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Chen B, Liu G, Chen Q, Wang H, Liu L, Tang K. Discovery of a novel marine Bacteroidetes with a rich repertoire of carbohydrate-active enzymes. Comput Struct Biotechnol J 2024; 23:406-416. [PMID: 38235362 PMCID: PMC10792170 DOI: 10.1016/j.csbj.2023.12.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024] Open
Abstract
Members of the phylum Bacteroidetes play a key role in the marine carbon cycle through their degradation of polysaccharides via carbohydrate-active enzymes (CAZymes) and polysaccharide utilization loci (PULs). The discovery of novel CAZymes and PULs is important for our understanding of the marine carbon cycle. In this study, we isolated and identified a potential new genus of the family Catalimonadaceae, in the phylum Bacteroidetes, from the southwest Indian Ocean. Strain TK19036, the type strain of the new genus, is predicted to encode CAZymes that are relatively abundant in marine Bacteroidetes genomes. Tunicatimonas pelagia NBRC 107804T, Porifericola rhodea NBRC 107748T and Catalinimonas niigatensis NBRC 109829T, which exhibit 16 S rRNA similarities exceeding 90% with strain TK19036, and belong to the same family, were selected as reference strains. These organisms possess a highly diverse repertoire of CAZymes and PULs, which may enable them to degrade a wide range of polysaccharides, especially pectin and alginate. In addition, some secretory CAZymes in strain TK19036 and its relatives were predicted to be transported by type IX secretion system (T9SS). Further, to the best of our knowledge, we propose the first reported "hybrid" PUL targeting alginates in T. pelagia NBRC 107804T. Our findings provide new insights into the polysaccharide degradation capacity of marine Bacteroidetes, and suggest that T9SS may play a more important role in this process than previously believed.
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Affiliation(s)
- Beihan Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Guohua Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Quanrui Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Huanyu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Le Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
| | - Kai Tang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Science, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, China
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2
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Zhang Y, Zheng L, Liu G, Shen J, Chen G, Mei X, Chang Y, Xue C. The α-linkage in funoran and agarose could be hydrolyzed by a GH96 family enzyme: Discovery of the α-funoranase. Carbohydr Polym 2024; 338:122201. [PMID: 38763726 DOI: 10.1016/j.carbpol.2024.122201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/27/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Agarans represent a group of galactans extracted from red algae. Funoran and agarose are the two major types and commercially applied polysaccharides of agaran. Although the glycoside hydrolases targeting β-glycosidic bonds of agaran have been widely investigated, those capable of degrading α-glycosidic bonds of agarose were limited, and the enzyme degrading α-linkages of funoran has not been reported till now. In this study, a GH96 family enzyme BiAF96A_Aq from a marine bacterium Aquimarina sp. AD1 was heterologously expressed in Escherichia coli. BiAF96A_Aq exhibited dual activities towards the characteristic structure of funoran and agarose, underscoring the multifunctionality of GH96 family members. Glycomics and NMR analysis revealed that BiAF96A_Aq hydrolyzed the α-1,3 glycosidic bonds between 3,6-anhydro-α-l-galactopyranose (LA) and β-d-galactopyranose-6-sulfate (G6S) of funoran, as well as LA and β-d-galactopyranose (G) of agarose, through an endo-acting manner. The end products of BiAF96A_Aq were majorly composed of disaccharides and tetrasaccharides. The identification of the activity of BiAF96A_Aq on funoran indicated the first discovery of the funoran hydrolase for α-1,3 linkage. Considering the novel catalytic reaction, we proposed to name this activity as "α-funoranase" and recommended the assignment of a dedicated EC number for its classification.
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Affiliation(s)
- Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Long Zheng
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guangning Chen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China; Qingdao Marine Science and Technology Center, 1 Wenhai Road, Qingdao 266237, China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China; Qingdao Marine Science and Technology Center, 1 Wenhai Road, Qingdao 266237, China
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3
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Kim M, Cha IT, Li M, Park SJ. Unraveling interspecies cross-feeding during anaerobic lignin degradation for bioenergy applications. CHEMOSPHERE 2024; 361:142588. [PMID: 38866340 DOI: 10.1016/j.chemosphere.2024.142588] [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: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024]
Abstract
Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - In-Tae Cha
- Climate Change and Environmental Biology Research Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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Shen J, Liu G, Chen G, Zhang Y, Mei X, Zheng L, Xue C, Chang Y. Biochemical characterization and cleavage specificities analyses of three endo-1,3-fucanases within glycoside hydrolase family 174. Carbohydr Polym 2024; 335:122083. [PMID: 38616101 DOI: 10.1016/j.carbpol.2024.122083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/05/2024] [Accepted: 03/21/2024] [Indexed: 04/16/2024]
Abstract
Sulfated fucans have garnered extensive research interest in recent decades due to their varied bioactivity. Fucanases are important tools for investigating sulfated fucans. This study reported the bioinformatic analysis and biochemical properties of three GH174 family endo-1,3-fucanases. Wherein, Fun174Rm and Fun174Sb showed the highest optimal reaction temperature among the reported fucanases, and Fun174Sb possessed favorable thermostability and catalysis efficiency. Fun174Rm displayed a random endo-acting manner, while Fun174Ri and Fun174Sb hydrolyzed sulfated fucan in processive manners. UPLC-MS and NMR analyses confirmed that the three enzymes catalyze cleavage of the α(1 → 3)-bonds between Fucp2S and Fucp2S in the sulfated fucan from Isostichopus badionotus. These enzymes demonstrated novel cleavage specificities, which could accept α-Fucp2S residues at subsites -1 and + 1. The acquiring of these biotechnological tools would be beneficial to the in-depth research of sulfated fucans.
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Affiliation(s)
- Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guangning Chen
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Long Zheng
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China.
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Wang S, Yuan C, Xu C, Li D, Zhang H, Wang J, Wang X, Li Y, Jiao D, Yuan S, Chen H, Qiu D. Denitrificimonas halotolerans sp. nov., a novel species isolated from UASB sludge treating landfill leachate. Antonie Van Leeuwenhoek 2024; 117:91. [PMID: 38907751 DOI: 10.1007/s10482-024-01987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/30/2024] [Indexed: 06/24/2024]
Abstract
A Gram-stain-negative, facultative anaerobe, rod-shaped strain JX-1T was isolated from UASB sludge treating landfill leachate in Wuhan, China. The isolate is capable of growing under conditions of pH 6.0-11.0 (optimum, pH 7.0-8.0), temperature 4-42 ℃ (optimum, 20-30 ℃), 0-8.0% (w/v) NaCl (optimum, 5.0%), and ammonia nitrogen concentration of 200-5000 mg/L (optimum, 500 mg/L) on LB plates. The microorganism can utilize malic acid, D-galactose, L-rhamnose, inosine, and L-glutamic acid as carbon sources, but does not reduce nitrates and nitrites. The major fatty acids are C18:1ω7c/C18:1ω6c, iso-C15:0, and anteiso-C15:0. The respiratory quinones are Q9 (91.92%) and Q8 (8.08%). Polar lipids include aminolipid, aminophospholipid, diphosphatidylglycerol, glycolipid, phosphatidylethanolamine, phosphatidylglycerol, and phospholipid. Compared with other strains, strain JX-1T and Denitrificimonas caeni HY-14T have the highest values in terms of 16S rRNA gene sequence similarity (96.79%), average nucleotide identity (ANI; 76.06%), and average amino acid identity (AAI; 78.89%). Its digital DNA-DNA hybridization (dDDH) result is 20.3%. The genome of strain JX-1T, with a size of 2.78 Mb and 46.12 mol% G + C content, lacks genes for denitrification and dissimilatory nitrate reduction to ammonium (DNRA), but contains genes for ectoine synthesis as a secondary metabolite. The results of this polyphasic study allow genotypic and phenotypic differentiation of the analysed strain from the closest related species and confirm that the strain represents a novel species within the genus Denitrificimonas, for which the name Denitrificimonas halotolerans sp. nov. is proposed with JX-1T (= MCCC 1K08958T = KCTC 8395T) as the type strain.
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Affiliation(s)
- Shanhui Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chu Yuan
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Chengbin Xu
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Ditian Li
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Han Zhang
- Unikleen Filtration Technology (Wuhan) Co., Ltd, Wuhan, 430205, China
| | - Jing Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Wang
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Li
- China University of Geosciences (CUG), Wuhan, 430074, China
| | - Dian Jiao
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siliang Yuan
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Han Chen
- Jingchu University of Technology, Jingmen, 448000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dongru Qiu
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture (CAS), Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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6
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Tran DM, Huynh TU, Do TO, Nguyen AD. Isolation, Plant Growth-Promoting Properties, and Whole-Genome Sequence of a Novel Paenibacillus Species. J Basic Microbiol 2024:e202400119. [PMID: 38894514 DOI: 10.1002/jobm.202400119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/27/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
This work aimed to isolate and characterize a novel chitin-degrading bacterium from Yok Don National Park, Vietnam, for crop production studies. Among the chitinolytic isolates, strain YSY-4.3 was selected, which grew rapidly and produced a large halo around the colony. 16S rDNA analysis indicated that the strain is a novel species in the genus paenibacillus, and an in vitro evaluation showed that the strain produced phytohormones (IAA, GA3, and zeatin), biofilms, and siderophores; possessed cellulase; and exerted antifungal activity. The whole genome of the strain was 5,628,400 bp with 49.3% GC content, 5056 coding sequences, 48 tRNA, and 1 rRNA. It shared the highest values of digital DNA-DNA hybridization (67.4%) and average nucleotide identity (89.54%) with those of Paenibacillus woosongensis B2_4 (CP126084.1), suggesting a novel species. Of the coding sequences, 4287 proteins were identified by COG, and 2561 were assigned by KEGG. The genome contained at least 51 genes involved in plant growth and resistance to heavy-metal toxicity and 359 carbohydrate-active enzymes. The chitinolytic system of the strain was composed of 15 enzymes, among them, PsChiC, which contained a GH18 catalytic domain and a GH5 catalytic domain, had not been previously reported. In addition, the genome possessed 15 gene clusters encoding antimicrobial metabolites, 10 of which are possible novel clusters. This study expands knowledge regarding novel chitinolytic bacteria from Yok Don National Park and provides a valuable gene resource for future studies.
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Affiliation(s)
- Dinh Minh Tran
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - To Uyen Huynh
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - Tu Oanh Do
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak, Vietnam
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Blair EM, Brown JL, Li D, Holden PA, O'Malley MA. Metagenomics analysis yields assembled genomes from prokaryotic anaerobes with polymer-degrading potential. Biotechnol Prog 2024:e3484. [PMID: 38881311 DOI: 10.1002/btpr.3484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024]
Abstract
Anaerobic microbial communities are often highly degradative, such as those found in the herbivore rumen and large-scale anaerobic digesters. Since the microbial communities in these systems degrade recalcitrant organic polymers, we hypothesize that some microbes in anaerobic environments may be involved in man-made plastic association, deformation, or even breakdown. While efforts have been put toward characterizing microbial communities, many microbes remain unidentified until they can be sufficiently cultivated to generate enough genetic material to assemble high-quality metagenome assemblies and reference genomes. In this study, microbial consortia from goat fecal pellets and anaerobic digester sludge were cultivated for over 6 weeks to assemble metagenomes from novel anaerobic taxa with potential degradative activity. To select for microbes with potential plastic-degrading abilities, plastic strips were included in culture, though the presence of plastic did not appear to enrich for particularly degradative consortia, yet it did select for novel species that otherwise may not have been characterized. Whole-genome shotgun sequencing enabled assembly of 72 prokaryotic metagenome-assembled genomes (MAGs) with >90% completion, <5% contamination, and an N50 >10,000 bp; 17 of these MAGs are classified as novel species given their lack of similarity to publicly available genomes and MAGs. These 72 MAGs vary in predicted carbohydrate-degrading abilities, with genes predicted to encode fewer than 10 or up to nearly 400 carbohydrate-active enzymes. Overall, this enrichment strategy enables characterization of less abundant MAGs in a community, and the MAGs identified here can be further mined to advance understanding of degradative anaerobic microbial consortia.
