), their relative abundances differed in each sample, resulting in different bacterial and archaeal assemblages. In winter, the abundance of the dominant bacterial phylotypes were mainly regulated by the increasing levels of total organic carbon in waters. Archaeal abundance and richness appeared mostly influenced by pH in winter and total nitrogen content in summer. The prokaryotic community composition at Témpanos lake, located most northerly and closer to a glacier, greatly differed in respect to the other two lakes. In this lake was detected the highest bacterial diversity, being Betaproteobacteria the most abundant group, whereas Alphaproteobacteria were distinctive of Mercedes. Archaeal community associated with sediments was mainly represent by members related to the order of Methanosarcinales at Mercedes and Las Torres lakes, and by Crenarchaeota at Témpanos lake. Our results indicate that the proximity to the glacier and the seasonality shape the composition of the prokaryotic communities in these remote lakes. These results may be used as baseline information to follow the microbial community responses to potential global changes and to anthropogenic impacts.
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Affiliation(s)
- Paulina Aguayo
- Department of Microbiology, Laboratory of Basic Microbiology and Bioremedation, University of Concepción, Concepción, Chile
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
| | - Paulina González
- Department of Microbiology, Laboratory of Basic Microbiology and Bioremedation, University of Concepción, Concepción, Chile
| | - Víctor Campos
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
- Department of Microbiology, Laboratory of Environmental Microbiology, University of Concepción, Concepción, Chile
| | - Teresa L Maugeri
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
| | - Maria Papale
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
| | - Concetta Gugliandolo
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy.
| | - Miguel A Martinez
- Department of Microbiology, Laboratory of Basic Microbiology and Bioremedation, University of Concepción, Concepción, Chile
- Research Centre for Extreme Environments and Extremophiles, Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres, 31, 98166, Messina, Italy
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60
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Casillo A, Parrilli E, Sannino F, Mitchell DE, Gibson MI, Marino G, Lanzetta R, Parrilli M, Cosconati S, Novellino E, Randazzo A, Tutino ML, Corsaro MM. Structure-activity relationship of the exopolysaccharide from a psychrophilic bacterium: A strategy for cryoprotection. Carbohydr Polym 2017; 156:364-371. [PMID: 27842835 PMCID: PMC5166977 DOI: 10.1016/j.carbpol.2016.09.037] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 08/25/2016] [Accepted: 09/13/2016] [Indexed: 11/19/2022]
Abstract
Microrganisms from sea ice, glacial and subglacial environments are currently under investigation due to their relevant ecological functions in these habitats, and to their potential biotechnological applications. The cold-adapted Colwellia psychrerythraea 34H produces extracellular polysaccharides with cryoprotection activity. We here describe the purification and detailed molecular primary and secondary structure of the exopolysaccharide (EPS) secreted by C. psychrerythraea 34H cells grown at 4°C. The structure was determined by chemical analysis and NMR. The trisaccharide repeating unit of the EPS is constituted by a N-acetyl quinovosamine unit and two residues of galacturonic acid both decorated with alanine. In addition, the EPS was tested in vitro showing a significant inhibitory effect on ice recrystallization. In-depth NMR and computational analysis suggest a pseudohelicoidal structure which seems to prevent the local tetrahedral order of the water molecules in the first hydration shell, and could be responsible of the inhibition of ice recrystallization. As cell cryopreservation is an essential tool in modern biotechnology and medicine, the observations reported in this paper could pave the way for a biotechnological application of Colwellia EPS.
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Affiliation(s)
- Angela Casillo
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Filomena Sannino
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Daniel E Mitchell
- Department of Chemistry and Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Matthew I Gibson
- Department of Chemistry and Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Gennaro Marino
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Rosa Lanzetta
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Michelangelo Parrilli
- Department of Biology, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, Second University of Naples, Via Vivaldi 43, 81100 Caserta, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, 80131 Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano, 49, 80131 Naples, Italy
| | - Maria L Tutino
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
| | - M Michela Corsaro
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy.
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61
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Sang P, Du X, Yang LQ, Meng ZH, Liu SQ. Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms. RSC Adv 2017. [DOI: 10.1039/c6ra23230b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The physicochemical bases for enzyme cold-adaptation remain elusive.
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Affiliation(s)
- Peng Sang
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| | - Xing Du
- Laboratory for Conservation and Utilization of Bio-Resources
- Yunnan University
- Kunming
- P. R. China
- Department of Biochemistry and Molecular Biology
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- P. R. China
| | - Zhao-Hui Meng
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
| | - Shu-Qun Liu
- Laboratory of Molecular Cardiology
- Department of Cardiology
- The First Affiliated Hospital of Kunming Medical University
- Kunming
- P. R. China
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62
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Fan L, Song C, Meng S, Qiu L, Zheng Y, Wu W, Qu J, Li D, Zhang C, Hu G, Chen J. Spatial distribution of planktonic bacterial and archaeal communities in the upper section of the tidal reach in Yangtze River. Sci Rep 2016; 6:39147. [PMID: 27966673 PMCID: PMC5155431 DOI: 10.1038/srep39147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/18/2016] [Indexed: 12/14/2022] Open
Abstract
Bacterioplankton and archaeaplankton communities play key roles in the biogeochemical processes of water, and they may be affected by many factors. In this study, we used high-throughput 16S rRNA gene sequencing to profile planktonic bacterial and archaeal community compositions in the upper section of the tidal reach in Yangtze River. We found that the predominant bacterial phyla in this river section were Proteobacteria, Firmicutes, and Actinobacteria, whereas the predominant archaeal classes were Halobacteria, Methanomicrobia, and unclassified Euryarchaeota. Additionally, the bacterial and archaeal community compositions, richnesses, functional profiles, and ordinations were affected by the spatial heterogeneity related to the concentration changes of sulphate or nitrate. Notably, the bacterial community was more sensitive than the archaeal community to changes in the spatial characteristics of this river section. These findings provide important insights into the distributions of bacterial and archaeal communities in natural water habitats.
