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Choudhary P, Bhatt S, Chatterjee S. From freezing to functioning: cellular strategies of cold-adapted bacteria for surviving in extreme environments. Arch Microbiol 2024; 206:329. [PMID: 38940837 DOI: 10.1007/s00203-024-04058-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 06/29/2024]
Abstract
The ability of cold-adapted bacteria to survive in extreme cold and diverse temperatures is due to their unique attributes like cell membrane stability, up-regulation of peptidoglycan biosynthesis, increased production of extracellular polymeric substances, and expansion of membrane pigment. Various cold-adapted proteins, including ice-nucleating proteins (INPs), antifreeze proteins (AFPs), cold shock proteins (Csps), and cold-acclimated proteins (CAPs), help the bacteria to survive in these environments. To sustain cells from extreme cold conditions and maintain stability in temperature fluctuations, survival strategies at the molecular level and their mechanism play significant roles in adaptations in cryospheric conditions. Furthermore, cold shock domains present in the multifunctional cold shock proteins play crucial roles in their adaptation strategies. The considerable contribution of lipopeptides, osmolytes, and membrane pigments plays an integral part in their survival in extreme environments. This review summarizes the evolutionary history of cold-adapted bacteria and their molecular and cellular adaptation strategies to thrive in harsh cold environments. It also discusses the importance of carotenoids produced, lipid composition, cryoprotectants, proteins, and chaperones related to this adaptation. Furthermore, the functions and mechanisms of adaptations within the cell are discussed briefly. One can utilize and explore their potential in various biotechnology applications and their evolutionary journey by knowing the inherent mechanism of their molecular and cellular adaptation to cold climatic conditions. This review will help all branches of the life science community understand the basic microbiology of psychrophiles and their hidden prospect in life science research.
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Affiliation(s)
- Priyanka Choudhary
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Sunidhi Bhatt
- Bioremediation and Metabolomics Research Group, Department of Environmental Sciences, Central University of Himachal Pradesh, Academic Block-Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Subhankar Chatterjee
- Bioremediation and Metabolomics Research Group, Dept. of Ecology & Environmental Sciences, School of Life Sciences, Pondicherry University, R.V. Nagar, Kalapet, Puducherry, 605014, India.
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Giovannini M, Vieri W, Bosi E, Riccardi C, Lo Giudice A, Fani R, Fondi M, Perrin E. Functional Genomics of a Collection of Gammaproteobacteria Isolated from Antarctica. Mar Drugs 2024; 22:238. [PMID: 38921549 PMCID: PMC11205219 DOI: 10.3390/md22060238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Antarctica, one of the most extreme environments on Earth, hosts diverse microbial communities. These microbes have evolved and adapted to survive in these hostile conditions, but knowledge on the molecular mechanisms underlying this process remains limited. The Italian Collection of Antarctic Bacteria (Collezione Italiana Batteri Antartici (CIBAN)), managed by the University of Messina, represents a valuable repository of cold-adapted bacterial strains isolated from various Antarctic environments. In this study, we sequenced and analyzed the genomes of 58 marine Gammaproteobacteria strains from the CIBAN collection, which were isolated during Italian expeditions from 1990 to 2005. By employing genome-scale metrics, we taxonomically characterized these strains and assigned them to four distinct genera: Pseudomonas, Pseudoalteromonas, Shewanella, and Psychrobacter. Genome annotation revealed a previously untapped functional potential, including secondary metabolite biosynthetic gene clusters and antibiotic resistance genes. Phylogenomic analyses provided evolutionary insights, while assessment of cold-shock protein presence shed light on adaptation mechanisms. Our study emphasizes the significance of CIBAN as a resource for understanding Antarctic microbial life and its biotechnological potential. The genomic data unveil new horizons for insight into bacterial existence in Antarctica.
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Affiliation(s)
- Michele Giovannini
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Walter Vieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Emanuele Bosi
- Department of Earth, Environment and Life Sciences—DISTAV, University of Genoa, Corso Europa 26, I-16132 Genova, Italy;
| | - Christopher Riccardi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
- Quantitative and Computational Biology Department, University of Southern California, Los Angeles, CA 90089, USA
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council, (CNR.ISP), Spianata San Raineri 86, I-98122 Messina, Italy;
- Italian Collection of Antarctic Bacteria, National Antarctic Museum (CIBAN-MNA), I-98122 Messina, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, I-90133 Palermo, Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Marco Fondi
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
| | - Elena Perrin
- Department of Biology, University of Florence, Via Madonna del Piano 6, I-50019 Sesto Fiorentino, Italy; (M.G.); (W.V.); (C.R.); (R.F.); (M.F.)
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García-Laviña CX, Morel MA, García-Gabarrot G, Castro-Sowinski S. Phenotypic and resistome analysis of antibiotic and heavy metal resistance in the Antarctic bacterium Pseudomonas sp. AU10. Braz J Microbiol 2023; 54:2903-2913. [PMID: 37783937 PMCID: PMC10689667 DOI: 10.1007/s42770-023-01135-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023] Open
Abstract
Resistance to antibiotics and heavy metals in Antarctic bacteria has been investigated due to anthropogenic impact on the continent. However, there is still much to learn about the genetic determinants of resistance in native bacteria. In this study, we investigated antibiotic, heavy metal, and metalloid resistance in Pseudomonas sp. AU10, isolated from King George Island (Antarctica), and analyzed its genome to look for all the associated genetic determinants (resistome). We found that AU10 displayed resistance to Cr(VI), Cu(II), Mn(II), Fe(II), and As(V), and produced an exopolysaccharide with high Cr(VI)-biosorption capacity. Additionaly, the strain showed resistance to aminopenicillins, cefotaxime, aztreonam, azithromycin, and intermediate resistance to chloramphenicol. Regarding the resistome, we did not find resistance genes in AU10's natural plasmid or in a prophage context. Only a copper resistance cluster indicated possible horizontal acquisition. The mechanisms of resistance found were mostly efflux systems, several sequestering proteins, and a few enzymes, such as an AmpC β-lactamase or a chromate reductase, which would account for the observed phenotypic profile. In contrast, the presence of a few gene clusters, including the terZABCDE operon for tellurite resistance, did not correlate with the expected phenotype. Despite the observed resistance to multiple antibiotics and heavy metals, the lack of resistance genes within evident mobile genetic elements is suggestive of the preserved nature of AU10's Antarctic habitat. As Pseudomonas species are good bioindicators of human impact in Antarctic environments, we consider that our results could help refine surveillance studies based on monitoring resistances and associated resistomes in these populations.
