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Bourgeois A, Lemos JAS, Roucheray S, Sergerie A, Richard D. The Paradigm Shift of Using Natural Molecules Extracted from Northern Canada to Combat Malaria. Infect Dis Rep 2024; 16:543-560. [PMID: 39051241 PMCID: PMC11270350 DOI: 10.3390/idr16040041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 07/27/2024] Open
Abstract
Parasitic diseases, such as malaria, are an immense burden to many low- and middle-income countries. In 2022, 249 million cases and 608,000 deaths were reported by the World Health Organization for malaria alone. Climate change, conflict, humanitarian crises, resource constraints and diverse biological challenges threaten progress in the elimination of malaria. Undeniably, the lack of a commercialized vaccine and the spread of drug-resistant parasites beg the need for novel approaches to treat this infectious disease. Most approaches for the development of antimalarials to date take inspiration from tropical or sub-tropical environments; however, it is necessary to expand our search. In this review, we highlight the origin of antimalarial treatments and propose new insights in the search for developing novel antiparasitic treatments. Plants and microorganisms living in harsh and cold environments, such as those found in the largely unexploited Northern Canadian boreal forest, often demonstrate interesting properties that are not found in other environments. Most prominently, the essential oil of Rhododendron tomentosum spp. Subarcticum from Nunavik and mortiamides isolated from Mortierella species found in Nunavut have shown promising activity against Plasmodium falciparum.
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Affiliation(s)
- Alexandra Bourgeois
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada; (A.B.); (J.A.S.L.); (S.R.); (A.S.)
- Department of Microbiology-Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Juliana Aline Souza Lemos
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada; (A.B.); (J.A.S.L.); (S.R.); (A.S.)
| | - Stéphanie Roucheray
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada; (A.B.); (J.A.S.L.); (S.R.); (A.S.)
- Department of Microbiology-Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Audrey Sergerie
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada; (A.B.); (J.A.S.L.); (S.R.); (A.S.)
- Department of Microbiology-Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Dave Richard
- Centre de Recherche en Infectiologie, CRCHU de Québec-Université Laval, Quebec City, QC G1V 4G2, Canada; (A.B.); (J.A.S.L.); (S.R.); (A.S.)
- Department of Microbiology-Infectious Diseases and Immunology, Faculty of Medicine, Laval University, Quebec City, QC G1V 0A6, Canada
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2
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Oliva B, Zervas A, Stougaard P, Westh P, Thøgersen MS. Metagenomic exploration of cold-active enzymes for detergent applications: Characterization of a novel, cold-active and alkali-stable GH8 endoglucanase from ikaite columns in SW Greenland. Microb Biotechnol 2024; 17:e14466. [PMID: 38829370 PMCID: PMC11146146 DOI: 10.1111/1751-7915.14466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 06/05/2024] Open
Abstract
Microbial communities from extreme environments are largely understudied, but are essential as producers of metabolites, including enzymes, for industrial processes. As cultivation of most microorganisms remains a challenge, culture-independent approaches for enzyme discovery in the form of metagenomics to analyse the genetic potential of a community are rapidly becoming the way forward. This study focused on analysing a metagenome from the cold and alkaline ikaite columns in Greenland, identifying 282 open reading frames (ORFs) that encoded putative carbohydrate-modifying enzymes with potential applications in, for example detergents and other processes where activity at low temperature and high pH is desired. Seventeen selected ORFs, representing eight enzyme families were synthesized and expressed in two host organisms, Escherichia coli and Aliivibrio wodanis. Aliivibrio wodanis demonstrated expression of a more diverse range of enzyme classes compared to E. coli, emphasizing the importance of alternative expression systems for enzymes from extremophilic microorganisms. To demonstrate the validity of the screening strategy, we chose a recombinantly expressed cellulolytic enzyme from the metagenome for further characterization. The enzyme, Cel240, exhibited close to 40% of its relative activity at low temperatures (4°C) and demonstrated endoglucanase characteristics, with a preference for cellulose substrates. Despite low sequence similarity with known enzymes, computational analysis and structural modelling confirmed its cellulase-family affiliation. Cel240 displayed activity at low temperatures and good stability at 25°C, activity at alkaline pH and increased activity in the presence of CaCl2, making it a promising candidate for detergent and washing industry applications.
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Affiliation(s)
- Bianca Oliva
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
- Present address:
Synthetic and Molecular Biology Laboratory, Department of Biotechnology, Lorena School of EngineeringUniversity of São PauloLorenaSPBrazil
| | - Athanasios Zervas
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
| | - Peter Stougaard
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
| | - Peter Westh
- Section for Protein Chemistry and Enzyme Technology, Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Mariane Schmidt Thøgersen
- Section for Environmental Microbiology, Department of Environmental ScienceAarhus UniversityRoskildeDenmark
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Yu X, Gao X, Shang L, Wang X, Jiao Y, Zhang XH, Shi X. Spatial and temporal change determined co-occurrence networks stability and community assembly processes of epipelagic seawater microbial community in the Nordic Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160321. [PMID: 36414066 DOI: 10.1016/j.scitotenv.2022.160321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/27/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
The Nordic Sea has a vital impact on the global climate change, occupies a significant status in the physical oceanography research, on account of its intersection of complex ocean currents. To explore the influence of seasonal and spatial heterogeneity in its epipelagic seawater on the microbial community structure, a total of 54 seawater samples from 18 stations and 3 water layers (0 m, 50 m, 100 m) were collected in the summer of 2017 and the autumn of 2018 from the Norwegian Sea, the Greenland Sea and the vicinity of Jan Mayen Island in the Nordic Sea. Alpha- and Beta- diversity analysis showed that significant differences were found between characteristic bacterial groups in detached or mixed currents of corresponding seasons, as endemic OTUs with seasonal and ocean current characteristics which revealed the existence of spatiotemporal patterns of microbial communities in the Nordic Sea. Moreover, co-occurrence networks were conducted to show different degree of complexity and stability of microbial community response to spatiotemporal dynamic changes. Furthermore, the flow and collision between ocean currents do have an impact on the community assembly processes by affecting the migration and dispersal of microbial communities. This study reflects the response of microbial communities to the spatiotemporal dynamics and reveals the microbial community assembly mechanisms under complex hydrological condition represented in the Nordic Sea.
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Affiliation(s)
- Xiaowen Yu
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xueyu Gao
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Li Shang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiaoyu Wang
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Yutian Jiao
- Frontier Science Center for Deep Ocean Multispheres and Earth System (FDOMES), Physical Oceanography Laboratory, Ocean University of China, Qingdao 266071, PR China
| | - Xiao-Hua Zhang
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China
| | - Xiaochong Shi
- College of Marine Life Science, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, PR China; Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, PR China.