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Affiliation(s)
- Elaina M Blair
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Jennifer L Brown
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
| | - Dong Li
- Bren School of Environmental Science & Management, University of California, Santa Barbara, California, USA
| | - Patricia A Holden
- Bren School of Environmental Science & Management, University of California, Santa Barbara, California, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, California, USA
- Joint BioEnergy Institute (JBEI), Emeryville, California, USA
- Department of Bioengineering, University of California, Santa Barbara, California, USA
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Radzlin N, Mohamad Ali MS, Goh KM, Yaakop AS, Zakaria II, Kahar UM. Exploring a novel GH13_5 α-amylase from Jeotgalibacillus malaysiensis D5 T for raw starch hydrolysis. AMB Express 2024; 14:71. [PMID: 38874807 PMCID: PMC11178733 DOI: 10.1186/s13568-024-01722-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024] Open
Abstract
α-Amylase plays a crucial role in the industrial degradation of starch. The genus Jeotgalibacillus of the underexplored marine bacteria family Caryophanaceae has not been investigated in terms of α-amylase production. Herein, we report the comprehensive analysis of an α-amylase (AmyJM) from Jeotgalibacillus malaysiensis D5T (= DSM28777T = KCTC33550T). Protein phylogenetic analysis indicated that AmyJM belongs to glycoside hydrolase family 13 subfamily 5 (GH13_5) and exhibits low sequence identity with known α-amylases, with its closest counterpart being the GH13_5 α-amylase from Bacillus sp. KSM-K38 (51.05% identity). Purified AmyJM (molecular mass of 70 kDa) is stable at a pH range of 5.5-9.0 and optimally active at pH 7.5. The optimum temperature for AmyJM is 40 °C, where the enzyme is reasonably stable at this temperature. Similar to other α-amylases, the presence of CaCl2 enhanced both the activity and stability of AmyJM. AmyJM exhibited activity toward raw and gelatinized forms of starches and related α-glucans, generating a mixture of reducing sugars, such as glucose, maltose, maltotriose, maltotetraose, and maltopentaose. In raw starch hydrolysis, AmyJM exhibited its highest efficiency (51.10% degradation) in hydrolyzing raw wheat starch after 3-h incubation at 40 °C. Under the same conditions, AmyJM also hydrolyzed tapioca, sago, potato, rice, and corn raw starches, yielding 16.01-30.05%. These findings highlight the potential of AmyJM as a biocatalyst for the saccharification of raw starches, particularly those derived from wheat.
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Affiliation(s)
- Nurfatini Radzlin
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Enzyme Technology Laboratory, Institute Bioscience, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | - Kian Mau Goh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Amira Suriaty Yaakop
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Pulau Pinang, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia.
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Sreya PK, Hari Naga Papa Rao A, Suresh G, Sasikala C, Venkata Ramana C. Genomic and functional insights of a mucin foraging Rhodopirellula halodulae sp. nov. Syst Appl Microbiol 2024; 47:126523. [PMID: 38897058 DOI: 10.1016/j.syapm.2024.126523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Nine novel strains were obtained from various algal and seagrass samples. The analysis of the 16S rRNA gene-based phylogenetic tree revealed monophyletic placement of all novel strains within the Rhodopirellula genus. The type strain was identified as JC737T, which shared 99.1 % 16S rRNA gene sequence identity with Rhodopirellula baltica SH1T, while strain JC740 was designated as an additional strain. The genome sizes of strains JC737T and JC740 were 6.6 and 6.7 Mb, respectively, and the G + C content was 56.2 %. The strains cladded distinctly in the phylogenomic tree, and the ANI and dDDH values of the strain JC737T were 75.8-76.1 % and 20.8-21.3 %, respectively, in comparison to other Rhodopirellula members. The strain demonstrated a versatile degradation capability, exhibiting a diverse array of complex polysaccharides, including mucin which had not been previously identified within the members of the phylum Planctomycetota. The phylogenomic, pan-genomic, morphological, physiological, and genomic characterization of the strain lead to the proposal to describe the strain as Rhodopirellula halodulae sp. nov.
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Affiliation(s)
- P K Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Atham Hari Naga Papa Rao
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | | | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.
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10
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Ghezzi D, Salvi L, Costantini PE, Firrincieli A, Iorio M, Lopo E, Sosio M, Elbanna AH, Khalil ZG, Capon RJ, De Waele J, Vergara F, Sauro F, Cappelletti M. Ancient and remote quartzite caves as a novel source of culturable microbes with biotechnological potential. Microbiol Res 2024; 286:127793. [PMID: 38901277 DOI: 10.1016/j.micres.2024.127793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024]
Abstract
Quartzite caves located on table-top mountains (tepuis) in the Guyana Shield, are ancient, remote, and pristine subterranean environments where microbes have evolved peculiar metabolic strategies to thrive in silica-rich, slightly acidic and oligotrophic conditions. In this study, we explored the culturable fraction of the microbiota inhabiting the (ortho)quartzite cave systems in Venezuelan tepui (remote table-top mountains) and we investigated their metabolic and enzymatic activities in relation with silica solubilization and extracellular hydrolytic activities as well as the capacity to produce antimicrobial compounds. Eighty microbial strains were isolated with a range of different enzymatic capabilities. More than half of the isolated strains performed at least three enzymatic activities and four bacterial strains displayed antimicrobial activities. The antimicrobial producers Paraburkholderia bryophila CMB_CA002 and Sphingomonas sp. MEM_CA187, were further analyzed by conducting chemotaxonomy, phylogenomics, and phenomics. While the isolate MEM_CA187 represents a novel species of the genus Sphingomonas, for which the name Sphingomonas imawarii sp. nov. is proposed, P. bryophila CMB_CA002 is affiliated with a few strains of the same species that are antimicrobial producers. Chemical analyses demonstrated that CMB_CA002 produces ditropolonyl sulfide that has a broad range of activity and a possibly novel siderophore. Although the antimicrobial compounds produced by MEM_CA187 could not be identified through HPLC-MS analysis due to the absence of reference compounds, it represents the first soil-associated Sphingomonas strain with the capacity to produce antimicrobials. This work provides first insights into the metabolic potential present in quartzite cave systems pointing out that these environments are a novel and still understudied source of microbial strains with biotechnological potential.
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Affiliation(s)
- Daniele Ghezzi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Luca Salvi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Paolo E Costantini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | - Andrea Firrincieli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; Department for Innovation in Biological, Agro-Food and Forest systems, University of Tuscia, Viterbo 01100, Italy
| | | | - Ettore Lopo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy
| | | | - Ahmed H Elbanna
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Department of Pharmacognosy, Cairo University, Cairo 11562, Egypt
| | - Zeinab G Khalil
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jo De Waele
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Freddy Vergara
- La Venta Geographic Explorations Association, Treviso 31100, Italy; Teraphosa Exploring Team, Puerto Ordaz, Venezuela
| | - Francesco Sauro
- La Venta Geographic Explorations Association, Treviso 31100, Italy
| | - Martina Cappelletti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna 40126, Italy; La Venta Geographic Explorations Association, Treviso 31100, Italy.
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11
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Hilário S, Gonçalves MFM, Matos I, Rangel LF, Sousa JA, Santos MJ, Ayra-Pardo C. Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter. Appl Microbiol Biotechnol 2024; 108:370. [PMID: 38861018 PMCID: PMC11166776 DOI: 10.1007/s00253-024-13210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.
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Affiliation(s)
- Sandra Hilário
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
- GreenUPorto, Sustainable Agrifood Production Research Centre/Inov4Agro, DGAOT, Faculty of Sciences, University of Porto, Campus de Vairão, 747, 4485-646, Vila do Conde, Portugal.
| | - Micael F M Gonçalves
- Department of Biology, Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Matos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - Luis F Rangel
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
| | - José A Sousa
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Maria J Santos
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, s/n, FC4, 4169-007, Porto, Portugal
| | - Camilo Ayra-Pardo
- Interdisciplinary Centre of Marine and Environmental Research, CIIMAR, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4450-208, Porto, Portugal.
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12
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Ercole TG, Kava VM, Petters-Vandresen DAL, Nassif Gomes ME, Aluizio R, Ribeiro RA, Hungria M, Galli LV. Unlocking the growth-promoting and antagonistic power: A comprehensive whole genome study on Bacillus velezensis strains. Gene 2024; 927:148669. [PMID: 38866259 DOI: 10.1016/j.gene.2024.148669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/14/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Abstract
Bacillus species are extensively documented as plant growth-promoting rhizobacteria, contributing significantly to the enhancement of soil fertility, nutrient recycling, and the control of phytopathogens. Utilizing them as biocontrol agents represents an environmentally friendly strategy, particularly within the rhizospheric community. This study presents the comprehensive genome sequences of three B. velezensis strains (LGMB12, LGMB319, and LGMB426) which were previously isolated from root samples of maize (Zea mays L.), along with a type strain FZB42. The research assesses the capability of the three strains for antagonizing fungi, specifically Fusarium graminearum, Fusarium verticillioides, Colletotrichum graminicola, and Stenocarpella sp. In paired cultures involving maize fungi, treatments containing bacteria B. velezensis exhibited statistically significant differences compared to both negative and positive treatments in terms of antagonism. Furthermore, genome mining techniques were employed to explore their inherent antagonistic potential. The assembly revealed that strains LGMB12, LGMB319, LGMB426, and FZB42 exhibit genome sizes of 4,187,541 bp, 4,244,954 bp, 3,976,537 bp, and 3,990,518 respectively. Their respective G + C content stands at 46.42 %, 46.50 %, 46.51 %, and 46.38 %. Moreover, the genomes present multiple gene clusters responsible for the synthesis of secondary metabolites and carbohydrate-active enzymes (CAZymes). These clusters highlight a diverse array of antibacterial and antifungal properties, complemented by numerous plant growth-promoting genes. These results highlight the potential of B. velezensis LGMB12, LGMB319, and LGMB426 strains as biocontrol and plant growth promotion agents, being promising candidates for further studies in agricultural production, including field trials.
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Affiliation(s)
- Tairine Graziella Ercole
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Vanessa Merlo Kava
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Desirrê Alexia Lourenço Petters-Vandresen
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Maria Eduarda Nassif Gomes
- Pontifical Catholic University of Paraná, Imaculada Conceição St., 1155, 80215-901 Curitiba, PR, Brazil.
| | - Rodrigo Aluizio
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
| | - Renan Augusto Ribeiro
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, SHIS QI 1 Conjunto B, Blocos A, B, C e D, Lago Sul, 71605-001 Brasília, Distrito Federal, Brazil.
| | | | - Lygia Vitoria Galli
- Department of Genetics, Laboratory of Genetics of Microorganisms, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100, 81531-980 Curitiba, PR, Brazil.
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13
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Wei J, Luo J, Yang F, Dai W, Huang Z, Yan Y, Luo M. Comparative genomic and metabolomic analysis reveals the potential of a newly isolated Enterococcus faecium B6 involved in lipogenic effects. Gene 2024; 927:148668. [PMID: 38852695 DOI: 10.1016/j.gene.2024.148668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/01/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Evidence has indicated that Enterococcus plays a vital role in non-alcoholic fatty liver disease (NAFLD) development. However, the microbial genetic basis and metabolic potential in the disease are yet unknown. We previously isolated a bacteria Enterococcus faecium B6 (E. faecium B6) from children with NAFLD for the first time. Here, we aim to systematically investigate the potential of strain B6 in lipogenic effects. The lipogenic effects of strain B6 were explored in vitro and in vivo. The genomic and functional characterizations were investigated by whole-genome sequencing and comparative genomic analysis. Moreover, the metabolite profiles were unraveled by an untargeted metabolomic analysis. We demonstrated that strain B6 could effectively induce lipogenic effects in the liver of mice. Strain B6 contained a circular chromosome and two circular plasmids and posed various functions. Compared to the other two probiotic strains of E. faecium, strain B6 exhibited unique functions in pathways of ABC transporters, phosphotransferase system, and amino sugar and nucleotide sugar metabolism. Moreover, strain B6 produced several metabolites, mainly enriched in the protein digestion and absorption pathway. The unique potential of strain B6 in lipogenic effects was probably associated with glycolysis, fatty acid synthesis, and glutamine and choline transport. This study pioneeringly revealed the metabolic characteristics and specific detrimental traits of strain B6. The findings provided new insights into the underlying mechanisms of E. faecium in lipogenic effects, and laid essential foundations for further understanding of E. faecium-related disease.
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Affiliation(s)
- Jia Wei
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Jiayou Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Fei Yang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang 421001, Hunan, China
| | - Wen Dai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Zhihang Huang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Yulin Yan
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China
| | - Miyang Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha 410078, Hunan, China.
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14
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An H, Ching XH, Cheah WJ, Lim WL, Ee KY, Chong CS, Lam MQ. Genomic analysis of a halophilic bacterium Nesterenkonia sp. CL21 with ability to produce a diverse group of lignocellulolytic enzymes. Folia Microbiol (Praha) 2024:10.1007/s12223-024-01178-9. [PMID: 38842626 DOI: 10.1007/s12223-024-01178-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 05/26/2024] [Indexed: 06/07/2024]
Abstract
Halophilic bacteria are extremophiles that thrive in saline environment. Their ability to withstand such harsh conditions makes them an ideal choice for industrial applications such as lignocellulosic biomass degradation. In this study, a halophilic bacterium with the ability to produce extracellular cellulases and hemicellulases, designated as Nesterenkonia sp. CL21, was isolated from mangrove sediment in Tanjung Piai National Park, Malaysia. Thus far, studies on lignocellulolytic enzymes concerning bacterial species under this genus are limited. To gain a comprehensive understanding of its lignocellulose-degrading potential, the whole genome was sequenced using the Illumina NovaSeq 6000 platform. The genome of strain CL21 was assembled into 25 contigs with 3,744,449 bp and a 69.74% GC content and was predicted to contain 3,348 coding genes. Based on taxonomy analysis, strain CL21 shares 73.8 to 82.0% average nucleotide identity with its neighbouring species, below the 95% threshold, indicating its possible status as a distinct species in Nesterenkonia genus. Through in-depth genomic mining, a total of 81 carbohydrate-active enzymes were encoded. Among these, 24 encoded genes were identified to encompass diverse cellulases (GH3), xylanases (GH10, GH11, GH43, GH51, GH127 and CE4), mannanases (GH38 and GH106) and pectinases (PL1, PL9, and PL11). The production of lignocellulolytic enzymes was tested in the presence of several substrates. This study revealed that strain CL21 can produce a diverse array of enzymes which are active at different time points. By combining experimental data with genomic information, the ability of strain CL21 to produce lignocellulolytic enzymes has been elucidated, with potential applications in biorefinery industry.