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Affiliation(s)
- César X García-Laviña
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
| | - María A Morel
- Laboratorio de Microbiología de Suelos, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Gabriela García-Gabarrot
- Departamento de Laboratorios, Ministerio de Salud Pública, Alfredo Navarro 3051, 11600, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable (IIBCE), Av. Italia 3318, 11600, Montevideo, Uruguay.
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Ramón A, Esteves A, Villadóniga C, Chalar C, Castro-Sowinski S. A general overview of the multifactorial adaptation to cold: biochemical mechanisms and strategies. Braz J Microbiol 2023; 54:2259-2287. [PMID: 37477802 PMCID: PMC10484896 DOI: 10.1007/s42770-023-01057-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023] Open
Abstract
Cold environments are more frequent than people think. They include deep oceans, cold lakes, snow, permafrost, sea ice, glaciers, cold soils, cold deserts, caves, areas at elevations greater than 3000 m, and also artificial refrigeration systems. These environments are inhabited by a diversity of eukaryotic and prokaryotic organisms that must adapt to the hard conditions imposed by cold. This adaptation is multifactorial and includes (i) sensing the cold, mainly through the modification of the liquid-crystalline membrane state, leading to the activation of a two-component system that transduce the signal; (ii) adapting the composition of membranes for proper functions mainly due to the production of double bonds in lipids, changes in hopanoid composition, and the inclusion of pigments; (iii) producing cold-adapted proteins, some of which show modifications in the composition of amino acids involved in stabilizing interactions and structural adaptations, e.g., enzymes with high catalytic efficiency; and (iv) producing ice-binding proteins and anti-freeze proteins, extracellular polysaccharides and compatible solutes that protect cells from intracellular and extracellular ice. However, organisms also respond by reprogramming their metabolism and specifically inducing cold-shock and cold-adaptation genes through strategies such as DNA supercoiling, distinctive signatures in promoter regions and/or the action of CSPs on mRNAs, among others. In this review, we describe the main findings about how organisms adapt to cold, with a focus in prokaryotes and linking the information with findings in eukaryotes.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Adriana Esteves
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Carolina Villadóniga
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Cora Chalar
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Sección Bioquímica, Instituto de Biología, Facultad de Ciencias, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
- Laboratorio de Biocatalizadores Y Sus Aplicaciones, Facultad de Ciencias, Instituto de Química Biológica, Universidad de La República, Igua 4225, 11400, Montevideo, Uruguay.
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Ramasamy KP, Mahawar L, Rajasabapathy R, Rajeshwari K, Miceli C, Pucciarelli S. Comprehensive insights on environmental adaptation strategies in Antarctic bacteria and biotechnological applications of cold adapted molecules. Front Microbiol 2023; 14:1197797. [PMID: 37396361 PMCID: PMC10312091 DOI: 10.3389/fmicb.2023.1197797] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Climate change and the induced environmental disturbances is one of the major threats that have a strong impact on bacterial communities in the Antarctic environment. To cope with the persistent extreme environment and inhospitable conditions, psychrophilic bacteria are thriving and displaying striking adaptive characteristics towards severe external factors including freezing temperature, sea ice, high radiation and salinity which indicates their potential in regulating climate change's environmental impacts. The review illustrates the different adaptation strategies of Antarctic microbes to changing climate factors at the structural, physiological and molecular level. Moreover, we discuss the recent developments in "omics" approaches to reveal polar "blackbox" of psychrophiles in order to gain a comprehensive picture of bacterial communities. The psychrophilic bacteria synthesize distinctive cold-adapted enzymes and molecules that have many more industrial applications than mesophilic ones in biotechnological industries. Hence, the review also emphasizes on the biotechnological potential of psychrophilic enzymes in different sectors and suggests the machine learning approach to study cold-adapted bacteria and engineering the industrially important enzymes for sustainable bioeconomy.
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Affiliation(s)
| | - Lovely Mahawar
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
| | - Raju Rajasabapathy
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, Tamilnadu, India
| | | | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Biodegradation of Naphthalene and Anthracene by Aspergillus glaucus Strain Isolated from Antarctic Soil. Processes (Basel) 2022. [DOI: 10.3390/pr10050873] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Biotechnologies based on microbial species capable of destroying harmful pollutants are a successful way to solve some of the most important problems associated with a clean environment. The subject of investigation is the Antarctic fungal strain Aspergillus glaucus AL1. The culturing of the examined strain was performed with 70 mg of wet mycelium being inoculated in a Czapek Dox liquid medium containing naphthalene, anthracene, or phenanthrene (0.3 g/L) as the sole carbon source. Progressively decreasing naphthalene and anthracene concentrations were monitored in the culture medium until the 15th day of the cultivation of A. glaucus AL1. The degradation was determined through gas chromatography–mass spectrometry. Both decreased by 66% and 44%, respectively, for this period. The GC-MS analyses were applied to identify salicylic acid, catechol, and ketoadipic acid as intermediates in the naphthalene degradation. The intermediates identified in anthracene catabolism are 2-hydroxy-1-naphthoic acid, o-phthalic acid, and protocatechuic acid. The enzyme activities for phenol 2-monooxygenase (1.14.13.7) and catechol 1,2-dioxygenase (1.13.11.1) were established. A gene encoding an enzyme with catechol 1,2-dioxygenase activity was identified and sequenced (GeneBank Ac. No KM360483). The recent study provides original data on the potential of an ascomycete’s fungal strain A. glaucus strain AL 1 to degrade naphthalene and anthracene.