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4
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Hu YW, Chen WH, Song MM, Pang XY, Tian XP, Wang FZ, Liu YH, Wang JF. Indole diketopiperazine alkaloids and aromatic polyketides from the Antarctic fungus Penicillium sp. SCSIO 05705. Nat Prod Res 2023; 37:389-396. [PMID: 34498972 DOI: 10.1080/14786419.2021.1973460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A new indole diketopiperazine alkaloid, named penilline D (1), together with five known indole alkaloid analogues (2-5, 11), two meroterpenoids (6 and 12), and four butenolide derivatives (7-10), were isolated from the Antarctic fungus Penicillium sp. SCSIO 05705. Extensive spectroscopic analysis and electronic circular dichroism (ECD) calculation were used to elucidate the structure of penilline D (1), including its absolute configuration. All isolated compounds (1-12) were evaluated for their cytotoxic, antibacterial and enzyme inhibitory activities against acetylcholinesterase (AChE) and pancreatic lipase (PL). Among them, compound 5 exhibited moderate in vitro cytotoxic activity against the 143B cell line with IC50 value of 12.64 ± 0.78 μM. Compound 6 showed strong inhibitory activity against AChE with IC50 value of 0.36 nM (IC50 18.7 nM for Tacrine), while compounds 6 and 11 showed weak PL enzyme inhibitory activity. Furthermore, an in silico molecular docking study was also performed between 6 and AChE.
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Affiliation(s)
- Yi-Wei Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wei-Hao Chen
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Meng-Meng Song
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao-Yan Pang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fa-Zuo Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Yong-Hong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Feng Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.,Sanya Institute of Oceanology, SCSIO, Yazhou Scientific Bay, Sanya, China.,University of Chinese Academy of Sciences, Beijing, China
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5
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Rego A, Fernandez-Guerra A, Duarte P, Assmy P, Leão PN, Magalhães C. Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes. Microb Genom 2021; 7. [PMID: 34904945 PMCID: PMC8767328 DOI: 10.1099/mgen.0.000731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.
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Affiliation(s)
- Adriana Rego
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Pedro Duarte
- Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway
| | - Philipp Assmy
- Norwegian Polar Institute, Fram Centre, N-9296 Tromsø, Norway
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- *Correspondence: Pedro N. Leão,
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- Faculty of Sciences, University of Porto, 4150-179 Porto, Portugal
- *Correspondence: Catarina Magalhães,
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6
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Floris R, Sanna G, Mura L, Fiori M, Culurgioni J, Diciotti R, Rizzo C, Lo Giudice A, Laganà P, Fois N. Isolation and Identification of Bacteria with Surface and Antibacterial Activity from the Gut of Mediterranean Grey Mullets. Microorganisms 2021; 9:microorganisms9122555. [PMID: 34946156 PMCID: PMC8703445 DOI: 10.3390/microorganisms9122555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022] Open
Abstract
Fish gut represents a peculiar ecological niche where bacteria can transit and reside to play vital roles by producing bio-compounds with nutritional, immunomodulatory and other functions. This complex microbial ecosystem reflects several factors (environment, feeding regimen, fish species, etc.). The objective of the present study was the identification of intestinal microbial strains able to produce molecules called biosurfactants (BSs), which were tested for surface and antibacterial activity in order to select a group of probiotic bacteria for aquaculture use. Forty-two bacterial isolates from the digestive tracts of twenty Mediterranean grey mullets were screened for testing emulsifying (E-24), surface and antibiotic activities. Fifty percent of bacteria, ascribed to Pseudomonas aeruginosa, Pseudomonas sp., P. putida and P. anguilliseptica, P. stutzeri, P. protegens and Enterobacter ludwigii were found to be surfactant producers. Of the tested strains, 26.6% exhibited an antibacterial activity against Staphylococcus aureus (10.0 ± 0.0–14.5 ± 0.7 mm inhibition zone), and among them, 23.3% of isolates also showed inhibitory activity vs. Proteus mirabilis (10.0 ± 0.0–18.5 ± 0.7 mm inhibition zone) and 6.6% vs. Klebsiella pneumoniae (11.5 ± 0.7–17.5 ± 0.7 mm inhibition zone). According to preliminary chemical analysis, the bioactive compounds are suggested to be ascribed to the class of glycolipids. This works indicated that fish gut is a source of bioactive compounds which deserves to be explored.
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Affiliation(s)
- Rosanna Floris
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
- Correspondence: ; Tel.: +39-079-284-2331
| | - Gabriele Sanna
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Laura Mura
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Myriam Fiori
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Jacopo Culurgioni
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Riccardo Diciotti
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
| | - Carmen Rizzo
- Stazione Zoologica Anton Dohrn-Ecosustainable Marine Biotechnology Department, Sicily Marine Centre, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy;
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy;
| | - Pasqualina Laganà
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Torre Biologica 3p, AOU ‘G. Martino, Via C. Valeria, s.n.c., 98125 Messina, Italy;
| | - Nicola Fois
- AGRIS-Sardegna, Agricultural Research Agency of Sardinia, Bonassai, 07100 Sassari, Italy; (G.S.); (L.M.); (M.F.); (J.C.); (R.D.); (N.F.)
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7
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Severgnini M, Canini F, Consolandi C, Camboni T, Paolo D'Acqui L, Mascalchi C, Ventura S, Zucconi L. Highly differentiated soil bacterial communities in Victoria Land macro-areas (Antarctica). FEMS Microbiol Ecol 2021; 97:6307020. [PMID: 34151349 DOI: 10.1093/femsec/fiab087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Abstract
Ice-free areas of Victoria Land, in Antarctica, are characterized by different terrestrial ecosystems, that are dominated by microorganisms supporting highly adapted communities. Despite the unique conditions of these ecosystems, reports on their bacterial diversity are still fragmentary. From this perspective, 60 samples from 14 localities were analyzed. These localities were distributed in coastal sites with differently developed biological soil crusts, inner sites in the McMurdo Dry Valleys with soils lacking of plant coverage, and a site called Icarus Camp, with a crust developed on a thin locally weathered substrate of the underlying parent granitic-rock. Bacterial diversity was studied through 16S rRNA metabarcoding sequencing. Communities diversity, composition and the abundance and composition of different taxonomic groups were correlated to soil physicochemical characteristics. Firmicutes, Bacteroidetes, Cyanobacteria and Proteobacteria dominated these communities. Most phyla were mainly driven by soil granulometry, an often disregarded parameter and other abiotic parameters. Bacterial composition differed greatly among the three macrohabitats, each having a distinct bacterial profile. Communities within the two main habitats (coastal and inner ones) were well differentiated from each other as well, therefore depending on site-specific physicochemical characteristics. A core community of the whole samples was observed, mainly represented by Firmicutes and Bacteroidetes.
