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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [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: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Panda B, Sundaray L, Mishra A, Palai S, Padhi SR, Patro S, Mohanty PK. Preliminary assessment of the water quality of Rushikulya estuary based on the abundance of pathogenic bacteria. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 195:1169. [PMID: 37682420 DOI: 10.1007/s10661-023-11784-8] [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: 01/24/2023] [Accepted: 08/24/2023] [Indexed: 09/09/2023]
Abstract
Estuaries are among the most dynamic ecosystems in coastal regions and are facing serious threats due to increasing anthropogenic activities. The aim of the present study is to evaluate the water quality of the Rushikulya estuary by analyzing the abundance of pathogenic bacteria in both its water and sediment. Water and sediment samples were collected from five different stations at the mouth of the Rushikulya estuary during the monsoon and post-monsoon seasons. These samples were analyzed to assess the abundance of pathogenic bacteria and environmental parameters. The results revealed that bacterial abundance is significantly higher in the sediment than in the water, possibly due to a longer residence time of pathogenic bacteria in the sediment. Seasonal observations indicated an increase in pathogenic bacterial abundance during the monsoon season, suggesting an impact from monsoonal discharge. Escherichia coli-like organism, faecal coliforms, Shigella-like organisms, and Vibrio cholera-like organisms were the dominant pathogenic bacteria in both the water and sediment of the Rushikulya estuary. The higher abundance of these pathogens and the results of statistical analysis, which showed a strong correlation between Total Streptococci and BOD (r = 0.79), indicate the influence of human settlement and the mixing of untreated sewage in the Rushikulya estuary. The elevated levels of E. coli, faecal coliforms, and Shigella-like organisms in the Rushikulya estuary raise significant concerns that require immediate attention.
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Affiliation(s)
- Bhubaneswari Panda
- Department of Marine Sciences, Berhampur University, Bhanjabihar, Berhampur, Odisha, 760007, India
| | - Lokeshwara Sundaray
- Department of Marine Sciences, Berhampur University, Bhanjabihar, Berhampur, Odisha, 760007, India
| | - Ankita Mishra
- Department of Marine Sciences, Berhampur University, Bhanjabihar, Berhampur, Odisha, 760007, India
| | - Subhadarshani Palai
- Department of Marine Sciences, Berhampur University, Bhanjabihar, Berhampur, Odisha, 760007, India
| | - Sanjukta Rani Padhi
- Department of Marine Sciences, Berhampur University, Bhanjabihar, Berhampur, Odisha, 760007, India
| | - Shesdev Patro
- Department of Marine Sciences, Berhampur University, Bhanjabihar, Berhampur, Odisha, 760007, India.
| | - Pratap Kumar Mohanty
- Department of Marine Sciences, Berhampur University, Bhanjabihar, Berhampur, Odisha, 760007, India
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Wainwright BJ, Millar T, Bowen L, Semon L, Hickman KJE, Lee JN, Yeo ZY, Zahn G. The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival. ENVIRONMENTAL MICROBIOME 2023; 18:47. [PMID: 37264467 DOI: 10.1186/s40793-023-00499-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 05/01/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Microbes have fundamental roles underpinning the functioning of our planet, they are involved in global carbon and nutrient cycling, and support the existence of multicellular life. The mangrove ecosystem is nutrient limited and if not for microbial cycling of nutrients, life in this harsh environment would likely not exist. The mangroves of Southeast Asia are the oldest and most biodiverse on the planet, and serve vital roles helping to prevent shoreline erosion, act as nursery grounds for many marine species and sequester carbon. Despite these recognised benefits and the importance of microbes in these ecosystems, studies examining the mangrove microbiome in Southeast Asia are scarce.cxs RESULTS: Here we examine the microbiome of Avicenia alba and Sonneratia alba and identify a core microbiome of 81 taxa. A further eight taxa (Pleurocapsa, Tunicatimonas, Halomonas, Marinomonas, Rubrivirga, Altererythrobacte, Lewinella, and Erythrobacter) were found to be significantly enriched in mangrove tree compartments suggesting key roles in this microbiome. The majority of those identified are involved in nutrient cycling or have roles in the production of compounds that promote host survival. CONCLUSION The identification of a core microbiome furthers our understanding of mangrove microbial biodiversity, particularly in Southeast Asia where studies such as this are rare. The identification of significantly different microbial communities between sampling sites suggests environmental filtering is occurring, with hosts selecting for a microbial consortia most suitable for survival in their immediate environment. As climate change advances, many of these microbial communities are predicted to change, however, without knowing what is currently there, it is impossible to determine the magnitude of any deviations. This work provides an important baseline against which change in microbial community can be measured.