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Analysis of Soil Fungal and Bacterial Communities in Tianchi Volcano Crater, Northeast China. Life (Basel) 2021; 11:life11040280. [PMID: 33810555 PMCID: PMC8066613 DOI: 10.3390/life11040280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 11/26/2022] Open
Abstract
High-altitude volcanoes, typical examples of extreme environments, are considered of particular interest in biology as a possible source of novel and exclusive microorganisms. We analyzed the crater soil microbial diversity of Tianchi Volcano, northeast China, by combining molecular and morphological analyses of culturable microbes, and metabarcoding based on Illumina sequencing, in order to increase our understanding of high-altitude volcanic microbial community structure. One-hundred and seventeen fungal strains belonging to 51 species and 31 genera of Ascomycota, Basidiomycota and Mucoromycota were isolated. Penicillium, Trichoderma, Cladosporium, Didymella, Alternaria and Fusarium dominated the culturable fungal community. A considerable number of isolated microbes, including filamentous fungi, such as Aureobasidium pullulans and Epicoccum nigrum, yeasts (Leucosporidium creatinivorum), and bacteria (Chryseobacterium lactis and Rhodococcus spp.), typical of high-altitude, cold, and geothermal extreme environments, provided new insights in the ecological characterization of the investigated environment, and may represent a precious source for the isolation of new bioactive compounds. A total of 1254 fungal and 2988 bacterial operational taxonomic units were generated from metabarcoding. Data analyses suggested that the fungal community could be more sensitive to environmental and geographical change compared to the bacterial community, whose network was characterized by more complicated and closer associations.
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Microbial Succession under Freeze-Thaw Events and Its Potential for Hydrocarbon Degradation in Nutrient-Amended Antarctic Soil. Microorganisms 2021; 9:microorganisms9030609. [PMID: 33809442 PMCID: PMC8000410 DOI: 10.3390/microorganisms9030609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 12/24/2022] Open
Abstract
The polar regions have relatively low richness and diversity of plants and animals, and the basis of the entire ecological chain is supported by microbial diversity. In these regions, understanding the microbial response against environmental factors and anthropogenic disturbances is essential to understand patterns better, prevent isolated events, and apply biotechnology strategies. The Antarctic continent has been increasingly affected by anthropogenic contamination, and its constant temperature fluctuations limit the application of clean recovery strategies, such as bioremediation. We evaluated the bacterial response in oil-contaminated soil through a nutrient-amended microcosm experiment using two temperature regimes: (i) 4 °C and (ii) a freeze–thaw cycle (FTC) alternating between −20 and 4 °C. Bacterial taxa, such as Myxococcales, Chitinophagaceae, and Acidimicrobiales, were strongly related to the FTC. Rhodococcus was positively related to contaminated soils and further stimulated under FTC conditions. Additionally, the nutrient-amended treatment under the FTC regime enhanced bacterial groups with known biodegradation potential and was efficient in removing hydrocarbons of diesel oil. The experimental design, rates of bacterial succession, and level of hydrocarbon transformation can be considered as a baseline for further studies aimed at improving bioremediation strategies in environments affected by FTC regimes.
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Alem D, Marizcurrena JJ, Saravia V, Davyt D, Martinez-Lopez W, Castro-Sowinski S. Production and antiproliferative effect of violacein, a purple pigment produced by an Antarctic bacterial isolate. World J Microbiol Biotechnol 2020; 36:120. [DOI: 10.1007/s11274-020-02893-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/11/2020] [Indexed: 12/22/2022]
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Yarzábal LA. Perspectives for using glacial and periglacial microorganisms for plant growth promotion at low temperatures. Appl Microbiol Biotechnol 2020; 104:3267-3278. [PMID: 32076773 DOI: 10.1007/s00253-020-10468-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/05/2020] [Accepted: 02/12/2020] [Indexed: 12/26/2022]
Abstract
Even though they are among the most extreme environments in which life can develop, glaciers are colonized by metabolically active microbes, some of which thrive-in their own particular way-under the prevailing harsh conditions. Glacial or periglacial microbes are often psychrophiles since they are able to grow optimally at low temperatures. This ability has evolved through a series of adaptations, both molecular and physiological, some of which have been exploited by the biotechnological industry to develop useful products and processes. The recent discovery of cold-adapted plant growth-promoting microorganisms (PGPM) in glacial ice or periglacial soils has opened a gate to a new trove of applications due to their potential use as biofertilizers or biocontrol agents, effective in cold climates. It has been claimed that this would be of profit to increase agriculture productivity in hilly terrains, like those prevailing in the Andes or the Himalayas, since-in addition to their ability to promote plant growth through direct or indirect mechanisms-they represent an environmentally friendly alternative to the use of pesticides and chemical fertilizers. In the following chapter, I summarize the current knowledge on the identity and characteristics of such PGPM and highlight the experiences in promoting the growth of a few plant species, at low temperatures.Key Points•Countless microbes are immured in glaciers and their surroundings.•Many glacial and periglacial microbes are cold-loving (i.e., psychrophiles).•Some glacial and periglacial psychrophiles promote plant growth and development.•Plant growth-promoting psychrophiles can be used to develop biofertilizers.
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Affiliation(s)
- Luis Andrés Yarzábal
- Carrera de Bioquímica y Farmacia, Unidad de Salud y Bienestar, Universidad Católica de Cuenca, Av. Las Américas y Calle Humboldt, Cuenca, Ecuador. .,Centro de Investigación, Innovación y Transferencia de Tecnología (CIITT), Universidad Católica de Cuenca. Campus Miracielos, Ricaurte, Ecuador.
