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Zhang DF, He W, Shao Z, Ahmed I, Zhang Y, Li WJ, Zhao Z. Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 37970897 DOI: 10.1099/ijsem.0.006156] [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: 11/19/2023] Open
Abstract
The families Paracoccaceae and
Roseobacteraceae
comprise metabolically, phenotypically and genotypically diverse members, and their descriptions rely heavily on 16S rRNA gene analysis. Hundreds of genera have been reported within the two families and misclassifications have been a reoccurring problem, even when the taxonomies have been established based on genome-scale phylogenetic reconstructions. In this study, we conducted a comprehensive phylotaxonomic assessment of the families Paracoccaceae and
Roseobacteraceae
based on four ubiquitous gene sets, bac120 (120 genes in Bacteria), rhodo268 (268 genes in ‘
Rhodobacteraceae
’, defined in this study), rp1 (16 ribosomal protein genes in Prokaryote) and rp2 (23 ribosomal protein genes in Prokaryote), using two tree-inferring applications and two approaches (supermatrix and consensus). The results suggested that the four supermatrix trees based on bac120 and rhodo268 shared a high proportion of common nodes (>88.4 %) and the topology was reproducible among all the trees within most of the genera. The evolutionary distance (ED) analysis showed significant overlapping between the intergeneric and intrageneric comparisons, implying that the proposal of some genera seemed to be unnecessary. In addition, the bac120 gene set and the FastTree program were found to be the most cost-effective way to conduct phylogenomic analysis of the families Paracoccaceae and
Roseobacteraceae
. An ED threshold of 0.21–0.23 based on either bac120 or rhodo268 was proposed as one standard for later genus delimitation in these families. A comprehensive phylogenetic framework is presented in this study and the proposed genus definition will help to establish a more reasonable taxonomy in the families Paracoccaceae and
Roseobacteraceae
.
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Affiliation(s)
- Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
| | - Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
| | - Zongze Shao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Iftikhar Ahmed
- National Agricultural Research Centre (NARC), Land Resources Research Institute (LRRI), National Culture Collection of Pakistan (NCCP), Islamabad, Pakistan
| | - Yuqin Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, PR China
| | - Wen-Jun Li
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
- State Key Laboratory of Biocontrol, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Zhe Zhao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing, PR China
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Román-Camacho JJ, García-García I, Santos-Dueñas IM, García-Martínez T, Mauricio JC. Latest Trends in Industrial Vinegar Production and the Role of Acetic Acid Bacteria: Classification, Metabolism, and Applications-A Comprehensive Review. Foods 2023; 12:3705. [PMID: 37835358 PMCID: PMC10572879 DOI: 10.3390/foods12193705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Vinegar is one of the most appreciated fermented foods in European and Asian countries. In industry, its elaboration depends on numerous factors, including the nature of starter culture and raw material, as well as the production system and operational conditions. Furthermore, vinegar is obtained by the action of acetic acid bacteria (AAB) on an alcoholic medium in which ethanol is transformed into acetic acid. Besides the highlighted oxidative metabolism of AAB, their versatility and metabolic adaptability make them a taxonomic group with several biotechnological uses. Due to new and rapid advances in this field, this review attempts to approach the current state of knowledge by firstly discussing fundamental aspects related to industrial vinegar production and then exploring aspects related to AAB: classification, metabolism, and applications. Emphasis has been placed on an exhaustive taxonomic review considering the progressive increase in the number of new AAB species and genera, especially those with recognized biotechnological potential.
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Affiliation(s)
- Juan J. Román-Camacho
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Isidoro García-García
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Inés M. Santos-Dueñas
- Department of Inorganic Chemistry and Chemical Engineering, Agrifood Campus of International Excellence ceiA3, Nano Chemistry Institute (IUNAN), University of Córdoba, 14014 Córdoba, Spain;
| | - Teresa García-Martínez
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
| | - Juan C. Mauricio
- Department of Agricultural Chemistry, Edaphology and Microbiology, Agrifood Campus of International Excellence ceiA3, University of Córdoba, 14014 Córdoba, Spain; (J.J.R.-C.); (T.G.-M.); (J.C.M.)
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Kazemzadeh K, Pelosi L, Chenal C, Chobert SC, Hajj Chehade M, Jullien M, Flandrin L, Schmitt W, He Q, Bouvet E, Jarzynka M, Varoquaux N, Junier I, Pierrel F, Abby SS. Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution. Mol Biol Evol 2023; 40:msad219. [PMID: 37788637 PMCID: PMC10597321 DOI: 10.1093/molbev/msad219] [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: 05/26/2023] [Revised: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/05/2023] Open
Abstract
The availability of an ever-increasing diversity of prokaryotic genomes and metagenomes represents a major opportunity to understand and decipher the mechanisms behind the functional diversification of microbial biosynthetic pathways. However, it remains unclear to what extent a pathway producing a specific molecule from a specific precursor can diversify. In this study, we focus on the biosynthesis of ubiquinone (UQ), a crucial coenzyme that is central to the bioenergetics and to the functioning of a wide variety of enzymes in Eukarya and Pseudomonadota (a subgroup of the formerly named Proteobacteria). UQ biosynthesis involves three hydroxylation reactions on contiguous carbon atoms. We and others have previously shown that these reactions are catalyzed by different sets of UQ-hydroxylases that belong either to the iron-dependent Coq7 family or to the more widespread flavin monooxygenase (FMO) family. Here, we combine an experimental approach with comparative genomics and phylogenetics to reveal how UQ-hydroxylases evolved different selectivities within the constrained framework of the UQ pathway. It is shown that the UQ-FMOs diversified via at least three duplication events associated with two cases of neofunctionalization and one case of subfunctionalization, leading to six subfamilies with distinct hydroxylation selectivity. We also demonstrate multiple transfers of the UbiM enzyme and the convergent evolution of UQ-FMOs toward the same function, which resulted in two independent losses of the Coq7 ancestral enzyme. Diversification of this crucial biosynthetic pathway has therefore occurred via a combination of parallel evolution, gene duplications, transfers, and losses.
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Affiliation(s)
- Katayoun Kazemzadeh
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ludovic Pelosi
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Clothilde Chenal
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie-Carole Chobert
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Mahmoud Hajj Chehade
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Margaux Jullien
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Laura Flandrin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - William Schmitt
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Qiqi He
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Emma Bouvet
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Manon Jarzynka
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Nelle Varoquaux
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Ivan Junier
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Fabien Pierrel
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Sophie S Abby
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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54
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Vishnoi V, Hoedt EC, Gould T, Carroll G, Carroll R, Lott N, Pockney P, Smith SR, Keely S. A pilot study: intraoperative 16S rRNA sequencing versus culture in predicting colorectal incisional surgical site infection. ANZ J Surg 2023; 93:2464-2472. [PMID: 37025037 DOI: 10.1111/ans.18455] [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: 01/27/2023] [Revised: 03/21/2023] [Accepted: 03/25/2023] [Indexed: 04/08/2023]
Abstract
BACKGROUND Surgical Site Infection (SSI) of the abdominal incision is a dreaded complication following colorectal surgery. Identifying the intraoperative surgical site microbes may provide clarity in the pathogenesis of SSIs. Genomic sequencing has revolutionized the ability to identify microbes from clinical samples. Utilization of 16S rRNA amplicon sequencing to characterize the intraoperative surgical site may provide the critical information required to predict and prevent infection in colorectal surgery. METHODS This is a pilot, prospective observational study of 50 patients undergoing elective colorectal resection. At completion of surgery, prior to skin closure, swabs were taken from the subcutaneous tissue of the abdominal incision to investigate the microbial profile. Dual swabs were taken to compare standard culture technique and 16S rRNA sequencing to establish if a microbial profile was associated with postoperative SSI. RESULTS 8/50 patients developed an SSI, which was more likely in those undergoing open surgery (5/15 33.3% versus 3/35, 8.6%; P = 0.029). 16S rRNA amplicon sequencing was more sensitive in microbial detection compared to traditional culture. Both culture and 16S rRNA demonstrated contamination of the surgical site, predominantly with anaerobes. Culture was not statistically predictive of infection. 16S rRNA amplicon sequencing was not statistically predictive of infection, however, it demonstrated patients with an SSI had an increased biodiversity (not significant) and a greater relative abundance (not significant) of pathogens such as Bacteroidacaea and Enterobacteriaceae within the intraoperative site. CONCLUSIONS 16S rRNA amplicon sequencing has demonstrated a potential difference in the intraoperative microbial profile of those that develop an infection. These findings require validation through powered experiments to determine the overall clinical significance.
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Affiliation(s)
- Veral Vishnoi
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Emily C Hoedt
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Tiffany Gould
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Georgia Carroll
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Rosemary Carroll
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Natalie Lott
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Peter Pockney
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - Stephen R Smith
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- Department of Surgical Services, John Hunter Hospital, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
- Department of Surgical Services, Calvary Mater Hospital, Newcastle, New South Wales, Australia
| | - Simon Keely
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, New South Wales, Australia
- Hunter Medical Research Institute, Immune Health Program, Newcastle, New South Wales, Australia
- NHMRC Centre for Research Excellence in Digestive Health, University of Newcastle, Newcastle, New South Wales, Australia
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Fufina TY, Vasilieva LG. Role of hydrogen-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. Biophys Rev 2023; 15:921-937. [PMID: 37974998 PMCID: PMC10643783 DOI: 10.1007/s12551-023-01109-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/01/2023] [Indexed: 11/19/2023] Open
Abstract
For the last decades, significant progress has been made in studying the biological functions of H-bond networks in membrane proteins, proton transporters, receptors, and photosynthetic reaction centers. Increasing availability of the X-ray crystal and cryo-electron microscopy structures of photosynthetic complexes resolved with high atomic resolution provides a platform for their comparative analysis. It allows identifying structural factors that are ensuring the high quantum yield of the photochemical reactions and are responsible for the stability of the membrane complexes. The H-bond networks are known to be responsible for proton transport associated with electron transfer from the primary to the secondary quinone as well as in the processes of water oxidation in photosystem II. Participation of such networks in reactions proceeding on the periplasmic side of bacterial photosynthetic reaction centers is less studied. This review summarizes the current understanding of the role of H-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. It is discussed that the networks may be involved in providing close association with mobile electron carriers, in light-induced proton transport, in regulation of the redox properties of bacteriochlorophyll cofactors, and in stabilization of the membrane protein structure at the interface of membrane and soluble phases.
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Affiliation(s)
- T. Yu. Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
| | - L. G. Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
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Coe LSY, Fei C, Weston J, Amin SA. Phycobacter azelaicus gen. nov. sp. nov., a diatom symbiont isolated from the phycosphere of Asterionellopsis glacialis. Int J Syst Evol Microbiol 2023; 73. [PMID: 37889154 DOI: 10.1099/ijsem.0.006104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
A diatom-associated bacterium, designated as strain F10T, was isolated from a pure culture of the pennate diatom Asterionellopsis glacialis A3 and has since been used to characterize molecular mechanisms of symbiosis between phytoplankton and bacteria, including interactions using diatom-derived azelaic acid. Its origin from a hypersaline environment, combined with its capacity for quorum sensing, biofilm formation, and potential for dimethylsulfoniopropionate methylation/cleavage, suggest it is within the family Roseobacteraceae. Initial phylogenetic analysis of the 16S rRNA gene sequence placed this isolate within the Phaeobacter genus, but recent genomic and phylogenomic analyses show strain F10T is a separate lineage diverging from the genus Pseudophaeobacter. The genomic DNA G+C content is 60.0 mol%. The predominant respiratory quinone is Q-10. The major fatty acids are C18 : 1 ω7c and C16 : 0. Strain F10T also contains C10 : 03-OH and the furan-containing fatty acid 10,13-epoxy-11-methyl-octadecadienoate (9-(3-methyl-5-pentylfuran-2-yl)nonanoic acid). The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on genomic, phylogenomic, phenotypic and chemotaxonomic characterizations, strain F10T represents a novel genus and species with the proposed name, Phycobacter azelaicus gen. nov. sp. nov. The type strain is F10T (=NCMA B37T=NCIMB 15470T=NRIC 2002T).