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Affiliation(s)
- Limin Fan
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Chao Song
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Shunlong Meng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Liping Qiu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Wei Wu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Jianhong Qu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Dandan Li
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Cong Zhang
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Gengdong Hu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
| | - Jiazhang Chen
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Scientific Observing and Experimental Station of Fishery Resources and Environment in the Lower Reaches of the Yangtze River, Wuxi 214081, China
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63
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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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64
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Liao Y, Williams TJ, Walsh JC, Ji M, Poljak A, Curmi PMG, Duggin IG, Cavicchioli R. Developing a genetic manipulation system for the Antarctic archaeon, Halorubrum lacusprofundi: investigating acetamidase gene function. Sci Rep 2016; 6:34639. [PMID: 27708407 PMCID: PMC5052560 DOI: 10.1038/srep34639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 09/16/2016] [Indexed: 01/04/2023] Open
Abstract
No systems have been reported for genetic manipulation of cold-adapted Archaea. Halorubrum lacusprofundi is an important member of Deep Lake, Antarctica (~10% of the population), and is amendable to laboratory cultivation. Here we report the development of a shuttle-vector and targeted gene-knockout system for this species. To investigate the function of acetamidase/formamidase genes, a class of genes not experimentally studied in Archaea, the acetamidase gene, amd3, was disrupted. The wild-type grew on acetamide as a sole source of carbon and nitrogen, but the mutant did not. Acetamidase/formamidase genes were found to form three distinct clades within a broad distribution of Archaea and Bacteria. Genes were present within lineages characterized by aerobic growth in low nutrient environments (e.g. haloarchaea, Starkeya) but absent from lineages containing anaerobes or facultative anaerobes (e.g. methanogens, Epsilonproteobacteria) or parasites of animals and plants (e.g. Chlamydiae). While acetamide is not a well characterized natural substrate, the build-up of plastic pollutants in the environment provides a potential source of introduced acetamide. In view of the extent and pattern of distribution of acetamidase/formamidase sequences within Archaea and Bacteria, we speculate that acetamide from plastics may promote the selection of amd/fmd genes in an increasing number of environmental microorganisms.
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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 C Walsh
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia.,The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - M Ji
- 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
| | - P M G Curmi
- School of Physics, The University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - I G Duggin
- The ithree institute, University of Technology Sydney, Broadway, New South Wales, 2007, 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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65
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França L, Sannino C, Turchetti B, Buzzini P, Margesin R. Seasonal and altitudinal changes of culturable bacterial and yeast diversity in Alpine forest soils. Extremophiles 2016; 20:855-873. [PMID: 27620454 PMCID: PMC5085987 DOI: 10.1007/s00792-016-0874-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/25/2016] [Indexed: 11/04/2022]
Abstract
The effect of altitude and season on abundance and diversity of the culturable heterotrophic bacterial and yeast community was examined at four forest sites in the Italian Alps along an altitude gradient (545–2000 m). Independently of altitude, bacteria isolated at 0 °C (psychrophiles) were less numerous than those recovered at 20 °C. In autumn, psychrophilic bacterial population increased with altitude. The 1194 bacterial strains were primarily affiliated with the classes Alpha-, Beta-, Gammaproteobacteria, Spingobacteriia and Flavobacteriia. Fifty-seven of 112 operational taxonomic units represented potential novel species. Strains isolated at 20 °C had a higher diversity and showed similarities in taxa composition and abundance, regardless of altitude or season, while strains isolated at 0 °C showed differences in community composition at lower and higher altitudes. In contrast to bacteria, yeast diversity was season-dependent: site- and altitude-specific effects on yeast diversity were only detected in spring. Isolation temperature affected the relative proportions of yeast genera. Isolations recovered 719 strains, belonging to the classes Dothideomycetes, Saccharomycetes, Tremellomycetes and Mycrobotryomycetes. The presence of few dominant bacterial OTUs and yeast species indicated a resilient microbial population that is not affected by season or altitude. Soil nutrient contents influenced significantly abundance and diversity of culturable bacteria, but not of culturable yeasts.
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Affiliation(s)
- Luís França
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
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66
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Abstract
The large diversity of marine microorganisms harboured by oceans plays an important role in planet sustainability by driving globally important biogeochemical cycles; all primary and most secondary production in the oceans is performed by microorganisms. The largest part of the planet is covered by cold environments; consequently, cold-adapted microorganisms have crucial functional roles in globally important environmental processes and biogeochemical cycles cold-adapted extremophiles are a remarkable model to shed light on the molecular basis of survival at low temperature. The indigenous populations of Antarctic and Arctic microorganisms are endowed with genetic and physiological traits that allow them to live and effectively compete at the temperatures prevailing in polar regions. Some genes, e.g. glycosyltransferases and glycosylsynthetases involved in the architecture of the cell wall, may have been acquired/retained during evolution of polar strains or lost in tropical strains. This present work focusses on temperature and its role in shaping microbial adaptations; however, in assessing the impacts of climate changes on microbial diversity and biogeochemical cycles in polar oceans, it should not be forgotten that physiological studies need to include the interaction of temperature with other abiotic and biotic factors.
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67
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The genome and transcriptome of Trichormus sp. NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau. Sci Rep 2016; 6:29404. [PMID: 27381465 PMCID: PMC4933973 DOI: 10.1038/srep29404] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 06/20/2016] [Indexed: 11/09/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP.
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68
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Peintner U, Knapp M, Fleischer V, Walch G, Dresch P. Myrmecridium hiemale sp. nov. from snow-covered alpine soil is the first eurypsychrophile in this genus of anamorphic fungi. Int J Syst Evol Microbiol 2016; 66:2592-2598. [PMID: 27088455 DOI: 10.1099/ijsem.0.001090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Myrmecridium hiemale sp. nov. was isolated from snow-covered alpine bare soil and is described as the first eurypsychrophilic species of this genus of filamentous fungi. Colony growth temperature experiments were carried out in the range 4-37 °C. Morphological characteristics and colony appearance were in accordance with characteristics typical for Myrmecridium, but M. hiemale does not grow at temperatures of 25 °C and above. Sequence analyses of the internal transcribed spacer and LSU rRNA D1/D2 regions indicated that the strain in question represents a distinct taxon within the genus Myrmecridium (Myrmecridiaceae, Sordariomycetes, Ascomycota). The type strain of M. hiemale is CBS 141017T(=JMRC 12083T). A morphological description is provided, and a key is presented for the currently known taxa of Myrmecridium, a group of interesting fungi that are either saprobes or plant endophytes.
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Affiliation(s)
- Ursula Peintner
- Institute of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Maria Knapp
- Institute of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Verena Fleischer
- Institute of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Georg Walch
- Institute of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Philipp Dresch
- Institute of Microbiology, University of Innsbruck, A-6020 Innsbruck, Austria
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69
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Characterization of a temperature-responsive two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii. Sci Rep 2016; 6:24278. [PMID: 27052690 PMCID: PMC4823666 DOI: 10.1038/srep24278] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/23/2016] [Indexed: 01/18/2023] Open
Abstract
Cold environments dominate the Earth’s biosphere and the resident microorganisms play critical roles in fulfilling global biogeochemical cycles. However, only few studies have examined the molecular basis of thermosensing; an ability that microorganisms must possess in order to respond to environmental temperature and regulate cellular processes. Two component regulatory systems have been inferred to function in thermal regulation of gene expression, but biochemical studies assessing these systems in Bacteria are rare, and none have been performed in Archaea or psychrophiles. Here we examined the LtrK/LtrR two component regulatory system from the Antarctic archaeon, Methanococcoides burtonii, assessing kinase and phosphatase activities of wild-type and mutant proteins. LtrK was thermally unstable and had optimal phosphorylation activity at 10 °C (the lowest optimum activity for any psychrophilic enzyme), high activity at 0 °C and was rapidly thermally inactivated at 30 °C. These biochemical properties match well with normal environmental temperatures of M. burtonii (0–4 °C) and the temperature this psychrophile is capable of growing at in the laboratory (−2 to 28 °C). Our findings are consistent with a role for LtrK in performing phosphotransfer reactions with LtrR that could lead to temperature-dependent gene regulation.