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Shah M, Sun C, Sun Z, Zhang G, Che Q, Gu Q, Zhu T, Li D. Antibacterial Polyketides from Antarctica Sponge-Derived Fungus Penicillium sp. HDN151272. Mar Drugs 2020; 18:md18020071. [PMID: 31979231 PMCID: PMC7073682 DOI: 10.3390/md18020071] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 10/30/2022] Open
Abstract
Three new polyketides, ketidocillinones A-C (1-3), were discovered from the extract of an Antarctica sponge-derived fungus Penicillium sp. HDN151272. All the structures were deduced by spectroscopic data, including NMR and HRESIMS. The absolute configuration of compound 3 was established by using ECD calculation. Compounds 1-3 can be slowly oxidized to quinone form when exposed to air. Ketidocillinones B and C (2 and 3) exhibited potent antibacterial activity against Pseudomonas aeurigenosa, Mycobacterium phlei, and MRCNS (methicillin-resistant coagulase-negative staphylococci) with MIC values ranging from 1.56 to 25.00 µg/mL.
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Affiliation(s)
- Mudassir Shah
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
| | - Chunxiao Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
| | - Zichao Sun
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
| | - Qianqun Gu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
- Correspondence: (T.Z.); (D.L.); Tel.: +86-532-82031632 (T.Z.); +86-532-82031619 (D.L.)
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (M.S.); (C.S.); (Z.S.); (G.Z.); (Q.C.); (Q.G.)
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Correspondence: (T.Z.); (D.L.); Tel.: +86-532-82031632 (T.Z.); +86-532-82031619 (D.L.)
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Diversity and Horizontal Transfer of Antarctic Pseudomonas spp. Plasmids. Genes (Basel) 2019; 10:genes10110850. [PMID: 31661808 PMCID: PMC6896180 DOI: 10.3390/genes10110850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/22/2019] [Accepted: 10/26/2019] [Indexed: 12/23/2022] Open
Abstract
Pseudomonas spp. are widely distributed in various environments around the world. They are also common in the Antarctic regions. To date, almost 200 plasmids of Pseudomonas spp. have been sequenced, but only 12 of them were isolated from psychrotolerant strains. In this study, 15 novel plasmids of cold-active Pseudomonas spp. originating from the King George Island (Antarctica) were characterized using a combined, structural and functional approach, including thorough genomic analyses, functional analyses of selected genetic modules, and identification of active transposable elements localized within the plasmids and comparative genomics. The analyses performed in this study increased the understanding of the horizontal transfer of plasmids found within Pseudomonas populations inhabiting Antarctic soils. It was shown that the majority of the studied plasmids are narrow-host-range replicons, whose transfer across taxonomic boundaries may be limited. Moreover, structural and functional analyses enabled identification and characterization of various accessory genetic modules, including genes encoding major pilin protein (PilA), that enhance biofilm formation, as well as active transposable elements. Furthermore, comparative genomic analyses revealed that the studied plasmids of Antarctic Pseudomonas spp. are unique, as they are highly dissimilar to the other known plasmids of Pseudomonas spp.
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Yuan K, Yu K, Yang R, Zhang Q, Yang Y, Chen E, Lin L, Luan T, Chen W, Chen B. Metagenomic characterization of antibiotic resistance genes in Antarctic soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:300-308. [PMID: 30947033 DOI: 10.1016/j.ecoenv.2019.03.099] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 03/01/2019] [Accepted: 03/25/2019] [Indexed: 05/20/2023]
Abstract
Antibiotic resistance genes (ARGs) are considered environmental pollutants. Comprehensive characterization of the ARGs in pristine environments is essential towards understanding the evolution of antibiotic resistance. Here, we analyzed ARGs in soil samples collected from relatively pristine Antarctica using metagenomic approaches. We identified 79 subtypes related to 12 antibiotic classes in Antarctic soils, in which ARGs related to multidrug and polypeptide were dominant. The characteristics of ARGs in Antarctic soils were significantly different from those in active sludge, chicken feces and swine feces, in terms of composition, abundance and potential transferability. ARG subtypes (e.g., bacA, ceoB, dfrE, mdtB, amrB, and acrB) were more abundant than others in Antarctic soils. Approximately 60% of the ARGs conferred antibiotic resistance via an efflux mechanism, and a low fraction of ARGs (∼16%) might be present on plasmids. Culturable bacterial consortiums isolated from Antarctic soils were consistently susceptible to most of the tested antibiotics frequently used in clinical therapies. The amrB and ceoB carried by culturable species did not express the resistance to aminoglycoside and fluoroquinolone at the levels of clinical concern. Our results suggest that the wide use of antibiotics may have contributed to developing higher antibiotic resistance and mobility.