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Affiliation(s)
- Marco Severgnini
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), via f.lli Cervi, 93, 20054, Segrate, Italy
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università s.n.c., 01100, Viterbo, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), via f.lli Cervi, 93, 20054, Segrate, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), via f.lli Cervi, 93, 20054, Segrate, Italy
| | - Luigi Paolo D'Acqui
- Terrestria Ecosystems Research Institute, National Research Council (IRET-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Cristina Mascalchi
- Terrestria Ecosystems Research Institute, National Research Council (IRET-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Stefano Ventura
- Terrestria Ecosystems Research Institute, National Research Council (IRET-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy.,The Italian Embassy in Israel, Trade Tower, 25 Hamered Street, 68125, Tel Aviv, Israel
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università s.n.c., 01100, Viterbo, Italy
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8
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Tedesco P, Palma Esposito F, Masino A, Vitale GA, Tortorella E, Poli A, Nicolaus B, van Zyl LJ, Trindade M, de Pascale D. Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier. Microorganisms 2021; 9:microorganisms9050890. [PMID: 33919419 PMCID: PMC8143284 DOI: 10.3390/microorganisms9050890] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Extremophilic microorganisms represent a unique source of novel natural products. Among them, cold adapted bacteria and particularly alpine microorganisms are still underexplored. Here, we describe the isolation and characterization of a novel Gram-positive, aerobic rod-shaped alpine bacterium (KRL4), isolated from sediments from the Karuola glacier in Tibet, China. Complete phenotypic analysis was performed revealing the great adaptability of the strain to a wide range of temperatures (5-40 °C), pHs (5.5-8.5), and salinities (0-15% w/v NaCl). Genome sequencing identified KRL4 as a member of the placeholder genus Exiguobacterium_A and annotation revealed that only half of the protein-encoding genes (1522 of 3079) could be assigned a putative function. An analysis of the secondary metabolite clusters revealed the presence of two uncharacterized phytoene synthase containing pathways and a novel siderophore pathway. Biological assays confirmed that the strain produces molecules with antioxidant and siderophore activities. Furthermore, intracellular extracts showed nematocidal activity towards C. elegans, suggesting that strain KRL4 is a source of anthelmintic compounds.
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Affiliation(s)
- Pietro Tedesco
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Fortunato Palma Esposito
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Antonio Masino
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy
| | - Giovanni Andrea Vitale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
| | - Emiliana Tortorella
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
| | - Annarita Poli
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, 80078 Naples, Italy; (A.P.); (B.N.)
| | - Barbara Nicolaus
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, 80078 Naples, Italy; (A.P.); (B.N.)
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, 7535 Cape Town, South Africa; (L.J.v.Z.); (M.T.)
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Bellville, 7535 Cape Town, South Africa; (L.J.v.Z.); (M.T.)
| | - Donatella de Pascale
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 80131 Naples, Italy; (P.T.); (F.P.E.); (A.M.); (G.A.V.); (E.T.)
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80122 Naples, Italy
- Correspondence:
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9
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Benaud N, Edwards RJ, Amos TG, D'Agostino PM, Gutiérrez-Chávez C, Montgomery K, Nicetic I, Ferrari BC. Antarctic desert soil bacteria exhibit high novel natural product potential, evaluated through long-read genome sequencing and comparative genomics. Environ Microbiol 2020; 23:3646-3664. [PMID: 33140504 DOI: 10.1111/1462-2920.15300] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 11/30/2022]
Abstract
Actinobacteria and Proteobacteria are important producers of bioactive natural products (NP), and these phyla dominate in the arid soils of Antarctica, where metabolic adaptations influence survival under harsh conditions. Biosynthetic gene clusters (BGCs) which encode NPs, are typically long and repetitious high G + C regions difficult to sequence with short-read technologies. We sequenced 17 Antarctic soil bacteria from multi-genome libraries, employing the long-read PacBio platform, to optimize capture of BGCs and to facilitate a comprehensive analysis of their NP capacity. We report 13 complete bacterial genomes of high quality and contiguity, representing 10 different cold-adapted genera including novel species. Antarctic BGCs exhibited low similarity to known compound BGCs (av. 31%), with an abundance of terpene, non-ribosomal peptide and polyketide-encoding clusters. Comparative genome analysis was used to map BGC variation between closely related strains from geographically distant environments. Results showed the greatest biosynthetic differences to be in a psychrotolerant Streptomyces strain, as well as a rare Actinobacteria genus, Kribbella, while two other Streptomyces spp. were surprisingly similar to known genomes. Streptomyces and Kribbella BGCs were predicted to encode antitumour, antifungal, antibacterial and biosurfactant-like compounds, and the synthesis of NPs with antibacterial, antifungal and surfactant properties was confirmed through bioactivity assays.
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Affiliation(s)
- Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Timothy G Amos
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Paul M D'Agostino
- Technische Universität Dresden, Chair of Technical Biochemistry, Bergstraße 66, 01602 Dresden, Germany
| | | | - Kate Montgomery
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Iskra Nicetic
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, 2052, Australia
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10
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Passarini MRZ, E Silva TR, Bernal SPF, Cecchet NL, Sartoratto A, Boroski M, Duarte AWF, Ottoni JR, Rosa LH, de Oliveira VM. Undecane production by cold-adapted bacteria from Antarctica. Extremophiles 2020; 24:863-873. [PMID: 32944821 DOI: 10.1007/s00792-020-01200-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/03/2020] [Indexed: 11/27/2022]
Abstract
In the last decades, efforts to reduce the use of fossil fuels have increased the search for alternative sustainable sources of renewable energy. In this scenario, hydrocarbons derived from fatty acids are among the compounds that have been drawing attention. The intracellular production of hydrocarbons by bacteria derived from cold environments such as the Antarctic continent is currently poorly investigated, as extremophilic microorganisms provide a great range of metabolic capabilities and may represent a key tool in the production of biofuels. The aim of this study was to explore the ability of bacterial cells derived from extreme environments to produce hydrocarbons with potential for further use as biofuels. Seven bacteria isolated from Antarctic samples were evaluated for hydrocarbon production using GC-MS approaches. Two isolates, identified as Arthrobacter livingstonensis 593 and Pseudoalteromonas arctica 628, were able to produce the hydrocarbon undecane (CH3-(CH2)9-CH3) in concentrations of 1.39 mg L-1 and 1.81 mg L-1, respectively. Results from the present work encourage further research focusing on the optimization of hydrocarbon production by the isolates identified as producers, which may be used in further aircraft biofuel production. This is the first report on the production of the undecane compound by bacteria isolated from waterlogged soil and sponge from Antarctica.