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Affiliation(s)
- Benjamin J Wainwright
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
| | - Trevor Millar
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lacee Bowen
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Lauren Semon
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - K J E Hickman
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Jen Nie Lee
- Faculty of Science and Marine Environment, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Malaysia
| | - Zhi Yi Yeo
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
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Yasar Yildiz S, Finore I, Leone L, Romano I, Lama L, Kasavi C, Nicolaus B, Toksoy Oner E, Poli A. Genomic Analysis Provides New Insights Into Biotechnological and Industrial Potential of Parageobacillus thermantarcticus M1. Front Microbiol 2022; 13:923038. [PMID: 35756030 PMCID: PMC9218356 DOI: 10.3389/fmicb.2022.923038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/18/2022] [Indexed: 02/02/2023] Open
Abstract
Parageobacillus thermantarcticus strain M1 is a Gram-positive, motile, facultative anaerobic, spore forming, and thermophilic bacterium, isolated from geothermal soil of the crater of Mount Melbourne (74°22′ S, 164°40′ E) during the Italian Antarctic Expedition occurred in Austral summer 1986–1987. Strain M1 demonstrated great biotechnological and industrial potential owing to its ability to produce exopolysaccharides (EPSs), ethanol and thermostable extracellular enzymes, such as an xylanase and a β-xylosidase, and intracellular ones, such as xylose/glucose isomerase and protease. Furthermore, recent studies revealed its high potential in green chemistry due to its use in residual biomass transformation/valorization and as an appropriate model for microbial astrobiology studies. In the present study, using a systems-based approach, genomic analysis of P. thermantarcticus M1 was carried out to enlighten its functional characteristics. The elucidation of whole-genome organization of this thermophilic cell factory increased our understanding of biological mechanisms and pathways, by providing valuable information on the essential genes related to the biosynthesis of nucleotide sugar precursors, monosaccharide unit assembly, as well as the production of EPSs and ethanol. In addition, gene prediction and genome annotation studies identified genes encoding xylanolytic enzymes that are required for the conversion of lignocellulosic materials to high-value added molecules. Our findings pointed out the significant potential of strain M1 in various biotechnological and industrial applications considering its capacity to produce EPSs, ethanol and thermostable enzymes via the utilization of lignocellulosic waste materials.