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Affiliation(s)
- Ke Yuan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Ke Yu
- School of Environmental and Energy, Peking University Shenzhen Graduate School, Guangdong, 518055, China
| | - Ruiqiang Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Qinghua Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Ying Yang
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Enzhong Chen
- Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, China
| | - Lan Lin
- Zhujiang Hospital of Southern Medical University, Guangzhou, 510282, China
| | - Tiangang Luan
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China; School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wen Chen
- School of Public Health, Sun Yat-sen University, Guangzhou, 510275, China
| | - Baowei Chen
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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14
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Reference genes for real-time RT-PCR expression studies in an Antarctic Pseudomonas exposed to different temperature conditions. Extremophiles 2019; 23:625-633. [DOI: 10.1007/s00792-019-01109-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/17/2019] [Indexed: 12/21/2022]
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15
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Herrera LM, Braña V, Franco Fraguas L, Castro-Sowinski S. Characterization of the cellulase-secretome produced by the Antarctic bacterium Flavobacterium sp. AUG42. Microbiol Res 2019; 223-225:13-21. [PMID: 31178046 DOI: 10.1016/j.micres.2019.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/28/2019] [Accepted: 03/22/2019] [Indexed: 10/27/2022]
Abstract
Flavobacterium sp. AUG42 is a cellulase-producing bacterium isolated from the Antarctic oligochaete Grania sp. (Annelida). In this work, we report that AUG42 produces a glycoside hydrolase cocktail with CMCase, PASCase and cellobiase activities (optimum pHs and temperatures ranging from 5.5 to 6.5 and 40 to 50 °C, respectively). The time-course analyses of the bacterial growth and cellulase production showed that the cocktail has maximal activity at the stationary phase when growing at 16 °C with filter paper as a cellulosic carbon source, among the tested substrates. The analyses of the CAZome and the identification of secreted proteins by shotgun Mass Spectrometry analysis showed that five glycoside hydrolyses are present in the bacterial secretome, which probably cooperate in the degradation of the cellulosic substrates. Two of these glycoside hydrolyses may harbor putative carbohydrate binding modules, both with a cleft-like active site. The cellulolytic cocktail was assayed in saccharification experiments using carboxymethylcellulose as a substrate and results showed the release of glucose (a fermentable sugar) and other reducing-sugars, after 24 h incubation. The ecological relevance of producing cellulases in the Antarctic environment, as well as their potential use in the bio-refinery industry, are discussed.
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Affiliation(s)
- Lorena M Herrera
- Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República (UdelaR), Iguá 4225, 11400, Montevideo, Uruguay
| | - Victoria Braña
- Molecular Microbiology, Institute Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay
| | - Laura Franco Fraguas
- Cátedra de Bioquímica, Departamento de Biociencias, Facultad de Química, Universidad de la República, Av. Gral. Flores 2124, 11800, Montevideo, Uruguay
| | - Susana Castro-Sowinski
- Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República (UdelaR), Iguá 4225, 11400, Montevideo, Uruguay; Molecular Microbiology, Institute Clemente Estable, Av. Italia 3318, 11600, Montevideo, Uruguay.
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16
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Antarctic Soil Microbial Communities in a Changing Environment: Their Contributions to the Sustainability of Antarctic Ecosystems and the Bioremediation of Anthropogenic Pollution. SPRINGER POLAR SCIENCES 2019. [DOI: 10.1007/978-3-030-02786-5_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Arai T, Fukami D, Hoshino T, Kondo H, Tsuda S. Ice-binding proteins from the fungus Antarctomyces psychrotrophicus possibly originate from two different bacteria through horizontal gene transfer. FEBS J 2018; 286:946-962. [PMID: 30548092 DOI: 10.1111/febs.14725] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 11/03/2018] [Accepted: 12/06/2018] [Indexed: 12/12/2022]
Abstract
Various microbes, including fungi and bacteria, that live in cold environments produce ice-binding proteins (IBPs) that protect them from freezing. Ascomycota and Basidiomycota are two major phyla of fungi, and Antarctomyces psychrotrophicus is currently designated as the sole ascomycete that produces IBP (AnpIBP). However, its complete amino acid sequence, ice-binding property, and evolutionary history have not yet been clarified. Here, we determined the peptide sequences of three new AnpIBP isoforms by total cDNA analysis and compared them with those of other microbial IBPs. The AnpIBP isoforms and ascomycete-putative IBPs were found to be phylogenetically close to the bacterial ones but far from the basidiomycete ones, which is supported by the higher sequence identities to bacterial IBPs than basidiomycete IBPs, although ascomycetes are phylogenetically distant from bacteria. In addition, two of the isoforms of AnpIBP share low sequence identity and are not close in the phylogenetic tree. It is hence presumable that these two AnpIBP isoforms were independently acquired from different bacteria through horizontal gene transfer (HGT), which implies that ascomycetes and bacteria frequently exchange their IBP genes. The non-colligative freezing-point depression ability of AnpIBP was not very high, whereas it exhibited significant abilities of ice recrystallization inhibition, ice shaping, and cryo-protection against freeze-thaw cycles even at submicromolar concentrations. These results suggest that HGT is crucial for the cold-adaptive evolution of ascomycetes, and their IBPs offer freeze resistance to organisms to enable them to inhabit the icy environments of Antarctica. DATABASES: Nucleotide sequence data are available in the DDBJ database under the accession numbers LC378707, LC378707, LC378707 for AnpIBP1a, AnpIBP1b, AnpIBP2, respectively.
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Affiliation(s)
- Tatsuya Arai
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Daichi Fukami
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Tamotsu Hoshino
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Hidemasa Kondo
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Sakae Tsuda
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan.,Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan.,OPERANDO Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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18
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A highly efficient and cost-effective recombinant production of a bacterial photolyase from the Antarctic isolate Hymenobacter sp. UV11. Extremophiles 2018; 23:49-57. [DOI: 10.1007/s00792-018-1059-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/24/2018] [Indexed: 01/12/2023]
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19
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Vásquez-Ponce F, Higuera-Llantén S, Pavlov MS, Marshall SH, Olivares-Pacheco J. Phylogenetic MLSA and phenotypic analysis identification of three probable novel Pseudomonas species isolated on King George Island, South Shetland, Antarctica. Braz J Microbiol 2018; 49:695-702. [PMID: 29598976 PMCID: PMC6175711 DOI: 10.1016/j.bjm.2018.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 02/03/2018] [Accepted: 02/14/2018] [Indexed: 02/07/2023] Open
Abstract
Antarctica harbors a great diversity of microorganisms, including bacteria, archaea, microalgae and yeasts. The Pseudomonas genus is one of the most diverse and successful bacterial groups described to date, but only eight species isolated from Antarctica have been characterized. Here, we present three potentially novel species isolated on King George Island. The most abundant isolates from four different environments, were genotypically and phenotypically characterized. Multilocus sequence analysis and 16S rRNA gene analysis of a sequence concatenate for six genes (16S, aroE, glnS, gyrB, ileS and rpoD), determined one of the isolates to be a new Pseudomonas mandelii strain, while the other three are good candidates for new Pseudomonas species. Additionally, genotype analyses showed the three candidates to be part of a new subgroup within the Pseudomonas fluorescens complex, together with the Antarctic species Pseudomonas antarctica and Pseudomonas extremaustralis. We propose terming this new subgroup P. antarctica. Likewise, phenotypic analyses using API 20 NE and BIOLOG® corroborated the genotyping results, confirming that all presented isolates form part of the P. fluorescens complex. Pseudomonas genus research on the Antarctic continent is in its infancy. To understand these microorganisms’ role in this extreme environment, the characterization and description of new species is vital.