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Affiliation(s)
- Michel Rodrigo Zambrano Passarini
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil.
| | - Tiago Rodrigues E Silva
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Suzan Prado Fernandes Bernal
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Nathália Luana Cecchet
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Biotecnologia Ambiental, Av. Tarquínio Joslin dos Santos, 1000-Jd Universitário, Foz do Iguaçu, PR, 85870-650, Brazil
| | - Adilson Sartoratto
- CPQBA/UNICAMP-Divisão de Química Orgânica e Farmacêutica, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
| | - Marcela Boroski
- UNILA-Universidade Federal da Integração Latino-Americana. Laboratório de Química, Av. Tancredo Neves 6731- Conjunto B, Foz do Iguaçu, PR, 85867-970, Brazil
| | - Alysson Wagner Fernandes Duarte
- UFAL-Universidade Federal de Alagoas, Av. Manoel Severino Barbosa-Rodovia AL-115, Bom Sucesso, Arapiraca, AL, 57309-005, Brazil
| | - Júlia Ronzella Ottoni
- UDC-Centro Universitário Dinâmica das Cataratas, Rua Castelo Branco, 349, Centro, Foz do Iguaçu, PR, Brazil
| | - Luiz Henrique Rosa
- UFMG-Departamento de Microbiologia, Universidade Federal de Minas Gerais, Instituto de Ciências Biológicas, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte, MG, 31270-901, Brazil
| | - Valéria Maia de Oliveira
- CPQBA/UNICAMP-Divisão de Recursos Microbianos, Rua Alexandre Caselatto 999, Vila Betel, CP 6171, Campinas, SP, 13083-970, Brazil
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11
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Rizzo C, Lo Giudice A. The Variety and Inscrutability of Polar Environments as a Resource of Biotechnologically Relevant Molecules. Microorganisms 2020; 8:microorganisms8091422. [PMID: 32947905 PMCID: PMC7564310 DOI: 10.3390/microorganisms8091422] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
The application of an ever-increasing number of methodological approaches and tools is positively contributing to the development and yield of bioprospecting procedures. In this context, cold-adapted bacteria from polar environments are becoming more and more intriguing as valuable sources of novel biomolecules, with peculiar properties to be exploited in a number of biotechnological fields. This review aims at highlighting the biotechnological potentialities of bacteria from Arctic and Antarctic habitats, both biotic and abiotic. In addition to cold-enzymes, which have been intensively analysed, relevance is given to recent advances in the search for less investigated biomolecules, such as biosurfactants, exopolysaccharides and antibiotics.
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Affiliation(s)
- Carmen Rizzo
- Stazione Zoologica Anton Dohrn, Department Marine Biotechnology, National Institute of Biology, Villa Pace, Contrada Porticatello 29, 98167 Messina, Italy
- Correspondence:
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (CNR-ISP), Spianata San Raineri 86, 98122 Messina, Italy;
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12
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Zucconi L, Canini F, Temporiti ME, Tosi S. Extracellular Enzymes and Bioactive Compounds from Antarctic Terrestrial Fungi for Bioprospecting. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17186459. [PMID: 32899827 PMCID: PMC7558612 DOI: 10.3390/ijerph17186459] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/26/2020] [Accepted: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Antarctica, one of the harshest environments in the world, has been successfully colonized by extremophilic, psychrophilic, and psychrotolerant microorganisms, facing a range of extreme conditions. Fungi are the most diverse taxon in the Antarctic ecosystems, including soils. Genetic adaptation to this environment results in the synthesis of a range of metabolites, with different functional roles in relation to the biotic and abiotic environmental factors, some of which with new biological properties of potential biotechnological interest. An overview on the production of cold-adapted enzymes and other bioactive secondary metabolites from filamentous fungi and yeasts isolated from Antarctic soils is here provided and considerations on their ecological significance are reported. A great number of researches have been carried out to date, based on cultural approaches. More recently, metagenomics approaches are expected to increase our knowledge on metabolic potential of these organisms, leading to the characterization of unculturable taxa. The search on fungi in Antarctica deserves to be improved, since it may represent a useful strategy for finding new metabolic pathways and, consequently, new bioactive compounds.
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Affiliation(s)
- Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence: (L.Z.); (F.C.); Tel.: +39-328-2741247 (L.Z.); +39-347-9288247 (F.C.)
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy
- Correspondence: (L.Z.); (F.C.); Tel.: +39-328-2741247 (L.Z.); +39-347-9288247 (F.C.)
| | - Marta Elisabetta Temporiti
- Department of Earth and Environmental Sciences, University of Pavia, via S. Epifanio 14, 27100 Pavia, Italy; (M.E.T.); (S.T.)
| | - Solveig Tosi
- Department of Earth and Environmental Sciences, University of Pavia, via S. Epifanio 14, 27100 Pavia, Italy; (M.E.T.); (S.T.)
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13
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Habib S, Ahmad SA, Wan Johari WL, Abd Shukor MY, Alias SA, Smykla J, Saruni NH, Abdul Razak NS, Yasid NA. Production of Lipopeptide Biosurfactant by a Hydrocarbon-Degrading Antarctic Rhodococcus. Int J Mol Sci 2020; 21:ijms21176138. [PMID: 32858859 PMCID: PMC7504157 DOI: 10.3390/ijms21176138] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/05/2020] [Accepted: 08/08/2020] [Indexed: 12/19/2022] Open
Abstract
Rhodococci are renowned for their great metabolic repertoire partly because of their numerous putative pathways for large number of specialized metabolites such as biosurfactant. Screening and genome-based assessment for the capacity to produce surface-active molecules was conducted on Rhodococcus sp. ADL36, a diesel-degrading Antarctic bacterium. The strain showed a positive bacterial adhesion to hydrocarbon (BATH) assay, drop collapse test, oil displacement activity, microplate assay, maximal emulsification index at 45% and ability to reduce water surface tension to < 30 mN/m. The evaluation of the cell-free supernatant demonstrated its high stability across the temperature, pH and salinity gradient although no correlation was found between the surface and emulsification activity. Based on the positive relationship between the assessment of macromolecules content and infrared analysis, the extracted biosurfactant synthesized was classified as a lipopeptide. Prediction of the secondary metabolites in the non-ribosomal peptide synthetase (NRPS) clusters suggested the likelihood of the surface-active lipopeptide production in the strain’s genomic data. This is the third report of surface-active lipopeptide producers from this phylotype and the first from the polar region. The lipopeptide synthesized by ADL36 has the prospect to be an Antarctic remediation tool while furnishing a distinctive natural product for biotechnological application and research.