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Affiliation(s)
- Hongxuan An
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Xin Huey Ching
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wai Jun Cheah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wei Lun Lim
- Faculty of Chemical Engineering Technology, Universiti Malaysia Perlis (UniMAP), 02600, Arau, Perlis, Malaysia
| | - Kah Yaw Ee
- Department of Agricultural and Food Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
- Centre for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Ming Quan Lam
- Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
- Centre for Agriculture and Food Research, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
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15
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Khomyakova MA, Merkel AY, Slobodkin AI. Anaerobaca lacustris gen. nov., sp. nov., an obligately anaerobic planctomycete of the widespread SG8-4 group, isolated from a coastal lake, and proposal of Anaerobacaceae fam. nov. Syst Appl Microbiol 2024; 47:126522. [PMID: 38852331 DOI: 10.1016/j.syapm.2024.126522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/11/2024]
Abstract
One of the numerous and widespread lineages of planctomycetes is the hitherto uncultured SG8-4 group inhabiting anoxic environments. A novel anaerobic, mesophilic, alkalitolerant, chemoorganotrophic bacterium (strain M17dextrT) was isolated from anaerobic sediment of a coastal lake (Taman Peninsula, Russia). The cell were mainly non-motile cocci, 0.3 to 1.0 µm in diameter forming chains or aggregates. The cells had a Gram-negative cell wall and divided by binary fission. The temperature range for growth was 20-37 0C (optimum at 30 0C). The pH range for growth was 6.5-10.0, with an optimum at pH 8.0-8.5. Strain M17dextrT fermented mono-, di- and polysaccharides (starch, xanthan gum, dextran, N-acetylglucosamine), but did not utilized proteinaceous compounds. Major cellular fatty acids were C16:0 and C18:0. The genome of strain M17dextrT had a size of 5.7 Mb with a G + C content of 62.49 %. The genome contained 345 CAZyme genes. The closest cultured phylogenetic relatives of strain M17dextrT were members of the order Sedimentisphaerales, class Phycisphaerae. Among characterized planctomycetes, the highest 16S rRNA gene sequence similarity (88.3 %) was observed with Anaerohalosphaera lusitana. According to phylogenomic analysis strain M17dextrT together with many uncultured representatives of Sedimentisphaerales forms a separate family-level lineage. We propose to assign strain M17dextrT to a novel genus and species, Anaerobaca lacustris gen. nov., sp. nov.; the type strain is M17dextrT (=VKM B-3571 T = DSM 113417 T = JCM 39238 T = KCTC 25381 T = UQM 41474 T). This genus is placed in a novel family, Anaerobacaceae fam. nov. within the order Sedimentisphaerales.
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Affiliation(s)
- M A Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia.
| | - A Y Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
| | - A I Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Leninskiy Prospect, 33, bld. 2, 119071, Moscow, Russia
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16
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Pellegrinetti TA, de Cássia Mesquita da Cunha I, Chaves MGD, Freitas ASD, Passos GS, Silva AVRD, Cotta SR, Tsai SM, Mendes LW. Genomic insights of Fictibacillus terranigra sp. nov., a versatile metabolic bacterium from Amazonian Dark Earths. Braz J Microbiol 2024; 55:1817-1828. [PMID: 38358421 PMCID: PMC11153436 DOI: 10.1007/s42770-024-01268-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
The Amazon rainforest, a hotspot for biodiversity, is a crucial research area for scientists seeking novel microorganisms with ecological and biotechnological significance. A key region within the Amazon rainforest is the Amazonian Dark Earths (ADE), noted for supporting diverse plant and microbial communities, and its potential as a blueprint for sustainable agriculture. This study delineates the isolation, morphological traits, carbon source utilization, and genomic features of Fictibacillus terranigra CENA-BCM004, a candidate novel species of the Fictibacillus genus isolated from ADE. The genome of Fictibacillus terranigra was sequenced, resulting in 16 assembled contigs, a total length of 4,967,627 bp, and a GC content of 43.65%. Genome annotation uncovered 3315 predicted genes, encompassing a wide range of genes linked to various metabolic pathways. Phylogenetic analysis indicated that CENA-BCM004 is a putative new species, closely affiliated with other unidentified Fictibacillus species and Bacillus sp. WQ 8-8. Moreover, this strain showcased a multifaceted metabolic profile, revealing its potential for diverse biotechnological applications. It exhibited capabilities to antagonize pathogens, metabolize multiple sugars, mineralize organic matter compounds, and solubilize several minerals. These insights substantially augment our comprehension of microbial diversity in ADE and underscore the potential of Fictibacillus terranigra as a precious resource for biotechnological endeavors. The genomic data generated from this study will serve as a foundational resource for subsequent research and exploration of the biotechnological capabilities of this newly identified species.
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Affiliation(s)
- Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
- Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Piracicaba, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Anderson Santos de Freitas
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Gabriel Schimmelpfeng Passos
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Simone Raposo Cotta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture, University of Sao Paulo, Piracicaba, Brazil.
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17
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Botero J, Peeters C, De Canck E, Laureys D, Vandamme P. Eupransor demetentiae gen. nov., sp. nov., a novel fructophilic lactic acid bacterium from bumble bees. Int J Syst Evol Microbiol 2024; 74. [PMID: 38833293 DOI: 10.1099/ijsem.0.006409] [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: 06/06/2024] Open
Abstract
Strain LMG 33000T was isolated from a Bombus lapidarius gut sample. It shared the highest percentage 16S rRNA sequence identity, average amino acid identity, and amino acid identity of conserved genes with Convivina intestini LMG 28291T (95.86 %, 69.9 and 76.2 %, respectively), and the highest percentage OrthoANIu value with Fructobacillus fructosus DSM 20349T (71.4 %). Phylogenomic analyses by means of 107 or 120 conserved genes consistently revealed Convivina as nearest neighbour genus. The draft genome of strain LMG 33000T was 1.44 Mbp in size and had a DNA G+C content of 46.1 mol%. Genomic and physiological analyses revealed that strain LMG 33000T was a typical obligately fructophilic lactic acid bacterium that lacked the adhE and aldh genes and that did not produce ethanol during glucose or fructose metabolism. In contrast, Convivina species have the adhE and aldh genes in their genomes and produced ethanol from glucose and fructose metabolism, which is typical for heterofermentative lactic acid bacteria. Moreover, strain LMG 33000T exhibited catalase activity, an unusual characteristic among lactic acid bacteria, that is not shared with Convivina species. Given its position in the phylogenomic trees, and the difference in genomic percentage G+C content and in physiological and metabolic characteristics between strain LMG 33000T and Convivina species, we considered it most appropriate to classify strain LMG 33000T into a novel genus and species within the Lactobacillaceae family for which we propose the name Eupransor demetentiae gen. nov., sp. nov., with LMG 33000T (=CECT 30958T) as the type strain.
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Affiliation(s)
- Juliana Botero
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Evelien De Canck
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - David Laureys
- Innovation Centre for Brewing & Fermentation, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, K. L. Ledeganckstraat 35, 9000 Ghent, Belgium
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18
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Navaratna TA, Alansari N, Eisenberg AR, O'Malley MA. Anaerobic fungi contain abundant, diverse, and transcriptionally active Long Terminal Repeat retrotransposons. Fungal Genet Biol 2024; 172:103897. [PMID: 38750926 DOI: 10.1016/j.fgb.2024.103897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/14/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024]
Abstract
Long Terminal Repeat (LTR) retrotransposons are a class of repetitive elements that are widespread in the genomes of plants and many fungi. LTR retrotransposons have been associated with rapidly evolving gene clusters in plants and virulence factor transfer in fungal-plant parasite-host interactions. We report here the abundance and transcriptional activity of LTR retrotransposons across several species of the early-branching Neocallimastigomycota, otherwise known as the anaerobic gut fungi (AGF). The ubiquity of LTR retrotransposons in these genomes suggests key evolutionary roles in these rumen-dwelling biomass degraders, whose genomes also contain many enzymes that are horizontally transferred from other rumen-dwelling prokaryotes. Up to 10% of anaerobic fungal genomes consist of LTR retrotransposons, and the mapping of sequences from LTR retrotransposons to transcriptomes shows that the majority of clusters are transcribed, with some exhibiting expression greater than 104 reads per kilobase million mapped reads (rpkm). Many LTR retrotransposons are strongly differentially expressed upon heat stress during fungal cultivation, with several exhibiting a nearly three-log10 fold increase in expression, whereas growth substrate variation modulated transcription to a lesser extent. We show that some LTR retrotransposons contain carbohydrate-active enzymes (CAZymes), and the expansion of CAZymes within genomes and among anaerobic fungal species may be linked to retrotransposon activity. We further discuss how these widespread sequences may be a source of promoters and other parts towards the bioengineering of anaerobic fungi.
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Affiliation(s)
- Tejas A Navaratna
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States
| | - Nabil Alansari
- Department of Chemical Engineering, UC Santa Barbara, United States
| | - Amy R Eisenberg
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States
| | - Michelle A O'Malley
- Department of Chemical Engineering, UC Santa Barbara, United States; California NanoSystems Institute, United States; Department of Bioengineering, UC Santa Barbara, United States.
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Mohapatra BR. Genome features and carbohydrate-active enzymes repertoire of a novel Stenotrophomonas sepilia Alg010 strain isolated from Sargassum seaweed waste. Data Brief 2024; 54:110533. [PMID: 38868382 PMCID: PMC11166690 DOI: 10.1016/j.dib.2024.110533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
This study reports the genome sequence data of a novel Stenotrophomonas sepilia Alg010 strain isolated from Sargassum seaweed waste accumulated on the coastline of Barbados. The genome sequence data was obtained via sequencing of the genomic DNA of this isolate with Illumina NextSeq2000 platform and paired-end library preparation protocol. The resulting reads were assembled with the SPAdes Genome Assembler (ver 3.15.4) and annotated with the DDBJ Fast Annotation and Submission Tool. The genome size of this novel isolate was recorded as 4,515,447 bp with a coverage of 270×, a GC content of 66.6 % and a gap ratio of 0.027 %. The lengths of the longest and the N50 contigs were estimated as 246,749 bp and 81,982 bp, respectively. The genome contains 2 rRNA, 66 tRNA, 2 CRISPR, 86 contigs and 4024 CDSs (coding sequences) with a coding ratio of 88.9 %. The annotation of the CDSs for COG (cluster of orthologous groups) and for subsystem features indicated that the metabolism and the amino acids and derivatives were the most dominant categories, respectively. The annotation of the genome via dbCAN3 server for carbohydrate-active genes revealed 98 genes encoding the six functional classes of carbohydrate-active enzymes. The genome sequence data is available in NCBI GenBank with the accession number BTRJ00000000.
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Affiliation(s)
- Bidyut R. Mohapatra
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown BB11000, Barbados
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20
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Li X, Yang M, Mo K, Hu Y, Gu H, Sun D, Bao S, Huang H. Genome Analysis of Multiple Polysaccharide-Degrading Bacterium Microbulbifer thermotolerans HB226069: Determination of Alginate Lyase Activity. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:488-499. [PMID: 38668917 DOI: 10.1007/s10126-024-10311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/05/2024] [Indexed: 06/15/2024]
Abstract
Polysaccharide-degrading bacteria are key participants in the global carbon cycle and algal biomass recycling. Herein, a polysaccharide lyase-producing strain HB226069 was isolated from Sargassum sp. from Qingge Port, Hainan, China. Results of the phylogenetic of the 16S rRNA gene and genotypic analysis indicated that the isolate should be classified as Microbulbifer thermotolerans. The whole genome is a 4,021,337 bp circular chromosome with a G+C content of 56.5%. Analysis of the predicted genes indicated that strain HB226069 encoded 161 carbohydrate-active enzymes (CAZymes), and abundant putative enzymes involved in polysaccharide degradation were predicted, including alginate lyase, fucosidase, agarase, xylanase, cellulase, pectate lyase, amylase, and chitinase. Three of the putative polysaccharide lyases from PL7 and PL17 families were involved in alginate degradation. The alginate lyases of strain HB226069 showed the maximum activity of 117.4 U/mL at 50 °C, pH 7.0, and 0.05 M FeCl3, while exhibiting the best stability at 30 °C and pH 7.0. The Thin Layer Chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analyses indicated that the alginate oligosaccharides (AOSs) degraded by the partially purified alginate lyases contained oligosaccharides of DP2-DP5 and monosaccharide while reacting for 36 h. The complete genome of M. thermotolerans HB226069 enriches our understanding of the mechanism of polysaccharide lyase production and supports its potential application in polysaccharide degradation.
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Affiliation(s)
- Xue Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163000, Heilongjiang, China
| | - Miao Yang
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- College of Life Science and Technology, Huazhong Agricultural University, CATAS, Wuhan, 430070, Hubei, China
| | - Kunlian Mo
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China
| | - Yonghua Hu
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China
| | - Hanjie Gu
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China
| | - Dongmei Sun
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163000, Heilongjiang, China.
| | - Shixiang Bao
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China.