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Affiliation(s)
- Lisa S Y Coe
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
| | - Cong Fei
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
| | - James Weston
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
- Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
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Romanenko L, Otstavnykh N, Tanaka N, Kurilenko V, Svetashev V, Tekutyeva L, Mikhailov V, Isaeva M. Characterization and Genomic Analysis of Fererhizobium litorale gen. nov., sp. nov., Isolated from the Sandy Sediments of the Sea of Japan Seashore. Microorganisms 2023; 11:2385. [PMID: 37894043 PMCID: PMC10609224 DOI: 10.3390/microorganisms11102385] [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: 08/15/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The taxonomic status of two gram-negative, whitish-pigmented motile bacteria KMM 9576T and KMM 9553 isolated from a sandy sediment sample from the Sea of Japan seashore was defined. Phylogenetic analysis revealed that strains KMM 9576T and KMM 9553 represent a distinct lineage within the family Rhizobiaceae, sharing 100% 16S rRNA sequence similarity and 99.5% average nucleotide identity (ANI) to each other. The strains showed the highest 16S rRNA sequence similarities of 97.4% to Sinorhizobium garamanticum LMG 24692T, 96.9% to Ensifer adhaerens NBRC 100388T, and 96.8% to Pararhizobium giardinii NBRC 107135T. The ANI values between strain KMM 9576T and Ensifer adhaerens NBRC 100388T, Sinorhizobium fredii USDA 205T, Pararhizobium giardinii NBRC 107135T, and Rhizobium leguminosarum NBRC 14778T were 79.9%, 79.6%, 79.4%, and 79.2%, respectively. The highest core-proteome average amino acid identity (cpAAI) values of 82.1% and 83.1% were estimated between strain KMM 9576T and Rhizobium leguminosarum NBRC 14778T and 'Rhizobium album' NS-104, respectively. The DNA GC contents were calculated from a genome sequence to be 61.5% (KMM 9576T) and 61.4% (KMM 9553). Both strains contained the major ubiquinone Q-10 and C18:1ω7c as the dominant fatty acid followed by 11-methyl C18:1ω7c and C19:0 cyclo, and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminophospholipid, and two unidentified phospholipids. Based on phylogenetic and phylogenomic analyses, and phenotypic characterization, strains KMM 9576T and KMM 9553 are concluded to represent a novel genus and species, for which the name Fererhizobium litorale gen. nov., sp. nov. is proposed. The type strain of the type species is strain KMM 9576T (=NRIC 0957T).
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Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Naoto Tanaka
- NODAI Culture Collection Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan;
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Vasily Svetashev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevskogo Street 17, Vladivostok 690041, Russia;
| | - Liudmila Tekutyeva
- ARNIKA, Territory of PDA Nadezhdinskaya, Centralnaya St. 42, Volno-Nadezhdinskoye, Primorsky krai, Vladivostok 692481, Russia;
| | - Valery Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
| | - Marina Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Prospect 100 Let Vladivostoku, 159, Vladivostok 690022, Russia; (N.O.); (V.K.); (V.M.)
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Wang N, Wang Y, Jin Y, Guo B, Cui H, Yang Y. Complete genome sequence of Brucella pseudintermedia ASAG-D25, isolated from the wheat ear. Microbiol Resour Announc 2023; 12:e0130022. [PMID: 37534895 PMCID: PMC10508100 DOI: 10.1128/mra.01300-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/16/2023] [Indexed: 08/04/2023] Open
Abstract
Brucella pseudintermedia ASAG-D25 was isolated from the wheat ear sample in Xuzhou City, Jiangsu Province, China. The complete genome sequence of B. pseudintermedia will provide an important resource for better understanding of the genetic features of the species within the family of Brucellaceae.
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Affiliation(s)
- Nanxi Wang
- Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Yang Wang
- Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Yi Jin
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
| | - Baoyuan Guo
- Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Hua Cui
- Academy of National Food and Strategic Reserves Administration, Beijing, China
| | - Yongtan Yang
- Academy of National Food and Strategic Reserves Administration, Beijing, China
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59
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Kretz J, Israel V, McIntosh M. Design-Build-Test of Synthetic Promoters for Inducible Gene Regulation in Alphaproteobacteria. ACS Synth Biol 2023; 12:2663-2675. [PMID: 37561940 DOI: 10.1021/acssynbio.3c00251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Inducible gene expression is useful for biotechnological applications and for studying gene regulation and function in bacteria. Many inducible systems that perform in model organisms such as the Gammaproteobacterium Escherichia coli do not perform well in other bacteria that are of biotechnological interest. Typical problems include weak or leaky expression. Here, we describe an invention named ACIT (Alphaproteobacteria chromosomally integrating transcription-control cassette) that is carried on a suicide plasmid to enable insertion into the chromosome of the host. ACIT consists of multiple DNA fragments specifically arranged in a cassette that allows tight transcription control over any gene or gene cluster of interest following homologous recombination. At the heart of the invention is the ability to modify or exchange parts, e.g., promoters, to suit particular bacteria and growth conditions, allowing for customized gene expression control. Furthermore, ACIT provides a basis for a design-build-test approach for controlling gene expression in less studied bacteria. We describe examples of its control over pigment and exopolysaccharide production, growth, cell form, and social behavior in various Alphaproteobacteria.
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Affiliation(s)
- Jonas Kretz
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Vera Israel
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
| | - Matthew McIntosh
- Institute of Microbiology and Molecular Biology, IFZ, Justus-Liebig-Universität, 35292 Giessen, Germany
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60
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Wang YH, Liu JC, Du YH, Xu JH, Du ZJ, Ye MQ. Psychromarinibacter sediminicola sp. nov., a novel moderately halophilic, metabolically diverse bacterium isolated from a solar saltern sediment, and comparison between members of family Roseobacteraceae. Arch Microbiol 2023; 205:331. [PMID: 37698663 DOI: 10.1007/s00203-023-03672-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/13/2023]
Abstract
Known for its species abundance and evolutionary status complexity, family Roseobacteraceae is an important subject of many studies on the discovery, identification, taxonomic status, and ecological properties of marine bacteria. This study compared and analyzed the phylogenetic, genomic, biochemical, and chemo taxonomical properties of seven species from three genera (Psychromarinibacter, Lutimaribacter, and Maritimibacter) of the family Roseobacteraceae. Moreover, a novel strain, named C21-152T was isolated from solar saltern sediment in Weihai, China. The values of 16S rRNA gene sequence similarity, the average nucleotide identity (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) between genomes of the novel strain and Psychromarinibacter halotolerans MCCC 1K03203T were 97.19, 78.49, 73.45, and 21.90%, respectively. Genome sequencing of strain C21-152T revealed a complete Sox enzyme system related to thiosulfate oxidization as well as a complete pathway for the final conversion of hydroxyproline to α-ketoglutarate. In addition, strain C21-152T was resistant to many antibiotics and had the ability to survive below 13% salinity. This strain had versatile survival strategies in saline environments including salt-in, compatible solute production and compatible solute transport. Some of its physiological features enriched and complemented the knowledge of the characteristics of the genus Psychromarinibacter. Optimum growth of strain C21-152T occurred at 37 ℃, with 5-6% (w/v) NaCl and at pH 7.5. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain C21-152T should represent a novel specie of the genus Psychromarinibacter, for which the name Psychromarinibacter sediminicola sp. nov. is proposed. The type strain is C21-152T (= MCCC 1H00808T = KCTC 92746T = SDUM1063002T).
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Affiliation(s)
- Yu-Hui Wang
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Jun-Cheng Liu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Yi-Heng Du
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Jin-Hao Xu
- SDU-ANU Joint Science College, Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, People's Republic of China
| | - Meng-Qi Ye
- Marine College, Shandong University, Weihai, Shandong, 264209, People's Republic of China.
- Shenzhen Research Institute of Shandong University, Shenzhen, 518057, Guangdong, People's Republic of China.
- Weihai Research Institute of Industrial Technology of Shandong University, Weihai, 264209, Shandong, People's Republic of China.
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61
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Lee HJ, Whang KS. Oryzibacter oryziterrae gen. nov., sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37737839 DOI: 10.1099/ijsem.0.006033] [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: 09/23/2023] Open
Abstract
A novel Gram-stain-negative, aerobic, motile and pleomorphic rod-shaped bacterial strain, designated COJ-58T, was isolated from rice paddy soil. Strain COJ-58T grew optimally at 20-30 °C, at pH 5.0-8.0 and with 0-1.0 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain COJ-58T forms a distinct lineage within the family Pleomorphomonadaceae, with highest similarity to Pleomorphomonas carboxyditropha SVCO-16T (95.9 %), Pleomorphomonas koreensis Y9T (95.8 %), Pleomorphomonas oryzae F-7T (95.7 %) and Pleomorphomonas diazotrophica R5-392T (95.6 %), respectively. The average nucleotide identity, digital DNA-DNA hybridization, average amino acid identity and percentage of conserved proteins values between the genomes of strain COJ-58T and its closely related taxa are ≤77.2 %, ≤21.6 %, ≤68.3 % and ≤61.3 %, respectively. The genome size of strain COJ-58T is 4.9 Mb and the genomic DNA G + C content is 63.7 mol%. The major fatty acids are C18 : 1 ω7c, C16 : 0 and summed feature 2 (C14 : 0 3-OH and/or iso-C16 : 1 I). The differential phenotypic and genotypic characteristics of strain COJ-58T indicate that it represents a novel genus and species, for which the name Oryzibacter oryziterrae gen. nov., sp. nov. is proposed, with strain COJ-58T (=KACC 22108T=JCM 34744T) as the type strain.
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Affiliation(s)
- Hyo-Jin Lee
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
| | - Kyung-Sook Whang
- Institute of Microbial Ecology & Resources, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
- Department of Microbial Biotechnology, Mokwon University, 88, Doanbuk-ro, Seo-gu, Daejeon, Republic of Korea
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Deshmukh UB, Oren A. Proposal of Thalassovita gen. nov. and Alloyangia gen. nov. as replacement names for the illegitimate prokaryotic generic names Thalassobius and Yangia, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37695726 DOI: 10.1099/ijsem.0.006025] [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: 09/13/2023] Open
Abstract
The prokaryotic generic names Thalassobius Arahal et al. 2005 and Yangia Dai et al. 2006 are illegitimate because they are later homonyms of the genus names Thalassobius Solier 1849 (Coleoptera) and Yangia Zheng 1997 (fossil Rodentia), respectively Principle two and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes]. We therefore propose the replacement generic names Thalassovita and Alloyangia, with type species Thalassovita gelatinovora and Alloyangia pacifica, respectively.
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Affiliation(s)
- Umakant Bhoopati Deshmukh
- Institution of Higher Learning, Research and Specialized Studies Centre, Department of Botany, Janata Mahavidyalaya, Chandrapur 442 401, Maharashtra, India
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 9190401, Israel
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Liu WL, Yang ZW, Guo DY, Deng QQ, Li JL, Wang PD, Chen SH, Liu L, Nie GX, Li WJ. Cereibacter flavus sp. nov., a novel member of the family Rhodobacteraceae isolated from seawater of the South China Sea and reclassification of Rhodobacter alkalitolerans as Cereibacter alkalitolerans comb. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37773605 DOI: 10.1099/ijsem.0.006051] [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: 10/01/2023] Open
Abstract
A Gram-stain-negative, aerobic, motile, ovoid-shaped and yellow-coloured strain, designated SYSU M79828T, was isolated from seawater collected from the South China Sea. Growth of this strain was observed at 4-37 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-6% NaCl (optimum, 3.0 %, w/v). The respiratory quinone was found to be Q-10. Major fatty acid constituents were C18 : 1 ω7c/C18 : 1 ω6c, C18 : 1 ω7c11-methyl and C18 : 0 (>5 % of total). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, two unidentified phospholipid, one unidentified lipid and an unidentified glycolipid. The genomic DNA G+C content was 64.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M79828T belonged to the genus Cereibacter and had the highest sequences similarity to 'Rhodobacter xinxiangensis' TJ48T (98.41 %). Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterizations, we consider that strain SYSU M79828T represents a novel species of the genus Cereibacter, for which the name Cereibacter flavus sp. nov. is proposed. The type strain is SYSU M79828T (=GDMCC 1.3803T=KCTC 92893T). In addition, according to the results of phylogenetic analysis and similar taxonomic characteristics, we propose that Rhodobacter alkalitolerans should be reclassified as Cereibacter alkalitolerans comb. nov.
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Affiliation(s)
- Wen-Li Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Zi-Wen Yang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Dan-Yuan Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Qi-Qi Deng
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Jia-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Pan-Deng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
| | - Sen-Hua Chen
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519000, PR China
| | - Guo-Xing Nie
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, PR China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, PR China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, PR China
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64
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Moreno E, Middlebrook EA, Altamirano-Silva P, Al Dahouk S, Araj GF, Arce-Gorvel V, Arenas-Gamboa Á, Ariza J, Barquero-Calvo E, Battelli G, Bertu WJ, Blasco JM, Bosilkovski M, Cadmus S, Caswell CC, Celli J, Chacón-Díaz C, Chaves-Olarte E, Comerci DJ, Conde-Álvarez R, Cook E, Cravero S, Dadar M, De Boelle X, De Massis F, Díaz R, Escobar GI, Fernández-Lago L, Ficht TA, Foster JT, Garin-Bastuji B, Godfroid J, Gorvel JP, Güler L, Erdenliğ-Gürbilek S, Gusi AM, Guzmán-Verri C, Hai J, Hernández-Mora G, Iriarte M, Jacob NR, Keriel A, Khames M, Köhler S, Letesson JJ, Loperena-Barber M, López-Goñi I, McGiven J, Melzer F, Mora-Cartin R, Moran-Gilad J, Muñoz PM, Neubauer H, O'Callaghan D, Ocholi R, Oñate Á, Pandey P, Pappas G, Pembroke JT, Roop M, Ruiz-Villalonos N, Ryan MP, Salcedo SP, Salvador-Bescós M, Sangari FJ, de Lima Santos R, Seimenis A, Splitter G, Suárez-Esquivel M, Tabbaa D, Trangoni MD, Tsolis RM, Vizcaíno N, Wareth G, Welburn SC, Whatmore A, Zúñiga-Ripa A, Moriyón I. If You're Not Confused, You're Not Paying Attention: Ochrobactrum Is Not Brucella. J Clin Microbiol 2023; 61:e0043823. [PMID: 37395662 PMCID: PMC10446859 DOI: 10.1128/jcm.00438-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.