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70
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Danovaro R, Molari M, Corinaldesi C, Dell’Anno A. Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems. SCIENCE ADVANCES 2016; 2:e1500961. [PMID: 27386507 PMCID: PMC4928989 DOI: 10.1126/sciadv.1500961] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 03/31/2016] [Indexed: 05/06/2023]
Abstract
Bacteria and archaea dominate the biomass of benthic deep-sea ecosystems at all latitudes, playing a crucial role in global biogeochemical cycles, but their macroscale patterns and macroecological drivers are still largely unknown. We show the results of the most extensive field study conducted so far to investigate patterns and drivers of the distribution and structure of benthic prokaryote assemblages from 228 samples collected at latitudes comprising 34°N to 79°N, and from ca. 400- to 5570-m depth. We provide evidence that, in deep-sea ecosystems, benthic bacterial and archaeal abundances significantly increase from middle to high latitudes, with patterns more pronounced for archaea, and particularly for Marine Group I Thaumarchaeota. Our results also reveal that different microbial components show varying sensitivities to changes in temperature conditions and food supply. We conclude that climate change will primarily affect deep-sea benthic archaea, with important consequences on global biogeochemical cycles, particularly at high latitudes.
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Affiliation(s)
- Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- Corresponding author.
| | - Massimiliano Molari
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- HGF MPG Joint Research for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
| | - Cinzia Corinaldesi
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Antonio Dell’Anno
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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71
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Qiao Q, Wang Q, Han X, Guan Y, Sun H, Zhong Y, Huang J, Zhang T. Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau. Sci Rep 2016; 6:21729. [PMID: 26906946 PMCID: PMC4764839 DOI: 10.1038/srep21729] [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: 10/09/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
The extreme environment of the Qinghai-Tibet Plateau (QTP) provides an ideal natural laboratory for studies on adaptive evolution. Few genome/transcriptome based studies have been conducted on how plants adapt to the environments of QTP compared to numerous studies on vertebrates. Crucihimalaya himalaica is a close relative of Arabidopsis with typical QTP distribution, and is hoped to be a new model system to study speciation and ecological adaptation in extreme environment. In this study, we de novo generated a transcriptome sequence of C. himalaica, with a total of 49,438 unigenes. Compared to five relatives, 10,487 orthogroups were shared by all six species, and 4,286 orthogroups contain putative single copy gene. Further analysis identified 487 extremely significantly positively selected genes (PSGs) in C. himalaica transcriptome. Theses PSGs were enriched in functions related to specific adaptation traits, such as response to radiation, DNA repair, nitrogen metabolism, and stabilization of membrane. These functions are responsible for the adaptation of C. himalaica to the high radiation, soil depletion and low temperature environments on QTP. Our findings indicate that C. himalaica has evolved complex strategies for adapting to the extreme environments on QTP and provide novel insights into genetic mechanisms of highland adaptation in plants.
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Affiliation(s)
- Qin Qiao
- School of Agriculture, Yunnan University, Kunming 650091, China
| | - Qia Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.,University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xi Han
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yanlong Guan
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yang Zhong
- Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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72
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Liu Y, Priscu JC, Xiong J, Conrad R, Vick-Majors T, Chu H, Hou J. Salinity drives archaeal distribution patterns in high altitude lake sediments on the Tibetan Plateau. FEMS Microbiol Ecol 2016; 92:fiw033. [DOI: 10.1093/femsec/fiw033] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2016] [Indexed: 11/13/2022] Open
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73
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Taha, Siddiqui KS, Campanaro S, Najnin T, Deshpande N, Williams TJ, Aldrich‐Wright J, Wilkins M, Curmi PMG, Cavicchioli R. Single
TRAM
domain
RNA
‐binding proteins in
A
rchaea
: functional insight from
C
tr3 from the
A
ntarctic methanogen
M
ethanococcoides burtonii. Environ Microbiol 2016; 18:2810-24. [DOI: 10.1111/1462-2920.13229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/13/2016] [Accepted: 01/13/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Taha
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - K. S. Siddiqui
- Life Sciences Department King Fahd University of Petroleum and Minerals Dhahran Kingdom of Saudi Arabia
| | - S. Campanaro
- Department of Biology University of Padua Via U. Bassi 58/B 35121 Padova Italy
| | - T. Najnin
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - N. Deshpande
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - T. J. Williams
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - J. Aldrich‐Wright
- Nanoscale Organization and Dynamic Group School of Science and Health Western Sydney University Penrith 2560 NSW Australia
| | - M. Wilkins
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
| | - P. M. G. Curmi
- School of Physics The University of New South Wales Sydney NSW 2052 Australia
| | - R. Cavicchioli
- School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 Australia
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Lario LD, Malpiedi LP, Pereira JFB, Sette LD, Pessoa-Junior A. Liquid-liquid extraction of protease from cold-adapted yeastRhodotorula mucilaginosaL7 using biocompatible and biodegradable aqueous two-phase systems. SEP SCI TECHNOL 2015. [DOI: 10.1080/01496395.2015.1080276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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75
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Taubner RS, Schleper C, Firneis MG, Rittmann SKMR. Assessing the Ecophysiology of Methanogens in the Context of Recent Astrobiological and Planetological Studies. Life (Basel) 2015; 5:1652-86. [PMID: 26703739 PMCID: PMC4695842 DOI: 10.3390/life5041652] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/15/2015] [Accepted: 11/10/2015] [Indexed: 12/31/2022] Open
Abstract
Among all known microbes capable of thriving under extreme and, therefore, potentially extraterrestrial environmental conditions, methanogens from the domain Archaea are intriguing organisms. This is due to their broad metabolic versatility, enormous diversity, and ability to grow under extreme environmental conditions. Several studies revealed that growth conditions of methanogens are compatible with environmental conditions on extraterrestrial bodies throughout the Solar System. Hence, life in the Solar System might not be limited to the classical habitable zone. In this contribution we assess the main ecophysiological characteristics of methanogens and compare these to the environmental conditions of putative habitats in the Solar System, in particular Mars and icy moons. Eventually, we give an outlook on the feasibility and the necessity of future astrobiological studies concerning methanogens.