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China.
| | - Huiqin Huang
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China.
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China.
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Wu J, Tang W, Li Z, Chakraborty A, Zhou C, Li F, He S. Duplications and Losses of the Detoxification Enzyme Glycosyltransferase 1 Are Related to Insect Adaptations to Plant Feeding. Int J Mol Sci 2024; 25:6080. [PMID: 38892266 PMCID: PMC11173166 DOI: 10.3390/ijms25116080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Insects have developed sophisticated detoxification systems to protect them from plant secondary metabolites while feeding on plants to obtain necessary nutrients. As an important enzyme in the system, glycosyltransferase 1 (GT1) conjugates toxic compounds to mitigate their harm to insects. However, the evolutionary link between GT1s and insect plant feeding remains elusive. In this study, we explored the evolution of GT1s across different insect orders and feeding niches using publicly available insect genomes. GT1 is widely present in insect species; however, its gene number differs among insect orders. Notably, plant-sap-feeding species have the highest GT1 gene numbers, whereas blood-feeding species display the lowest. GT1s appear to be associated with insect adaptations to different plant substrates in different orders, while the shift to non-plant feeding is related to several losses of GT1s. Most large gene numbers are likely the consequence of tandem duplications showing variations in collinearity among insect orders. These results reveal the potential relationships between the evolution of GT1s and insect adaptation to plant feeding, facilitating our understanding of the molecular mechanisms underlying insect-plant interactions.
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Affiliation(s)
- Jinyu Wu
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Wanjiang Tang
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Zhengyang Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Amrita Chakraborty
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic;
| | - Cao Zhou
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Fei Li
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
| | - Shulin He
- College of Life Science, Chongqing Normal University, Chongqing 401331, China; (J.W.)
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Li W, Lin X, Liang H, Wu Z, Wang M, Sun J, Li X, He W, Gao X, Hu T, Xiao L, Zou Y. Genomic and functional diversity of the human-derived isolates of Faecalibacterium. Front Microbiol 2024; 15:1379500. [PMID: 38873165 PMCID: PMC11169845 DOI: 10.3389/fmicb.2024.1379500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/06/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Faecalibacterium is one of the most abundant bacteria in the gut microbiota of healthy adults, highly regarded as a next-generation probiotic. However, the functions of Faecalibacterium genomes from cultured strains and the distribution of different species in populations may differ among different sources. Methods We here performed an extensive analysis of pan-genomes, functions, and safety evaluation of 136 Faecalibacterium genomes collected from 10 countries. Results The genomes are clustered into 11 clusters, with only five of them were characterized and validly nomenclated. Over 80% of the accessory genes and unique genes of Faecalibacterium are found with unknown function, which reflects the importance of expanding the collection of Faecalibacterium strains. All the genomes have the potential to produce acetic acid and butyric acid. Nine clusters of Faecalibacterium are found significantly enriched in the healthy individuals compared with patients with type II diabetes.. Discussion This study provides a comprehensive view of genomic characteristic and functions and of culturable Faecalibacterium bacterium from human gut, and enables clinical advances in the future.
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Affiliation(s)
- Wenxi Li
- BGI-Shenzhen, Shenzhen, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaoqian Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Hewei Liang
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Zhinan Wu
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengmeng Wang
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingxi Sun
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofang Li
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | | | | | - Tongyuan Hu
- BGI-Shenzhen, Shenzhen, China
- BGI Research, Wuhan, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
| | - Yuanqiang Zou
- BGI-Shenzhen, Shenzhen, China
- BGI College and Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen, China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken, Copenhagen, Denmark
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Logachev A, Kanapin A, Rozhmina T, Stanin V, Bankin M, Samsonova A, Orlova E, Samsonova M. Pangenomics of flax fungal parasite Fusarium oxysporum f. sp. lini. FRONTIERS IN PLANT SCIENCE 2024; 15:1383914. [PMID: 38872883 PMCID: PMC11169931 DOI: 10.3389/fpls.2024.1383914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/16/2024] [Indexed: 06/15/2024]
Abstract
To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.
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Affiliation(s)
- Anton Logachev
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Alexander Kanapin
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Tatyana Rozhmina
- Flax Institute, Federal Research Center for Bast Fiber Crops, Torzhok, Russia
| | - Vladislav Stanin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Mikhail Bankin
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Anastasia Samsonova
- Center for Computational Biology, Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Ekaterina Orlova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
| | - Maria Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great St.Petersburg Polytechnic University, Saint Petersburg, Russia
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Mu W, Liu H, Guo B, Wang K, Hu J, Song J, Li X, Wei S, Liu A, Liu H. Paracoccus benzoatiresistens sp. nov., a benzoate resistance and selenite reduction bacterium isolated from wetland. Antonie Van Leeuwenhoek 2024; 117:81. [PMID: 38777900 DOI: 10.1007/s10482-024-01969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/13/2024] [Indexed: 05/25/2024]
Abstract
A Gram-stain-negative, aerobic, non-motile, catalase- and oxidase-positive, pale orange, rod-shaped strain EF6T, was isolated from a natural wetland reserve in Hebei province, China. The strain grew at 25-37 °C (optimum, 30 °C), pH 5-9 (optimum, pH 7), and in the presence of 1.0-4.0% (w/v) NaCl (optimum, 2%). A phylogenetic analysis based on 16S rRNA gene sequence revealed that strain EF6T belongs to the genus Paracoccus, and the closest members were Paracoccus shandongensis wg2T with 98.1% similarity, Paracoccus fontiphilus MVW-1 T (97.9%), Paracoccus everestensis S8-55 T (97.7%), Paracoccus subflavus GY0581T (97.6%), Paracoccus sediminis CMB17T (97.3%), Paracoccus caeni MJ17T (97.0%), and Paracoccus angustae E6T (97.0%). The genome size of strain EF6T was 4.88 Mb, and the DNA G + C content was 65.3%. The digital DNA-DNA hybridization, average nucleotide identity, and average amino acid identity values between strain EF6T and the reference strains were all below the threshold limit for species delineation (< 32.8%, < 88.0%, and < 86.7%, respectively). The major fatty acids (≥ 5.0%) were summed feature 8 (86.3%, C18:1 ω6c and/or C18:1 ω7c) and C18:1 (5.0%) and the only isoprenoid quinone was Q-10. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, two unidentified glycolipids, five unidentified phospholipids, and an unidentified aminolipid. Strain EF6T displays notable resistance to benzoate and selenite, with higher tolerance levels (25 g/L for benzoate and 150 mM for selenite) compared to the closely related species. Genomic analysis identified six benzoate resistance genes (acdA, pcaF, fadA, pcaC, purB, and catA) and twenty selenite resistance and reduction-related genes (iscR, ssuB, ssuD, selA, selD and so on). Additionally, EF6T possesses unique genes (catA, ssuB, and ssuC) absent in the closely related species for benzoate and selenite resistance. Its robust resistance to benzoate and selenite, coupled with its genomic makeup, make EF6T a promising candidate for the remediation of both organic and inorganic pollutants. It is worth noting that the specific resistance phenotypes described above were not reported in other novel species in Paracoccus. Based on the results of biochemical, physiological, phylogenetic, and chemotaxonomic analyses, combined with comparisons of the 16S rRNA gene sequence and the whole genome sequence, strain EF6T is considered to represent a novel species of the genus Paracoccus within the family Rhodobacteraceae, for which the name Paracoccus benzoatiresistens sp. nov. is proposed. The type strain is EF6T (= GDMCC 1.3400 T = JCM 35642 T = MCCC 1K08702T).
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Affiliation(s)
- Weidong Mu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Haoran Liu
- College of Life Sciences, Shandong Agricultural University, Taian, 271018, People's Republic of China
| | - Bai Guo
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Kaiyue Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Jinhua Hu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Jianjun Song
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Xiuyun Li
- Shandong Provincial Maternal and Child Health Care Hospital, Jinan, 250014, People's Republic of China
| | - Shuzhen Wei
- Center for Wetland Conservation and Research, Hengshui University, Hengshui, 053000, People's Republic of China.
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
- Hebei Key Laboratory of Wetland Ecology and Conservation, Hengshui, 053000, People's Republic of China.
| | - Aijv Liu
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China
- School of Resources and Environmental Engineering, Shandong University of Technology, Zibo, 255000, People's Republic of China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, People's Republic of China.
- Collaborative Innovation Center for Wetland Conservation and Green Development of Hebei Province, Hengshui, 053000, People's Republic of China.
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Zhao Y, Ding WJ, Xu L, Sun JQ. A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas. Front Microbiol 2024; 15:1395477. [PMID: 38817968 PMCID: PMC11138164 DOI: 10.3389/fmicb.2024.1395477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/29/2024] [Indexed: 06/01/2024] Open
Abstract
Stenotrophomonas strains, which are often described as plant growth promoting (PGP) bacteria, are ubiquitous in many environments. A total of 213 genomes of strains of Stenotrophomonas were analyzed using comparative genomics to better understand the ecological roles of these bacteria in the environment. The pan-genome of the 213 strains of Stenotrophomonas consists of 27,186 gene families, including 710 core gene families, 11,039 unique genes and 15,437 accessory genes. Nearly all strains of Stenotrophomonas harbor the genes for GH3-family cellulose degradation and GH2- and GH31-family hemicellulose hydrolase, as well as intact glycolysis and tricarboxylic acid cycle pathways. These abilities suggest that the strains of this genus can easily obtain carbon and energy from the environment. The Stenotrophomonas strains can respond to oxidative stress by synthesizing catalase, superoxide dismutase, methionine sulfoxide reductase, and disulfide isomerase, as well as managing their osmotic balance by accumulating potassium and synthesizing compatible solutes, such as betaine, trehalose, glutamate, and proline. Each Stenotrophomonas strain also contains many genes for resistance to antibiotics and heavy metals. These genes that mediate stress tolerance increase the ability of Stenotrophomonas strains to survive in extreme environments. In addition, many functional genes related to attachment and plant colonization, growth promotion and biocontrol were identified. In detail, the genes associated with flagellar assembly, motility, chemotaxis and biofilm formation enable the strains of Stenotrophomonas to effectively colonize host plants. The presence of genes for phosphate-solubilization and siderophore production and the polyamine, indole-3-acetic acid, and cytokinin biosynthetic pathways confer the ability to promote plant growth. These strains can produce antimicrobial compounds, chitinases, lipases and proteases. Each Stenotrophomonas genome contained 1-9 prophages and 17-60 genomic islands, and the genes related to antibiotic and heavy metal resistance and the biosynthesis of polyamines, indole-3-acetic acid, and cytokinin may be acquired by horizontal gene transfer. This study demonstrates that strains of Stenotrophomonas are highly adaptable for different environments and have strong potential for use as plant growth-promoting bacteria.
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Affiliation(s)
- Yang Zhao
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Wen-Jing Ding
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Lian Xu
- Jiangsu Key Lab for Organic Solid Waste Utilization, Educational Ministry Engineering Center of Resource-saving Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Ji-Quan Sun
- Lab for Microbial Resources, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
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26
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Sorokin DY, Merkel AY, Kolganova TV, Bale NJ, Sinninghe Damsté JS. Natronospira bacteriovora sp. nov., and Natronospira elongata sp. nov., extremely salt-tolerant predatory proteolytic bacteria from soda lakes and proposal to classify the genus Natronospira into Natronospiraceae fam. nov., and Natronospirales ord. nov., within the class Gammaproteobacteria. Syst Appl Microbiol 2024; 47:126519. [PMID: 38759530 DOI: 10.1016/j.syapm.2024.126519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
The genus Natronospira is represented by a single species of extremely salt-tolerant aerobic alkaliphilic proteolytic bacterium, isolated from hypersaline soda lakes. When cells of Gram-positive cocci were used as a substrate instead of proteins at extremely haloalkaline conditions, two new members of this genus were enriched and isolated in pure culture from the same sites. Strains AB-CW1 and AB-CW4 are obligate aerobic heterotrophic proteolytic bacteria able to feed on both live and dead cells of staphylococci and a range of proteins and peptides. Similar to the type species, N. proteinivora, the isolates are extremely salt-tolerant obligate alkaliphiles. However, N. proteinivora was unable to use bacterial cells as a substrate. Electron microscopy showed direct contact between the prey and predator cells. Functional analysis of the AB-CW1 and AB-CW4 genomes identified two sets of genes coding for extracellular enzymes potentially involved in the predation and proteolysis, respectively. The first set includes several copies of lysozyme-like GH23 peptidoglycan-lyase and murein-specific M23 [Zn]-di-peptidase enabling the cell wall degradation. The second set features multiple copies of secreted serine and metallopeptidases apparently allowing for the strong proteolytic phenotype. Phylogenomic analysis placed the isolates into the genus Natronospira as two novel species members, and furthermore indicated that this genus forms a deep-branching lineage of a new family (Natronospiraceae) and order (Natronospirales) within the class Gammaproteobacteria. On the basis of distinct phenotypic and genomic properties, strain AB-CW1T (JCM 335396 = UQM 41579) is proposed to be classified as Natronospira elongata sp. nov., and AB-CW4T (JCM 335397 = UQM 41580) as Natronospira bacteriovora sp. nov.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, TU Delft, The Netherlands.