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Affiliation(s)
- Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Earl A. Middlebrook
- Genomics and Bioanalytics, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Sascha Al Dahouk
- Department of Environmental Hygiene, German Environment Agency, Berlin, Germany
| | - George F. Araj
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Vilma Arce-Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, CNRS, INSERM, Marseille, France
| | - Ángela Arenas-Gamboa
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Javier Ariza
- Infectious Disease Department, Hospital Universitario de Bellvitge, Universidad de Barcelona, Barcelona, Spain
| | - Elías Barquero-Calvo
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Giorgio Battelli
- Department of Medical Veterinary Sciences, University of Bologna, Bologna, Italy
| | - Wilson J. Bertu
- Brucellosis Research Laboratory, Bacterial Research Division, National Veterinary Research Institute, Vom, Nigeria
| | - José María Blasco
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain
| | - Mile Bosilkovski
- University Hospital for Infectious Diseases and Febrile Conditions, Medical Faculty, Saints Cyril and Methodius University, Skopje, Republic of North Macedonia
| | - Simeon Cadmus
- Centre for Control and Prevention of Zoonoses, Faculty of Veterinary Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clayton C. Caswell
- Center for One Health Research, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia, USA
| | - Jean Celli
- Larner College of Medicine at the University of Vermont, Department of Microbiology and Molecular Genetics, Burlington, Vermont, USA
| | - Carlos Chacón-Díaz
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Diego J. Comerci
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Raquel Conde-Álvarez
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Elizabeth Cook
- International Livestock Research Institute, Nairobi, Kenya
| | - Silvio Cravero
- Centro de Investigación en Ciencias Veterinarias y Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Xavier De Boelle
- Research Unit in Biology of Microorganisms, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Fabrizio De Massis
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Teramo, Italy
| | - Ramón Díaz
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Gabriela I. Escobar
- Laboratorio de Brucelosis, Laboratorio Nacional de Referencia, INEI-ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Luis Fernández-Lago
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Thomas A. Ficht
- Texas A&M University, Veterinary Pathobiology, College Station, Texas, USA
| | - Jeffrey T. Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Bruno Garin-Bastuji
- French Agency for Food, Environmental, and Occupational Health and Safety, Maisons-Alfort, France
| | - Jacques Godfroid
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Jean-Pierre Gorvel
- Centre d'Immunologie de Marseille-Luminy, Aix-Marseille Université, CNRS, INSERM, Marseille, France
| | - Leyla Güler
- MG Veterinary Diagnostic Laboratory, Meram, Konya, Turkey
| | - Sevil Erdenliğ-Gürbilek
- Harran University, Faculty of Veterinary Medicine, Microbiology Department, Şanlıurfa, Şanlıurfa, Turkey
| | - Amayel M. Gusi
- Brucellosis Research Laboratory, Bacterial Research Division, National Veterinary Research Institute, Vom, Nigeria
| | - Caterina Guzmán-Verri
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Jiang Hai
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, People's Republic of China
| | - Gabriela Hernández-Mora
- Servicio Nacional de Salud Animal, Ministerio de Agricultura y Ganadería, Heredia, Costa Rica
| | - Maite Iriarte
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Nestor R. Jacob
- Hospital Argerich, Department of Infectious Diseases, Buenos Aires, Argentina
| | - Anne Keriel
- Centre National de Référence des Brucella, U1047, University of Montpellier/INSERM, CHU de Nîmes, Nimes, France
| | - Maamar Khames
- University of Medea, Faculty of Sciences, Department of Biology, Medea, Algeria
| | - Stephan Köhler
- Institut de Recherche en Infectiologie de Montpellier, CNRS, University of Montpellier, Montpellier, France
| | - Jean-Jacques Letesson
- Research Unit in Biology of Microorganisms, Namur Research Institute for Life Sciences, University of Namur, Namur, Belgium
| | - Maite Loperena-Barber
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ignacio López-Goñi
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - John McGiven
- WOAH Reference Laboratory for Brucellosis, Animal and Plant Health Agency, Weybridge, United Kingdom
- FAO Reference Centre for Brucellosis, Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Falk Melzer
- Friedrich Loeffler Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Ricardo Mora-Cartin
- Section of Rheumatology, Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Jacob Moran-Gilad
- Microbiology, Advanced Genomics, and Infection Control Applications Laboratory, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Pilar M. Muñoz
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón, Zaragoza, Spain
| | - Heinrich Neubauer
- Friedrich Loeffler Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - David O'Callaghan
- Centre National de Référence des Brucella, U1047, University of Montpellier/INSERM, CHU de Nîmes, Nimes, France
| | - Reuben Ocholi
- Bacteriology, Parasitology, and Virology Department, National Veterinary Research Institute, Vom, Nigeria
| | - Ángel Oñate
- Laboratory of Molecular Immunology, Department of Microbiology, Faculty of Biological Sciences, Universidad de Concepción, Concepción, Chile
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, India
| | - Georgios Pappas
- Institute of Continuing Medical Education of Ioannina, Ioannina, Greece
| | - J. Tony Pembroke
- School of Natural Sciences and Bernal Institute, University of Limerick, Limerick, Ireland
| | - Martin Roop
- Department of Microbiology and Immunology, East Carolina University School of Medicine, Greenville, North Carolina, USA
| | - Nazaret Ruiz-Villalonos
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Michael P. Ryan
- Department of Applied Science, Technological University of the Shanno, Limerick, Ireland
| | - Suzana P. Salcedo
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Miriam Salvador-Bescós
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Félix J. Sangari
- Instituto de Biomedicina y Biotecnología de Cantabria, Consejo Superior de Investigaciones Científicas, Universidad de Cantabria, Santander, Spain
| | - Renato de Lima Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Aristarchos Seimenis
- Mediterranean Zoonoses Control Centre, World Health Organization, Athens, Greece
| | - Gary Splitter
- School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marcela Suárez-Esquivel
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Darem Tabbaa
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Hama University, Hama, Syria
| | - Marcos David Trangoni
- Centro de Investigación en Ciencias Veterinarias y Agropecuarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Argentina
| | - Renee M. Tsolis
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, Davis, California, USA
| | - Nieves Vizcaíno
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Gamal Wareth
- Friedrich Loeffler Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Susan C. Welburn
- Division of Infection and Pathway Medicine, Centre for Infectious Diseases, School of Biomedical Sciences, College of Medicine and Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Whatmore
- WOAH Reference Laboratory for Brucellosis, Animal and Plant Health Agency, Weybridge, United Kingdom
- FAO Reference Centre for Brucellosis, Department of Bacteriology, Animal and Plant Health Agency, Weybridge, United Kingdom
| | - Amaia Zúñiga-Ripa
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ignacio Moriyón
- Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
- Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
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65
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Mendoza-Hoffmann F, Yang L, Buratto D, Brito-Sánchez J, Garduño-Javier G, Salinas-López E, Uribe-Álvarez C, Ortega R, Sotelo-Serrano O, Cevallos MÁ, Ramírez-Silva L, Uribe-Carvajal S, Pérez-Hernández G, Celis-Sandoval H, García-Trejo JJ. Inhibitory to non-inhibitory evolution of the ζ subunit of the F 1F O-ATPase of Paracoccus denitrificans and α-proteobacteria as related to mitochondrial endosymbiosis. Front Mol Biosci 2023; 10:1184200. [PMID: 37664184 PMCID: PMC10469736 DOI: 10.3389/fmolb.2023.1184200] [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: 03/11/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction: The ζ subunit is a potent inhibitor of the F1FO-ATPase of Paracoccus denitrificans (PdF1FO-ATPase) and related α-proteobacteria different from the other two canonical inhibitors of bacterial (ε) and mitochondrial (IF1) F1FO-ATPases. ζ mimics mitochondrial IF1 in its inhibitory N-terminus, blocking the PdF1FO-ATPase activity as a unidirectional pawl-ratchet and allowing the PdF1FO-ATP synthase turnover. ζ is essential for the respiratory growth of P. denitrificans, as we showed by a Δζ knockout. Given the vital role of ζ in the physiology of P. denitrificans, here, we assessed the evolution of ζ across the α-proteobacteria class. Methods: Through bioinformatic, biochemical, molecular biology, functional, and structural analyses of several ζ subunits, we confirmed the conservation of the inhibitory N-terminus of ζ and its divergence toward its C-terminus. We reconstituted homologously or heterologously the recombinant ζ subunits from several α-proteobacteria into the respective F-ATPases, including free-living photosynthetic, facultative symbiont, and intracellular facultative or obligate parasitic α-proteobacteria. Results and discussion: The results show that ζ evolved, preserving its inhibitory function in free-living α-proteobacteria exposed to broad environmental changes that could compromise the cellular ATP pools. However, the ζ inhibitory function was diminished or lost in some symbiotic α-proteobacteria where ζ is non-essential given the possible exchange of nutrients and ATP from hosts. Accordingly, the ζ gene is absent in some strictly parasitic pathogenic Rickettsiales, which may obtain ATP from the parasitized hosts. We also resolved the NMR structure of the ζ subunit of Sinorhizobium meliloti (Sm-ζ) and compared it with its structure modeled in AlphaFold. We found a transition from a compact ordered non-inhibitory conformation into an extended α-helical inhibitory N-terminus conformation, thus explaining why the Sm-ζ cannot exert homologous inhibition. However, it is still able to inhibit the PdF1FO-ATPase heterologously. Together with the loss of the inhibitory function of α-proteobacterial ε, the data confirm that the primary inhibitory function of the α-proteobacterial F1FO-ATPase was transferred from ε to ζ and that ζ, ε, and IF1 evolved by convergent evolution. Some key evolutionary implications on the endosymbiotic origin of mitochondria, as most likely derived from α-proteobacteria, are also discussed.
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Affiliation(s)
- Francisco Mendoza-Hoffmann
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Lingyun Yang
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jorge Brito-Sánchez
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Gilberto Garduño-Javier
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Emiliano Salinas-López
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Cristina Uribe-Álvarez
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Raquel Ortega
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Oliver Sotelo-Serrano
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Miguel Ángel Cevallos
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Leticia Ramírez-Silva
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Salvador Uribe-Carvajal
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - Gerardo Pérez-Hernández
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México, México
| | - Heliodoro Celis-Sandoval
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
| | - José J. García-Trejo
- Departamento de Biología, Facultad de Química, Ciudad Universitaria, Universidad Nacional Autónoma de México (U.N.A.M.), Ciudad de México, México
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Moriyón I, Blasco JM, Letesson JJ, De Massis F, Moreno E. Brucellosis and One Health: Inherited and Future Challenges. Microorganisms 2023; 11:2070. [PMID: 37630630 PMCID: PMC10459711 DOI: 10.3390/microorganisms11082070] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
One Health is the collaborative efforts of multiple disciplines to attain optimal health for people, animals and the environment, a concept that historically owes much to the study of brucellosis, including recent political and ethical considerations. Brucellosis One Health actors include Public Health and Veterinary Services, microbiologists, medical and veterinary practitioners and breeders. Brucellosis awareness, and the correct use of diagnostic, epidemiological and prophylactic tools is essential. In brucellosis, One Health implementation faces inherited and new challenges, some aggravated by global warming and the intensification of breeding to meet growing food demands. In endemic scenarios, disease awareness, stakeholder sensitization/engagement and the need to build breeder trust are unresolved issues, all made difficult by the protean characteristics of this zoonosis. Extended infrastructural weaknesses, often accentuated by geography and climate, are critically important. Capacity-building faces misconceptions derived from an uncritical adoption of control/eradication strategies applied in countries with suitable means, and requires additional reference laboratories in endemic areas. Challenges for One Health implementation include the lack of research in species other than cattle and small ruminants, the need for a safer small ruminant vaccine, the need to fill in the infrastructure gap, the need for realistic capacity-building, the creation of reference laboratories in critical areas, and the stepwise implementation of measures not directly transposed from the so-called developed countries.