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Affiliation(s)
- Songul Yasar Yildiz
- Department of Bioengineering, Istanbul Medeniyet University, Istanbul, Turkey
| | - Ilaria Finore
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Luigi Leone
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Ida Romano
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Licia Lama
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Ceyda Kasavi
- Department of Bioengineering, Industrial Biotechnology and Systems Biology (IBSB), Marmara University, Istanbul, Turkey
| | - Barbara Nicolaus
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
| | - Ebru Toksoy Oner
- Department of Bioengineering, Industrial Biotechnology and Systems Biology (IBSB), Marmara University, Istanbul, Turkey
| | - Annarita Poli
- Institute of Biomolecular Chemistry (ICB), National Research Council, Naples, Italy
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Björnsdóttir SH, Pétursdóttir SK, Gudmundsdóttir EE, Olgudóttir E, Stefansson SK, Róbertsdóttir T, Sigurpálsson ÁH, Ólafsdóttir SK, Fridjónsson ÓH, Hreggvidsson GÓ. Rhodocaloribacter litoris gen. nov., sp. nov., isolated from an intertidal hot spring. Int J Syst Evol Microbiol 2021; 71. [PMID: 34672921 DOI: 10.1099/ijsem.0.005073] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Red-pigmented strains of non-sporeforming, aerobic, chemoorganotrophic bacteria were isolated from intertidal hot springs in Laugarvík, NW-Iceland. Cells stained Gram-negative and formed pleomorphic rods that often had swollen ends and occurred singly or in filaments. Growth was observed at 40-65 °C (optimum at 60 °C), pH 6-9 (optimum at 6.5-8) and 0.5-5% (optimum at 1-2%) (w/v) NaCl. Strain ISCAR-4553T contained MK-7 as the main respiratory quinone and saturated iso and anteiso branched chains of 17 and 15 carbons as the main cellular fatty acids (83.4%). The G+C content of the DNA is 67.3 mol%. The highest 16S rRNA gene sequence similarity was with the genus Roseithermus (92.0%) and followed by Rhodothermus, Rubrivirga and Rubricoccus (88-90%). Genome and phenotype comparisons supported the affiliation of the novel isolates and the genus Roseithermus to the family Rhodothermaceae of the phylum Rhodothermaeota. The described isolates are proposed to be classified as representatives of a novel species belonging to a novel genus, with the name Rhodocaloribacter litoris gen. nov., sp. nov. The type strain is ISCAR-4553T (=DSM 110790T = ATCC TSD-179T).
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Affiliation(s)
- Snædís H Björnsdóttir
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | | | | | | | - Sigmar K Stefansson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | - Tara Róbertsdóttir
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | - Ásbjörn H Sigurpálsson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland
| | | | | | - Gudmundur Ó Hreggvidsson
- University of Iceland, Institute of Life and Environmental Sciences, Sturlugata 7, IS-101 Reykjavík, Iceland.,Matis, Vínlandsleið 12, IS-113 Reykjavík, Iceland
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6
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Liew KJ, Bruce NC, Sani RK, Chong CS, Yaakop AS, Shamsir MS, Goh KM. Global Transcriptomic Responses of Roseithermus sacchariphilus Strain RA in Media Supplemented with Beechwood Xylan. Microorganisms 2020; 8:E976. [PMID: 32610703 PMCID: PMC7409140 DOI: 10.3390/microorganisms8070976] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/23/2020] [Accepted: 06/27/2020] [Indexed: 11/17/2022] Open
Abstract
The majority of the members in order Rhodothermales are underexplored prokaryotic extremophiles. Roseithermus, a new genus within Rhodothermales, was first described in 2019. Roseithermus sacchariphilus is the only species in this genus. The current report aims to evaluate the transcriptomic responses of R. sacchariphilus strain RA when cultivated on beechwood xylan. Strain RA doubled its growth in Marine Broth (MB) containing xylan compared to Marine Broth (MB) alone. Strain RA harbors 54 potential glycosyl hydrolases (GHs) that are affiliated with 30 families, including cellulases (families GH 3, 5, 9, and 44) and hemicellulases (GH 2, 10, 16, 29, 31,43, 51, 53, 67, 78, 92, 106, 113, 130, and 154). The majority of these GHs were upregulated when the cells were grown in MB containing xylan medium and enzymatic activities for xylanase, endoglucanase, β-xylosidase, and β-glucosidase were elevated. Interestingly, with the introduction of xylan, five out of six cellulolytic genes were upregulated. Furthermore, approximately 1122 genes equivalent to one-third of the total genes for strain RA were upregulated. These upregulated genes were mostly involved in transportation, chemotaxis, and membrane components synthesis.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Neil C. Bruce
- Centre for Novel Agricultural Products, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK;
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA;
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, Pulau Pinang 11800, Malaysia;
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Johor 84600, Malaysia
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Johor 81310, Malaysia; (K.J.L.); (C.S.C.); (M.S.S.)