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Affiliation(s)
- Felipe Vásquez-Ponce
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Sebastián Higuera-Llantén
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - María S Pavlov
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Jorge Olivares-Pacheco
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile.
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20
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Cid FP, Maruyama F, Murase K, Graether SP, Larama G, Bravo LA, Jorquera MA. Draft genome sequences of bacteria isolated from the Deschampsia antarctica phyllosphere. Extremophiles 2018; 22:537-552. [PMID: 29492666 DOI: 10.1007/s00792-018-1015-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/18/2018] [Indexed: 11/28/2022]
Abstract
Genome analyses are being used to characterize plant growth-promoting (PGP) bacteria living in different plant compartiments. In this context, we have recently isolated bacteria from the phyllosphere of an Antarctic plant (Deschampsia antarctica) showing ice recrystallization inhibition (IRI), an activity related to the presence of antifreeze proteins (AFPs). In this study, the draft genomes of six phyllospheric bacteria showing IRI activity were sequenced and annotated according to their functional gene categories. Genome sizes ranged from 5.6 to 6.3 Mbp, and based on sequence analysis of the 16S rRNA genes, five strains were identified as Pseudomonas and one as Janthinobacterium. Interestingly, most strains showed genes associated with PGP traits, such as nutrient uptake (ammonia assimilation, nitrogen fixing, phosphatases, and organic acid production), bioactive metabolites (indole acetic acid and 1-aminocyclopropane-1-carboxylate deaminase), and antimicrobial compounds (hydrogen cyanide and pyoverdine). In relation with IRI activity, a search of putative AFPs using current bioinformatic tools was also carried out. Despite that genes associated with reported AFPs were not found in these genomes, genes connected to ice-nucleation proteins (InaA) were found in all Pseudomonas strains, but not in the Janthinobacterium strain.
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Affiliation(s)
- Fernanda P Cid
- Programa de Doctorado en Ciencias de Recursos Naturales, Universidad de La Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- The Japan Science and Technology Agency/Japan International Cooperation Agency, Science and Technology Research Partnership for Sustainable Development (JST/JICA, SATREPS), Tokyo, Japan
| | - Kazunori Murase
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Steffen P Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Giovanni Larama
- Department of Mathematical Engineering, Universidad de La Frontera, Temuco, Chile
| | - Leon A Bravo
- Departamento de Ciencias Agronómicas y Recursos Naturales, Facultad de Ciencias Agropecuarias y Forestales, Universidad de la Frontera, Temuco, Chile
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile
| | - Milko A Jorquera
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile.
- Applied Microbial Ecology Laboratory, Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, Temuco, Chile.
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21
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Carvalho EL, Maciel LF, Macedo PE, Dezordi FZ, Abreu MET, Victória FDC, Pereira AB, Boldo JT, Wallau GDL, Pinto PM. De novo Assembly and Annotation of the Antarctic Alga Prasiola crispa Transcriptome. Front Mol Biosci 2018; 4:89. [PMID: 29359133 PMCID: PMC5766667 DOI: 10.3389/fmolb.2017.00089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Evelise L Carvalho
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Lucas F Maciel
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Pablo E Macedo
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Filipe Z Dezordi
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | - Maria E T Abreu
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | | | - Antônio B Pereira
- Núcleo de Estudos da Vegetação Antártica, Federal University of Pampa, São Gabriel, Brazil
| | - Juliano T Boldo
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
| | | | - Paulo M Pinto
- Applied Proteomics Laboratory, Federal University of Pampa, São Gabriel, Brazil
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22
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Zhang M, Wang W, Wang J, Teng Y, Xu Z. Dynamics of biochemical properties associated with soil nitrogen mineralization following nitrification inhibitor and fungicide applications. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:11340-11348. [PMID: 28303541 DOI: 10.1007/s11356-017-8762-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 03/07/2017] [Indexed: 06/06/2023]
Abstract
Agrochemical applications may have side effects on soil biochemical properties related to soil nitrogen (N) mineralization and thus affect N cycling. The present study aimed to evaluate the effects of nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) and fungicide iprodione on soil neutral protease (NPR), alkaline protease (APR), chitinase (CHI), and their functional genes (nprA, aprA, and chiA) related to soil N mineralization. The following four treatments were included: blank control (CK), single DMPP application (DAA), weekly iprodione applications (IPR), and the combined applications of DMPP and iprodione (DI). Compared with the CK treatment, DMPP application significantly inhibited the CHI activity in the first 14 days of incubation, and iprodione applications, particularly when applied alone, decreased the NPR, APR, and CHI activities. Relative to the IPR treatment, extra DMPP application had the potential to alleviate the inhibitory effects of iprodione on the activities of these enzymes. DMPP application significantly increased aprA gene abundances after 14 days of incubation. However, repeated iprodione applications, alone or with the DMPP, decreased nprA and chiA gene abundances. Relative to the CK treatment, DMPP application generated negligible effects on the positive/negative correlations between soil enzyme activities and the corresponding functional gene abundances. However, the positive correlation between the CHI activity and chiA gene abundance was changed to negative correlation by repeated iprodione applications, alone or together with the DMPP. Our results demonstrated that agrochemical applications, particularly repeated fungicide applications, can have inadvertent effects on enzyme activities and functional gene abundances associated with soil N mineralization.