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Affiliation(s)
- Ignacio Moriyón
- Microbiology and Parasitology Department, Medical School, Universidad de Navarra, 31008 Pamplona, Spain
| | - José María Blasco
- Departamento de Ciencia Animal, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), 50059 Zaragoza, Spain;
| | - Jean Jacques Letesson
- Research Unit in Biology of Microorganisms, Narilis, University of Namur, 5000 Namur, Belgium;
| | - Fabrizio De Massis
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, 64100 Teramo, Italy;
| | - Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia 40104, Costa Rica;
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Oladipupo SO, Laidoudi Y, Beckmann JF, Hu XP, Appel AG. The prevalence of Wolbachia in multiple cockroach species and its implication for urban insect management. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:1307-1316. [PMID: 37247378 DOI: 10.1093/jee/toad098] [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: 02/23/2023] [Revised: 04/25/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
Cockroach management relies heavily on the use of conventional insecticides in urban settings, which no longer provide the anticipated level of control. Knowledge of cockroach endosymbionts, like Wolbachia, might provide novel avenues for control. Therefore, we screened 16 cockroach species belonging to 3 families (Ectobiidae, Blattidae, and Blaberidae) for the presence of Wolbachia. We mapped the evolution of Wolbachia-cockroach relationships based on maximum likelihood phylogeny and phylogenetic species clustering on a multi-loci sequence dataset (i.e., coxA, virD4, hcpA, and gatB) of Wolbachia genes. We confirmed the previous report of Wolbachia in 1 Ectobiid species; Supella longipalpa (Fab.), and detected the presence of Wolbachia in 2 Ectobiid species; Balta notulata (Stål) and Pseudomops septentrionalis Hebard, and 1 Blaberid species; Gromphadorhina portentosa (Schaum). All cockroach-associated Wolbachia herein detected were clustered with the ancestor of F clade Wolbachia of Cimex lectularius L. (bed bugs). Since Wolbachia provision C. lectularius with biotin vitamins that confer reproductive fitness, we screened the cockroach-associated Wolbachia for the presence of biotin genes. In toto, our results reveal 2 important findings: (i) Wolbachia is relatively uncommon among cockroach species infecting about 25% of species investigated, and (ii) cockroach-associated Wolbachia have biotin genes that likely provide nutritional benefits to their hosts. Thus, we discuss the potential of exploring Wolbachia as a tool for urban insect management.
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Affiliation(s)
- Seun O Oladipupo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Younes Laidoudi
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
| | - John F Beckmann
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Xing Ping Hu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - Arthur G Appel
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
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68
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Geiger O, Sanchez-Flores A, Padilla-Gomez J, Degli Esposti M. Multiple approaches of cellular metabolism define the bacterial ancestry of mitochondria. SCIENCE ADVANCES 2023; 9:eadh0066. [PMID: 37556552 PMCID: PMC10411912 DOI: 10.1126/sciadv.adh0066] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/11/2023] [Indexed: 08/11/2023]
Abstract
We breathe at the molecular level when mitochondria in our cells consume oxygen to extract energy from nutrients. Mitochondria are characteristic cellular organelles that derive from aerobic bacteria and carry out oxidative phosphorylation and other key metabolic pathways in eukaryotic cells. The precise bacterial origin of mitochondria and, consequently, the ancestry of the aerobic metabolism of our cells remain controversial despite the vast genomic information that is now available. Here, we use multiple approaches to define the most likely living relatives of the ancestral bacteria from which mitochondria originated. These bacteria live in marine environments and exhibit the highest frequency of aerobic traits and genes for the metabolism of fundamental lipids that are present in the membranes of eukaryotes, sphingolipids, and cardiolipin.
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Affiliation(s)
- Otto Geiger
- Center for Genomic Sciences, UNAM Campus de Morelos, Cuernavaca, México
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformatica, Institute of Biotechnology, UNAM, Cuernavaca, México
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Ma T, Xue H, Piao C, Jiang N, Li Y. Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov. Front Microbiol 2023; 14:1207256. [PMID: 37601364 PMCID: PMC10434624 DOI: 10.3389/fmicb.2023.1207256] [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: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).
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Affiliation(s)
| | | | | | | | - Yong Li
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing, China
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70
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Hong YW, Jang GI, Kim SY, Choi JY, Kim BJ, Shin DY, Kang JK, Kim SK, Cho BC, Hwang CY. Roseovarius pelagicus sp. nov., a facultatively anaerobic bacterium with potential for degrading polypropylene, isolated from Arctic seawater. Int J Syst Evol Microbiol 2023; 73. [PMID: 37561014 DOI: 10.1099/ijsem.0.005999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023] Open
Abstract
A Gram-stain-negative, facultatively anaerobic, non-motile, rod-shaped bacterial strain, designated HL-MP18T, was isolated from Arctic seawater after a prolonged incubation employing polypropylene as the sole carbon source. Phylogenetic analyses of the 16S rRNA gene sequence revealed that strain HL-MP18T was affiliated to the genus Roseovarius with close relatives Roseovarius carneus LXJ103T (96.8 %) and Roseovarius litorisediminis KCTC 32327T (96.5 %). The complete genome sequence of strain HL-MP18T comprised a circular chromosome of 3.86 Mbp and two circular plasmids of 0.17 and 0.24 Mbp. Genomic comparisons based on average nucleotide identity and digital DNA-DNA hybridization showed that strain HL-MP18T was consistently discriminated from its closely related taxa in the genus Roseovarius. Strain HL-MP18T showed optimal growth at 25 °C, pH 7.0 and 2.5 % (w/v) sea salts. The major cellular fatty acids were C18 : 1 ω6c and/or C18 : 1 ω7c (49.6 %), C19 : 0 cyclo ω8c (13.5 %), and C16 : 0 (12.8 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of the strain was 59.2 mol%. The phylogenetic, genomic, phenotypic and chemotaxonomic results indicate that strain HL-MP18T is distinguishable from the recognized species of the genus Roseovarius. Therefore, we propose that strain HL-MP18T represents a novel species belonging to the genus Roseovarius, for which the name Roseovarius pelagicus sp. nov. is proposed. The type strain is HL-MP18T (=KCCM 90405T=JCM 35639T).
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Affiliation(s)
- Yeon Woo Hong
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Gwang Il Jang
- Aquatic Disease Control Division, National Fishery Products Quality Management Service, Busan 46083, Republic of Korea
| | - Soo Yoon Kim
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Jy Young Choi
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Bok Jin Kim
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Dong Young Shin
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin Kyeong Kang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung-Kyu Kim
- Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon 22012, Republic of Korea
| | - Byung Cheol Cho
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
- Saemangeum Environmental Research Center, Kunsan National University, Kunsan 54150, Republic of Korea
| | - Chung Yeon Hwang
- Microbial Oceanography Laboratory, School of Earth and Environmental Sciences and Research Institute of Oceanography, Seoul National University, Seoul 08826, Republic of Korea
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Wang XN, Wang L, He W, Yang Q, Zhang DF. Description of Flavimaribacter sediminis gen. nov., sp. nov., a New Member of the Family Rhizobiaceae Isolated from Marine Sediment. Curr Microbiol 2023; 80:301. [PMID: 37493780 DOI: 10.1007/s00284-023-03402-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023]
Abstract
A novel Gram-staining-negative, aerobic and rod-shaped bacterium, designated WL0058T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51' 13″ E, 32° 6' 26″ N) in October 2020. Strain WL0058T was found to grow at 4-37 °C (optimum, 28 °C) with 1.5-4.0% NaCl (optimum, 4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0-10.0 (optimum, pH 6.0). Phylogenetic trees constructed based on 16S rRNA gene sequence indicated that strain WL0058T is a member of the family Rhizobiaceae, shared the highest similarity with "Hoeflea prorocentri" CCTCC AB 2016294T (97.7%) and constituted a sub-cluster within the family with it, while the similarity with others in the family Rhizobiaceae was lower than 97.0%. The G + C content of genomic DNA was 59.5 mol%. Polar lipids profile of strain WL0058T included phosphatidylcholine (PC), phosphatidylethanolamine (PE), and glycolipid (GL), phosphatidylmonomethylethanolamine (PME) and two unidentified polar lipids (L). The major isoprenoid quinone was determined to be Q-10 and the major fatty acids were C16:0, C18:0, summed features 4 (iso-C17:1 and/or anteiso-C17:1), and summed features 8 (C18:1ω6c and/or C18:1ω7c). As inferred from the morphology, physiology, and biochemical analysis, genotypic characteristics, and the phylogenetic trees, strain WL0058T ought to be recognized as a novel genus in the family Rhizobiaceae, for which the name Flavimaribacter sediminis gen. nov., sp. nov. The type strain of Flavimaribacter sediminis gen. nov., sp. nov. is WL0058T (= MCCC 1K06063T = JCM 34659T = GDMCC 1.2448T).
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Affiliation(s)
- Xiang-Ning Wang
- Nanjing Forestry University, Nanjing, 210037, People's Republic of China.
| | - Lu Wang
- Nanjing Forestry University, Nanjing, 210037, People's Republic of China
- Institute of Marine Biotechnology and Bio-resource Utilization, College of Oceanography, Hohai University, Nanjing, 201198, People's Republic of China
| | - Wei He
- Institute of Marine Biotechnology and Bio-resource Utilization, College of Oceanography, Hohai University, Nanjing, 201198, People's Republic of China
| | - Qiao Yang
- Laboratory of Marine Environment and Ecology, College of Marine Science and Technology, Zhejiang Ocean University, Zhoushan, 316022, People's Republic of China
| | - Dao-Feng Zhang
- Institute of Marine Biotechnology and Bio-resource Utilization, College of Oceanography, Hohai University, Nanjing, 201198, People's Republic of China.
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Ishaq SE, Ahmad T, Liang L, Hou J, Dong Y, Yu T, Wang F. Mariluticola halotolerans gen. nov., sp. nov., a novel member of the family Devosiaceae isolated from South China Sea sediment. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486324 DOI: 10.1099/ijsem.0.005972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
A novel member of class Alphaproteobacteria was isolated from marine sediment of the South China Sea. Cells of strain LMO-2T were Gram-stain negative, greyish in colour, motile, with a single lateral flagellum and short rod in shape with a slight curve. Strain LMO-2T was positive for oxidase and negative for catalase. The bacterium grew aerobically at 10-40 °C (optimum, 25-30 °C), pH 5.5-10.0 (optimum, pH 7.0) and 0-9 % NaCl (w/v; optimum, 2-3 %). Phylogenetic analysis of the 16S rRNA gene sequence and phylogenomic analysis of the whole genome sequence indicated that strain LMO-2T represents a new genus and a new species within the family Devosiaceae, class Alphaproteobacteria, phylum Pseudomonadota. Comparisons of the 16S rRNA gene sequences of strain LMO-2T showed 94.8 % similarity to its closest relative. The genome size is ~3.45 Mbp with a DNA G+C content of 58.17 mol%. The strain possesses potential capability for the degradation of complex organic matter, i.e. fatty acid and benzoate. The predominant cellular fatty acids (>10 %) were C16 : 0 and C18 : 1 ω7c 11-methyl. The sole respiratory quinone was ubiquinone-10. The major identified polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phospholipid. Based on the polyphasic taxonomic data, strain LMO-2T represents a novel genus and a novel species for which the name Mariluticola halotolerans gen. nov., sp. nov., was proposed in the family Devosiaceae. The type strain is LMO-2T (=CGMCC 1.19273T=JCM 34934T).
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Affiliation(s)
- Sidra Erum Ishaq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Tariq Ahmad
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Lewen Liang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Tiantian Yu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240, PR China
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73
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McLean R, Schwander T, Diehl C, Cortina NS, Paczia N, Zarzycki J, Erb TJ. Exploring alternative pathways for the in vitro establishment of the HOPAC cycle for synthetic CO 2 fixation. SCIENCE ADVANCES 2023; 9:eadh4299. [PMID: 37315145 DOI: 10.1126/sciadv.adh4299] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
Nature has evolved eight different pathways for the capture and conversion of CO2, including the Calvin-Benson-Bassham cycle of photosynthesis. Yet, these pathways underlie constrains and only represent a fraction of the thousands of theoretically possible solutions. To overcome the limitations of natural evolution, we introduce the HydrOxyPropionyl-CoA/Acrylyl-CoA (HOPAC) cycle, a new-to-nature CO2-fixation pathway that was designed through metabolic retrosynthesis around the reductive carboxylation of acrylyl-CoA, a highly efficient principle of CO2 fixation. We realized the HOPAC cycle in a step-wise fashion and used rational engineering approaches and machine learning-guided workflows to further optimize its output by more than one order of magnitude. Version 4.0 of the HOPAC cycle encompasses 11 enzymes from six different organisms, converting ~3.0 mM CO2 into glycolate within 2 hours. Our work moves the hypothetical HOPAC cycle from a theoretical design into an established in vitro system that forms the basis for different potential applications.