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Tatyana V Kolganova
- Skryabin Insitutute of Bioengineering, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, and Utrecht University, Den Burg, Texel, The Netherlands
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Beidler I, Steinke N, Schulze T, Sidhu C, Bartosik D, Zühlke MK, Martin LT, Krull J, Dutschei T, Ferrero-Bordera B, Rielicke J, Kale V, Sura T, Trautwein-Schult A, Kirstein IV, Wiltshire KH, Teeling H, Becher D, Bengtsson MM, Hehemann JH, Bornscheuer UT, Amann RI, Schweder T. Alpha-glucans from bacterial necromass indicate an intra-population loop within the marine carbon cycle. Nat Commun 2024; 15:4048. [PMID: 38744821 PMCID: PMC11093988 DOI: 10.1038/s41467-024-48301-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Phytoplankton blooms provoke bacterioplankton blooms, from which bacterial biomass (necromass) is released via increased zooplankton grazing and viral lysis. While bacterial consumption of algal biomass during blooms is well-studied, little is known about the concurrent recycling of these substantial amounts of bacterial necromass. We demonstrate that bacterial biomass, such as bacterial alpha-glucan storage polysaccharides, generated from the consumption of algal organic matter, is reused and thus itself a major bacterial carbon source in vitro and during a diatom-dominated bloom. We highlight conserved enzymes and binding proteins of dominant bloom-responder clades that are presumably involved in the recycling of bacterial alpha-glucan by members of the bacterial community. We furthermore demonstrate that the corresponding protein machineries can be specifically induced by extracted alpha-glucan-rich bacterial polysaccharide extracts. This recycling of bacterial necromass likely constitutes a large-scale intra-population energy conservation mechanism that keeps substantial amounts of carbon in a dedicated part of the microbial loop.
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Affiliation(s)
- Irena Beidler
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany
| | - Nicola Steinke
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany
| | - Tim Schulze
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Daniel Bartosik
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, 17489, Greifswald, Germany
| | - Marie-Katherin Zühlke
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany
| | - Laura Torres Martin
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany
| | - Joris Krull
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Theresa Dutschei
- Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Borja Ferrero-Bordera
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Julia Rielicke
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Vaikhari Kale
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Thomas Sura
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Anke Trautwein-Schult
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Inga V Kirstein
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, 27483, Helgoland, Germany
| | - Karen H Wiltshire
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, 27483, Helgoland, Germany
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Dörte Becher
- Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Mia Maria Bengtsson
- Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, 17489, Greifswald, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
- University of Bremen, Center for Marine Environmental Sciences, MARUM, 28359, Bremen, Germany
| | - Uwe T Bornscheuer
- Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17489, Greifswald, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, 28359, Bremen, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University of Greifswald, 17489, Greifswald, Germany.
- Institute of Marine Biotechnology, 17489, Greifswald, Germany.
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, 27483, Helgoland, Germany.
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Cai Z, Wang Y, You Y, Yang N, Lu S, Xue J, Xing X, Sha S, Zhao L. Introduction of Cellulolytic Bacterium Bacillus velezensis Z2.6 and Its Cellulase Production Optimization. Microorganisms 2024; 12:979. [PMID: 38792808 PMCID: PMC11124521 DOI: 10.3390/microorganisms12050979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Enzyme-production microorganisms typically occupy a dominant position in composting, where cellulolytic microorganisms actively engage in the breakdown of lignocellulose. Exploring strains with high yields of cellulose-degrading enzymes holds substantial significance for the industrial production of related enzymes and the advancement of clean bioenergy. This study was inclined to screen cellulolytic bacteria, conduct genome analysis, mine cellulase-related genes, and optimize cellulase production. The potential carboxymethylcellulose-hydrolyzing bacterial strain Z2.6 was isolated from the maturation phase of pig manure-based compost with algae residuals as the feedstock and identified as Bacillus velezensis. In the draft genome of strain Z2.6, 31 related cellulolytic genes were annotated by the CAZy database, and further validation by cloning documented the existence of an endo-1,4-β-D-glucanase (EC 3.2.1.4) belonging to the GH5 family and a β-glucosidase (EC 3.2.1.21) belonging to the GH1 family, which are predominant types of cellulases. Through the exploration of ten factors in fermentation medium with Plackett-Burman and Box-Behnken design methodologies, maximum cellulase activity was predicted to reach 2.98 U/mL theoretically. The optimal conditions achieving this response were determined as 1.09% CMC-Na, 2.30% salinity, and 1.23% tryptone. Validation under these specified conditions yielded a cellulose activity of 3.02 U/mL, demonstrating a 3.43-fold degree of optimization. In conclusion, this comprehensive study underscored the significant capabilities of strain Z2.6 in lignocellulolytic saccharification and its potentialities for future in-depth exploration in biomass conversion.
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Affiliation(s)
- Zhi Cai
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China; (Z.C.); (Y.W.); (Y.Y.); (N.Y.); (S.L.); (J.X.); (X.X.)
- Marine College, Shandong University, Weihai 264209, China
| | - Yi Wang
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China; (Z.C.); (Y.W.); (Y.Y.); (N.Y.); (S.L.); (J.X.); (X.X.)
| | - Yang You
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China; (Z.C.); (Y.W.); (Y.Y.); (N.Y.); (S.L.); (J.X.); (X.X.)
| | - Nan Yang
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China; (Z.C.); (Y.W.); (Y.Y.); (N.Y.); (S.L.); (J.X.); (X.X.)
| | - Shanshan Lu
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China; (Z.C.); (Y.W.); (Y.Y.); (N.Y.); (S.L.); (J.X.); (X.X.)
| | - Jianheng Xue
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China; (Z.C.); (Y.W.); (Y.Y.); (N.Y.); (S.L.); (J.X.); (X.X.)
| | - Xiang Xing
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China; (Z.C.); (Y.W.); (Y.Y.); (N.Y.); (S.L.); (J.X.); (X.X.)
- Marine College, Shandong University, Weihai 264209, China
| | - Sha Sha
- Marine College, Shandong University, Weihai 264209, China
| | - Lihua Zhao
- Marine College, Shandong University, Weihai 264209, China
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Kawamoto H, Watanabe M, Mochimaru H, Nakahara N, Meng XY, Sakamoto S, Morinaga K, Katayama T, Yoshioka H, Nomura N, Tamaki H. Atrimonas thermophila gen. nov., sp. nov., a novel anaerobic thermophilic bacterium of the phylum Atribacterota isolated from deep subsurface gas field and proposal of Atrimonadaceae fam. nov. within the class Atribacteria in the phylum Atribacterota. Syst Appl Microbiol 2024; 47:126515. [PMID: 38776610 DOI: 10.1016/j.syapm.2024.126515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 04/08/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024]
Abstract
A novel anaerobic, thermophilic bacterium of the class Atribacteria, strain M15T, was isolated from a high-temperature gas reservoir, Japan. Cells of strain M15T were gram-negative, short oval-shaped, and lacked flagella. Growth occurred at 45-75 °C (optimum 70-75 °C) and pH 6.5-8.5 (optimum pH 7.5-8.0) and was fast under optimal conditions (doubling time 11.4 h). Yeast extract was required for growth. Fermentative growth with glucose, arabinose, xylose, and cellobiose was observed. The major fermentative end products of glucose were acetate and hydrogen. The major cellular fatty acids were C16:0, iso-C15:0, and C18:0. The genomic G + C content was 46.0 mol%. Fluorescence and electron microscopy observations revealed the intracellular localization of genomic DNA surrounded by a membrane in the cells of strain M15T as reported in a sole validly described species of the class Atribacteria in the phylum Atribacterota, Atribacter laminatus strain RT761T, suggesting that the unique morphological traits are widely shared in this class. Phylogenetic analyses indicated that strain M15T belongs to a distinct family-level lineage in the class Atribacteria and shows low similarities to Atribacter laminatus strain RT761T (16S rRNA gene sequence identity of 90.1 %, average nucleotide identity [ANI] of 66.1 %, average amino acid identity [AAI] of 55.8 %). Phenotypic traits of strain M15T (thermophilic, fast-growing, relatively high G + C content, etc.) were clearly distinct from A. laminatus. Based on these phenotypic and genomic properties, we propose a novel genus and species, Atrimonas thermophila gen. nov., sp. nov. for strain M15T (=JCM39389T, =KCTC25731T) representing a novel family Atrimonadaceae fam., nov. in the class Atribacteria.
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Affiliation(s)
- Hiroki Kawamoto
- Graduate School of Science and Technology, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Miho Watanabe
- Department of Biological Environment, Faculty of Bioresource Sciences, Akita Prefectural University, Shimo-Shinjyo Nakano, Akita 010-0195, Japan
| | - Hanako Mochimaru
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nozomi Nakahara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan; Environmental Management Center, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Xiang-Ying Meng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Sachiko Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Kana Morinaga
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Taiki Katayama
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Hideyoshi Yoshioka
- Research Institute for Geo-Resources and Environment, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Nobuhiko Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; MiCS (Microbiology Research Center for Sustainability), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1, Higashi, Tsukuba, Ibaraki 305-8566, Japan; Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan; MiCS (Microbiology Research Center for Sustainability), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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30
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Da Silva Morais E, Grimaud GM, Warda A, Stanton C, Ross P. Genome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus. Sci Rep 2024; 14:10109. [PMID: 38698002 PMCID: PMC11066082 DOI: 10.1038/s41598-024-59148-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.
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Affiliation(s)
- Emilene Da Silva Morais
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Microbiology Department, University College Cork, Co. Cork, Ireland
| | - Ghjuvan Micaelu Grimaud
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Alicja Warda
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Paul Ross
- APC Microbiome Ireland, University College Cork, Co. Cork, Ireland.
- Microbiology Department, University College Cork, Co. Cork, Ireland.
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31
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Han DM, Baek JH, Choi DG, Jeon MS, Eyun SI, Jeon CO. Comparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity. Food Microbiol 2024; 119:104435. [PMID: 38225047 DOI: 10.1016/j.fm.2023.104435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/25/2023] [Indexed: 01/17/2024]
Abstract
Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.
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Affiliation(s)
- Dong Min Han
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Ju Hye Baek
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae Gyu Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Seong-Il Eyun
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea.
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32
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Sorokin DY, Elcheninov AG, Bale NJ, Sininghe Damsté J, Kublanov IV. Natronosalvus hydrolyticus sp. nov., a beta-1,3-glucan utilizing natronoarchaeon from hypersaline soda lakes. Syst Appl Microbiol 2024; 47:126514. [PMID: 38735274 DOI: 10.1016/j.syapm.2024.126514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/23/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Use of curldlan, an insoluble β-1,3-glucan, as an enrichment substrate under aerobic conditions resulted in the selection from hypersaline soda lakes of a single natronarchaeon, strain AArc-curdl1. This organism is an obligately aerobic saccharolytic, possessing a poorly explored (in Archaea) potential to utilize beta-1-3 glucans, being only a second example of a haloarchaeon with this ability known in pure culture. The main phenotypic property of the isolate is the ability to grow with insoluble β-1,3-backboned glucans, i.e. curdlan and pachyman. Furthermore, the strain utilized starch family α-glucans, beta-fructan inulin and a limited spectrum of sugars. The major ether-bound membrane polar phospholipids included PGP-Me and PG. The glyco- and sulfolipids were absent. The major respiratory menaquinone is MK-8:8. According to phylogenomic analysis, AArc-curdl1 represents a separate species in the recently described genus Natronosalvus within the family Natrialbaceae. The closest related species is Natronosalvus amylolyticus (ANI, AAI and DDH values of 90.2, 91.6 and 44 %, respectively). On the basis of its unique physiological properties and phylogenomic distance, strain AArc-curdl1T is classified as a novel species Natronosalvus hydrolyticus sp. nov. (=JCM 34865 = UQM 41566).
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia; Department of Biotechnology, Delft University of Technology, Delft, the Netherlands.
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Nicole J Bale
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Jaap Sininghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Den Burg, Texel, the Netherlands
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia
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33
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Pang SL, Wang YY, Wang L, Zhang XJ, Li YH. The CBM91 module enhances the activity of β-xylosidase/α-L-arabinofuranosidase PphXyl43B from Paenibacillus physcomitrellae XB by adopting a unique loop conformation at the top of the active pocket. Int J Biol Macromol 2024; 266:131275. [PMID: 38556222 DOI: 10.1016/j.ijbiomac.2024.131275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Carbohydrate-binding module (CBM) family 91 is a novel module primarily associated with glycoside hydrolase (GH) family 43 enzymes. However, our current understanding of its function remains limited. PphXyl43B is a β-xylosidase/α-L-arabinofuranosidase bifunctional enzyme from physcomitrellae patens XB belonging to the GH43_11 subfamily and containing CBM91 at its C terminus. To fully elucidate the contributions of the CBM91 module, the truncated proteins consisting only the GH43_11 catalytic module (rPphXyl43B-dCBM91) and only the CBM91 module (rCBM91) of PphXyl43B were constructed, respectively. The result showed that rPphXyl43B-dCBM91 completely lost hydrolysis activity against both p-nitrophenyl-β-D-xylopyranoside and p-nitrophenyl-α-L-arabinofuranoside; it also exhibited significantly reduced activity towards xylobiose, xylotriose, oat spelt xylan and corncob xylan compared to the control. Thus, the CBM91 module is crucial for the β-xylosidase/α-L-arabinofuranosidase activities in PphXyl43B. However, rCBM91 did not exhibit any binding capability towards corncob xylan. Structural analysis indicated that CBM91 of PphXyl43B might adopt a loop conformation (residues 496-511: ILSDDYVVQSYGGFFT) to actively contribute to the catalytic pocket formation rather than substrate binding capability. This study provides important insights into understanding the function of CBM91 and can be used as a reference for analyzing the action mechanism of GH43_11 enzymes and their application in biomass energy conversion.