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Affiliation(s)
- Manyun Zhang
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia.
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Weijin Wang
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia
- Department of Science, Information Technology and Innovation, Dutton Park, QLD, 4102, Australia
| | - Jun Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- Chongqing Research Academy of Environmental Sciences, Chongqing, 401147, China
| | - Ying Teng
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
| | - Zhihong Xu
- Environmental Futures Research Institute, School of Natural Sciences, Griffith University, Brisbane, QLD, 4111, Australia.
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23
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Fullana N, Braña V, José Marizcurrena J, Morales D, Betton JM, Marín M, Castro-Sowinski S. Identification, recombinant production and partial biochemical characterization of an extracellular cold-active serine-metalloprotease from an Antarctic Pseudomonas isolate. AIMS BIOENGINEERING 2017. [DOI: 10.3934/bioeng.2017.3.386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Chen B, Yuan K, Chen X, Yang Y, Zhang T, Wang Y, Luan T, Zou S, Li X. Metagenomic Analysis Revealing Antibiotic Resistance Genes (ARGs) and Their Genetic Compartments in the Tibetan Environment. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:6670-9. [PMID: 27111002 DOI: 10.1021/acs.est.6b00619] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Comprehensive profiles of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in a minimally impacted environment are essential to understanding the evolution and dissemination of modern antibiotic resistance. Chemical analyses of the samples collected from Tibet demonstrated that the region under investigation was almost devoid of anthropogenic antibiotics. The soils, animal wastes, and sediments were different from each other in terms of bacterial community structures, and in the typical profiles of ARGs and MGEs. Diverse ARGs that encoded resistance to common antibiotics (e.g., beta-lactams, fluoroquinolones, etc.) were found mainly via an efflux mechanism completely distinct from modern antibiotic resistome. In addition, a very small fraction of ARGs in the Tibetan environment were carried by MGEs, indicating the low potential of these ARGs to be transferred among bacteria. In comparison to the ARG profiles in relatively pristine Tibet, contemporary ARGs and MGEs in human-impacted environments have evolved substantially since the broad use of anthropogenic antibiotics.
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Affiliation(s)
- Baowei Chen
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University , Guangzhou 510275, China
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University , Hung Hom, Kowloon Hong Kong
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University , Guangzhou 510275, China
| | - Ke Yuan
- MOE Key Laboratory of Aquatic Product Safety, School of Life Sciences, Sun Yat-Sen University , Guangzhou 510275, China
| | - Xin Chen
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University , Guangzhou 510275, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, School of Marine Sciences, Sun Yat-Sen University , Guangzhou 510275, China
| | - Ying Yang
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University , Guangzhou 510275, China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong , Pokfulam, Hong Kong
| | - Yawei Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center of Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085, China
| | - Tiangang Luan
- MOE Key Laboratory of Aquatic Product Safety, School of Life Sciences, Sun Yat-Sen University , Guangzhou 510275, China
| | - Shichun Zou
- South China Sea Resource Exploitation and Protection Collaborative Innovation Center, School of Marine Sciences, Sun Yat-sen University , Guangzhou 510275, China
| | - Xiangdong Li
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University , Hung Hom, Kowloon Hong Kong
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25
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Matsui K, Yoshinami S, Narita M, Chien MF, Phung LT, Silver S, Endo G. Mercury resistance transposons in Bacilli strains from different geographical regions. FEMS Microbiol Lett 2016; 363:fnw013. [PMID: 26802071 DOI: 10.1093/femsle/fnw013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/30/2015] [Indexed: 11/14/2022] Open
Abstract
A total of 65 spore-forming mercury-resistant bacteria were isolated from natural environments worldwide in order to understand the acquisition of additional genes by and dissemination of mercury resistance transposons across related Bacilli genera by horizontal gene movement. PCR amplification using a single primer complementary to the inverted repeat sequence of TnMERI1-like transposons showed that 12 of 65 isolates had a transposon-like structure. There were four types of amplified fragments: Tn5084, Tn5085, Tn(d)MER3 (a newly identified deleted transposon-like fragment) and Tn6294 (a newly identified transposon). Tn(d)MER3 is a 3.5-kb sequence that carries a merRETPA operon with no merB or transposase genes. It is related to the mer operon of Bacillus licheniformis strain FA6-12 from Russia. DNA homology analysis shows that Tn6294 is an 8.5-kb sequence that is possibly derived from Tn(d)MER3 by integration of a TnMERI1-type transposase and resolvase genes and in addition the merR2 and merB1 genes. Bacteria harboring Tn6294 exhibited broad-spectrum mercury resistance to organomercurial compounds, although Tn6294 had only merB1 and did not have the merB2 and merB3 sequences for organomercurial lyases found in Tn5084 of B. cereus strain RC607. Strains with Tn6294 encode mercuric reductase (MerA) of less than 600 amino acids in length with a single N-terminal mercury-binding domain, whereas MerA encoded by strains MB1 and RC607 has two tandem domains. Thus, Tn(d)MER3 and Tn6294 are shorter prototypes for TnMERI1-like transposons. Identification of Tn6294 in Bacillus sp. from Taiwan and in Paenibacillus sp. from Antarctica indicates the wide horizontal dissemination of TnMERI1-like transposons across bacterial species and geographical barriers.