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Affiliation(s)
- Richard McLean
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Schwander
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Niña Socorro Cortina
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- SYNMIKRO Center of Synthetic Microbiology, Marburg, Germany
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Netrusov AI, Liyaskina EV, Kurgaeva IV, Liyaskina AU, Yang G, Revin VV. Exopolysaccharides Producing Bacteria: A Review. Microorganisms 2023; 11:1541. [PMID: 37375041 DOI: 10.3390/microorganisms11061541] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial exopolysaccharides (EPS) are essential natural biopolymers used in different areas including biomedicine, food, cosmetic, petroleum, and pharmaceuticals and also in environmental remediation. The interest in them is primarily due to their unique structure and properties such as biocompatibility, biodegradability, higher purity, hydrophilic nature, anti-inflammatory, antioxidant, anti-cancer, antibacterial, and immune-modulating and prebiotic activities. The present review summarizes the current research progress on bacterial EPSs including their properties, biological functions, and promising applications in the various fields of science, industry, medicine, and technology, as well as characteristics and the isolation sources of EPSs-producing bacterial strains. This review provides an overview of the latest advances in the study of such important industrial exopolysaccharides as xanthan, bacterial cellulose, and levan. Finally, current study limitations and future directions are discussed.
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Affiliation(s)
- Alexander I Netrusov
- Department of Microbiology, Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Biology and Biotechnology, High School of Economics, 119991 Moscow, Russia
| | - Elena V Liyaskina
- Department of Biotechnology, Biochemistry and Bioengineering, National Research Ogarev Mordovia State University, 430005 Saransk, Russia
| | - Irina V Kurgaeva
- Department of Biotechnology, Biochemistry and Bioengineering, National Research Ogarev Mordovia State University, 430005 Saransk, Russia
| | - Alexandra U Liyaskina
- Institute of the World Ocean, Far Eastern Federal University, 690922 Vladivostok, Russia
| | - Guang Yang
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Viktor V Revin
- Department of Biotechnology, Biochemistry and Bioengineering, National Research Ogarev Mordovia State University, 430005 Saransk, Russia
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75
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Zhang X, Bi L, Gentekaki E, Zhao J, Shen P, Zhang Q. Culture-Independent Single-Cell PacBio Sequencing Reveals Epibiotic Variovorax and Nucleus Associated Mycoplasma in the Microbiome of the Marine Benthic Protist Geleia sp. YT (Ciliophora, Karyorelictea). Microorganisms 2023; 11:1500. [PMID: 37375002 DOI: 10.3390/microorganisms11061500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Microbes in marine sediments constitute up to five-sixths of the planet's total biomass, but their diversity is little explored, especially for those forming associations with unicellular protists. Heterotrophic ciliates are among the most dominant and diversified marine benthic protists and comprise hotspot niches of bacterial colonization. To date, studies using culture-independent single-cell approaches to explore microbiomes of marine benthic ciliates in nature are almost absent, even for the most ubiquitous species. Here, we characterize the major bacterial groups associated with a representative marine benthic ciliate, Geleia sp. YT, collected directly from the coastal zone of Yantai, China. PacBio sequencing of the nearly full-length 16Sr RNA genes was performed on single cells of Geleia. Fluorescence in situ hybridization (FISH) analysis with genus-specific probes was further applied to locate the dominant bacterial groups. We identified a Variovorax-like bacterium as the major epibiotic symbiont residing in the kineties of the ciliate host. We provide evidence of a nucleus-associated bacterium related to the human pathogen Mycoplasma, which appeared prevalently in the local populations of Geleia sp. YT for 4 months. The most abundant bacterial taxa associated with Geleia sp. YT likely represent its core microbiome, hinting at the important roles of the ciliate-bacteria consortium in the marine benthos. Overall, this work has contributed to the knowledge of the diversity of life in the enigmatic marine benthic ciliate and its symbioses.
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Affiliation(s)
- Xiaoxin Zhang
- School of Ocean, Yantai University, Yantai 264003, China
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Luping Bi
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Gut Microbiome Research Group, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Jianmin Zhao
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Pingping Shen
- School of Ocean, Yantai University, Yantai 264003, China
| | - Qianqian Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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76
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Kaise H, Sawadogo JB, Alam MS, Ueno C, Dianou D, Shinjo R, Asakawa S. Methylocystis iwaonis sp. nov., a type II methane-oxidizing bacterium from surface soil of a rice paddy field in Japan, and emended description of the genus Methylocystis ( ex Whittenbury et al. 1970) Bowman et al. 1993. Int J Syst Evol Microbiol 2023; 73. [PMID: 37279153 DOI: 10.1099/ijsem.0.005925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
A novel methane-oxidizing bacterial strain SS37A-ReT was isolated from surface soil of a rice paddy field in Japan. Cells were Gram-stain-negative, motile rods with single polar flagellum and type II intracytoplasmic membrane arrangement. The strain grew on methane or methanol as the sole carbon and energy source. It grew at 15–37 °C (optimum 25–30 °C), pH 6.0–9.0 (optimum 7.0–8.0) and with 0–0.1 % (w/w) NaCl (no growth at 0.5 % or above). Cells formed cysts, but not exospores. The results of sequence analysis of the 16S rRNA gene indicated that SS37A-ReT represented a member of the family
Methylocystaceae
, with the highest similarity (98.9 %) to Methylocystis parva corrig. OBBPT. Phylogenetic analysis of pmoA and mxaF genes and core genes in the genome indicated that the strain was closely related to the members of the genus
Methylocystis
, while the analysis of the mmoX gene indicated the close relationships with the genus
Methylosinus
. The values of genome relatedness between SS37A-ReT and species of the genera
Methylocystis
and
Methylosinus
were 78.6–82.5% and 21.7–24.9 % estimated by the average nucleotide identity and digital DNA–DNA hybridisation, respectively, showing the highest values with
Methylocystis echinoides
LMG 27198T. The DNA G+C content was 63.2 mol% (genome). The major quinone and fatty acids were Q-8 and, C18 : 1 (C18 : 1ω8t and C18 : 1ω8c) and C18 : 2, respectively. On the basis of the phenotypic and phylogenetic features, the strain represents a novel species of the genus
Methylocystis
, for which the name Methylocystis iwaonis sp. nov. is proposed. The type strain is SS37A-ReT (=JCM 34278T =NBRC 114996T=KCTC 82710T).
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Affiliation(s)
- Hirotaka Kaise
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Joseph Benewindé Sawadogo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Université Nazi BONI, Bobo-Dioulasso, 01 BP 1091 Bobo-Dioulasso 01, Burkina Faso
| | - Mohammad Saiful Alam
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur 1706, Bangladesh
| | - Chihoko Ueno
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Dayéri Dianou
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
- Centre National de la Recherche Scientifique et Technologique, Ouagadougou, 03 BP 7047 Ouagadougou 03, Burkina Faso
| | - Rina Shinjo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
| | - Susumu Asakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furocho, Chikusa, Nagoya 464-8601, Japan
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Dadar M, Brangsch H, Alamian S, Neubauer H, Wareth G. Whole-genome sequencing for genetic diversity analysis of Iranian Brucella spp. isolated from humans and livestock. One Health 2023; 16:100483. [PMID: 36632477 PMCID: PMC9827381 DOI: 10.1016/j.onehlt.2023.100483] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
Brucellosis is one of the most common zoonoses in the Middle East. It is causing economic losses to the livestock industry and has a great public health concern. Little is known about the genetic diversity and distribution of brucellae in Iran. Therefore, forty Brucella spp. strains (B. abortus and B. melitensis) isolated from animals and humans were analyzed by whole genome sequencing (WGS) technology using single nucleotide polymorphism (SNP) analysis and core genome multilocus sequence typing (cgMLST). Brucella isolates were obtained from lymph nodes (cows and camels), milk (cows, camels and sheep), and aborted foetus samples (sheep and goats), as well as cerebrospinal fluid and blood of humans. The isolates were originating from thirteen provinces of Iran and isolated between 2015 and 2020. According to in-silico MLST, ST8 and ST2 were the most frequent sequence types in B. melitensis and B. abortus, respectively. Based on phylogeographic reconstruction using cgSNP analysis, the investigated Iranian B. melitensis strains belonged to the American and Mediterranean lineages of the B. melitensis phylogeny. Furthermore, cgSNP analysis revealed a similarity between Iranian B. abortus isolates and strains from Iraq and Egypt. Therefore, the origin of the Iranian strains can be suggested to be strains from neighboring and Middle East countries. Moreover, cgMLST analysis showed that the Iranian B. melitensis strains were closely relative to strains recovered from sheep and humans in Iraq, Afghanistan, Syria, Turkmenistan, and Pakistan. In the current panel of strains, cgMLST and cgSNP analysis provided an appropriate and accurate tool for effective traceback analyses for Brucella spp. from Iran. The results of cgSNP and cgMLST helped to understand the geographic distribution and interspecies transmission of Iranian strains and highlight the importance of specific brucellosis control measures in Iran with regard to the One-Health approach.
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Affiliation(s)
- Maryam Dadar
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Hanka Brangsch
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Saeed Alamian
- Razi Vaccine and Serum Research Institute (RVSRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
| | - Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany
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78
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Grützner J, Börner J, Jäger A, Klug G. The Small RNA-Binding Protein CcaF1 Promotes Formation of Photosynthetic Complexes in Rhodobacter sphaeroides. Int J Mol Sci 2023; 24:ijms24119515. [PMID: 37298460 DOI: 10.3390/ijms24119515] [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: 05/12/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In natural habitats, bacteria frequently need to adapt to changing environmental conditions. Regulation of transcription plays an important role in this process. However, riboregulation also contributes substantially to adaptation. Riboregulation often acts at the level of mRNA stability, which is determined by sRNAs, RNases, and RNA-binding proteins. We previously identified the small RNA-binding protein CcaF1, which is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides. Rhodobacter is a facultative phototroph that can perform aerobic and anaerobic respiration, fermentation, and anoxygenic photosynthesis. Oxygen concentration and light conditions decide the pathway for ATP production. Here, we show that CcaF1 promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins. Levels of mRNAs for transcriptional regulators of photosynthesis genes are not affected by CcaF1. RIP-Seq analysis compares the binding of CcaF1 to RNAs during microaerobic and photosynthetic growth. The stability of the pufBA mRNA for proteins of the light-harvesting I complex is increased by CcaF1 during phototrophic growth but decreased during microaerobic growth. This research underlines the importance of RNA-binding proteins in adaptation to different environments and demonstrates that an RNA-binding protein can differentially affect its binding partners in dependence upon growth conditions.
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Affiliation(s)
- Julian Grützner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Andreas Jäger
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gabriele Klug
- Institute of Microbiology and Molecular Biology, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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79
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Aljanazreh B, Shamseye AA, Abuawad A, Ashhab Y. Genomic distribution of the insertion sequence IS711 reveal a potential role in Brucella genome plasticity and host preference. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023:105457. [PMID: 37257801 DOI: 10.1016/j.meegid.2023.105457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/10/2023] [Accepted: 05/25/2023] [Indexed: 06/02/2023]
Abstract
The Insertion Sequence 711 (IS711) is linked to the Brucella genus. Mapping the genomic distribution of IS711 can help understand this insertion element's biological and evolutionary role. This work aimed to delineate the genomic distribution of the IS711 element and to study its association with Brucella evolution. A total of 124 genomes representing 9 Brucella species were searched using BLASTn sequence alignment tool to identify complete and truncated copies of IS711. Based on the genomic context, each IS711 locus was assigned a code using the initial letters of its neighboring genes. Various tools were used to annotate the neighboring genes and determine the shared synteny around orthologous IS711 loci. The tool Islandviewer 4 was used to scan for genomic islands. The Codon Tree method was used to build phylogenetic trees of B. melitensis, B. abortus, and B. suis genomes. The phylogenetic trees of the three species were analyzed, taking into account the genomic distribution patterns of IS711. The result of IS711 frequency analysis showed a relatively conserved number of copies/genome for the different species and for some biovars. The analysis showed that Brucella species with a relatively low IS711 copy number (4-8 copies/genome) are linked to domestic animals as primary hosts and have potential for zoonotic transmission. However, species with a relatively higher copy number (12-30 copies/genome) are less zoonotic and tend to be linked with wild animals as primary hosts. Analyzing the genomic distribution map of IS711 loci showed several unique patterns of IS711 distribution that are correlated with the evolution of Brucella species and biovars. The results also showed that 46.2% of the conserved IS711 elements are located within genomic islands. Based on our results and previous data, we postulate a model explaining the IS711 role in Brucella evolution. We assume that during the transition from a free-living to an intracellular lifestyle, a descendant of the Brucella genus had acquired a progenitor sequence of the IS711. Subsequently, a burst in IS711 transposition occurred. This parasitic expansion can be deleterious and has to be counteracted by evolutionary forces to prevent lineage extension and to promote adaptation to host. Similar to other plasmid-free pathogenic α-Proteobacteria bacteria, the balance of expansion and reduction of insertion elements could be one of the mechanisms to control genome reduction and streamlining. We hypothesize that the IS711-mediated genomic changes and other small sequence nucleotide changes in specific orthologous genes could significantly contribute to Brucella's evolution and adaptation to different animal hosts.