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Affiliation(s)
- Ruth-Sophie Taubner
- Research Platform: ExoLife, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
- Institute of Astrophysics, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
| | - Maria G Firneis
- Research Platform: ExoLife, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
- Institute of Astrophysics, University of Vienna, Türkenschanzstraße 17, 1180 Vienna, Austria.
| | - Simon K-M R Rittmann
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
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76
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Some like it hot, some like it cold: Temperature dependent biotechnological applications and improvements in extremophilic enzymes. Biotechnol Adv 2015; 33:1912-22. [DOI: 10.1016/j.biotechadv.2015.11.001] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 11/12/2015] [Accepted: 11/12/2015] [Indexed: 11/23/2022]
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77
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78
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Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures. J Theor Biol 2015; 383:130-7. [DOI: 10.1016/j.jtbi.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/21/2015] [Accepted: 07/16/2015] [Indexed: 11/21/2022]
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79
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80
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δ(13)C-CH4 reveals CH4 variations over oceans from mid-latitudes to the Arctic. Sci Rep 2015; 5:13760. [PMID: 26323236 PMCID: PMC4555175 DOI: 10.1038/srep13760] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 08/05/2015] [Indexed: 11/09/2022] Open
Abstract
The biogeochemical cycles of CH4 over oceans are poorly understood, especially over the Arctic Ocean. Here we report atmospheric CH4 levels together with δ(13)C-CH4 from offshore China (31°N) to the central Arctic Ocean (up to 87°N) from July to September 2012. CH4 concentrations and δ(13)C-CH4 displayed temporal and spatial variation ranging from 1.65 to 2.63 ppm, and from -50.34% to -44.94% (mean value: -48.55 ± 0.84%), respectively. Changes in CH4 with latitude were linked to the decreasing input of enriched δ(13)C and chemical oxidation by both OH and Cl radicals as indicated by variation of δ(13)C. There were complex mixing sources outside and inside the Arctic Ocean. A keeling plot showed the dominant influence by hydrate gas in the Nordic Sea region, while the long range transport of wetland emissions were one of potentially important sources in the central Arctic Ocean. Experiments comparing sunlight and darkness indicate that microbes may also play an important role in regional variations.
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81
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Ding C, Ma T, Hu A, Dai L, He Q, Cheng L, Zhang H. Enrichment and Characterization of a Psychrotolerant Consortium Degrading Crude Oil Alkanes Under Methanogenic Conditions. MICROBIAL ECOLOGY 2015; 70:433-444. [PMID: 25783218 DOI: 10.1007/s00248-015-0590-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 02/26/2015] [Indexed: 06/04/2023]
Abstract
Anaerobic alkane degradation via methanogenesis has been intensively studied under mesophilic and thermophilic conditions. While there is a paucity of information on the ability and composition of anaerobic alkane-degrading microbial communities under low temperature conditions. In this study, we investigated the ability of consortium Y15, enriched from Shengli oilfield, to degrade hydrocarbons under different temperature conditions (5-35 °C). The consortium could use hexadecane over a low temperature range (15-30 °C). No growth was detected below 10 °C and above 35 °C, indicating the presence of cold-tolerant species capable of alkane degradation. The preferential degradation of short chain n-alkanes from crude oil was observed by this consortium. The structure and dynamics of the microbial communities were examined using terminal restriction fragment length polymorphism (T-RFLP) fingerprinting and Sanger sequencing of 16S rRNA genes. The core archaeal communities were mainly composed of aceticlastic Methanosaeta spp. Syntrophaceae-related microorganisms were always detected during consecutive transfers and dominated the bacterial communities, sharing 94-96 % sequence similarity with Smithella propionica strain LYP(T). Phylogenetic analysis of Syntrophaceae-related clones in diverse methanogenic alkane-degrading cultures revealed that most of them were clustered into three sublineages. Syntrophaceae clones retrieved from this study were mainly clustered into sublineage I, which may represent psychrotolerant, syntrophic alkane degraders. These results indicate the wide geographic distribution and ecological function of syntrophic alkane degraders.
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Affiliation(s)
- Chen Ding
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin South Road, Chengdu, 610041, People's Republic of China
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82
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Blake LI, Tveit A, Øvreås L, Head IM, Gray ND. Response of Methanogens in Arctic Sediments to Temperature and Methanogenic Substrate Availability. PLoS One 2015; 10:e0129733. [PMID: 26083466 PMCID: PMC4471053 DOI: 10.1371/journal.pone.0129733] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/12/2015] [Indexed: 01/06/2023] Open
Abstract
Although cold environments are major contributors to global biogeochemical cycles, comparatively little is known about their microbial community function, structure, and limits of activity. In this study a microcosm based approach was used to investigate the effects of temperature, and methanogenic substrate amendment, (acetate, methanol and H2/CO2) on methanogen activity and methanogen community structure in high Arctic wetlands (Solvatnet and Stuphallet, Svalbard). Methane production was not detected in Stuphallet sediment microcosms (over a 150 day period) and occurred within Solvatnet sediments microcosms (within 24 hours) at temperatures from 5 to 40°C, the maximum temperature being at far higher than in situ maximum temperatures (which range from air temperatures of -1.4 to 14.1°C during summer months). Distinct responses were observed in the Solvatnet methanogen community under different short term incubation conditions. Specifically, different communities were selected at higher and lower temperatures. At lower temperatures (5°C) addition of exogenous substrates (acetate, methanol or H2/CO2) had no stimulatory effect on the rate of methanogenesis or on methanogen community structure. The community in these incubations was dominated by members of the Methanoregulaceae/WCHA2-08 family-level group, which were most similar to the psychrotolerant hydrogenotrophic methanogen Methanosphaerula palustris strain E1-9c. In contrast, at higher temperatures, substrate amendment enhanced methane production in H2/CO2 amended microcosms, and played a clear role in structuring methanogen communities. Specifically, at 30°C members of the Methanoregulaceae/WCHA2-08 predominated following incubation with H2/CO2, and Methanosarcinaceaeand Methanosaetaceae were enriched in response to acetate addition. These results may indicate that in transiently cold environments, methanogen communities can rapidly respond to moderate short term increases in temperature, but not necessarily to the seasonal release of previously frozen organic carbon from thawing permafrost soils. However, as temperatures increase such inputs of carbon will likely have a greater influence on methane production and methanogen community structure. Understanding the action and limitations of anaerobic microorganisms within cold environments may provide information which can be used in defining region-specific differences in the microbial processes; which ultimately control methane flux to the atmosphere.