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Liew KJ, Ngooi CY, Shamsir MS, Sani RK, Chong CS, Goh KM. Heterologous expression, purification and biochemical characterization of a new endo-1,4-β-xylanase from Rhodothermaceae bacterium RA. Protein Expr Purif 2019; 164:105464. [DOI: 10.1016/j.pep.2019.105464] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/10/2019] [Accepted: 07/31/2019] [Indexed: 11/28/2022]
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8
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Goh KM, Shahar S, Chan KG, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current Status and Potential Applications of Underexplored Prokaryotes. Microorganisms 2019; 7:E468. [PMID: 31635256 PMCID: PMC6843859 DOI: 10.3390/microorganisms7100468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
- International Genome Centre, Jiangsu University, ZhenJiang 212013, China.
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Syazwani Itri Amran
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Mohd Helmi Sani
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
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Characterizing a Halo-Tolerant GH10 Xylanase from Roseithermus sacchariphilus Strain RA and Its CBM-Truncated Variant. Int J Mol Sci 2019; 20:ijms20092284. [PMID: 31075847 PMCID: PMC6539836 DOI: 10.3390/ijms20092284] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/22/2019] [Accepted: 05/07/2019] [Indexed: 11/26/2022] Open
Abstract
A halo-thermophilic bacterium, Roseithermus sacchariphilus strain RA (previously known as Rhodothermaceae bacterium RA), was isolated from a hot spring in Langkawi, Malaysia. A complete genome analysis showed that the bacterium harbors 57 glycoside hydrolases (GHs), including a multi-domain xylanase (XynRA2). The full-length XynRA2 of 813 amino acids comprises a family 4_9 carbohydrate-binding module (CBM4_9), a family 10 glycoside hydrolase catalytic domain (GH10), and a C-terminal domain (CTD) for type IX secretion system (T9SS). This study aims to describe the biochemical properties of XynRA2 and the effects of CBM truncation on this xylanase. XynRA2 and its CBM-truncated variant (XynRA2ΔCBM) was expressed, purified, and characterized. The purified XynRA2 and XynRA2ΔCBM had an identical optimum temperature at 70 °C, but different optimum pHs of 8.5 and 6.0 respectively. Furthermore, XynRA2 retained 94% and 71% of activity at 4.0 M and 5.0 M NaCl respectively, whereas XynRA2ΔCBM showed a lower activity (79% and 54%). XynRA2 exhibited a turnover rate (kcat) of 24.8 s−1, but this was reduced by 40% for XynRA2ΔCBM. Both the xylanases hydrolyzed beechwood xylan predominantly into xylobiose, and oat-spelt xylan into a mixture of xylo-oligosaccharides (XOs). Collectively, this work suggested CBM4_9 of XynRA2 has a role in enzyme performance.