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Affiliation(s)
- Bessan Aljanazreh
- Palestine-Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine
| | - Assalla Abu Shamseye
- Palestine-Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine
| | - Abdalhalim Abuawad
- Palestine-Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine
| | - Yaqoub Ashhab
- Palestine-Korea Biotechnology Center, Palestine Polytechnic University, Hebron, Palestine.
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80
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Patwardhan S, Phan J, Smedile F, Vetriani C. The Genome of Varunaivibrio sulfuroxidans Strain TC8 T, a Metabolically Versatile Alphaproteobacterium from the Tor Caldara Gas Vents in the Tyrrhenian Sea. Microorganisms 2023; 11:1366. [PMID: 37374867 DOI: 10.3390/microorganisms11061366] [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: 04/05/2023] [Revised: 05/02/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
Varunaivibrio sulfuroxidans type strain TC8T is a mesophilic, facultatively anaerobic, facultatively chemolithoautotrophic alphaproteobacterium isolated from a sulfidic shallow-water marine gas vent located at Tor Caldara, Tyrrhenian Sea, Italy. V. sulfuroxidans belongs to the family Thalassospiraceae within the Alphaproteobacteria, with Magnetovibrio blakemorei as its closest relative. The genome of V. sulfuroxidans encodes the genes involved in sulfur, thiosulfate and sulfide oxidation, as well as nitrate and oxygen respiration. The genome encodes the genes involved in carbon fixation via the Calvin-Benson-Bassham cycle, in addition to genes involved in glycolysis and the TCA cycle, indicating a mixotrophic lifestyle. Genes involved in the detoxification of mercury and arsenate are also present. The genome also encodes a complete flagellar complex, one intact prophage and one CRISPR, as well as a putative DNA uptake mechanism mediated by the type IVc (aka Tad pilus) secretion system. Overall, the genome of Varunaivibrio sulfuroxidans highlights the organism's metabolic versatility, a characteristic that makes this strain well-adapted to the dynamic environmental conditions of sulfidic gas vents.
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Affiliation(s)
- Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jonathan Phan
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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81
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Safronova V, Sazanova A, Belimov A, Guro P, Kuznetsova I, Karlov D, Chirak E, Yuzikhin O, Verkhozina A, Afonin A, Tikhonovich I. Synergy between Rhizobial Co-Microsymbionts Leads to an Increase in the Efficiency of Plant-Microbe Interactions. Microorganisms 2023; 11:1206. [PMID: 37317180 DOI: 10.3390/microorganisms11051206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 05/02/2023] [Indexed: 06/16/2023] Open
Abstract
Combined inoculation of legumes with rhizobia and plant growth-promoting rhizobacteria or endophytes is a known technique for increasing the efficiency of nitrogen-fixing symbiosis and plant productivity. The aim of this work was to expand knowledge about the synergistic effects between commercial rhizobia of pasture legumes and root nodule bacteria of relict legume species. Pot experiments were performed on common vetch (Vicia sativa L.) and red clover (Trifolium pratense L.) co-inoculated with the participation of the corresponding commercial rhizobial strains (R. leguminosarum bv. viciae RCAM0626 and R. leguminosarum bv. trifolii RCAM1365) and seven strains isolated from nodules of relict legumes inhabiting the Baikal Lake region and the Altai Republic: Oxytropis popoviana, Astragalus chorinensis, O. tragacanthoides and Vicia costata. The inoculation of plants with combinations of strains (commercial strain plus the isolate from relict legume) had a different effect on symbiosis depending on the plant species: the increase in the number of nodules was mainly observed on vetch, whereas increased acetylene reduction activity was evident on clover. It was shown that the relict isolates differ significantly in the set of genes related to different genetic systems that affect plant-microbe interactions. At the same time, they had additional genes that are involved in the formation of symbiosis and determine its effectiveness, but are absent in the used commercial strains: symbiotic genes fix, nif, nod, noe and nol, as well as genes associated with the hormonal status of the plant and the processes of symbiogenesis (acdRS, genes for gibberellins and auxins biosynthesis, genes of T3SS, T4SS and T6SS secretion systems). It can be expected that the accumulation of knowledge about microbial synergy on the example of the joint use of commercial and relict rhizobia will allow in the future the development of methods for the targeted selection of co-microsymbionts to increase the efficiency of agricultural legume-rhizobia systems.
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Affiliation(s)
- Vera Safronova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Anna Sazanova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Andrey Belimov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Polina Guro
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Irina Kuznetsova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Denis Karlov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Elizaveta Chirak
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Oleg Yuzikhin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Alla Verkhozina
- Siberian Institute of Plant Physiology and Biochemistry (SIPPB), P.O. Box 1243, 664033 Irkutsk, Russia
| | - Alexey Afonin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Sh. Podbelskogo 3, 196608 St. Petersburg, Russia
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 St. Petersburg, Russia
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Yoon J. Thetidibacter halocola gen. nov., sp. nov., a novel member within the family Roseobacteraceae isolated from seawater. Antonie Van Leeuwenhoek 2023:10.1007/s10482-023-01832-1. [PMID: 37133556 DOI: 10.1007/s10482-023-01832-1] [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: 12/07/2022] [Accepted: 04/17/2023] [Indexed: 05/04/2023]
Abstract
A Gram-staining-negative, strictly aerobic, dark beige-colored, rod-shaped, chemoorganoheterotrophic, and catalase- and oxidase-positive bacterium, designated as KMU-90T, was isolated from coastal seawater in the Republic of Korea, and subjected to a polyphasic study. The novel isolate was able to grow at 0-6.0% NaCl concentrations (w/v), pH 6.5-9.5, and 4-45 °C. The 16S rRNA gene sequences-based phylogeny revealed that the novel marine isolate belongs to the family Roseobacteraceae of class Alphaproteobacteria and that it shared the greatest sequence similarity (97.3%) with Aestuariicoccus marinus NAP41T. The novel strain could be distinguished phenotypically from related representatives of the family Roseobacteraceae. The major (> 10%) fatty acids of strain KMU-90T were C18:1 ω7c and C18:1 ω7c 11-methyl and the only respiratory quinone was ubiquinone-10 (Q-10). Strain KMU-90T contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, two unidentified aminolipids, an unidentified phospholipid, and three unidentified glycolipids as polar lipids. The assembled draft genome size of strain KMU-90T was 4.84 Mbp with a DNA G + C content of 66.5%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values between the genomes of strain KMU-90T and its closely related representatives were 77.0-79.0%, 14.6-20.0%, and 60.0-69.9%, respectively. From the polyphasic taxonomic results obtained, the strain is considered to represent a novel genus and a new species of the family Roseobacteraceae, for which the name Thetidibacter halocola gen. nov., sp. nov. is proposed. The type species is T. halocola, with the type strain KMU-90T (= KCCM 90287T = NBRC 113375T).
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Affiliation(s)
- Jaewoo Yoon
- College of Pharmacy, Keimyung University, 1095 Dalgubeoldaero, Dalseo-gu, Daegu, 42601, Republic of Korea.
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83
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Gupta RS, Kanter-Eivin DA. AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species. Int J Syst Evol Microbiol 2023; 73. [PMID: 37159410 DOI: 10.1099/ijsem.0.005844] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
Taxon-specific conserved signature indels (CSIs) in genes/proteins provide reliable molecular markers (synapomorphies) for unambiguous demarcation of taxa of different ranks in molecular terms and for genetic, biochemical and diagnostic studies. Because of their predictive abilities, the shared presence of known taxon-specific CSIs in genome sequences has proven useful for taxonomic purposes. However, the lack of a convenient method for identifying the presence of known CSIs in genome sequences has limited their utility for taxonomic and other studies. We describe here a web-based tool/server (AppIndels.com) that identifies the presence of known and validated CSIs in genome sequences and uses this information for predicting taxonomic affiliation. The utility of this server was tested by using a database of 585 validated CSIs, which included 350 CSIs specific for ≈45 Bacillales genera, with the remaining CSIs being specific for members of the orders Neisseriales, Legionellales and Chlorobiales, family Borreliaceae, and some Pseudomonadaceae species/genera. Using this server, genome sequences were analysed for 721 Bacillus strains of unknown taxonomic affiliation. Results obtained showed that 651 of these genomes contained significant numbers of CSIs specific for the following Bacillales genera/families: Alkalicoccus, 'Alkalihalobacillaceae', Alteribacter, Bacillus Cereus clade, Bacillus Subtilis clade, Caldalkalibacillus, Caldibacillus, Cytobacillus, Ferdinandcohnia, Gottfriedia, Heyndrickxia, Lederbergia, Litchfieldia, Margalitia, Mesobacillus, Metabacillus, Neobacillus, Niallia, Peribacillus, Priestia, Pseudalkalibacillus, Robertmurraya, Rossellomorea, Schinkia, Siminovitchia, Sporosarcina, Sutcliffiella, Weizmannia and Caryophanaceae. Validity of the taxon assignment made by the server was examined by reconstructing phylogenomic trees. In these trees, all Bacillus strains for which taxonomic predictions were made correctly branched with the indicated taxa. The unassigned strains likely correspond to taxa for which CSIs are lacking in our database. Results presented here show that the AppIndels server provides a useful new tool for predicting taxonomic affiliation based on shared presence of the taxon-specific CSIs. Some caveats in using this server are discussed.
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Affiliation(s)
- Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
| | - David A Kanter-Eivin
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario CA L8N 3Z5, Canada
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84
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Dick JM, Tan J. Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences. MICROBIAL ECOLOGY 2023; 85:1338-1355. [PMID: 35503575 DOI: 10.1007/s00248-022-01988-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/28/2022] [Indexed: 05/10/2023]
Abstract
Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.
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Affiliation(s)
- Jeffrey M Dick
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China.
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou, 510640, China.
| | - Jingqiang Tan
- Key Laboratory of Metallogenic Prediction of Nonferrous Metals and Geological Environment Monitoring, Ministry of Education, School of Geosciences and Info-Physics, Central South University, Changsha, 410083, China
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85
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Dorneles EMS, Santana JA, Costa ACTRB, Júnior DGJ, Heinemann MB, Lage AP. Equine brucellosis: current understanding and challenges. J Equine Vet Sci 2023:104298. [PMID: 37072072 DOI: 10.1016/j.jevs.2023.104298] [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: 11/08/2022] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/20/2023]
Abstract
Brucellosis in equines, including horses, donkeys, and mules, is characterized by abscesses in tendons, bursae, and joints. Reproductive disorders, which are common in other animals, are rare in both males and females. Joint breeding of horses, cattle, and pigs was found as the main risk factor for equine brucellosis, with the transmission from equines to cattle or among equines possible, although unlikely. Hence, evaluation of the disease in equines can be considered an indirect indicator of the effectiveness of brucellosis control measures employed for other domestic species. Generally, the disease in equines reflects disease status in the sympatric domestic species, mainly cattle. It is important to note that in equines, the disease has no validated diagnostic test, which limits the interpretation of available data. Finally, it is important to mention that equines also represent significant Brucella spp. infection sources for humans. Considering the zoonotic aspect of brucellosis, the significant losses due to infection, and the representativeness of horses, mules, and donkeys in the society, as well as the continuous efforts to control and eradicate the disease in livestock, in this review, we covered the various aspects of brucellosis in equines and compile the sparse and diffuse information on the subject.
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Affiliation(s)
- Elaine Maria Seles Dorneles
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais. Caixa Postal 3037, Campus Universitário, 37200-900, Brazil.
| | - Jordana Almeida Santana
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Campus Pampulha da, Av. Pres. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Anna Cecília Trolesi Reis Borges Costa
- Departamento de Medicina Veterinária, Faculdade de Zootecnia e Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais. Caixa Postal 3037, Campus Universitário, 37200-900, Brazil
| | - Danilo Guedes Junqueira Júnior
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Campus Pampulha da, Av. Pres. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil
| | - Marcos Bryan Heinemann
- Departamento de Medicina Veterinária Preventiva e Saúde Pública, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Professor Orlando Marques de Paiva, 87. Butantã. São Paulo, São Paulo, 05508-270, Brazil
| | - Andrey Pereira Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Campus Pampulha da, Av. Pres. Antônio Carlos, 6627, Belo Horizonte, Minas Gerais, 31270-901, Brazil..