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Affiliation(s)
- Kazuaki Matsui
- Department of Civil and Environmental Engineering, Kinki University, Higashiosaka, Osaka 577-8502, Japan
| | - Satoshi Yoshinami
- Department of Civil and Environmental Engineering, Kinki University, Higashiosaka, Osaka 577-8502, Japan
| | - Masaru Narita
- Tohoku Afforestation and Environmental Protection Co, Sendai, Miyagi 980-0014, Japan Laboratory of Environmental Biotechnology, Tohoku Gakuin University, Tagajo, Miyagi 985-8537, Japan
| | - Mei-Fang Chien
- Laboratory of Environmental Biotechnology, Tohoku Gakuin University, Tagajo, Miyagi 985-8537, Japan Graduate School of Environmental Studies, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Le T Phung
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612 USA
| | - Simon Silver
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612 USA
| | - Ginro Endo
- Laboratory of Environmental Biotechnology, Tohoku Gakuin University, Tagajo, Miyagi 985-8537, Japan
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26
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Dziewit L, Bartosik D. Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. Front Microbiol 2014; 5:596. [PMID: 25426110 PMCID: PMC4224046 DOI: 10.3389/fmicb.2014.00596] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/21/2014] [Indexed: 11/24/2022] Open
Abstract
Extremely cold environments are a challenge for all organisms. They are mostly inhabited by psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the cold. Such harsh environments are often highly vulnerable to the influence of external factors and may undergo frequent dynamic changes. The rapid adjustment of bacteria to changing environmental conditions is crucial for their survival. Such “short-term” evolution is often enabled by plasmids—extrachromosomal replicons that represent major players in horizontal gene transfer. The genomic sequences of thousands of microorganisms, including those of many cold-active bacteria have been obtained over the last decade, but the collected data have yet to be thoroughly analyzed. This report describes the results of a meta-analysis of the NCBI sequence databases to identify and characterize plasmids of psychrophilic and psychrotolerant bacteria. We have performed in-depth analyses of 66 plasmids, almost half of which are cryptic replicons not exceeding 10 kb in size. Our analyses of the larger plasmids revealed the presence of numerous genes, which may increase the phenotypic flexibility of their host strains. These genes encode enzymes possibly involved in (i) protection against cold and ultraviolet radiation, (ii) scavenging of reactive oxygen species, (iii) metabolism of amino acids, carbohydrates, nucleotides and lipids, (iv) energy production and conversion, (v) utilization of toxic organic compounds (e.g., naphthalene), and (vi) resistance to heavy metals, metalloids and antibiotics. Some of the plasmids also contain type II restriction-modification systems, which are involved in both plasmid stabilization and protection against foreign DNA. Moreover, approx. 50% of the analyzed plasmids carry genetic modules responsible for conjugal transfer or mobilization for transfer, which may facilitate the spread of these replicons among various bacteria, including across species boundaries.
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Affiliation(s)
- Lukasz Dziewit
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
| | - Dariusz Bartosik
- Department of Bacterial Genetics, Faculty of Biology, Institute of Microbiology, University of Warsaw Warsaw, Poland
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Lewin A, Wentzel A, Valla S. Metagenomics of microbial life in extreme temperature environments. Curr Opin Biotechnol 2013; 24:516-25. [DOI: 10.1016/j.copbio.2012.10.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/15/2012] [Accepted: 10/17/2012] [Indexed: 02/04/2023]
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Dziewit L, Grzesiak J, Ciok A, Nieckarz M, Zdanowski MK, Bartosik D. Sequence determination and analysis of three plasmids of Pseudomonas sp. GLE121, a psychrophile isolated from surface ice of Ecology Glacier (Antarctica). Plasmid 2013; 70:254-62. [PMID: 23721858 DOI: 10.1016/j.plasmid.2013.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 05/12/2013] [Accepted: 05/17/2013] [Indexed: 11/24/2022]
Abstract
Pseudomonas sp. GLE121 (a psychrophilic Antarctic strain) carries three plasmids: pGLE121P1 (6899 bp), pGLE121P2 (8330 bp) and pGLE121P3 (39,583 bp). Plasmids pGLE121P1 and pGLE121P2 show significant sequence similarity to members of the IncP-9 and IncP-7 incompatibility groups, respectively, while the largest replicon, pGLE121P3, is highly related to plasmid pNCPPB880-40 of Pseudomonas syringae pathovar tomato NCPPB880. All three plasmids have a narrow host range, limited to members of the genus Pseudomonas. Plasmid pGLE121P3 encodes a conjugal transfer system, while pGLE121P1 carries only a putative MOB module, conserved in many mobilizable plasmids. Plasmid pGLE121P3 contains an additional load of genetic information, including a pair of genes with homology to the rulAB operon, responsible for ultraviolet radiation (UVR) tolerance. Given the increasing UV exposure in Antarctic regions, the expression of these genes is likely to be an important adaptive response.
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Affiliation(s)
- Lukasz Dziewit
- University of Warsaw, Faculty of Biology, Institute of Microbiology, Department of Bacterial Genetics, Miecznikowa 1, 02-096 Warsaw, Poland.
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Van Houdt R, Deghorain M, Vermeersch M, Provoost A, Lo Giudice A, Leys N, Perez-Morga D, Van Melderen L, Michaud L. Characterization of culturable Paenibacillus spp. from the snow surface on the high Antarctic Plateau (DOME C) and their dissemination in the Concordia research station. Extremophiles 2013; 17:565-73. [DOI: 10.1007/s00792-013-0539-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 03/26/2013] [Indexed: 10/27/2022]
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Microbial competition in polar soils: a review of an understudied but potentially important control on productivity. BIOLOGY 2013; 2:533-54. [PMID: 24832797 PMCID: PMC3960893 DOI: 10.3390/biology2020533] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 03/11/2013] [Accepted: 03/12/2013] [Indexed: 01/29/2023]
Abstract
Intermicrobial competition is known to occur in many natural environments, and can result from direct conflict between organisms, or from differential rates of growth, colonization, and/or nutrient acquisition. It has been difficult to extensively examine intermicrobial competition in situ, but these interactions may play an important role in the regulation of the many biogeochemical processes that are tied to microbial communities in polar soils. A greater understanding of how competition influences productivity will improve projections of gas and nutrient flux as the poles warm, may provide biotechnological opportunities for increasing the degradation of contaminants in polar soil, and will help to predict changes in communities of higher organisms, such as plants.
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