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Affiliation(s)
- Shuai Li Pang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yan Yan Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Le Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xiao Jie Zhang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yan Hong Li
- College of Life Sciences, Capital Normal University, Beijing 100048, China.
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34
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Lee JK, Choi DG, Choi BJ, Kim JM, Jeon CO. Coraliomargarita algicola sp. nov., isolated from a marine green alga. Int J Syst Evol Microbiol 2024; 74:006367. [PMID: 38717925 PMCID: PMC11165907 DOI: 10.1099/ijsem.0.006367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 04/18/2024] [Indexed: 06/13/2024] Open
Abstract
A Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, non-motile, non-flagellated, and coccus-shaped bacterium, strain J2-16T, isolated from a marine green alga, was characterized taxonomically. Strain J2-16T grew at 20-40 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0), and 1.0-4.0 % (w/v) NaCl (optimum, 3.0 %). Menaquinone-7 was identified as the sole respiratory quinone, and major fatty acids (>5 %) were C18 : 1 ω9c, iso-C14 : 0, C14 : 0, anteiso-C15 : 0, C18 : 0, C16 : 0, and C17 : 1 ω8c. The polar lipids of strain J2-16T consisted of phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, and three unidentified lipids. The genome size of strain J2-16T was 5384 kb with a G+C content of 52.0 mol%. Phylogenetic analyses based on 16S rRNA gene and 120 protein marker sequences revealed that strain J2-16T formed a distinct phyletic lineage within the genus Coraliomargarita, closely related to Coraliomargarita sinensis WN38T and Coraliomargarita akajimensis DSM 45221T with 16S rRNA gene sequence similarities of 95.7 and 94.4 %, respectively. Average nucleotide identity and digital DNA-DNA hybridization values between strain J2-16T and Coraliomargarita species were lower than 71.2 and 20.0 %, respectively. The phenotypic, chemotaxonomic, and molecular features support that strain J2-16T represents a novel species of the genus Coraliomargarita, for which the name Coraliomargarita algicola sp. nov. is proposed. The type strain is J2-16T (=KACC 22590T=JCM 35407T).
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Affiliation(s)
- Jae Kyeong Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Dae Gyu Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Byeong Jun Choi
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jeong Min Kim
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
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35
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St John E, Reysenbach AL. Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae. Syst Appl Microbiol 2024; 47:126507. [PMID: 38703419 DOI: 10.1016/j.syapm.2024.126507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/02/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
Deep-sea hydrothermal vents host archaeal and bacterial thermophilic communities, including taxonomically and functionally diverse Thermoproteota. Despite their prevalence in high-temperature submarine communities, Thermoproteota are chronically under-represented in genomic databases and issues have emerged regarding their nomenclature, particularly within the Aeropyrum-Thermodiscus-Caldisphaera. To resolve some of these problems, we identified 47 metagenome-assembled genomes (MAGs) within this clade, from 20 previously published deep-sea hydrothermal vent and submarine volcano metagenomes, and 24 MAGs from public databases. Using phylogenomic analysis, Genome Taxonomy Database Toolkit (GTDB-Tk) taxonomic assessment, 16S rRNA gene phylogeny, average amino acid identity (AAI) and functional gene patterns, we re-evaluated of the taxonomy of the Aeropyrum-Thermodiscus-Caldisphaera. At least nine genus-level clades were identified with two or more MAGs. In accordance with SeqCode requirements and recommendations, we propose names for three novel genera, viz. Tiamatella incendiivivens, Hestiella acidicharens and Calypsonella navitae. A fourth genus was also identified related to Thermodiscus maritimus, for which no available sequenced genome exists. We propose the novel species Thermodiscus eudorianus to describe our high-quality Thermodiscus MAG, which represents the type genome for the genus. All three novel genera and T. eudorianus are likely anaerobic heterotrophs, capable of fermenting protein-rich carbon sources, while some Tiamatella, Calypsonella and T. eudorianus may also reduce polysulfides, thiosulfate, sulfur and/or selenite, and the likely acidophile, Hestiella, may reduce nitrate and/or perchlorate. Based on phylogenomic evidence, we also propose the family Acidilobaceae be amended to include Caldisphaera, Aeropyrum, Thermodiscus and Stetteria and the novel genera described here.
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Affiliation(s)
- Emily St John
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA.
| | - Anna-Louise Reysenbach
- Center for Life in Extreme Environments, Portland State University, Portland, OR 97201, USA.
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Li J, Luo J, Li M, Wang C, Hu S, Lu K, Wang G. Splendidivirga corallicola gen. nov., sp. nov. and Agaribacillus aureus gen. nov., sp. nov., two bacteria isolated from coral Porites lutea, and proposal of Splendidivirgaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38739684 DOI: 10.1099/ijsem.0.006376] [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: 05/16/2024] Open
Abstract
The Bacteroidota is one of the dominant bacterial phyla in corals. However, the exact taxa of those coral bacteria under the Bacteroidota are still unclear. Two aerobic, Gram-stain-negative, non-motile rods, designated strains BMA10T and BMA12T, were isolated from stony coral Porites lutea collected from Weizhou Island, PR China. Global alignment of 16S rRNA gene sequences indicated that both strains are closest to species of Fulvivirga with the highest identities being lower than 93 %, and the similarity value between these two strains was 92.3 %. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that these two strains form an monophylogenetic lineage alongside the families Fulvivirgaceae, Reichenbachiellaceae, Roseivirgaceae, Marivirgaceae, Cyclobacteriaceae, and Cesiribacteraceae in the order Cytophagales, phylum Bacteroidota. The genomic DNA G+C contents of BMA10T and BMA12T were 38.4 and 41.9 mol%, respectively. The major polar lipids of BMA10T were phosphatidylethanolamine, unidentified aminophospholipid, four unidentified aminolipids, and five unidentified lipids. While those of BMA12T were phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids. The major cellular fatty acids detected in both isolates were iso-C15 : 0 and C16 : 1 ω5c. Carbohydrate-active enzyme analysis indicated these two strains may utilize coral mucus or chitin. Based on above characteristics, these two strains are suggested to represent two new species in two new genera of a new family in the order Cytophagales, for which the name Splendidivirga corallicola gen. nov., sp. nov., Agaribacillus aureus gen. nov., sp. nov. and Splendidivirgaceae fam. nov. are proposed. The type strain of S. corallicola is BMA10T (=MCCC 1K08300T=KCTC 102045T), and that for A. aureus is BMA12T (=MCCC 1K08309T=KCTC 102046T).
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Affiliation(s)
- Jin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Jixin Luo
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Mi Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Chenyan Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Siyu Hu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Kun Lu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
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Gong Y, Shang DD, Sun CL, Du ZJ, Chen GJ. Direct Degradation of Fresh and Dried Macroalgae by Agarivorans albus B2Z047. Mar Drugs 2024; 22:203. [PMID: 38786594 PMCID: PMC11122777 DOI: 10.3390/md22050203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Marine macroalgae are increasingly recognized for their significant biological and economic potential. The key to unlocking this potential lies in the efficient degradation of all carbohydrates from the macroalgae biomass. However, a variety of polysaccharides (alginate, cellulose, fucoidan, and laminarin), are difficult to degrade simultaneously in a short time. In this study, the brown alga Saccharina japonica was found to be rapidly and thoroughly degraded by the marine bacterium Agarivorans albus B2Z047. This strain harbors a broad spectrum of carbohydrate-active enzymes capable of degrading various polysaccharides, making it uniquely equipped to efficiently break down both fresh and dried kelp, achieving a hydrolysis rate of up to 52%. A transcriptomic analysis elucidated the presence of pivotal enzyme genes implicated in the degradation pathways of alginate, cellulose, fucoidan, and laminarin. This discovery highlights the bacterium's capability for the efficient and comprehensive conversion of kelp biomass, indicating its significant potential in biotechnological applications for macroalgae resource utilization.
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Affiliation(s)
- Ya Gong
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai 264209, China
| | - Dan-Dan Shang
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
| | - Cheng-Lin Sun
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai 264209, China
| | - Guan-Jun Chen
- Marine College, Shandong University, Weihai 264209, China; (Y.G.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China
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Nakamura S, Kurata R, Miyazaki T. Structural insights into α-(1→6)-linkage preference of GH97 glucodextranase from Flavobacterium johnsoniae. FEBS J 2024. [PMID: 38661728 DOI: 10.1111/febs.17139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/07/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Glycoside hydrolase family 97 (GH97) comprises enzymes like anomer-inverting α-glucoside hydrolases (i.e., glucoamylase) and anomer-retaining α-galactosidases. In a soil bacterium, Flavobacterium johnsoniae, we previously identified a GH97 enzyme (FjGH97A) within the branched dextran utilization locus. It functions as an α-glucoside hydrolase, targeting α-(1→6)-glucosidic linkages in dextran and isomaltooligosaccharides (i.e., glucodextranase). FjGH97A exhibits a preference for α-(1→6)-glucoside linkages over α-(1→4)-linkages, while Bacteroides thetaiotaomicron glucoamylase SusB (with 69% sequence identity), which is involved in the starch utilization system, exhibits the highest specificity for α-(1→4)-glucosidic linkages. Here, we examined the crystal structures of FjGH97A in complexes with glucose, panose, or isomaltotriose, and analyzed the substrate preferences of its mutants to identify the amino acid residues that determine the substrate specificity for α-(1→4)- and α-(1→6)-glucosidic linkages. The overall structure of FjGH97A resembles other GH97 enzymes, with conserved catalytic residues similar to anomer-inverting GH97 enzymes. A comparison of active sites between FjGH97A and SusB revealed differences in amino acid residues at subsites +1 and +2 (specifically Ala195 and Ile378 in FjGH97A). Among the three mutants (A195S, I378F, and A195S-I378F), A195S and A195S-I378F exhibited increased activity toward α-(1→4)-glucoside bonds compared to α-(1→6)-glucoside bonds. This suggests that Ala195, located on the Gly184-Thr203 loop (named loop-N) conserved within the GH97 subgroup, including FjGH97A and SusB, holds significance in determining linkage specificity. The conservation of alanine in the active site of the GH97 enzymes, within the same gene cluster as the putative dextranase, indicates its crucial role in determining the specificity for α-(1→6)-glucoside linkage.
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Affiliation(s)
- Shuntaro Nakamura
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Japan
| | - Rikuya Kurata
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Japan
| | - Takatsugu Miyazaki
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Japan
- Department of Agriculture, Graduate School of Integrated Science and Technology, Shizuoka University, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Japan
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Gajda Ł, Daszkowska-Golec A, Świątek P. Trophic Position of the White Worm ( Enchytraeus albidus) in the Context of Digestive Enzyme Genes Revealed by Transcriptomics Analysis. Int J Mol Sci 2024; 25:4685. [PMID: 38731903 PMCID: PMC11083476 DOI: 10.3390/ijms25094685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/20/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
To assess the impact of Enchytraeidae (potworms) on the functioning of the decomposer system, knowledge of the feeding preferences of enchytraeid species is required. Different food preferences can be explained by variations in enzymatic activities among different enchytraeid species, as there are no significant differences in the morphology or anatomy of their alimentary tracts. However, it is crucial to distinguish between the contribution of microbial enzymes and the animal's digestive capacity. Here, we computationally analyzed the endogenous digestive enzyme genes in Enchytraeus albidus. The analysis was based on RNA-Seq of COI-monohaplotype culture (PL-A strain) specimens, utilizing transcriptome profiling to determine the trophic position of the species. We also corroborated the results obtained using transcriptomics data from genetically heterogeneous freeze-tolerant strains. Our results revealed that E. albidus expresses a wide range of glycosidases, including GH9 cellulases and a specific digestive SH3b-domain-containing i-type lysozyme, previously described in the earthworm Eisenia andrei. Therefore, E. albidus combines traits of both primary decomposers (primary saprophytophages) and secondary decomposers (sapro-microphytophages/microbivores) and can be defined as an intermediate decomposer. Based on assemblies of publicly available RNA-Seq reads, we found close homologs for these cellulases and i-type lysozymes in various clitellate taxa, including Crassiclitellata and Enchytraeidae.
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Affiliation(s)
| | | | - Piotr Świątek
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, 9 Bankowa St., 40-007 Katowice, Poland; (Ł.G.); (A.D.-G.)