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Affiliation(s)
- Syahir Habib
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Siti Aqlima Ahmad
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Wan Lutfi Wan Johari
- Department of Environment, Faculty of Forestry and Environment, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia;
| | - Mohd Yunus Abd Shukor
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Siti Aisyah Alias
- Institute of Ocean and Earth Sciences, C308 Institute of Postgraduate Studies, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - Jerzy Smykla
- Institute of Nature Conservation, Polish Academy of Sciences, Mickiewicza 33, 31-120 Kraków, Poland;
| | - Nurul Hani Saruni
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Nur Syafiqah Abdul Razak
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
| | - Nur Adeela Yasid
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor 43400, Malaysia; (S.H.); (S.A.A.); (M.Y.A.S.); (N.H.S.); (N.S.A.R.)
- Correspondence: ; Tel.: +603-9769-8297
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14
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Benaud N, Zhang E, van Dorst J, Brown MV, Kalaitzis JA, Neilan BA, Ferrari BC. Harnessing long-read amplicon sequencing to uncover NRPS and Type I PKS gene sequence diversity in polar desert soils. FEMS Microbiol Ecol 2020; 95:5372416. [PMID: 30848780 DOI: 10.1093/femsec/fiz031] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/07/2019] [Indexed: 02/02/2023] Open
Abstract
The severity of environmental conditions at Earth's frigid zones present attractive opportunities for microbial biomining due to their heightened potential as reservoirs for novel secondary metabolites. Arid soil microbiomes within the Antarctic and Arctic circles are remarkably rich in Actinobacteria and Proteobacteria, bacterial phyla known to be prolific producers of natural products. Yet the diversity of secondary metabolite genes within these cold, extreme environments remain largely unknown. Here, we employed amplicon sequencing using PacBio RS II, a third generation long-read platform, to survey over 200 soils spanning twelve east Antarctic and high Arctic sites for natural product-encoding genes, specifically targeting non-ribosomal peptides (NRPS) and Type I polyketides (PKS). NRPS-encoding genes were more widespread across the Antarctic, whereas PKS genes were only recoverable from a handful of sites. Many recovered sequences were deemed novel due to their low amino acid sequence similarity to known protein sequences, particularly throughout the east Antarctic sites. Phylogenetic analysis revealed that a high proportion were most similar to antifungal and biosurfactant-type clusters. Multivariate analysis showed that soil fertility factors of carbon, nitrogen and moisture displayed significant negative relationships with natural product gene richness. Our combined results suggest that secondary metabolite production is likely to play an important physiological component of survival for microorganisms inhabiting arid, nutrient-starved soils.
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Affiliation(s)
- Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, 2052, Australia
| | - Eden Zhang
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, 2052, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, 2052, Australia
| | - Mark V Brown
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - John A Kalaitzis
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, 2052, Australia
| | - Brett A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, 2052, Australia
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15
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Lo Giudice A, Poli A, Finore I, Rizzo C. Peculiarities of extracellular polymeric substances produced by Antarctic bacteria and their possible applications. Appl Microbiol Biotechnol 2020; 104:2923-2934. [PMID: 32076778 DOI: 10.1007/s00253-020-10448-8] [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: 12/28/2019] [Revised: 01/31/2020] [Accepted: 02/06/2020] [Indexed: 10/25/2022]
Abstract
Extracellular polymeric substances (EPSs) possess diversified ecological role, including the cell adhesion to surfaces and cell protection, and are highly involved in the interactions between the bacterial cells and the bulk environments. Interestingly, EPSs find valuable applications in the industrial field, due to their chemical versatility. In this context, Antarctic bacteria have not been given the attention they deserve as producers of EPS molecules and a very limited insight into their EPS production capabilities and biotechnological potential is available in literature to date. Antarctic EPS-producing bacteria are mainly psychrophiles deriving from the marine environments (generally sea ice and seawater) around the continent, whereas a unique thermophilic bacterium, namely Parageobacillus thermantarcticus strain M1, was isolated from geothermal soil of the crater of Mount Melbourne. This mini-review is aimed at showcasing the current knowledge on EPS-producing Antarctic bacteria and the chemical peculiarities of produced EPSs, highlighting their biotechnological potential and the yet unexplored treasure they represent for biodiscovery.
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Affiliation(s)
- Angelina Lo Giudice
- National Research Council (CNR-ISP), Institute of Polar Sciences, Spianata S. Raineri 86, 98122, Messina, Italy.
| | - Annarita Poli
- National Research Council (CNR-ICB), Institute of Biomolecular Chemistry, Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Ilaria Finore
- National Research Council (CNR-ICB), Institute of Biomolecular Chemistry, Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Carmen Rizzo
- Department BIOTECH, Stazione Zoologica Anton Dohrn,, National Institute of Biology, Villa Pace, Contrada Porticatello 29, 98167, Messina, Italy
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16
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Characterization of amylase produced by cold-adapted bacteria from Antarctic samples. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2019.101452] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Li AZ, Han XB, Zhang MX, Zhou Y, Chen M, Yao Q, Zhu HH. Culture-Dependent and -Independent Analyses Reveal the Diversity, Structure, and Assembly Mechanism of Benthic Bacterial Community in the Ross Sea, Antarctica. Front Microbiol 2019; 10:2523. [PMID: 31787942 PMCID: PMC6856632 DOI: 10.3389/fmicb.2019.02523] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/21/2019] [Indexed: 11/22/2022] Open
Abstract
The benthic bacterial community in Antarctic continental shelf ecosystems are not well-documented. We collected 13 surface sediments from the Ross Sea, a biological hotspot in high-latitude maritime Antarctica undergoing rapid climate change and possible microflora shift, and aimed to study the diversity, structure and assembly mechanism of benthic bacterial community using both culture-dependent and -independent approaches. High-throughput sequencing of 16S rRNA gene amplicons revealed 370 OTUs distributed in 21 phyla and 284 genera. The bacterial community was dominated by Bacteroidetes, Gamma- and Alphaproteobacteria, and constituted by a compact, conserved and positively-correlated group of anaerobes and other competitive aerobic chemoheterotrophs. Null-model test based on βNTI and RCBray indicated that stochastic processes, including dispersal limitation and undominated fractions, were the main forces driving community assembly. On the other hand, environmental factors, mainly temperature, organic matter and chlorophyll, were significantly correlated with bacterial richness, diversity and community structure. Moreover, metabolic and physiological features of the prokaryotic taxa were mapped to evaluate the adaptive mechanisms and functional composition of the benthic bacterial community. Our study is helpful to understand the structural and functional aspects, as well as the ecological and biogeochemical role of the benthic bacterial community in the Ross Sea.