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10
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Park MJ, Oh JH, Yang SH, Kwon KK. Roseithermus sacchariphilus gen. nov., sp. nov. and proposal of Salisaetaceae fam. nov., representing new family in the order Rhodothermales. Int J Syst Evol Microbiol 2019; 69:1213-1219. [PMID: 30777820 DOI: 10.1099/ijsem.0.003293] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium with cells that were pinkish-cream-coloured, aerobic, rod-shaped, 0.62-1.00 µm wide and 2.3-3.3 µm long, designated as strain MEBiC09517T, was isolated from Buksung-Po, a small port in Incheon, Republic of Korea. Strain MEBiC09517T had low 16S rRNA gene sequence similarity to validly reported strains; among them, Rubrivirgaprofundi SAORIC-476T displayed highest sequence similarity (89.9 %). Nevertheless, the novel strain shared a phylogenetic line with members of the genus Rhodothermus, not the genus Rubrivirga. Optimum growth conditions of strain MEBiC09517T were at 50-55 °C, pH 7 and in 2.0-4.0 % salt concentration. Strain MEBiC09517T was found to be an obligate marine bacterium that requires KCl, MgCl2 and CaCl2 as well as NaCl for growth. A phosphatidylethanolamine, a diphosphatidylglycerol, three glycolipids and four unidentified lipids were the strain's predominant polar lipid components. The fatty acid of the cell wall mainly consisted of carbons with 16 or 18 chain lengths such as C16 : 0, C18 : 0, C18 : 1 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c). The predominant menaquinone was MK-7. The DNA G+C content is 68.65 mol%. Strain MEBiC09517T differs from genera of the order Rhodothermales in terms of fatty acid composition, growth conditions, and range of carbon source utilization. Based on phylogenetic analysis using the strain's 16S rRNA gene sequence and results of physiological tests, strain MEBiC09517T (KCCM=43267T, JCM=32374T) is proposed as Roseithermus sacchariphilus gen. nov., sp. nov. Additionally, the novel family Salisaetaceae fam. nov. based on phylogenetic analysis and physiological characteristics is suggested.
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Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea.,Major of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea
| | - Ji Hye Oh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Sung-Hyun Yang
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
| | - Kae Kyoung Kwon
- Major of Marine Biotechnology, University of Science and Technology, Daejeon, Republic of Korea.,Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan, Republic of Korea
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11
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Wang J, Goh KM, Salem DR, Sani RK. Genome analysis of a thermophilic exopolysaccharide-producing bacterium - Geobacillus sp. WSUCF1. Sci Rep 2019; 9:1608. [PMID: 30733471 PMCID: PMC6367360 DOI: 10.1038/s41598-018-36983-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/16/2018] [Indexed: 11/23/2022] Open
Abstract
Geobacillus sp. WSUCF1 is a Gram-positive, spore-forming, aerobic and thermophilic bacterium, isolated from a soil sample obtained from a compost facility. Strain WSUCF1 demonstrated EPS producing capability using different sugars as the carbon source. The whole-genome analysis of WSUCF1 was performed to disclose the essential genes correlated with nucleotide sugar precursor biosynthesis, assembly of monosaccharide units, export of the polysaccharide chain, and regulation of EPS production. Both the biosynthesis pathway and export mechanism of EPS were proposed based on functional annotation. Additionally, the genome description of strain WSUCF1 suggests sophisticated systems for its adaptation under thermophilic conditions. The presence of genes associated with CRISPR-Cas system, quorum quenching lactonase, polyketide synthesis and arsenic resistance makes this strain a potential candidate for various applications in biotechnology and biomedicine. The present study indicates that strain WSUCF1 has promise as a thermophilic EPS producer for a broad range of industrial applications. To the best of our knowledge, this is the first report on genome analysis of a thermophilic Geobacillus species focusing on its EPS biosynthesis and transportation, which will likely pave the way for both enhanced yield and tailor-made EPS production by thermophilic bacteria.
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Affiliation(s)
- Jia Wang
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Skudai, Johor, 81300, Malaysia
| | - David R Salem
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
- Department of Materials and Metallurgical Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
- Composite and Nanocomposite Advanced Manufacturing - Biomaterials Center (CNAM-Bio Center), Rapid City, SD, 57701, USA.
| | - Rajesh K Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
- Composite and Nanocomposite Advanced Manufacturing - Biomaterials Center (CNAM-Bio Center), Rapid City, SD, 57701, USA.
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, 57701, USA.
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Liew KJ, Teo SC, Shamsir MS, Sani RK, Chong CS, Chan KG, Goh KM. Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities. 3 Biotech 2018; 8:376. [PMID: 30105201 PMCID: PMC6087703 DOI: 10.1007/s13205-018-1391-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/06/2018] [Indexed: 11/26/2022] Open
Abstract
Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, β-glucosidase, and β-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes.