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Affiliation(s)
- Lynsay I. Blake
- Newcastle University, School of Civil engineering and Geosciences, Newcastle upon Tyne, United Kingdom
| | - Alexander Tveit
- Department of Arctic and Marine Biology, University of Tromsø, Tromsø, Norway
| | - Lise Øvreås
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Ian M. Head
- Newcastle University, School of Civil engineering and Geosciences, Newcastle upon Tyne, United Kingdom
| | - Neil D. Gray
- Newcastle University, School of Civil engineering and Geosciences, Newcastle upon Tyne, United Kingdom
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83
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Wang M, Jiang X, Wu W, Hao Y, Su Y, Cai L, Xiang M, Liu X. Psychrophilic fungi from the world's roof. PERSOONIA 2015; 34:100-12. [PMID: 26240448 PMCID: PMC4510274 DOI: 10.3767/003158515x685878] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 03/05/2014] [Indexed: 12/05/2022]
Abstract
During a survey of cold-adapted fungi in alpine glaciers on the Qinghai-Tibet Plateau, 1 428 fungal isolates were obtained of which 150 species were preliminary identified. Phoma sclerotioides and Pseudogymnoascus pannorum were the most dominant species. Psychrotolerant species in Helotiales (Leotiomycetes, Ascomycota) were studied in more detail as they represented the most commonly encountered group during this investigation. Two phylogenetic trees were constructed based on the partial large subunit nrDNA (LSU) to infer the taxonomic placements of these strains. Our strains nested in two well-supported major clades, which represented Tetracladium and a previously unknown lineage. The unknown lineage is distant to any other currently known genera in Helotiales. Psychrophila gen. nov. was therefore established to accommodate these strains which are characterised by globose or subglobose conidia formed from phialides on short or reduced conidiophores. Our analysis also showed that an LSU-based phylogeny is insufficient in differentiating strains at species level. Additional analyses using combined sequences of ITS+TEF1+TUB regions were employed to further investigate the phylogenetic relationships of these strains. Together with the recognisable morphological distinctions, six new species (i.e. P. antarctica, P. lutea, P. olivacea, T. ellipsoideum, T. globosum and T. psychrophilum) were described. Our preliminary investigation indicates a high diversity of cold-adapted species in nature, and many of them may represent unknown species.
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Affiliation(s)
- M. Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 1st Beichen West Road, Chaoyang District, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - X. Jiang
- Novozymes (China) Investment Co. Ltd., China Headquarters, 14 Xinxi Road, Shangdi Zone, Haidian District, 100085 Beijing, China
| | - W. Wu
- Novozymes (China) Investment Co. Ltd., China Headquarters, 14 Xinxi Road, Shangdi Zone, Haidian District, 100085 Beijing, China
| | - Y. Hao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 1st Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Y. Su
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 1st Beichen West Road, Chaoyang District, Beijing 100101, China
| | - L. Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 1st Beichen West Road, Chaoyang District, Beijing 100101, China
| | - M. Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 1st Beichen West Road, Chaoyang District, Beijing 100101, China
| | - X. Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 3 1st Beichen West Road, Chaoyang District, Beijing 100101, China
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84
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Hu W, Zhang Q, Tian T, Cheng G, An L, Feng H. The microbial diversity, distribution, and ecology of permafrost in China: a review. Extremophiles 2015; 19:693-705. [PMID: 25925876 DOI: 10.1007/s00792-015-0749-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 04/04/2015] [Indexed: 11/29/2022]
Abstract
Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.
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Affiliation(s)
- Weigang Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
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85
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Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs 2015; 13:1925-65. [PMID: 25854643 PMCID: PMC4413194 DOI: 10.3390/md13041925] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 12/26/2022] Open
Abstract
The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. Extremozymes are adapted to work in harsh physical-chemical conditions and their use in various industrial applications such as the biofuel, pharmaceutical, fine chemicals and food industries has increased. The understanding of the specific factors that confer the ability to withstand extreme habitats on such enzymes has become a priority for their biotechnological use. The most studied marine extremophiles are prokaryotes and in this review, we present the most studied archaea and bacteria extremophiles and their hydrolases, and discuss their use for industrial applications.
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86
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Li J, Qi L, Guo Y, Yue L, Li Y, Ge W, Wu J, Shi W, Dong X. Global mapping transcriptional start sites revealed both transcriptional and post-transcriptional regulation of cold adaptation in the methanogenic archaeon Methanolobus psychrophilus. Sci Rep 2015; 5:9209. [PMID: 25784521 PMCID: PMC5378194 DOI: 10.1038/srep09209] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/23/2015] [Indexed: 11/12/2022] Open
Abstract
Psychrophilic methanogenic Archaea contribute significantly to global methane emissions, but archaeal cold adaptation mechanisms remain poorly understood. Hinted by that mRNA architecture determined secondary structure respond to cold more promptly than proteins, differential RNA-seq was used in this work to examine the genome-wide transcription start sites (TSSs) of the psychrophilic methanogen Methanolobus psychrophilus R15 and its response to cold. Unlike most prokaryotic mRNAs with short 5' untranslated regions (5' UTR, median lengths of 20-40 nt), 51% mRNAs of this methanogen have large 5' UTR (>50 nt). For 24% of the mRNAs, the 5' UTR is >150 nt. This implies that post-transcriptional regulation may be significance in the psychrophile. Remarkably, 219 (14%) genes possessed multiple gene TSSs (gTSSs), and 84 genes exhibited temperature-regulated gTSS selection to express alternative 5' UTR. Primer extension studies confirmed the temperature-dependent TSS selection and a stem-loop masking of ribosome binding sites was predicted from the longer 5' UTRs, suggesting alternative 5' UTRs-mediated translation regulation in the cold adaptation as well. In addition, 195 small RNAs (sRNAs) were detected, and Northern blots confirmed that many sRNAs were induced by cold. Thus, this study revealed an integrated transcriptional and post-transcriptional regulation for cold adaptation in a psychrophilic methanogen.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Yang Guo
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Lei Yue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
| | - Yanping Li
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Weizhen Ge
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Jun Wu
- Novogene Bioinformatics Institute, 21st Floor, Jinma building B area, Xueqing Road, Beijing 100083, People's Republic of China
| | - Wenyuan Shi
- Department of Microbiology, Immunology and Molecular Genetics, University of California, 10833 Le Conte Avenue, Los Angeles, CA90095, USA
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Beijing 100101, People's Republic of China
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87
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Carillo S, Casillo A, Pieretti G, Parrilli E, Sannino F, Bayer-Giraldi M, Cosconati S, Novellino E, Ewert M, Deming JW, Lanzetta R, Marino G, Parrilli M, Randazzo A, Tutino ML, Corsaro MM. A unique capsular polysaccharide structure from the psychrophilic marine bacterium Colwellia psychrerythraea 34H that mimics antifreeze (glyco)proteins. J Am Chem Soc 2015; 137:179-89. [PMID: 25525681 DOI: 10.1021/ja5075954] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The low temperatures of polar regions and high-altitude environments, especially icy habitats, present challenges for many microorganisms. Their ability to live under subfreezing conditions implies the production of compounds conferring cryotolerance. Colwellia psychrerythraea 34H, a γ-proteobacterium isolated from subzero Arctic marine sediments, provides a model for the study of life in cold environments. We report here the identification and detailed molecular primary and secondary structures of capsular polysaccharide from C. psychrerythraea 34H cells. The polymer was isolated in the water layer when cells were extracted by phenol/water and characterized by one- and two-dimensional NMR spectroscopy together with chemical analysis. Molecular mechanics and dynamics calculations were also performed. The polysaccharide consists of a tetrasaccharidic repeating unit containing two amino sugars and two uronic acids bearing threonine as substituent. The structural features of this unique polysaccharide resemble those present in antifreeze proteins and glycoproteins. These results suggest a possible correlation between the capsule structure and the ability of C. psychrerythraea to colonize subfreezing marine environments.