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Affiliation(s)
- An-Zhang Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xi-Bin Han
- Key Laboratory of Submarine Geosciences, Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, China
| | - Ming-Xia Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yang Zhou
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Meng Chen
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qing Yao
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangdong Engineering Research Center for Grass Science, Guangdong Engineering Center for Litchi, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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18
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Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. Mar Drugs 2019; 17:md17100576. [PMID: 31614509 PMCID: PMC6835618 DOI: 10.3390/md17100576] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/13/2022] Open
Abstract
The sea represents a major source of biodiversity. It exhibits many different ecosystems in a huge variety of environmental conditions where marine organisms have evolved with extensive diversification of structures and functions, making the marine environment a treasure trove of molecules with potential for biotechnological applications and innovation in many different areas. Rapid progress of the omics sciences has revealed novel opportunities to advance the knowledge of biological systems, paving the way for an unprecedented revolution in the field and expanding marine research from model organisms to an increasing number of marine species. Multi-level approaches based on molecular investigations at genomic, metagenomic, transcriptomic, metatranscriptomic, proteomic, and metabolomic levels are essential to discover marine resources and further explore key molecular processes involved in their production and action. As a consequence, omics approaches, accompanied by the associated bioinformatic resources and computational tools for molecular analyses and modeling, are boosting the rapid advancement of biotechnologies. In this review, we provide an overview of the most relevant bioinformatic resources and major approaches, highlighting perspectives and bottlenecks for an appropriate exploitation of these opportunities for biotechnology applications from marine resources.
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19
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Enzymes from Marine Polar Regions and Their Biotechnological Applications. Mar Drugs 2019; 17:md17100544. [PMID: 31547548 PMCID: PMC6835263 DOI: 10.3390/md17100544] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
The microorganisms that evolved at low temperatures express cold-adapted enzymes endowed with unique catalytic properties in comparison to their mesophilic homologues, i.e., higher catalytic efficiency, improved flexibility, and lower thermal stability. Cold environments are therefore an attractive research area for the discovery of enzymes to be used for investigational and industrial applications in which such properties are desirable. In this work, we will review the literature on cold-adapted enzymes specifically focusing on those discovered in the bioprospecting of polar marine environments, so far largely neglected because of their limited accessibility. We will discuss their existing or proposed biotechnological applications within the framework of the more general applications of cold-adapted enzymes.
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20
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Hamilton EF, Element G, van Coeverden de Groot P, Engel K, Neufeld JD, Shah V, Walker VK. Anadromous Arctic Char Microbiomes: Bioprospecting in the High Arctic. Front Bioeng Biotechnol 2019; 7:32. [PMID: 30863748 PMCID: PMC6399304 DOI: 10.3389/fbioe.2019.00032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 02/05/2019] [Indexed: 01/31/2023] Open
Abstract
Northern populations of Arctic char (Salvelinus alpinus) can be anadromous, migrating annually from the ocean to freshwater lakes and rivers in order to escape sub-zero temperatures. Such seasonal behavior demands that these fish and their associated microbiomes adapt to changes in salinity, temperature, and other environmental challenges. We characterized the microbial community composition of anadromous S. alpinus, netted by Inuit fishermen at freshwater and seawater fishing sites in the high Arctic, both under ice and in open water. Bacterial profiles were generated by DNA extraction and high-throughput sequencing of PCR-amplified 16S ribosomal RNA genes. Results showed that microbial communities on the skin and intestine of Arctic char were statistically different when sampled from freshwater or saline water sites. This association was tested using hierarchical Ward's linkage clustering, showing eight distinct clusters in each of the skin and intestinal microbiomes, with the clusters reflecting sampling location between fresh and saline environments, confirming a salinity-linked turnover. This analysis also provided evidence for a core composition of skin and intestinal bacteria, with the phyla Proteobacteria, Firmicutes, and Cyanobacteria presenting as major phyla within the skin-associated microbiomes. The intestine-associated microbiome was characterized by unidentified genera from families Fusobacteriaceae, Comamonadaceae, Pseudomonadaceae, and Vibrionaceae. The salinity-linked turnover was further tested through ordinations that showed samples grouping based on environment for both skin- and intestine-associated microbiomes. This finding implies that core microbiomes between fresh and saline conditions could be used to assist in regulating optimal fish health in aquaculture practices. Furthermore, identified taxa from known psychrophiles and with nitrogen cycling properties suggest that there is additional potential for biotechnological applications for fish farm and waste management practices.
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Affiliation(s)
| | - Geraint Element
- Department of Biology, Queen's University, Kingston, ON, Canada
| | | | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Josh D. Neufeld
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Vishal Shah
- College of the Sciences and Mathematics, West Chester University, West Chester, PA, United States
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21
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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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Muralidharan A, Josyula VR, Hariharapura RC. Exploring the potential of marine microbes in clinical management of Alzheimer's disease: A road map for bioprospecting and identifying promising isolates. Life Sci 2018; 208:149-160. [PMID: 30031811 DOI: 10.1016/j.lfs.2018.07.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
Abstract
Pervasiveness of Alzheimer's disease (AD) across the globe is on rise, devitalizing the essential brain functions of the afflicted individual. Multiple neurological pathways viz., cholinergic, amyloidogenic and tau protein pathways underlying the disease and interdependence make it more complex to develop effective treatment strategies. Existing drug treatments for Alzheimer's disease majorly belong to the class of cholinergic inhibitors which improve the behavioral symptoms. But there are no drugs that could arrest the disease progression. Inhibition of beta secretase enzyme could prevent the deposition of amyloid plaques in the neurons, thereby arresting the disease progression. Search for novel drugs to treat the underlying pathogenesis of the disease is pivotal in this day and age. The source of most active lead molecules discovered recently is from the nature. Marine ecosystem provides a plethora of pharmacologically lead molecules from various living organisms inhabiting the sea. Among all, marine microbes are the most under-explored and indispensable source of many bioactive metabolites. Studies have been reported on potent metabolites from marine microbes which could inhibit the key enzymes involved in the AD pathogenesis. The advancement in microbial bioprospecting and molecular biology techniques have eased the process of cultivation and identification of microbes, isolation of novel bioactive metabolites of clinical use. Exploring such marine natural resources for pharmacological lead molecules could give a breakthrough in the drug discovery domain for treating AD such debilitating diseases. In this review, a comprehensive account of bioprospecting methods and reports of marine microbial isolates are discussed.