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Affiliation(s)
- Kok Jun Liew
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Seng Chong Teo
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, USA
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, 212013 People’s Republic of China
| | - Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, 81300 Skudai, Johor Malaysia
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13
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Viver T, Orellana L, González-Torres P, Díaz S, Urdiain M, Farías ME, Benes V, Kaempfer P, Shahinpei A, Ali Amoozegar M, Amann R, Antón J, Konstantinidis KT, Rosselló-Móra R. Genomic comparison between members of the Salinibacteraceae family, and description of a new species of Salinibacter (Salinibacter altiplanensis sp. nov.) isolated from high altitude hypersaline environments of the Argentinian Altiplano. Syst Appl Microbiol 2018; 41:198-212. [DOI: 10.1016/j.syapm.2017.12.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/22/2017] [Accepted: 12/23/2017] [Indexed: 01/08/2023]
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14
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Lee LS, Goh KM, Chan CS, Annie Tan GY, Yin WF, Chong CS, Chan KG. Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring. Microbiologyopen 2018; 7:e00615. [PMID: 29602271 PMCID: PMC6291792 DOI: 10.1002/mbo3.615] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 11/12/2022] Open
Abstract
The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.
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Affiliation(s)
- Li Sin Lee
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Kian Mau Goh
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Chia Sing Chan
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Geok Yuan Annie Tan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia
| | - Chun Shiong Chong
- Faculty of Biosciences and Medical Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Kok-Gan Chan
- ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Lumpur, Malaysia.,Jiangsu University, Zhenjiang, China
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15
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Pérez V, Dorador C, Molina V, Yáñez C, Hengst M. Rhodobacter sp. Rb3, an aerobic anoxygenic phototroph which thrives in the polyextreme ecosystem of the Salar de Huasco, in the Chilean Altiplano. Antonie van Leeuwenhoek 2018; 111:1449-1465. [PMID: 29569108 DOI: 10.1007/s10482-018-1067-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/16/2018] [Indexed: 10/17/2022]
Abstract
The Salar de Huasco is an evaporitic basin located in the Chilean Altiplano, which presents extreme environmental conditions for life, i.e. high altitude (3800 m.a.s.l.), negative water balance, a wide salinity range, high daily temperature changes and the occurrence of the highest registered solar radiation on the planet (> 1200 W m-2). This ecosystem is considered as a natural laboratory to understand different adaptations of microorganisms to extreme conditions. Rhodobacter, an anoxygenic aerobic phototrophic bacterial genus, represents one of the most abundant groups reported based on taxonomic diversity surveys in this ecosystem. The bacterial mat isolate Rhodobacter sp. strain Rb3 was used to study adaptation mechanisms to stress-inducing factors potentially explaining its success in a polyextreme ecosystem. We found that the Rhodobacter sp. Rb3 genome was characterized by a high abundance of genes involved in stress tolerance and adaptation strategies, among which DNA repair and oxidative stress were the most conspicuous. Moreover, many other molecular mechanisms associated with oxidative stress, photooxidation and antioxidants; DNA repair and protection; motility, chemotaxis and biofilm synthesis; osmotic stress, metal, metalloid and toxic anions resistance; antimicrobial resistance and multidrug pumps; sporulation; cold shock and heat shock stress; mobile genetic elements and toxin-antitoxin system were detected and identified as potential survival mechanism features in Rhodobacter sp. Rb3. In total, these results reveal a wide set of strategies used by the isolate to adapt and thrive under environmental stress conditions as a model of polyextreme environmental resistome.
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Affiliation(s)
- Vilma Pérez
- Laboratory of Molecular Ecology and Applied Microbiology, Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Cristina Dorador
- Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile
| | - Verónica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaiso, Chile
| | - Carolina Yáñez
- Laboratorio Microbiología, Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaiso, Chile
| | - Martha Hengst
- Laboratory of Molecular Ecology and Applied Microbiology, Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile. .,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile.
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