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Affiliation(s)
- Sara Carillo
- Department of Chemical Sciences, University of Naples Federico II , Complesso Universitario Monte S. Angelo, Via Cintia 4, 80126 Naples, Italy
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88
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Rice CV, Middaugh A, Wickham JR, Friedline A, Thomas KJ, Scull E, Johnson K, Zachariah M, Garimella R. Bacterial lipoteichoic acid enhances cryosurvival. Extremophiles 2014; 19:297-305. [PMID: 25477208 DOI: 10.1007/s00792-014-0714-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 11/16/2014] [Indexed: 11/24/2022]
Abstract
Antifreeze proteins in fish, plants, and insects provide protection to a few degrees below freezing. Microbes have been found to survive at even lower temperatures, and with a few exceptions, antifreeze proteins are missing. We show that lipoteichoic acid (LTA), a biopolymer in the cell wall of Gram-positive bacteria, can be added to B. subtilis cultures and increase freeze tolerance. At 1 % w/v, LTA enables a 50 % survival rate, similar to the results obtained with 1 % w/v glycerol as measured with the resazurin cell viability assay. In the absence of added LTA or glycerol, a very small number of B. subtilis cells survive freezing. This suggests that an innate freeze tolerance mechanism exists. While cryoprotection can be provided by extracellular polymeric substances, our data demonstrate a role for LTA in cryoprotection. Currently, the exact mode of action for LTA cryoprotection is unknown. With a molecular weight of 3-5 kDa, it is unlikely to enter the cell cytoplasm. However, low temperature microscopy data show small ice crystals aligned along channels of liquid water. Our observations suggest that teichoic acids could protect liquid water within biofilms and planktonic bacteria, augmenting the role of brine while also raising the possibility for survival without brine present.
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Affiliation(s)
- Charles V Rice
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA,
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89
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Pessi IS, Osorio-Forero C, Gálvez EJC, Simões FL, Simões JC, Junca H, Macedo AJ. Distinct composition signatures of archaeal and bacterial phylotypes in the Wanda Glacier forefield, Antarctic Peninsula. FEMS Microbiol Ecol 2014; 91:1-10. [PMID: 25764530 DOI: 10.1093/femsec/fiu005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several studies have shown that microbial communities in Antarctic environments are highly diverse. However, considering that the Antarctic Peninsula is among the regions with the fastest warming rates, and that regional climate change has been linked to an increase in the mean rate of glacier retreat, the microbial diversity in Antarctic soil is still poorly understood. In this study, we analysed more than 40 000 sequences of the V5-V6 hypervariable region of the 16S rRNA gene obtained by 454 pyrosequencing from four soil samples from the Wanda Glacier forefield, King George Island, Antarctic Peninsula. Phylotype diversity and richness were surprisingly high, and taxonomic assignment of sequences revealed that communities are dominated by Proteobacteria, Bacteroidetes and Euryarchaeota, with a high frequency of archaeal and bacterial phylotypes unclassified at the genus level and without cultured representative strains, representing a distinct microbial community signature. Several phylotypes were related to marine microorganisms, indicating the importance of the marine environment as a source of colonizers for this recently deglaciated environment. Finally, dominant phylotypes were related to different microorganisms possessing a large array of metabolic strategies, indicating that early successional communities in Antarctic glacier forefield can be also functionally diverse.
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Affiliation(s)
- Igor S Pessi
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500 - Agronomia, Porto Alegre - RS, 91501-970, Brazil
| | - César Osorio-Forero
- Research Group Microbial Ecology: Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen, Carrera 5 66A-34, 110231, Bogotá, DC, Colombia
| | - Eric J C Gálvez
- Research Group Microbial Ecology: Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen, Carrera 5 66A-34, 110231, Bogotá, DC, Colombia
| | - Felipe L Simões
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500 - Agronomia, Porto Alegre - RS, 91501-970, Brazil
| | - Jefferson C Simões
- Centro Polar e Climático, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500 - Agronomia, Porto Alegre - RS, 91501-970, Brazil
| | - Howard Junca
- Research Group Microbial Ecology: Metabolism, Genomics and Evolution of Communities of Environmental Microorganisms, CorpoGen, Carrera 5 66A-34, 110231, Bogotá, DC, Colombia
| | - Alexandre J Macedo
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500 - Agronomia, Porto Alegre - RS, 91501-970, Brazil Faculdade de Farmácia, Universidade Federal do Rio Grande do Sul, Avenida Ipiranga, 2752 - Azenha, Porto Alegre - RS, 90610-000, Brazil
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90
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Adaptational properties and applications of cold-active lipases from psychrophilic bacteria. Extremophiles 2014; 19:235-47. [PMID: 25472009 DOI: 10.1007/s00792-014-0710-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/16/2014] [Indexed: 10/24/2022]
Abstract
Psychrophilic microorganisms are cold-adapted with distinct properties from other thermal classes thriving in cold conditions in large areas of the earth's cold environment. Maintenance of functional membranes, evolving cold-adapted enzymes and synthesizing a range of structural features are basic adaptive strategies of psychrophiles. Among the cold-evolved enzymes are the cold-active lipases, a group of microbial lipases with inherent stability-activity-flexibility property that have engaged the interest of researchers over the years. Current knowledge regarding these cold-evolved enzymes in psychrophilic bacteria proves a display of high catalytic efficiency with low thermal stability, which is a differentiating feature with that of their mesophilic and thermophilic counterparts. Improvement strategies of their adaptive structural features have significantly benefited the enzyme industry. Based on their homogeneity and purity, molecular characterizations of these enzymes have been successful and their properties make them unique biocatalysts for various industrial and biotechnological applications. Although, strong association of lipopolysaccharides from Antarctic microorganisms with lipid hydrolases pose a challenge in their purification, heterologous expression of the cold-adapted lipases with affinity tags simplifies purification with higher yield. The review discusses these cold-evolved lipases from bacteria and their peculiar properties, in addition to their potential biotechnological and industrial applications.
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91
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Diversity and distribution of archaea community along a stratigraphic permafrost profile from Qinghai-Tibetan Plateau, China. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:240817. [PMID: 25525409 PMCID: PMC4261641 DOI: 10.1155/2014/240817] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/22/2014] [Accepted: 11/03/2014] [Indexed: 02/07/2023]
Abstract
Accompanying the thawing permafrost expected to result from the climate change, microbial decomposition of the massive amounts of frozen organic carbon stored in permafrost is a potential emission source of greenhouse gases, possibly leading to positive feedbacks to the greenhouse effect. In this study, the community composition of archaea in stratigraphic soils from an alpine permafrost of Qinghai-Tibetan Plateau was investigated. Phylogenic analysis of 16S rRNA sequences revealed that the community was predominantly constituted by
Crenarchaeota and Euryarchaeota. The active layer contained a proportion of
Crenarchaeota at 51.2%, with the proportion of Euryarchaeota at 48.8%, whereas the permafrost
contained 41.2% Crenarchaeota and 58.8% Euryarchaeota, based on 16S rRNA gene sequence analysis.