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Affiliation(s)
- Anuraag Muralidharan
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Udupi, Karnataka, India
| | - Venkata Rao Josyula
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Udupi, Karnataka, India.
| | - Raghu Chandrashekhar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Udupi, Karnataka, India
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Robertson AW, McCarville NG, MacIntyre LW, Correa H, Haltli B, Marchbank DH, Kerr RG. Isolation of Imaqobactin, an Amphiphilic Siderophore from the Arctic Marine Bacterium Variovorax Species RKJM285. JOURNAL OF NATURAL PRODUCTS 2018; 81:858-865. [PMID: 29616814 DOI: 10.1021/acs.jnatprod.7b00943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The amphiphilic siderophore imaqobactin was isolated from the Arctic bacterium Variovorax sp. RKJM285, a strain isolated from marine sediment collected from an inlet near Clyde River, Nunavut, Canada. The 2D structure of imaqobactin was determined by a combination of LC-HRMS, MS/MS, and NMR spectroscopic methods. The absolute configuration of the depsipeptide core was determined by Marfey's analysis, and the relative configuration of the 4,7-diamino-3-hydroxy-2-methylheptanoic acid moiety was determined by NOESY and selective NOE experiments. The photoreductive properties of imaqobactin were tested and are discussed. Initial tests for antimicrobial and cytotoxic activity of imaqobactin were also performed, identifying moderate antimicrobial activity.
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Affiliation(s)
- Andrew W Robertson
- Department of Chemistry , University of Prince Edward Island , Charlottetown , PEI , Canada C1A 4P3
- Nautilus Biosciences Canada Inc. , Duffy Research Center , 550 University Avenue , Charlottetown , PEI , Canada C1A 4P3
| | - Nicholas G McCarville
- Nautilus Biosciences Canada Inc. , Duffy Research Center , 550 University Avenue , Charlottetown , PEI , Canada C1A 4P3
| | - Logan W MacIntyre
- Department of Biomedical Sciences, Atlantic Veterinary College , University of Prince Edward Island , Charlottetown , PEI , Canada C1A 4P3
| | - Hebelin Correa
- Nautilus Biosciences Canada Inc. , Duffy Research Center , 550 University Avenue , Charlottetown , PEI , Canada C1A 4P3
| | - Brad Haltli
- Department of Chemistry , University of Prince Edward Island , Charlottetown , PEI , Canada C1A 4P3
- Nautilus Biosciences Canada Inc. , Duffy Research Center , 550 University Avenue , Charlottetown , PEI , Canada C1A 4P3
- Department of Biomedical Sciences, Atlantic Veterinary College , University of Prince Edward Island , Charlottetown , PEI , Canada C1A 4P3
| | - Douglas H Marchbank
- Department of Chemistry , University of Prince Edward Island , Charlottetown , PEI , Canada C1A 4P3
- Nautilus Biosciences Canada Inc. , Duffy Research Center , 550 University Avenue , Charlottetown , PEI , Canada C1A 4P3
| | - Russell G Kerr
- Department of Chemistry , University of Prince Edward Island , Charlottetown , PEI , Canada C1A 4P3
- Nautilus Biosciences Canada Inc. , Duffy Research Center , 550 University Avenue , Charlottetown , PEI , Canada C1A 4P3
- Department of Biomedical Sciences, Atlantic Veterinary College , University of Prince Edward Island , Charlottetown , PEI , Canada C1A 4P3
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24
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Baeza M, Barahona S, Alcaíno J, Cifuentes V. Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats. Front Microbiol 2017; 8:2235. [PMID: 29184546 PMCID: PMC5694453 DOI: 10.3389/fmicb.2017.02235] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/31/2017] [Indexed: 01/08/2023] Open
Abstract
In cold environments such as polar regions, microorganisms play important ecological roles, and most of our knowledge about them comes from studies of cultivable microorganisms. Metagenomic technologies are powerful tools that can give a more comprehensive assessment of microbial communities, and the amplification of rDNA followed by next-generation sequencing has given good results in studies aimed particularly at environmental microorganisms. Culture-independent studies of microbiota in terrestrial habitats of Antarctica, which is considered the driest, coldest climate on Earth, are increasing and indicate that micro-diversity is much higher than previously thought. In this work, the microbial diversity of terrestrial habitats including eight islands of the South Shetland Archipelago, two islands on the Antarctic Peninsula and Union Glacier, was studied by amplicon-metagenome analysis. Molecular analysis of the studied localities clustered together the islands of the South Shetland Archipelago, except Greenwich Island, and separated them from the Litchfield and Lagotellerie islands and Union Glacier, which is in agreement with the latitudinal difference among them. Among fungi, 87 genera and 123 species were found, of which species belonging to 37 fungal genera not previously cultivated from Antarctica were detected. Phylogenetic analysis, including the closest BLAST-hit sequences, clustered fungi in 11 classes being the most represented Lecanoromycetes and Eurotiomycetes.
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Affiliation(s)
- Marcelo Baeza
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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25
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Secondary Metabolites from Polar Organisms. Mar Drugs 2017; 15:md15030028. [PMID: 28241505 PMCID: PMC5367009 DOI: 10.3390/md15030028] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 01/24/2017] [Accepted: 01/29/2017] [Indexed: 01/11/2023] Open
Abstract
Polar organisms have been found to develop unique defences against the extreme environment environment, leading to the biosynthesis of novel molecules with diverse bioactivities. This review covers the 219 novel natural products described since 2001, from the Arctic and the Antarctic microoganisms, lichen, moss and marine faunas. The structures of the new compounds and details of the source organism, along with any relevant biological activities are presented. Where reported, synthetic and biosynthetic studies on the polar metabolites have also been included.
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26
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Rao TE, Imchen M, Kumavath R. Marine Enzymes: Production and Applications for Human Health. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 80:149-163. [PMID: 28215323 DOI: 10.1016/bs.afnr.2016.11.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Marine microbial enzymes have wide applications in bioindustries. Selection of microorganisms for enzyme production at the industrial level requires good yield and high production rate. A number of enzymes such as amylase, caseinase, lipase, gelatinase, and DNases have been discovered from microbes isolated from extreme marine environments. Such enzymes are thermostable, tolerant to a varied range of pH and other harsh conditions required in industrial applications. Novelty in their structure and characteristics has shown promising scope to the researchers in academia and industry. In this chapter, we present a bird's eye view on recent research works in the field of enzyme production from marine origin as well as their potential biological applications relevant to human health.
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Affiliation(s)
- T Eswara Rao
- Central University of Kerala, Padannakkad, Kerala, India
| | - M Imchen
- Central University of Kerala, Padannakkad, Kerala, India
| | - R Kumavath
- Central University of Kerala, Padannakkad, Kerala, India.