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86
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Sigida EN, Zdorovenko EL, Shashkov AS, Dmitrenok AS, Fedonenko YP. Structure of the O-specific polysaccharide of Ochrobactrum endophyticum KCTC 42485 T containing 3-(3-hydroxy-2,3-dimethyl-5-oxoprolyl)amino-3,6-dideoxy-d-galactose. Carbohydr Res 2023; 527:108810. [PMID: 37040681 DOI: 10.1016/j.carres.2023.108810] [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: 02/25/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/13/2023]
Abstract
Ochrobactrum endophyticum (syn. Brucella endophytica) is an aerobic species of Alphaproteobacteria isolated from healthy roots of Glycyrrhiza uralensis. Here we report the structure of the O-specific polysaccharide obtained by mild acid hydrolysis of the lipopolysaccharide of the type strain KCTC 42485:→3)-α-l-FucpNAc-(1→3)-β-d-QuipNAc-(1→2)-β-d-Fucp3NAcyl-(1→ where Acyl is 3-hydroxy-2,3-dimethyl-5-oxoprolyl. The structure was elucidated using chemical analyses along with 1H and 13C NMR spectroscopy (including 1H,1H COSY, TOCSY, ROESY and 1H,13C HSQC, HMBC, HSQC-TOCSY and HSQC-NOESY experiments). To our knowledge the OPS structure is novel and has not been previously published.
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Affiliation(s)
- Elena N Sigida
- Institute of Biochemistry and Physiology of Plants and Microorganisms, FRC Saratov Scientific Centre of Russian Academy of Sciences, 13, Prospekt Entuziastov, Saratov, 410049, Russia; N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Evelina L Zdorovenko
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Alexander S Shashkov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Andrey S Dmitrenok
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia
| | - Yulia P Fedonenko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, FRC Saratov Scientific Centre of Russian Academy of Sciences, 13, Prospekt Entuziastov, Saratov, 410049, Russia; Chernyshevsky Saratov State University, Ulitsa Astrakhanskaya 83, 410012, Saratov, Russia
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87
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Li FN, Zheng ZQ, Chen MS, Chen XH, Tuo L. Ancylobacter mangrovi sp. nov., a novel endophytic bacterium isolated form mangrove plant☆. Syst Appl Microbiol 2023; 46:126419. [PMID: 37030242 DOI: 10.1016/j.syapm.2023.126419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 03/27/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Two novel strains GSK1Z-4-2T and MQZ15Z-1 were isolated from branches of mangrove plants collected from Guangxi Zhuang Autonomous Region, China. Both strains were Gram-negative, aerobic, non-flagellated and non-spore-forming bacteria. The comparison of 16S rRNA gene sequences initially indicated that the two strains were assigned to the genus Ancylobacter with sharing the highest similarity to Ancylobacter pratisalsi DSM 102029T (97.3%). The 16S rRNA gene sequence similarity, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strains GSK1Z-4-2T and MQZ15Z-1 were 99.9%, 97.4% and 77.4%, respectively, which revealed that the two strains belonged to the same species. Phylogenetic analyses based on 16S rRNA gene sequences and the core proteome showed that the two strains formed a well-supported cluster with A. pratisalsi DSM 102029T. Moreover, the ANI and isDDH values between strain GSK1Z-4-2T and A. pratisalsi DSM 102029T were 83.0% and 25.8%, respectively, demonstrating that strain GSK1Z-4-2T was a previously undescribed species. Meanwhile, strains GSK1Z-4-2T and MQZ15Z-1 exhibited most of chemotaxonomic and phenotypic features consistent with the description of the genus Ancylobacter. Based on the polyphasic data, strains GSK1Z-4-2T and MQZ15Z-1 should represent a novel species of the genus Ancylobacter, for which the name Ancylobacter mangrovi sp. nov. is proposed. The type strain is GSK1Z-4-2T (=MCCC 1K07181T = JCM 34924T).
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Affiliation(s)
- Fei-Na Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing 100045, PR China
| | - Zhou-Qing Zheng
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Ming-Sheng Chen
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Xiao-Hui Chen
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China
| | - Li Tuo
- Life Sciences Institute, Zunyi Medical University, Zunyi 563006, PR China.
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88
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Du J, Zhang Y, Xin D, Xin Y, Zhang J. Antarcticirhabdus aurantiaca gen. nov., sp. nov., isolated from Antarctic gravel soil. Int J Syst Evol Microbiol 2023; 73. [PMID: 37068122 DOI: 10.1099/ijsem.0.005814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Strain R10T was isolated from a gravel soil sample obtained from Deception Island, Antarctica. The isolate was a Gram-stain-negative, strictly aerobic, motile, short-rod-shaped bacterium, and its colonies were orange yellow in colour. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain R10T belonged to the family Aurantimonadaceae and shared highest sequence similarity with Jiella aquimaris LZB041T (96.3 % sequence similarity), Aurantimonas aggregata R14M6T (96.0 %) and Aureimonas frigidaquae JCM 14755T (96.0 %). Phylogenetic analysis showed that strain R10T affiliated with members of the family Aurantimonadaceae and represented an independent lineage. Growth occurred at 10-37 °C (optimum, 28-32 °C), up to 1.0 % (w/v) NaCl (optimum, 0 %) and pH 5.5-9.0 (optimum, pH 7.0). The major respiratory quinone of strain R10T was Q-10. Its major fatty acids were C18 : 1 ω7c and C16 : 0. The polar lipid profile of strain R10T comprised diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, two unknown phospholipids and two unknown aminophospholipids. The genome of strain R10T was 5.92 Mbp with a G+C content of 69.1 % based on total genome calculations. Average nucleotide identity (ANI) values between R10T and other related species of the family Aurantimonadaceae were found to be low (ANIm <87.0 %, ANIb <75.0 % and OrthoANIu <77.0 %). Furthermore, digital DNA-DNA hybridization (dDDH) and average amino acid identity (AAI) values between strain R10T and the closely related species ranged from 19.5-20.6% and from 60.6-64.0 %, respectively. Based on the results of our phylogenetic, phenotypic, genotypic and chemotaxonomic analyses, it is concluded that strain R10T represents a novel genus and species of the family Aurantimonadaceae, for which the name Antarcticirhabdus aurantiaca gen. nov., sp. nov. is proposed. The type strain is R10T (=KCTC 72466T=CGMCC 1.17155T).
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Affiliation(s)
- Jie Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Ying Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Di Xin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jianli Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
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89
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Hu W, Li Z, Ou H, Wang X, Wang Q, Tao Z, Huang S, Huang Y, Wang G, Pan X. Novosphingobium album sp. nov., Novosphingobium organovorum sp. nov. and Novosphingobium mangrovi sp. nov. with the organophosphorus pesticides degrading ability isolated from mangrove sediments. Int J Syst Evol Microbiol 2023; 73. [PMID: 37115596 DOI: 10.1099/ijsem.0.005843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
Members of the genus Novosphingobium were frequently isolated from polluted environments and possess great bioremediation potential. Here, three species, designated B2637T, B2580T and B1949T, were isolated from mangrove sediments and might represent novel species in the genus Novosphingobium based on a polyphasic taxonomy study. Phylogenomic analysis revealed that strains B2580T, B1949T and B2637T clustered with Novosphingobium naphthalenivorans NBRC 102051T, 'N. profundi' F72 and N. decolorationis 502str22T, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between isolates and their closely related species were less than 94 and 54 %, respectively, all below the threshold of species discrimination. The sizes of the genomes of isolates B2580T, B2637T and B1949T ranged from 4.4 to 4.6 Mb, containing 63.3-66.4 % G+C content. Analysis of their genomic sequences identified genes related to pesticide degradation, heavy-metal resistance, nitrogen fixation, antibiotic resistance and sulphur metabolism, revealing the biotechnology potential of these isolates. Except for B2637T, B1949T and B2580T were able to grow in the presence of quinalphos. Results from these polyphasic taxonomic analyses support the affiliation of these strains to three novel species within the genus Novosphingobium, for which we propose the name Novosphingobium album sp. nov. B2580T (=KCTC 72967T=MCCC 1K04555T), Novosphingobium organovorum sp. nov. B1949T (=KCTC 92158T=MCCC 1K03763T) and Novosphingobium mangrovi sp. nov. B2637T (KCTC 72969T=MCCC 1K04460T).
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Affiliation(s)
- Wenjin Hu
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Zhe Li
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Haisheng Ou
- Guangxi Normal University School of Physical Science and Technology, Guilin, 541004, PR China
| | - Xiaochun Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Qiaozhen Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Zhanhua Tao
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Shushi Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Yuanlin Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Guiwen Wang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
| | - Xinli Pan
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Institute of Eco-Environmental Research, Guangxi Academy of Sciences, Nanning, 530007, PR China
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90
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Seidel L, Broman E, Nilsson E, Ståhle M, Ketzer M, Pérez-Martínez C, Turner S, Hylander S, Pinhassi J, Forsman A, Dopson M. Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities. THE ISME JOURNAL 2023; 17:855-869. [PMID: 36977742 DOI: 10.1038/s41396-023-01395-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/10/2023] [Indexed: 03/30/2023]
Abstract
Besides long-term average temperature increases, climate change is projected to result in a higher frequency of marine heatwaves. Coastal zones are some of the most productive and vulnerable ecosystems, with many stretches already under anthropogenic pressure. Microorganisms in coastal areas are central to marine energy and nutrient cycling and therefore, it is important to understand how climate change will alter these ecosystems. Using a long-term heated bay (warmed for 50 years) in comparison with an unaffected adjacent control bay and an experimental short-term thermal (9 days at 6-35 °C) incubation experiment, this study provides new insights into how coastal benthic water and surface sediment bacterial communities respond to temperature change. Benthic bacterial communities in the two bays reacted differently to temperature increases with productivity in the heated bay having a broader thermal tolerance compared with that in the control bay. Furthermore, the transcriptional analysis showed that the heated bay benthic bacteria had higher transcript numbers related to energy metabolism and stress compared to the control bay, while short-term elevated temperatures in the control bay incubation experiment induced a transcript response resembling that observed in the heated bay field conditions. In contrast, a reciprocal response was not observed for the heated bay community RNA transcripts exposed to lower temperatures indicating a potential tipping point in community response may have been reached. In summary, long-term warming modulates the performance, productivity, and resilience of bacterial communities in response to warming.
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Affiliation(s)
- Laura Seidel
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden.
| | - Elias Broman
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Emelie Nilsson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Magnus Ståhle
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Marcelo Ketzer
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Clara Pérez-Martínez
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Stephanie Turner
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Samuel Hylander
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Mark Dopson
- Centre for ecology and evolution in microbial model systems (EEMiS), Linnaeus University, Kalmar, Sweden
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91
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Complete Genome Sequence of Roseibium sp. Strain Sym1, a Bacterial Associate of Symbiodinium linucheae, the Microalgal Symbiont of the Anemone Aiptasia. Microbiol Resour Announc 2023; 12:e0111822. [PMID: 36790190 PMCID: PMC10019159 DOI: 10.1128/mra.01118-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
We sequenced the genome of Roseibium sp. strain Sym1, a strain isolated from a monoculture of a Symbiodiniaceae marine dinoflagellate, Symbiodinium linucheae, a microalgal symbiont of cnidarians. The completed genome consists of one circular chromosome of 6,694,563 bp and four plasmids of 192,102 bp, 160,136 bp, 120,881 bp, and 89,413 bp.
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92
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Degli Esposti M. The bacterial origin of mitochondria: Incorrect phylogenies and the importance of metabolic traits. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 374:1-35. [PMID: 36858653 DOI: 10.1016/bs.ircmb.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This article provides an updated review on the evolution of mitochondria from bacteria, which were likely related to extant alphaproteobacteria. Particular attention is given to the timeline of oxygen history on Earth and the entwined phases of eukaryotic evolution that produced the animals that still populate our planet. Mitochondria of early-branching unicellular eukaryotes and plants appear to retain partial or vestigial traits that were directly inherited from the alphaproteobacterial ancestors of the organelles. Most of such traits define the current aerobic physiology of mitochondria. Conversely, the anaerobic traits that would be essential in the syntrophic associations postulated for the evolution of eukaryotic cells are scantly present in extant alphaproteobacteria, and therefore cannot help defining from which bacterial lineage the ancestors of mitochondria originated. This question has recently been addressed quantitatively, reaching the novel conclusion that marine bacteria related to Iodidimonas may be the living relatives of protomitochondria. Additional evidence is presented that either support or does not contrast this novel view of the bacterial origin of mitochondria.