OTU1 and OTU11, affiliated to Group 1.3b/MCG-A within Crenarchaeota and the unclassified group within Euryarchaeota, respectively,
were widely distributed in all sediment layers. However, OTU5 affiliated to Group 1.3b/MCG-A was primarily distributed in the active layers.
Sequence analysis of the DGGE bands from the 16S rRNAs of methanogenic archaea showed that the majority of methanogens belonged
to Methanosarcinales and Methanomicrobiales affiliated to Euryarchaeota and the uncultured ZC-I cluster affiliated to Methanosarcinales distributed in all the depths along the permafrost profile, which indicated a dominant group of methanogens occurring in the cold ecosystems.
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92
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Rummel JD, Beaty DW, Jones MA, Bakermans C, Barlow NG, Boston PJ, Chevrier VF, Clark BC, de Vera JPP, Gough RV, Hallsworth JE, Head JW, Hipkin VJ, Kieft TL, McEwen AS, Mellon MT, Mikucki JA, Nicholson WL, Omelon CR, Peterson R, Roden EE, Sherwood Lollar B, Tanaka KL, Viola D, Wray JJ. A new analysis of Mars "Special Regions": findings of the second MEPAG Special Regions Science Analysis Group (SR-SAG2). ASTROBIOLOGY 2014; 14:887-968. [PMID: 25401393 DOI: 10.1089/ast.2014.1227] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
A committee of the Mars Exploration Program Analysis Group (MEPAG) has reviewed and updated the description of Special Regions on Mars as places where terrestrial organisms might replicate (per the COSPAR Planetary Protection Policy). This review and update was conducted by an international team (SR-SAG2) drawn from both the biological science and Mars exploration communities, focused on understanding when and where Special Regions could occur. The study applied recently available data about martian environments and about terrestrial organisms, building on a previous analysis of Mars Special Regions (2006) undertaken by a similar team. Since then, a new body of highly relevant information has been generated from the Mars Reconnaissance Orbiter (launched in 2005) and Phoenix (2007) and data from Mars Express and the twin Mars Exploration Rovers (all 2003). Results have also been gleaned from the Mars Science Laboratory (launched in 2011). In addition to Mars data, there is a considerable body of new data regarding the known environmental limits to life on Earth-including the potential for terrestrial microbial life to survive and replicate under martian environmental conditions. The SR-SAG2 analysis has included an examination of new Mars models relevant to natural environmental variation in water activity and temperature; a review and reconsideration of the current parameters used to define Special Regions; and updated maps and descriptions of the martian environments recommended for treatment as "Uncertain" or "Special" as natural features or those potentially formed by the influence of future landed spacecraft. Significant changes in our knowledge of the capabilities of terrestrial organisms and the existence of possibly habitable martian environments have led to a new appreciation of where Mars Special Regions may be identified and protected. The SR-SAG also considered the impact of Special Regions on potential future human missions to Mars, both as locations of potential resources and as places that should not be inadvertently contaminated by human activity.
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Affiliation(s)
- John D Rummel
- 1 Department of Biology, East Carolina University , Greenville, North Carolina, USA
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93
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Barahona S, Dorador C, Zhang R, Aguilar P, Sand W, Vera M, Remonsellez F. Isolation and characterization of a novel Acidithiobacillus ferrivorans strain from the Chilean Altiplano: attachment and biofilm formation on pyrite at low temperature. Res Microbiol 2014; 165:782-93. [PMID: 25111023 DOI: 10.1016/j.resmic.2014.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 12/17/2022]
Abstract
Microorganisms are used to aid the extraction of valuable metals from low-grade sulfide ores in mines worldwide, but relatively little is known about this process in cold environments. This study comprises a preliminary analysis of the bacterial diversity of the polyextremophilic acid River Aroma located in the Chilean Altiplano, and revealed that Betaproteobacteria was the most dominant bacterial group (Gallionella-like and Thiobacillus-like). Taxa characteristic of leaching environments, such Acidithiobacillus and Leptospirillum, were detected at low abundances. Also, bacteria not associated with extremely acidic, metal-rich environments were found. After enrichment in iron- and sulfur-oxidizing media, we isolated and identified a novel psychrotolerant Acidithiobacillus ferrivorans strain ACH. This strain can grow using ferrous iron, sulfur, thiosulfate, tetrathionate and pyrite, as energy sources. Optimal growth was observed in the presence of pyrite, where cultures reached a cell number of 6.5 · 10(7) cells mL(-1). Planktonic cells grown with pyrite showed the presence of extracellular polymeric substances (10 °C and 28 °C), and a high density of cells attached to pyrite grains were observed at 10 °C by electron microscopy. The attachment of cells to pyrite coupons and the presence of capsular polysaccharides were visualized by using epifluorescence microscopy, through nucleic acid and lectin staining with Syto(®)9 and TRITC-Con A, respectively. Interestingly, we observed high cell adhesion including the formation of microcolonies within 21 days of incubation at 4 °C, which was correlated with a clear induction of capsular polysaccharides production. Our data suggests that attachment to pyrite is not temperature-dependent in At. ferrivorans ACH. The results of this study highlight the potential of this novel psychrotolerant strain in oxidation and attachment to minerals under low-temperature conditions.
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Affiliation(s)
- Sergio Barahona
- Laboratorio de Tecnología de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Centro de Bioinnovación, Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Avenida Angamos 0601, Antofagasta, Chile.
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Centro de Bioinnovación, Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Avenida Angamos 0601, Antofagasta, Chile.
| | - Ruiyong Zhang
- Biofilm Centre, University of Dusiburg-Essen, 5, 45141 Essen, Germany.
| | - Pablo Aguilar
- Laboratorio de Tecnología de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta, Chile; Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Centro de Bioinnovación, Facultad de Ciencias del Mar y Recursos Biológicos, Departamento de Biotecnología, Universidad de Antofagasta, Avenida Angamos 0601, Antofagasta, Chile.
| | - Wolfgang Sand
- Biofilm Centre, University of Dusiburg-Essen, 5, 45141 Essen, Germany.
| | - Mario Vera
- Biofilm Centre, University of Dusiburg-Essen, 5, 45141 Essen, Germany.
| | - Francisco Remonsellez
- Laboratorio de Tecnología de Membranas, Biotecnología y Medio Ambiente, Departamento de Ingeniería Química, Universidad Católica del Norte, Avenida Angamos 0610, Antofagasta, Chile.
