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Chen G, He M, Li KJ, Zheng KW, Tang XX, Debnath SC, Wang PM, Guo Z, Hong Y, Zheng DQ. Shinella sedimenti sp. nov., isolated from sediment of Zhairuo Island located in the East China Sea. Int J Syst Evol Microbiol 2023; 73. [PMID: 37589186 DOI: 10.1099/ijsem.0.006000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023] Open
Abstract
A Gram-negative, rod-shaped and aerobic bacterial strain B3.7T, was isolated from the sediment of Zhairuo Island, Zhoushan city, Zhejiang Province, PR China. Maximum growth of strain B3.7T was observed at 30 °C when cultured in a medium containing 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain B3.7T belonged to the genus Shinella; it showed the highest sequence similarity of 98.47 % to Shinella kummerowiae CCBAU 25048T. The average nucleotide identity and digital DNA-DNA hybridization values between strain B3.7T and its reference strains were 82.9-84.2 % and 26.1-27.3 %, respectively. Chemotaxonomic analysis indicated that the sole respiratory quinone was Q-10 and the predominant cellular fatty acids were C19 : 0 cyclo ω8c, C16 : 0, C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unidentified phospholipids and two unidentified aminolipids. Collectively, strain B3.7T can be considered to represent a novel species, for which the name Shinella sedimenti sp. nov. is proposed. The type strain is B3.7T (=MCCC 1K07163T=LMG 32559T).
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Affiliation(s)
- Gen Chen
- Hainan Institute of Zhejiang University, Sanya, 572000, PR China
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
| | - Min He
- Hainan Institute of Zhejiang University, Sanya, 572000, PR China
| | - Ke-Jing Li
- Hainan Institute of Zhejiang University, Sanya, 572000, PR China
| | - Kai-Wen Zheng
- Hainan Institute of Zhejiang University, Sanya, 572000, PR China
| | - Xing-Xing Tang
- Hainan Institute of Zhejiang University, Sanya, 572000, PR China
| | | | - Pin-Mei Wang
- Hainan Institute of Zhejiang University, Sanya, 572000, PR China
| | - Zhen Guo
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058, PR China
| | - Yi Hong
- College of Civil Engineering and Architecture, Zhejiang University, Hangzhou, 310058, PR China
| | - Dao-Qiong Zheng
- Hainan Institute of Zhejiang University, Sanya, 572000, PR China
- Ocean College, Zhejiang University, Zhoushan, 316021, PR China
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Mousavi SA, Young JPW. International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria. Minutes of the closed annual meeting: videoconference on 11 October 2022 followed by online discussion until 31 December 2022. Int J Syst Evol Microbiol 2023; 73. [PMID: 37115621 DOI: 10.1099/ijsem.0.005856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Affiliation(s)
- Seyed Abdollah Mousavi
- Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland
| | - J Peter W Young
- Department of Biology, University of York, York YO10 5DD, UK
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Kaur A, Scott NE, Herisse M, Goddard-Borger ED, Pidot S, Williams SJ. Identification of levoglucosan degradation pathways in bacteria and sequence similarity network analysis. Arch Microbiol 2023; 205:155. [PMID: 37000297 PMCID: PMC10066097 DOI: 10.1007/s00203-023-03506-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/01/2023]
Abstract
Levoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degrading Paenarthrobacter spp. (Paenarthrobacter nitrojuajacolis LG01 and Paenarthrobacter histidinolovorans LG02) that were isolated from soil by metabolic enrichment using levoglucosan as the sole carbon source. Genome sequencing and proteomics analysis revealed the expression of a series of genes encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan β -eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and an associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident, while the expressed genes contained a range of putative sugar phosphate isomerases/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbours of LgdA revealed that homologues of LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One group of sugar phosphate isomerase/xylose isomerase homologues (named LgdB3) was identified with limited distribution that is mutually exclusive with LgdB2, and we propose that they may fulfil a similar function. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds, suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight diversity within the LGDH pathway, through which bacteria utilize levoglucosan as a nutrient source.
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Affiliation(s)
- Arashdeep Kaur
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, 3000, Australia
| | - Marion Herisse
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, 3000, Australia
| | - Ethan D Goddard-Borger
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- ACRF Chemical Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3010, Australia
| | - Sacha Pidot
- Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, 3000, Australia
| | - Spencer J Williams
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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Arhin SG, Cesaro A, Di Capua F, Esposito G. Recent progress and challenges in biotechnological valorization of lignocellulosic materials: Towards sustainable biofuels and platform chemicals synthesis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159333. [PMID: 36220479 DOI: 10.1016/j.scitotenv.2022.159333] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Lignocellulosic materials (LCM) have garnered attention as feedstocks for second-generation biofuels and platform chemicals. With an estimated annual production of nearly 200 billion tons, LCM represent an abundant source of clean, renewable, and sustainable carbon that can be funneled to numerous biofuels and platform chemicals by sustainable microbial bioprocessing. However, the low bioavailability of LCM due to the recalcitrant nature of plant cell components, the complexity and compositional heterogeneity of LCM monomers, and the limited metabolic flexibility of wild-type product-forming microorganisms to simultaneously utilize various LCM monomers are major roadblocks. Several innovative strategies have been proposed recently to counter these issues and expedite the widespread commercialization of biorefineries using LCM as feedstocks. Herein, we critically summarize the recent advances in the biological valorization of LCM to value-added products. The review focuses on the progress achieved in the development of strategies that boost efficiency indicators such as yield and selectivity, minimize carbon losses via integrated biorefinery concepts, facilitate carbon co-metabolism and carbon-flux redirection towards targeted products using recently engineered microorganisms, and address specific product-related challenges, to provide perspectives on future research needs and developments. The strategies and views presented here could guide future studies in developing feasible and economically sustainable LCM-based biorefineries as a crucial node in achieving carbon neutrality.
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Affiliation(s)
- Samuel Gyebi Arhin
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy.
| | - Alessandra Cesaro
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
| | - Francesco Di Capua
- School of Engineering, University of Basilicata, via dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Giovanni Esposito
- Department of Civil, Architectural and Environmental Engineering, University of Naples Federico II, Via Claudio 21, 80125 Naples, Italy
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