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27
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Affiliation(s)
- M. Kavitha
- School of Biosciences and Technology, VIT University, Vellore, India
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28
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Barahona S, Yuivar Y, Socias G, Alcaíno J, Cifuentes V, Baeza M. Identification and characterization of yeasts isolated from sedimentary rocks of Union Glacier at the Antarctica. Extremophiles 2016; 20:479-91. [PMID: 27215207 DOI: 10.1007/s00792-016-0838-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022]
Abstract
The study of the yeasts that inhabit cold environments, such as Antarctica, is an active field of investigation oriented toward understanding their ecological roles in these ecosystems. In a great part, the interest in cold-adapted yeasts is due to several industrial and biotechnological applications that have been described for them. The aim of this work was to isolate and identify yeasts from sedimentary rock samples collected at the Union Glacier, Antarctica. Furthermore, the yeasts were physiologically characterized, including the production of metabolites of biotechnological interest. The yeasts isolated that were identified at the molecular level belonged to genera Collophora (1 isolate), Cryptococcus (2 isolates), Sporidiobolus (4 isolates), Sporobolomyces (1 isolate) and Torrubiella (2 isolates). The majority of yeasts were basidiomycetous and psychrotolerant. By cross-test assays for anti-yeast activity, it was determined that Collophora sp., Sporidiobolus salmonicolor, and Sporobolomyces roseus secreted a protein factor that kills Sporidiobolus metaroseus. The colored yeasts Sp. salmonicolor, Sp. metaroseus and Collophora sp. produced several carotenoid pigments that were identified as 2,3 dihydroxy-γ-carotene, -carotene, 4-ketotorulene, torulene β-cryptoxanthin and spirilloxanthin. Concerning analysis of mycosporines, these metabolites were only found in the yeasts Torrubiella sp. and Cryptococcus sp. T11-10-1. Furthermore, the yeasts were evaluated for the production of extracellular hydrolytic activities. Of the twelve activities analyzed, alkaline phosphatase, invertase, gelatinase, cellulase, amylase, and protease enzyme activities were detected. The yeasts Cryptococcus sp. T11-10-1 and Sporidiobolus metaroseus showed the highest number of different enzyme activities.
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Affiliation(s)
- Salvador Barahona
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Yassef Yuivar
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Gabriel Socias
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Jennifer Alcaíno
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Víctor Cifuentes
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile
| | - Marcelo Baeza
- Laboratorio de Genética, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago, Chile.
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Vester JK, Glaring MA, Stougaard P. Improved cultivation and metagenomics as new tools for bioprospecting in cold environments. Extremophiles 2014; 19:17-29. [PMID: 25399309 PMCID: PMC4272415 DOI: 10.1007/s00792-014-0704-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022]
Abstract
Only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. This resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent DNA sequence information can be combined with functional screening. The coupling of these two approaches circumvents the need for pure, cultured isolates and can be used to generate targeted information on communities enriched for specific activities or properties. Bioprospecting in extreme environments is often associated with additional challenges such as low biomass, slow cell growth, complex sample matrices, restricted access, and problematic in situ analyses. In addition, the choice of vector system and expression host may be limited as few hosts are available for expression of genes with extremophilic properties. This review summarizes the methods developed for improved cultivation as well as the metagenomic approaches for bioprospecting with focus on the challenges faced by bioprospecting in cold environments.
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Affiliation(s)
- Jan Kjølhede Vester
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark,
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Moreno R, Rojo F. Features of pseudomonads growing at low temperatures: another facet of their versatility. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:417-426. [PMID: 25646532 DOI: 10.1111/1758-2229.12150] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pseudomonads are a diverse and ecologically successful group of γ-proteobacteria present in many environments (terrestrial, freshwater and marine), either free living or associated with plants or animals. Their success is at least partly based on their ability to grow over a wide range of temperatures, their capacity to withstand different kinds of stress and their great metabolic versatility. Although the optimal growth temperature of pseudomonads is usually close to 25–30°C, many strains can also grow between 5°C and 10°C, and some of them even close to 0°C. Such low temperatures strongly affect the physicochemical properties of macromolecules, forcing cells to evolve traits that optimize growth and help them withstand cold-induced stresses such as increased levels of reactive oxygen species, reduced membrane fluidity and enzyme activity, cold-induced protein denaturation and the greater stability of DNA and RNA secondary structures. This review gathers the information available on the strategies used by pseudomonads to adapt to low temperature growth, and briefly describes some of the biotechnological applications that might benefit from cold-adapted bacterial strains and enzymes, e.g., biotransformation or bioremediation processes to be performed at low temperatures.
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31
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De Santi C, Tedesco P, Ambrosino L, Altermark B, Willassen NP, de Pascale D. A New Alkaliphilic Cold-Active Esterase from the Psychrophilic Marine Bacterium Rhodococcus sp.: Functional and Structural Studies and Biotechnological Potential. Appl Biochem Biotechnol 2014; 172:3054-68. [DOI: 10.1007/s12010-013-0713-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/25/2013] [Indexed: 11/28/2022]
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32
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Papaleo MC, Romoli R, Bartolucci G, Maida I, Perrin E, Fondi M, Orlandini V, Mengoni A, Emiliani G, Tutino ML, Parrilli E, de Pascale D, Michaud L, Lo Giudice A, Fani R. Bioactive volatile organic compounds from Antarctic (sponges) bacteria. N Biotechnol 2013; 30:824-38. [DOI: 10.1016/j.nbt.2013.03.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 11/16/2022]
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Chong CW, Goh YS, Convey P, Pearce D, Tan IKP. Spatial pattern in Antarctica: what can we learn from Antarctic bacterial isolates? Extremophiles 2013; 17:733-45. [PMID: 23812890 DOI: 10.1007/s00792-013-0555-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 06/13/2013] [Indexed: 11/30/2022]
Abstract
A range of small- to moderate-scale studies of patterns in bacterial biodiversity have been conducted in Antarctica over the last two decades, most suggesting strong correlations between the described bacterial communities and elements of local environmental heterogeneity. However, very few of these studies have advanced interpretations in terms of spatially associated patterns, despite increasing evidence of patterns in bacterial biogeography globally. This is likely to be a consequence of restricted sampling coverage, with most studies to date focusing only on a few localities within a specific Antarctic region. Clearly, there is now a need for synthesis over a much larger spatial to consolidate the available data. In this study, we collated Antarctic bacterial culture identities based on the 16S rRNA gene information available in the literature and the GenBank database (n > 2,000 sequences). In contrast to some recent evidence for a distinct Antarctic microbiome, our phylogenetic comparisons show that a majority (~75 %) of Antarctic bacterial isolates were highly similar (≥99 % sequence similarity) to those retrieved from tropical and temperate regions, suggesting widespread distribution of eurythermal mesophiles in Antarctic environments. However, across different Antarctic regions, the dominant bacterial genera exhibit some spatially distinct diversity patterns analogous to those recently proposed for Antarctic terrestrial macroorganisms. Taken together, our results highlight the threat of cross-regional homogenisation in Antarctic biodiversity, and the imperative to include microbiota within the framework of biosecurity measures for Antarctica.
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Affiliation(s)
- Chun Wie Chong
- Department of Life Sciences, International Medical University, Kuala Lumpur, Malaysia.
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