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40
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Xu Y, Liang X, Hyun CG. Isolation, Characterization, Genome Annotation, and Evaluation of Hyaluronidase Inhibitory Activity in Secondary Metabolites of Brevibacillus sp. JNUCC 41: A Comprehensive Analysis through Molecular Docking and Molecular Dynamics Simulation. Int J Mol Sci 2024; 25:4611. [PMID: 38731830 PMCID: PMC11083829 DOI: 10.3390/ijms25094611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Brevibacillus sp. JNUCC 41, characterized as a plant-growth-promoting rhizobacterium (PGPR), actively participates in lipid metabolism and biocontrol based on gene analysis. This study aimed to investigate the crucial secondary metabolites in biological metabolism; fermentation, extraction, and isolation were performed, revealing that methyl indole-3-acetate showed the best hyaluronidase (HAase) inhibitory activity (IC50: 343.9 μM). Molecular docking results further revealed that the compound forms hydrogen bonds with the residues Tyr-75 and Tyr-247 of HAase (binding energy: -6.4 kcal/mol). Molecular dynamics (MD) simulations demonstrated that the compound predominantly binds to HAase via hydrogen bonding (MM-PBSA binding energy: -24.9 kcal/mol) and exhibits good stability. The residues Tyr-247 and Tyr-202, pivotal for binding in docking, were also confirmed via MD simulations. This study suggests that methyl indole-3-acetate holds potential applications in anti-inflammatory and anti-aging treatments.
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Affiliation(s)
| | | | - Chang-Gu Hyun
- Department of Beauty and Cosmetology, Jeju Inside Agency and Cosmetic Science Center, Jeju National University, Jeju 63243, Republic of Korea; (Y.X.); (X.L.)
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41
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Knobloch S, Skirnisdóttir S, Dubois M, Mayolle L, Kolypczuk L, Leroi F, Leeper A, Passerini D, Marteinsson VÞ. The gut microbiome of farmed Arctic char ( Salvelinus alpinus) is shaped by feeding stage and nutrient presence. FEMS MICROBES 2024; 5:xtae011. [PMID: 38745980 PMCID: PMC11092275 DOI: 10.1093/femsmc/xtae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/06/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
The gut microbiome plays an important role in maintaining health and productivity of farmed fish. However, the functional role of most gut microorganisms remains unknown. Identifying the stable members of the gut microbiota and understanding their functional roles could aid in the selection of positive traits or act as a proxy for fish health in aquaculture. Here, we analyse the gut microbial community of farmed juvenile Arctic char (Salvelinus alpinus) and reconstruct the metabolic potential of its main symbionts. The gut microbiota of Arctic char undergoes a succession in community composition during the first weeks post-hatch, with a decrease in Shannon diversity and the establishment of three dominant bacterial taxa. The genome of the most abundant bacterium, a Mycoplasma sp., shows adaptation to rapid growth in the nutrient-rich gut environment. The second most abundant taxon, a Brevinema sp., has versatile metabolic potential, including genes involved in host mucin degradation and utilization. However, during periods of absent gut content, a Ruminococcaceae bacterium becomes dominant, possibly outgrowing all other bacteria through the production of secondary metabolites involved in quorum sensing and cross-inhibition while benefiting the host through short-chain fatty acid production. Whereas Mycoplasma is often present as a symbiont in farmed salmonids, we show that the Ruminococcaceae species is also detected in wild Arctic char, suggesting a close evolutionary relationship between the host and this symbiotic bacterium.
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Affiliation(s)
- Stephen Knobloch
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Food Technology, University of Applied Sciences Fulda, Leipziger Strasse 123, 36037 Fulda, Germany
| | | | - Marianne Dubois
- ESBS/University of Strasbourg, 300 Bd Sébastien Brant, 67085 Strasbourg, France
| | - Lucie Mayolle
- University of Technology of Compiègne, Rue Roger Couttolenc, 60203 Compiègne, France
| | - Laetitia Kolypczuk
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Françoise Leroi
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Alexandra Leeper
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Arboretveien 6, 1430 Ås, Norway
- Iceland Ocean Cluster, Department of Research and Innovation, Grandagarður 16, 101 Reykjavík, Iceland
| | - Delphine Passerini
- Ifremer, MASAE Microbiologie Aliment Santé Environnement, BP 21105, F-44000 Nantes, France
| | - Viggó Þ Marteinsson
- Matís ohf., Microbiology Research Group, Vínlandsleið 12, 113 Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Sæmundargata 2, 101 Reykjavik, Iceland
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Salas-Veizaga DM, Rocabado-Villegas LR, Linares-Pastén JA, Gudmundsdottir EE, Hreggvidsson GO, Álvarez-Aliaga MT, Adlercreutz P, Nordberg Karlsson E. A novel glycoside hydrolase 43-like enzyme from Clostridium boliviensis is an endo-xylanase and a candidate for xylooligosaccharide production from different xylan substrates. Appl Environ Microbiol 2024; 90:e0222323. [PMID: 38497645 PMCID: PMC11022575 DOI: 10.1128/aem.02223-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/09/2024] [Indexed: 03/19/2024] Open
Abstract
An uncharacterized gene encoding a glycoside hydrolase family 43-like enzyme from Clostridium boliviensis strain E-1 was identified from genomic sequence data, and the encoded enzyme, CbE1Xyn43-l, was produced in Escherichia coli. CbE1Xyn43-l (52.9 kDa) is a two-domain endo-β-xylanase consisting of a C-terminal CBM6 and a GH43-like catalytic domain. The positions of the catalytic dyad conserved in GH43, the catalytic base (Asp74), and proton donor (Glu240) were identified in alignments including GH43-enzymes of known 3D-structure from different subfamilies. CbE1Xyn43-l is active at pH 7.0-9.0, with optimum temperature at 65°C, and a more than 7 days' half-life in irreversible deactivation studies at this temperature. The enzyme hydrolyzed birchwood xylan, quinoa stalks glucuronoarabinoxylan, and wheat arabinoxylan with xylotriose and xylotetraose as major hydrolysis products. CbE1Xyn43-l also released xylobiose from pNPX2 with low turnover (kcat of 0.044 s-1) but was inactive on pNPX, showing that a degree of polymerization of three (DP3) was the smallest hydrolyzable substrate. Divalent ions affected the specific activity on xylan substrates, which dependent on the ion could be increased or decreased. In conclusion, CbE1Xyn43-l from C. boliviensis strain E-1 is the first characterized member of a large group of homologous hypothetical proteins annotated as GH43-like and is a thermostable endo-xylanase, producing xylooligosaccharides of high DP (xylotriose and xylotetraose) producer. IMPORTANCE The genome of Clostridium boliviensis strain E-1 encodes a number of hypothetical enzymes, annotated as glycoside hydrolase-like but not classified in the Carbohydrate Active Enzyme Database (CAZy). A novel thermostable GH43-like enzyme is here characterized as an endo-β-xylanase of interest in the production of prebiotic xylooligosaccharides (XOs) from different xylan sources. CbE1Xyn43-l is a two-domain enzyme composed of a catalytic GH43-l domain and a CBM6 domain, producing xylotriose as main XO product. The enzyme has homologs in many related Clostridium strains which may indicate a similar function and be a previously unknown type of endo-xylanase in this evolutionary lineage of microorganisms.
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Affiliation(s)
- Daniel Martin Salas-Veizaga
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
- Instituto de Investigaciones Fármaco Bioquímicas, Universidad Mayor de San Andrés, La Paz, Bolivia
| | | | | | | | | | | | - Patrick Adlercreutz
- Division of Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
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Kalenborn S, Zühlke D, Riedel K, Amann RI, Harder J. Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72. FEMS Microbiol Ecol 2024; 100:fiae045. [PMID: 38569650 PMCID: PMC11036162 DOI: 10.1093/femsec/fiae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024] Open
Abstract
Arabinose and galactose are major, rapidly metabolized components of marine particulate and dissolved organic matter. In this study, we observed for the first time large microbiomes for the degradation of arabinogalactan and report a detailed investigation of arabinogalactan utilization by the flavobacterium Maribacter sp. MAR_2009_72. Cellular extracts hydrolysed arabinogalactan in vitro. Comparative proteomic analyses of cells grown on arabinogalactan, arabinose, galactose, and glucose revealed the expression of specific proteins in the presence of arabinogalactan, mainly glycoside hydrolases (GH). Extracellular glycan hydrolysis involved five alpha-l-arabinofuranosidases affiliating with glycoside hydrolase families 43 and 51, four unsaturated rhamnogalacturonylhydrolases (GH105) and a protein with a glycoside hydrolase family-like domain. We detected expression of three induced TonB-dependent SusC/D transporter systems, one SusC, and nine glycoside hydrolases with a predicted periplasmatic location. These are affiliated with the families GH3, GH10, GH29, GH31, GH67, GH78, and GH115. The genes are located outside of and within canonical polysaccharide utilization loci classified as specific for arabinogalactan, for galactose-containing glycans, and for arabinose-containing glycans. The breadth of enzymatic functions expressed in Maribacter sp. MAR_2009_72 as response to arabinogalactan from the terrestrial plant larch suggests that Flavobacteriia are main catalysts of the rapid turnover of arabinogalactans in the marine environment.
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Affiliation(s)
- Saskia Kalenborn
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Daniela Zühlke
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, D-17489 Greifswald, Germany
| | - Rudolf I Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
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Cohen AB, Cai G, Price DC, Molnar TJ, Zhang N, Hillman BI. The massive 340 megabase genome of Anisogramma anomala, a biotrophic ascomycete that causes eastern filbert blight of hazelnut. BMC Genomics 2024; 25:347. [PMID: 38580927 PMCID: PMC10998396 DOI: 10.1186/s12864-024-10198-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The ascomycete fungus Anisogramma anomala causes Eastern Filbert Blight (EFB) on hazelnut (Corylus spp.) trees. It is a minor disease on its native host, the American hazelnut (C. americana), but is highly destructive on the commercially important European hazelnut (C. avellana). In North America, EFB has historically limited commercial production of hazelnut to west of the Rocky Mountains. A. anomala is an obligately biotrophic fungus that has not been grown in continuous culture, rendering its study challenging. There is a 15-month latency before symptoms appear on infected hazelnut trees, and only a sexual reproductive stage has been observed. Here we report the sequencing, annotation, and characterization of its genome. RESULTS The genome of A. anomala was assembled into 108 scaffolds totaling 342,498,352 nt with a GC content of 34.46%. Scaffold N50 was 33.3 Mb and L50 was 5. Nineteen scaffolds with lengths over 1 Mb constituted 99% of the assembly. Telomere sequences were identified on both ends of two scaffolds and on one end of another 10 scaffolds. Flow cytometry estimated the genome size of A. anomala at 370 Mb. The genome exhibits two-speed evolution, with 93% of the assembly as AT-rich regions (32.9% GC) and the other 7% as GC-rich (57.1% GC). The AT-rich regions consist predominantly of repeats with low gene content, while 90% of predicted protein coding genes were identified in GC-rich regions. Copia-like retrotransposons accounted for more than half of the genome. Evidence of repeat-induced point mutation (RIP) was identified throughout the AT-rich regions, and two copies of the rid gene and one of dim-2, the key genes in the RIP mutation pathway, were identified in the genome. Consistent with its homothallic sexual reproduction cycle, both MAT1-1 and MAT1-2 idiomorphs were found. We identified a large suite of genes likely involved in pathogenicity, including 614 carbohydrate active enzymes, 762 secreted proteins and 165 effectors. CONCLUSIONS This study reveals the genomic structure, composition, and putative gene function of the important pathogen A. anomala. It provides insight into the molecular basis of the pathogen's life cycle and a solid foundation for studying EFB.
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Affiliation(s)
- Alanna B Cohen
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Guohong Cai
- Crop Production and Pest Control Research Unit, USDA-ARS, West Lafayette, IN, 47907, USA.
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Dana C Price
- Department of Entomology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Center for Vector Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Thomas J Molnar
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Ning Zhang
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
- Department of Biochemistry and Microbiology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Bradley I Hillman
- Department of Plant Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
- Graduate Program in Microbial Biology, Rutgers The State University of New Jersey, New Brunswick, NJ, 08901, USA.
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Luo J, Li J, Wang C, Li M, Hu S, Lu K, Wang G. Rubellicoccus peritrichatus gen. nov., sp. nov., isolated from crustose coralline algae in a coral aquarium. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568201 DOI: 10.1099/ijsem.0.006325] [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: 04/05/2024] Open
Abstract
A Gram-stain-negative, motile, aerobic, non-spore-forming coccus, designated strain CR14T, was isolated from crustose coralline algae. Cells grew at 20-30 °C (optimum, 25 °C), at pH 6-9 (optimum, pH 7.6) and with NaCl concentrations of 0.5-9 % (w/v; optimum, 2-4 %). Global alignment based on 16S rRNA gene sequences indicated strain CR14T is closest to Ruficoccus amylovorans JCM 31066T with an identity of 92 %. The average nucleotide identity and average amino acid identity values between CR14T and R. amylovorans JCM 31066T were 68.4 and 59.9 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CR14T forms an independent branch within the family Cerasicoccaeae, which was consistent with the phylogenomic results. The sole isoprenoid quinone was MK-7. The major fatty acids were C14 : 0, C18 : 1 ω9c, C19 : 0 cyc 9,10 DMA, C16 : 0, and C18 : 2 ω6c. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The genome DNA G+C content was 48.7 mol%. Based on morphological, physiological and chemotaxonomic characteristics, strain CR14T is suggested to represent a novel species in a new genus, for which the name Rubellicoccus peritrichatus gen. nov., sp. nov. is proposed. The type strain is CR14T (=MCCC 1K03845T=KCTC 72139T).