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94
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Reddy B, Singh KM, Patel AK, Antony A, Panchasara HJ, Joshi CG. Insights into resistome and stress responses genes in Bubalus bubalis rumen through metagenomic analysis. Mol Biol Rep 2014; 41:6405-17. [DOI: 10.1007/s11033-014-3521-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 06/19/2014] [Indexed: 01/05/2023]
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95
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General Characteristics and Important Model Organisms. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014. [DOI: 10.1128/9781555815516.ch2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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96
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Bakermans C, Skidmore ML, Douglas S, McKay CP. Molecular characterization of bacteria from permafrost of the Taylor Valley, Antarctica. FEMS Microbiol Ecol 2014; 89:331-46. [DOI: 10.1111/1574-6941.12310] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 12/01/2022] Open
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97
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Stoeva MK, Aris-Brosou S, Chételat J, Hintelmann H, Pelletier P, Poulain AJ. Microbial community structure in lake and wetland sediments from a high Arctic polar desert revealed by targeted transcriptomics. PLoS One 2014; 9:e89531. [PMID: 24594936 PMCID: PMC3940601 DOI: 10.1371/journal.pone.0089531] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/22/2014] [Indexed: 11/18/2022] Open
Abstract
While microbial communities play a key role in the geochemical cycling of nutrients and contaminants in anaerobic freshwater sediments, their structure and activity in polar desert ecosystems are still poorly understood, both across heterogeneous freshwater environments such as lakes and wetlands, and across sediment depths. To address this question, we performed targeted environmental transcriptomics analyses and characterized microbial diversity across three depths from sediment cores collected in a lake and a wetland, located on Cornwallis Island, NU, Canada. Microbial communities were characterized based on 16S rRNA and two functional gene transcripts: mcrA, involved in archaeal methane cycling and glnA, a bacterial housekeeping gene implicated in nitrogen metabolism. We show that methane cycling and overall bacterial metabolic activity are the highest at the surface of lake sediments but deeper within wetland sediments. Bacterial communities are highly diverse and structured as a function of both environment and depth, being more diverse in the wetland and near the surface. Archaea are mostly methanogens, structured by environment and more diverse in the wetland. McrA transcript analyses show that active methane cycling in the lake and wetland corresponds to distinct communities with a higher potential for methane cycling in the wetland. Methanosarcina spp., Methanosaeta spp. and a group of uncultured Archaea are the dominant methanogens in the wetland while Methanoregula spp. predominate in the lake.
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Affiliation(s)
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
| | - John Chételat
- Environment Canada, National Wildlife Research Centre, Ottawa, Ontario, Canada
| | - Holger Hintelmann
- Department of Chemistry, Trent University, Peterborough, Ontario, Canada
| | - Philip Pelletier
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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98
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Merlino A, Russo Krauss I, Castellano I, Ruocco MR, Capasso A, De Vendittis E, Rossi B, Sica F. Structural and denaturation studies of two mutants of a cold adapted superoxide dismutase point to the importance of electrostatic interactions in protein stability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:632-40. [DOI: 10.1016/j.bbapap.2014.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 01/07/2014] [Accepted: 01/10/2014] [Indexed: 10/25/2022]
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99
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Leuko S, Rettberg P, Pontifex AL, Burns BP. On the response of halophilic archaea to space conditions. Life (Basel) 2014; 4:66-76. [PMID: 25370029 PMCID: PMC4187150 DOI: 10.3390/life4010066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 02/10/2014] [Accepted: 02/17/2014] [Indexed: 11/16/2022] Open
Abstract
Microorganisms are ubiquitous and can be found in almost every habitat and ecological niche on Earth. They thrive and survive in a broad spectrum of environments and adapt to rapidly changing external conditions. It is of great interest to investigate how microbes adapt to different extreme environments and with modern human space travel, we added a new extreme environment: outer space. Within the last 50 years, technology has provided tools for transporting microbial life beyond Earth's protective shield in order to study in situ responses to selected conditions of space. This review will focus on halophilic archaea, as, due to their ability to survive in extremes, they are often considered a model group of organisms to study responses to the harsh conditions associated with space. We discuss ground-based simulations, as well as space experiments, utilizing archaea, examining responses and/or resistance to the effects of microgravity and UV in particular. Several halophilic archaea (e.g., Halorubrum chaoviator) have been exposed to simulated and actual space conditions and their survival has been determined as well as the protective effects of halite shown. Finally, the intriguing potential of archaea to survive on other planets or embedded in a meteorite is postulated.
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Affiliation(s)
- Stefan Leuko
- Deutsches Zentrum für Luft- und Raumfahrt, Institut für Luft- und Raumfahrtmedizin, Abteilung Strahlenbiologie, Arbeitsgruppe Astrobiologie, Linder Höhe, Köln 51147, Germany.
| | - Petra Rettberg
- Deutsches Zentrum für Luft- und Raumfahrt, Institut für Luft- und Raumfahrtmedizin, Abteilung Strahlenbiologie, Arbeitsgruppe Astrobiologie, Linder Höhe, Köln 51147, Germany.
| | - Ashleigh L Pontifex
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia.
| | - Brendan P Burns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia.
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100
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Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature. Int J Syst Evol Microbiol 2014; 64:180-186. [DOI: 10.1099/ijs.0.056218-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A psychrotolerant hydrogenotrophic methanogen, strain Pt1, was isolated from a syntrophic propionate-oxidizing methanogenic consortium obtained from granulated biomass of a two-stage low-temperature (3–8 °C) anaerobic expanded granular sludge bed (EGSB) bioreactor, fed with a mixture of volatile fatty acids (VFAs) (acetate, propionate and butyrate). The strain was strictly anaerobic, and cells were curved rods, 0.4–0.5×7.5–25 µm, that sometimes formed wavy filaments from 25 to several hundred micrometres in length. Cells stained Gram-negative and were non-sporulating. They were gently motile by means of tufted flagella. The strain grew at 5–37 °C (optimum at 20–30 °C), at pH 6.0–10 (optimum 7.0–7.5) and with 0–0.3 M NaCl (optimum 0 M NaCl). Growth and methane production was found with H2/CO2 and very weak growth with formate. Acetate and yeast extract stimulated growth, but were not essential. The G+C content of the DNA of strain Pt1 was 40 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Pt1 was a member of the genus
Methanospirillum
and showed 97.5 % sequence similarity to
Methanospirillum hungatei
JF1T and 94 % sequence similarity to
Methanospirillum lacunae
Ki8-1T. DNA–DNA hybridization of strain Pt1 with
Methanospirillum hungatei
JF1T revealed 39 % relatedness. On the basis of its phenotypic characteristics and phylogenetic position, strain Pt1 is a representative of a novel species of the genus
Methanospirillum
, for which the name Methanospirillum stamsii sp. nov. is proposed. The type strain is Pt1T ( = DSM 26304T = VKM B-2808T).
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