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93
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Xu CH, Chen G, Liu Y, Xiao W, Cui XL, Ding ZG, Liu WH, Wang YX. Azospirillum Aestuarii sp. nov., a Novel Nitrogen-Fixting and Aerobic Denitrifying Bacteria Isolated from an Estuary of a Freshwater River. Curr Microbiol 2023; 80:113. [PMID: 36823402 DOI: 10.1007/s00284-023-03213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
A novel Gram-staining negative, aerobic, rod-shaped bacterium, designated strain YIM DDC1T, was isolated from an estuary sediment sample of Dongda River flowing into Dianchi lake in Yunnan, southwest China. The strain displayed growth at 10-40 °C (optimum of 28 °C), pH 5.0-9.0 (optimum of 7.0-8.0) and in presence of 0-3% (w/v) NaCl (optimum of 0-1%). Strain YIM DDC1T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and two unidentified aminolipids as the predominant polar lipids; the ubiquinone 10 as the major respiratory quinone; and summed feature 8 (C18:1ω6c and/or C18:1ω7c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C18:1 2-OH as the major cellular fatty acids. Analysis of 16S rRNA showed that YIM DDC1T represents a member of the genus Azospirillum, and was closely related to A. brasilense ATCC 29145 T (98.9%), A. baldaniorum Sp245T (98.2%), A. argentinense Az39T (98.2%) and A. formosense CC-Nfb-7 T (98.2%). The draft genome size was 7.15 Mbp with a 68.4% G + C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain YIM DDC1T and the aforementioned closely related strains exhibited similarity in the range of 93.8-93.5% and 53.7-52.7%, respectively. nif gene cluster (nifHDK) and denitrification genes ((napA, nirS, nirK, norBC and nosZ) detected in the genome indicated its potential nitrogen fixation and full-fledged denitrifying function. Based on combined genotypic and phenotypic data, strain YIM DDC1T represents a novel species of the genus Azospirillum, for which the name Azospirillum aestuarii sp. nov. is proposed. The type strain is YIM DDC1T (= KCTC 42887 T = CGMCC 1.17325 T).
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Affiliation(s)
- Can-Hai Xu
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Gen Chen
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Yan Liu
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Wei Xiao
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Xiao-Long Cui
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Zhang-Gui Ding
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Wei-Hong Liu
- College of Agriculture and Biological Sciences, Dali University, Dali, Yunnan, 671003, People's Republic of China
| | - Yong-Xia Wang
- School of Life Sciences, Yunnan Institute of Microbiology, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.
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94
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An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0028122. [PMID: 36533907 PMCID: PMC9945509 DOI: 10.1128/jcm.00281-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.
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Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Nondomestic Animals Described in 2018 to 2021. J Clin Microbiol 2023; 61:e0142522. [PMID: 36533958 PMCID: PMC9945507 DOI: 10.1128/jcm.01425-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Revisions and new additions to bacterial taxonomy can have a significant widespread impact on clinical practice, infectious disease epidemiology, veterinary microbiology laboratory operations, and wildlife conservation efforts. The expansion of genome sequencing technologies has revolutionized our knowledge of the microbiota of humans, animals, and insects. Here, we address novel taxonomy and nomenclature revisions of veterinary significance that impact bacteria isolated from nondomestic wildlife, with emphasis being placed on bacteria that are associated with disease in their hosts or were isolated from host animal species that are culturally significant, are a target of conservation efforts, or serve as reservoirs for human pathogens.
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96
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Isolation and Genomics of Futiania mangrovii gen. nov., sp. nov., a Rare and Metabolically Versatile Member in the Class Alphaproteobacteria. Microbiol Spectr 2023; 11:e0411022. [PMID: 36541777 PMCID: PMC9927469 DOI: 10.1128/spectrum.04110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mangrove microorganisms are a major part of the coastal ecosystem and are directly associated with nutrient cycling. Despite their ecological significance, the collection of culturable mangrove microbes is limited due to difficulties in isolation and cultivation. Here, we report the isolation and genome sequence of strain FT118T, the first cultured representative of a previously uncultivated order UBA8317 within Alphaproteobacteria, based on the combined results of 16S rRNA gene similarity, phylogenomic, and average amino acid identity analyses. We propose Futianiales ord. nov. and Futianiaceae fam. nov. with Futiania as the type genus, and FT118T represents the type species with the name Futiania mangrovii gen. nov, sp. nov. The 16S rRNA gene sequence comparison reveals that this novel order is a rare member but has a ubiquitous distribution across various habitats worldwide, which is corroborated by the experimental confirmation that this isolate can physiologically adapt to a wide range of oxygen levels, temperatures, pH and salinity levels. Biochemical characterization, genomic annotation, and metatranscriptomic analysis of FT118T demonstrate that it is metabolically versatile and active in situ. Genomic analysis reveals adaptive features of Futianiales to fluctuating mangrove environments, including the presence of high- and low-affinity terminal oxidases, N-type ATPase, and the genomic capability of producing various compatible solutes and polyhydroxybutyrate, which possibly allow for the persistence of this novel order across various habitats. Collectively, these results expand the current culture collection of mangrove microorganisms, providing genomic insights of how this novel taxon adapts to fluctuating environments and the culture reference to unravel possible microbe-environment interactions. IMPORTANCE The rare biosphere constitutes an essential part of the microbial community and may drive nutrient cycling and other geochemical processes. However, the difficulty in microbial isolation and cultivation has hampered our understanding of the physiology and ecology of uncultured rare lineages. In this study, we successfully isolated a novel alphaproteobacterium, designated as FT118T, and performed a combination of phenotypic, phylogenetic, and phylogenomic analyses, confirming that this isolate represents the first cultured member of a previously uncultivated order UBA8317 within Alphaproteobacteria. It is a rare species with a ubiquitous distribution across different habitats. Genomic and metatranscriptomic analyses demonstrate that it is metabolically versatile and active in situ, suggesting its potential role in nutrient cycling despite being scarce. This work not only expands the current phylogeny of isolated Alphaproteobacteria but also provides genomic and culture reference to unravel microbial adaptation strategies in mangrove sediments and possible microbe-environment interactions.
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Ancylobacter moscoviensis sp. nov., novel facultatively methylotrophic bacteria from activated sludge and the reclassification of Starkeya novella (Starkey 1934) Kelly et al. 2000 as Ancylobacter novellus comb. nov., Starkeya koreensis Im et al. 2006 as Ancylobacter koreensis comb.nov., Angulomicrobium tetraedrale Vasil'eva et al. 1986 as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme Fritz et al. 2004 as Ancylobacter amanitiformis comb. nov., and Methylorhabdus multivorans Doronina et al. 1996 as Ancylobacter multivorans comb. nov., and emended description of the genus Ancylobacter. Antonie Van Leeuwenhoek 2023; 116:153-170. [PMID: 36462112 DOI: 10.1007/s10482-022-01788-8] [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: 05/16/2022] [Accepted: 10/23/2022] [Indexed: 12/04/2022]
Abstract
Three novel facultatively methylotrophic bacteria, strains 3CT, 1A, 8P, were isolated from activated sludges. The isolates were aerobic, Gram-stain-negative, non-motile, non-spore forming rods multiplying by binary fission. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethylethanolamine, phosphatidylmonomethylethanolamine, and diphosphatidylglycerol. The major fatty acids of cells were С18:1ω7c, C19:0ω8c cyclo and C16:0. Levels of 16S rRNA gene similarity indicates that the closely relatives are representatives of the genera Starkeya, Ancylobacter, Angulomicrobium and Methylorhabdus (96.4-99.4%). Genomic comparisons of 3CT and its closest relatives, S. novella DSM 506T and S. koreensis Jip08T, shared 87.3 and 86.8% nucleotide identity and 28.3 and 26.8% digital DNA-DNA hybridization values, respectively. The average amino acid identities between the strain 3CT and representatives of Starkeya, Ancylobacter and Angulomicrobium were in the range of 75.6-84.3%, which combines these strains into a single genus and gives rise to their reclassification. Based on polyphasic analyses, the strains 3CT, 1A, 8P represents a novel species of the genus Ancylobacter, for which the name Ancylobacter moscoviensis sp. nov. is proposed. The type strain is 3CT (= VKM B-3218T = KCTC 62336T). Furthermore, we also suggested the reclassification of Starkeya novella as Ancylobacter novellus comb. nov., Starkeya koreensis as Ancylobacter koreensis comb. nov., Angulomicrobium tetraedrale as Ancylobacter tetraedralis comb. nov., Angulomicrobium amanitiforme as Ancylobacter amanitiformis comb. nov. and Methylorhabdus multivorans as Ancylobacter multivorans comb. nov. with the emended description of the genus Ancylobacter.
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Guzman J, Won M, Poehlein A, Sombolestani AS, Mayorga-Ch D, Laureys D, Clippeleer JD, Kämpfer P, Daniel R, Vilcinskas A, Vandamme P, Kwon SW. Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749681 DOI: 10.1099/ijsem.0.005699] [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: 02/08/2023] Open
Abstract
Acetic acid bacteria (family Acetobacteraceae) are found in the gut of most insects. Two clades are currently recognized: Commensalibacter-Entomobacter and Bombella-Oecophyllibacter. The latter group is only found in hymenopteran insects and the described species have been isolated from bees and ants. In this study, two new strains DDB2-T1T (=KACC 21507T=LMG 31759T) and DM15PD (=CCM 9165=DSM 112731=KACC 22353=LMG 32454) were isolated from wasps collected in the Republic of Korea and Germany, respectively. Molecular and phenotypic analysis revealed that the strains are closely related, with 16S rRNA gene sequences showing 100 % identity and genomic average nucleotide identity (ANI) values ≥99 %. The closest related species based on type strain 16S rRNA gene sequences are Swingsia samuiensis, Acetobacter peroxydans, Bombella favorum and Bombella intestini (94.8-94.7% identity), whereas the closest related species based on type strain genome analysis are Saccharibacter floricola and Bombella intestini (ANI values of 68.8 and 68.2 %, respectively). The reconstruction of a phylogenomic tree based on 107 core proteins revealed that the branch leading to DDB2-T1T and DM15PD is localized between Oecophyllibacter and Saccharibacter-Bombella. Further genomic distance metrics such as ANI, percentage of conserved proteins and alignment fraction values were consistent with these strains belonging to a new genus. The key phenotypic characteristics were one MALDI-TOF-MS peak (m/z=4601.9±2.0) and the ability to produce acid from d-arabinose. Based on this polyphasic approach, including phylogenetics, phylogenomics, genome distance calculations, ecology and phenotypic characteristics, we propose to name the novel strains Aristophania vespae gen. nov., sp. nov., with the type strain DDB2-T1T (=KACC 21507T=LMG 31759T).
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Affiliation(s)
- Juan Guzman
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Miyoung Won
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Atena Sadat Sombolestani
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Daniela Mayorga-Ch
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - David Laureys
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jessika De Clippeleer
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University of Giessen, Giessen, Germany
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, Republic of Korea
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Gam ZBA, Thioye A, Cayol JL, Postec A, Bartoli-Joseph M, Vandecasteele C, Erauso G, Labat M. Thermospira aquatica gen. nov., sp. nov., a novel thermophilic spirochete isolated from a Tunisian hot spring, and description of the novel family Thermospiraceae. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748411 DOI: 10.1099/ijsem.0.005690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A novel thermophilic, anaerobic bacterium, strain F1F22T, was isolated from hot spring water collected in northern Tunisia. The cells were non-motile, Gram-negative and helical with hooked ends, 0.5×10-32 µm in size. Growth of the strain was observed at 45-70 °C (optimum, 55 °C), in 0.0-1.0 % (w/v) NaCl (optimum without NaCl) and at pH 6.5-8.5 (optimum, pH 7.5). Yeast extract was required for growth, and the strain grew on glucose, sucrose and maltose. The major fatty acids were C16:0 (40.2 %), iso-C16: 0 (30.2 %) and C16 :0 DMA (14.5 %). The genome consisted of a circular chromosome (2.5 Mb) containing 2672 predicted protein-encoding genes with a G+C content of 43.15 mol %. Based on a comparative 16S rRNA gene sequence analysis, strain F1F22T formed a deeply branching lineage within the phylum Spirochaetota, class Spirochaetia, order Brevinematales, and had only low sequence similarity to other species of the phylum (lower than 83 %). Genome-based analysis of average nucleotide identity and digital DNA-DNA hybridization of strain F1F22T with Treponema caldarium DSM 7334T, Brevinema andersonii ATCC 43811T and Spirochaeta thermophila DSM 6578T showed values between 63.26 and 63.52 %, and between 20 and 25 %. Hence, we propose strain F1F22T as a representative of a novel family (Thermospiraceae fam. nov.), genus and species of Brevinematales: Thermospira aquatica gen. nov., sp. nov. (type strain F1F22T=JCM 31314T=DSM 101182T).
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Affiliation(s)
- Zouhaier Ben Ali Gam
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Abdoulaye Thioye
- Université Cheikh Anta Diop, Ecole Supérieure Polytechnique, Laboratoire de Microbiologie Appliquée et de Génie Industriel, BP 5005, Dakar-Fann, Dakar, Sénégal
| | - Jean-Luc Cayol
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Anne Postec
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Manon Bartoli-Joseph
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | | | - Gaël Erauso
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
| | - Marc Labat
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Mediterranean Institute of Oceanography, 163 avenue de Luminy, F-13288, Marseille, France
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Rai A, Suresh G, Ria B, L V, Pk S, Ipsita S, Sasikala C, Venkata Ramana C. Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 36748586 DOI: 10.1099/ijsem.0.005672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.
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Affiliation(s)
- Anusha Rai
- 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
| | - Biswas Ria
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Vighnesh L
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sreya Pk
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Sahu Ipsita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad-500 085, 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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