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Affiliation(s)
- Jixin Luo
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Jin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Chenyan Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Mi Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Siyu Hu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Kun Lu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
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Lick S, Wibberg D, Busche T, Blom J, Grimmler C, Goesmann A, Kalinowski J. Pseudomonas kulmbachensis sp. nov. and Pseudomonas paraveronii sp. nov., originating from chilled beef and chicken breast. Int J Syst Evol Microbiol 2024; 74. [PMID: 38587505 DOI: 10.1099/ijsem.0.006293] [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: 04/09/2024] Open
Abstract
By investigating wet and dry age-related ripening of beef, Pseudomonas strains V3/3/4/13T and V3/K/3/5T were isolated. Strain V3/3/4/13T exhibited more than 99 % 16S rRNA gene-based similarity to Pseudomonas fragi and other members of this group, while isolate V3/K/3/5T was very close to Pseudomonas veronii and a number of relatives within the Pseudomonas fluorescens group. Additional comparisons of complete rpoB sequences and draft genomes allowed us to place isolate V3/3/4/13T close to Pseudomonas deceptionensis DSM 26521T. In the case of V3/K/3/5T the closest relative was P. veronii DSM 11331T. Average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values calculated from the draft genomes of V3/3/4/13T and P. deceptionensis DSM 26521T were 88.5 and 39.8 %, respectively. For V3/K/3/5T and its closest relative P. veronii DSM 11331T, the ANIb value was 95.1 % and the dDDH value was 60.7 %. The DNA G+C contents of V3/3/4/13T and V3/K/3/5T were 57.4 and 60.8 mol%, respectively. Predominant fatty acids were C16 : 0, C18 : 1 ω7c, C17 : 0 cyclo and summed feature C16 : 1 ω7ct/C15 : 0 iso 2OH. The main respiratory quinones were Q9, with minor proportions of Q8 and, in the case of V3/K/3/5T, additional Q10. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and, in the case of V3/K/3/5T, additional phosphatidylcholine. Based on the combined data, isolates V3/3/4/13T and V3/K/3/5T should be considered as representatives of two novel Pseudomonas species. The type strain of the newly proposed Pseudomonas kulmbachensis sp. nov. is V3/3/4/13T (=DSM 113654T=LMG 32520T), a second strain belonging to the same species is FLM 004-28 (=DSM 113604=LMG 32521); the type strain for the newly proposed Pseudomonas paraveronii sp. nov. is V3/K/3/5T (=DSM 113573T=LMG 32518T) with a second isolate FLM 11 (=DSM 113572=LMG 32519).
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Affiliation(s)
- Sonja Lick
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- ELIXIR DE Administration Office, Institute of Bio- and Geosciences IBG-5, Forschungszentrum Jülich GmbH - Branch office Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
- Medical School East Westphalia-Lippe, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Christina Grimmler
- Max Rubner-Institut, Federal Research Institute for Nutrition and Food, Department of Safety and Quality of Meat, E.-C.-Baumann Straße 20, D-95326 Kulmbach, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Gießen, Ludwigsstraße 23, D-35392 Gießen, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, Universitätsstraße 27, D-33615 Bielefeld, Germany
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Wang ML, Fu GY, Xu XW. Flagellimonas baculiformis sp. nov. and Flagellimonas crocea sp. nov., isolated from surface seawater of the Pacific Ocean. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568198 DOI: 10.1099/ijsem.0.006316] [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: 04/05/2024] Open
Abstract
Two Gram-negative, non-spore-forming, non-motile, non-flagellated bacteria, designated strains D6T and DH64T, were isolated from surface water of the Pacific Ocean. For strain D6T, growth occurred at 10-40 °C, pH 5.5-9.0 and in the presence of 0-8.0 % NaCl (w/v). For strain DH64T, growth occurred at 10-40 °C, pH 5.5-8.5 and in the presence of 0.5-8.0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains D6T and DH64T both belonged to the genera Flagellimonas, with the highest sequence identities to Flagellimonas taeanensis JCM 17757T (98.2 %) and Flagellimonas marinaquae JCM 11811T (98.6 %), respectively. The 16S rRNA gene sequence identity between strains D6T and DH64T was 95.9 %. The average amino acid identity and digital DNA-DNA hybridization values between the two strains and the nearest phylogenetic neighbours were 66.7-93.3 % and 16.1-38.5 %, respectively. The major respiratory quinone of both strains was menaquinone-6. The major polar lipid was phosphatidylethanolamine. The major fatty acids were identified similarly as iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH. The genomic G+C contents of strains D6T and DH64T were determined to be 45.5 and 42.6 mol%, respectively. The combined genotypic and phenotypic data show that the strains represent two novel species within genera Flagellimonas, for which the names Flagellimonas baculiformis sp. nov. and Flagellimonas crocea sp. nov. are proposed, with type strains D6T (=MCCC M28982T=KCTC 92604T) and DH64T (=MCCC M28986T=KCTC 92975T).
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Affiliation(s)
- Ming-Lei Wang
- Ocean College, Zhejiang University, Zhoushan 316000, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 316021, PR China
| | - Ge-Yi Fu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 316021, PR China
| | - Xue-Wei Xu
- Ocean College, Zhejiang University, Zhoushan 316000, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 316021, PR China
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Sawada H, Someya N, Morohoshi T, Ono M, Satou M. Pectobacterium araliae sp. nov., a pathogen causing bacterial soft rot of Japanese angelica tree in Japan. Int J Syst Evol Microbiol 2024; 74. [PMID: 38625720 DOI: 10.1099/ijsem.0.006326] [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: 04/17/2024] Open
Abstract
Phytopathogenic bacteria (MAFF 302110T and MAFF 302107) were isolated from lesions on Japanese angelica trees affected by bacterial soft rot in Yamanashi Prefecture, Japan. The strains were Gram-reaction-negative, facultatively anaerobic, motile with peritrichous flagella, rod-shaped, and non-spore-forming. The genomic DNA G+C content was 51.1 mol % and the predominant cellular fatty acids included summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0, summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 2 (comprising any combination of C12 : 0 aldehyde, an unknown fatty acid with an equivalent chain length of 10.928, C16 : 1 iso I, and C14 : 0 3OH), and C12 : 0. Phylogenetic analyses based on 16S rRNA and gyrB gene sequences, along with phylogenomic analysis utilizing whole-genome sequences, consistently placed these strains within the genus Pectobacterium. However, their phylogenetic positions did not align with any known species within the genus. Comparative studies involving average nucleotide identity and digital DNA-DNA hybridization with the closely related species indicated values below the thresholds employed for the prokaryotic species delineation (95-96 % and 70 %, respectively), with the highest values observed for Pectobacterium polonicum DPMP315T (92.10 and 47.1 %, respectively). Phenotypic characteristics, cellular fatty acid composition, and a repertoire of secretion systems could differentiate the strains from their closest relatives. The phenotypic, chemotaxonomic, and genotypic data obtained in this study show that MAFF 302110T/MAFF 302107 represent a novel species of the genus Pectobacterium, for which we propose the name Pectobacterium araliae sp. nov., designating MAFF 302110T (=ICMP 25161T) as the type strain.
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Affiliation(s)
- Hiroyuki Sawada
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobutaka Someya
- Institute for Plant Protection, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Tomohiro Morohoshi
- Graduate School of Regional Development and Creativity, Utsunomiya University, 7-1-2 Yoto, Utsunomiya, Tochigi 321-8585, Japan
| | - Mitsuaki Ono
- Yamanashi Agritechnology Center (retired), 1100 Shimoimai, Kai, Yamanashi 400-0105, Japan
| | - Mamoru Satou
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Yang F, Jiang H, Ma K, Hegazy A, Wang X, Liang S, Chang G, Yu L, Tian B, Shi X. Genomic and phenotypic analyses reveal Paenibacillus polymyxa PJH16 is a potential biocontrol agent against cucumber fusarium wilt. Front Microbiol 2024; 15:1359263. [PMID: 38591040 PMCID: PMC11000672 DOI: 10.3389/fmicb.2024.1359263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/10/2024] Open
Abstract
In recent years, bacterial-based biocontrol agents (BCA) have become a new trend for the control of fungal diseases such as fusarium wilt that seriously threaten the yield and quality of cucumber, which are transmitted through infested soil and water. This study was set out with the aim of figuring the mechanism of the isolated rhizobacterial strain Paenibacillus polymyxa PJH16 in preventing Fusarium oxysporum f. sp. cucumerinum (Foc). Biocontrol and growth-promoting experiments revealed that bacterial strain causes effective inhibition of the fungal disease through a significant growth-promoting ability of plants, and had activities of β-1,3-glucanase, cellulase, amylase and protease. It could produce siderophore and indole-3-acetic acid, too. Using the high-throughput sequencing tool PacBio Sequel II system and the database annotation, the bacterial strain was identified as P. polymyxa PJH16 and contained genes encoding for presence of biofilm formation, antimicrobial peptides, siderophores and hydrolyases. From comparing data between the whole genome of P. polymyxa PJH16 with four closely related P. polymyxa strains, findings revealed markedly the subtle differences in their genome sequences and proposed new antifungal substances present in P. polymyxa PJH16. Therefore, P. polymyxa PJH16 could be utilized in bioengineering a microbial formulation for application as biocontrol agent and bio-stimulant, in the future.
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Affiliation(s)
- Fan Yang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Huayan Jiang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Kai Ma
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Abeer Hegazy
- National Water Research Center, Shubra El Kheima, Egypt
| | - Xin Wang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Shen Liang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Gaozheng Chang
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Liqin Yu
- Henan Natural Products Biotechnology Co., Ltd., Zhengzhou, China
| | - Baoming Tian
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Xuanjie Shi
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Graduate T&R Base of Zhengzhou University, Zhengzhou, Henan, China
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Roager L, Athena-Vasileiadi D, Gram L, Sonnenschein EC. Antagonistic activity of Phaeobacter piscinae against the emerging fish pathogen Vibrio crassostreae in aquaculture feed algae. Appl Environ Microbiol 2024; 90:e0143923. [PMID: 38349149 PMCID: PMC10952492 DOI: 10.1128/aem.01439-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/21/2023] [Indexed: 03/21/2024] Open
Abstract
Aquaculture provides a rich resource of high-quality protein; however, the production is challenged by emerging pathogens such as Vibrio crassostreae. While probiotic bacteria have been proposed as a sustainable solution to reduce pathogen load in aquaculture, their application requires a comprehensive assessment across the aquaculture food chain. The purpose of this study was to determine the antagonistic effect of the potential probiotic bacterium Phaeobacter piscinae against the emerging fish pathogen V. crassostreae in aquaculture feed algae that can be an entry point for pathogens in fish and shellfish aquaculture. P. piscinae strain S26 produces the antibacterial compound tropodithietic acid (TDA). In a plate-based assay, P. piscinae S26 was equally to more effective than the well-studied Phaeobacter inhibens DSM17395 in its inhibition of the fish pathogens Vibrio anguillarum 90-11-286 and V. crassostreae DMC-1. When co-cultured with the microalgae Tetraselmis suecica and Isochrysis galbana, P. piscinae S26 reduced the maximum cell density of V. crassostreae DMC-1 by 2 log and 3-4 log fold, respectively. A TDA-deficient mutant of P. piscinae S26 inhibited V. crassostreae DMC-1 to a lesser extent than the wild type, suggesting that the antagonistic effect involves TDA and other factors. TDA is the prime antagonistic agent of the inhibition of V. anguillarum 90-11-286. Comparative genomics of V. anguillarum 90-11-286 and V. crassostreae DMC-1 revealed that V. crassostreae DMC-1 carries a greater arsenal of antibiotic resistance genes potentially contributing to the reduced effect of TDA. In conclusion, P. piscinae S26 is a promising new candidate for inhibition of emerging pathogens such as V. crassostreae DMC-1 in algal feed systems and could contribute to a more sustainable aquaculture industry.IMPORTANCEThe globally important production of fish and shellfish in aquaculture is challenged by disease outbreaks caused by pathogens such as Vibrio crassostreae. These outbreaks not only lead to substantial economic loss and environmental damage, but treatment with antibiotics can also lead to antibiotic resistance affecting human health. Here, we evaluated the potential of probiotic bacteria, specifically the newly identified strain Phaeobacter piscinae S26, to counteract these threats in a sustainable manner. Through a systematic assessment of the antagonistic effect of P. piscinae S26 against V. crassostreae DMC-1, particularly within the context of algal feed systems, the study demonstrates the effectiveness of P. piscinae S26 as probiotic and thereby provides a strategic pathway for addressing disease outbreaks in aquaculture. This finding has the potential of significantly contributing to the long-term stability of the industry, highlighting the potential of probiotics as an efficient and environmentally conscious approach to safeguarding aquaculture productivity against the adverse impact of pathogens.
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Affiliation(s)
- Line Roager
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Eva C. Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
- Swansea University, College of Science and Engineering, Swansea, Wales, United Kingdom
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