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Luo J, Li J, Wang C, Li M, Hu S, Lu K, Wang G. Rubellicoccus peritrichatus gen. nov., sp. nov., isolated from crustose coralline algae in a coral aquarium. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568201 DOI: 10.1099/ijsem.0.006325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
A Gram-stain-negative, motile, aerobic, non-spore-forming coccus, designated strain CR14T, was isolated from crustose coralline algae. Cells grew at 20-30 °C (optimum, 25 °C), at pH 6-9 (optimum, pH 7.6) and with NaCl concentrations of 0.5-9 % (w/v; optimum, 2-4 %). Global alignment based on 16S rRNA gene sequences indicated strain CR14T is closest to Ruficoccus amylovorans JCM 31066T with an identity of 92 %. The average nucleotide identity and average amino acid identity values between CR14T and R. amylovorans JCM 31066T were 68.4 and 59.9 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CR14T forms an independent branch within the family Cerasicoccaeae, which was consistent with the phylogenomic results. The sole isoprenoid quinone was MK-7. The major fatty acids were C14 : 0, C18 : 1 ω9c, C19 : 0 cyc 9,10 DMA, C16 : 0, and C18 : 2 ω6c. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and two unidentified lipids. The genome DNA G+C content was 48.7 mol%. Based on morphological, physiological and chemotaxonomic characteristics, strain CR14T is suggested to represent a novel species in a new genus, for which the name Rubellicoccus peritrichatus gen. nov., sp. nov. is proposed. The type strain is CR14T (=MCCC 1K03845T=KCTC 72139T).
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Affiliation(s)
- Jixin Luo
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Jin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Chenyan Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Mi Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Siyu Hu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Kun Lu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
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Discovering symbiosis in the supralittoral: bacterial metabarcoding analysis from the hepatopancreas of Orchestia and Tylos (Crustacea). Symbiosis 2021. [DOI: 10.1007/s13199-021-00749-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Feng X, Zou QH, Zhang XY, Ye MQ, Du ZJ. Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae. Int J Syst Evol Microbiol 2020; 70:5654-5664. [PMID: 32931410 DOI: 10.1099/ijsem.0.004458] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic coccus, designated CK1056T, was isolated from coastal sediment of Xiaoshi Island, Weihai, PR China. Strain CK1056T was found to grow at 15-37 °C (optimum, 30 °C), with 0.5-6.5 % (w/v) NaCl (optimum, 3.5 %) and displayed alkaliphilic growth within the pH range of pH 6.5-10.0 (optimum, pH 8.0). The major fatty acids identified were iso-C15 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The main polar lipids consisted of aminophosphoglycolipid and phosphatidylethanolamine. The predominant respiratory quinone was MK-7. The G+C content of the genomic DNA was 54.0 mol%. The result of the 16S rRNA gene sequence analysis confirmed the affiliation of this micro-organism to the family Puniceicoccaceae, with Coraliomargarita akajimensis KCTC 12865T as its closest relative with only 88.0 % sequence similarity. From the taxonomic data obtained in this study, we propose that the new marine isolate be placed into a novel species within a novel genus in the family Puniceicoccaceae, phylum Verrucomicrobia, for which the name Oceanipulchritudo coccoides gen. nov., sp. nov. is proposed. The type strain is CK1056T (=KCTC 72798T=MCCC 1H00425T).
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Affiliation(s)
- Xi Feng
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Qi-Hang Zou
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Xiao-Yu Zhang
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Meng-Qi Ye
- Marine College, Shandong University, Weihai, Shandong 264209, PR China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.,Marine College, Shandong University, Weihai, Shandong 264209, PR China
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Sizikov S, Burgsdorf I, Handley KM, Lahyani M, Haber M, Steindler L. Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales. Environ Microbiol 2020; 22:4669-4688. [PMID: 32840024 DOI: 10.1111/1462-2920.15210] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/18/2020] [Accepted: 08/22/2020] [Indexed: 12/13/2022]
Abstract
Bacteria of the phylum Verrucomicrobia are ubiquitous in marine environments and can be found as free-living organisms or as symbionts of eukaryotic hosts. Little is known about host-associated Verrucomicrobia in the marine environment. Here we reconstructed two genomes of symbiotic Verrucomicrobia from bacterial metagenomes derived from the Atlanto-Mediterranean sponge Petrosia ficiformis and three genomes from strains that we isolated from offshore seawater of the Eastern Mediterranean Sea. Phylogenomic analysis of these five strains indicated that they are all members of Verrucomicrobia subdivision 4, order Opitutales. We compared these novel sponge-associated and seawater-isolated genomes to closely related Verrucomicrobia. Genomic analysis revealed that Planctomycetes-Verrucomicrobia microcompartment gene clusters are enriched in the genomes of symbiotic Opitutales including sponge symbionts but not in free-living ones. We hypothesize that in sponge symbionts these microcompartments are used for degradation of l-fucose and l-rhamnose, which are components of algal and bacterial cell walls and therefore may be found at high concentrations in the sponge tissue. Furthermore, we observed an enrichment of toxin-antitoxin modules in symbiotic Opitutales. We suggest that, in sponges, verrucomicrobial symbionts utilize these modules as a defence mechanism against antimicrobial activity deriving from the abundant microbial community co-inhabiting the host.
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Affiliation(s)
- Sofia Sizikov
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Kim Marie Handley
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Matan Lahyani
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel.,Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
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Doherty M, Yager PL, Moran MA, Coles VJ, Fortunato CS, Krusche AV, Medeiros PM, Payet JP, Richey JE, Satinsky BM, Sawakuchi HO, Ward ND, Crump BC. Bacterial Biogeography across the Amazon River-Ocean Continuum. Front Microbiol 2017; 8:882. [PMID: 28588561 PMCID: PMC5440517 DOI: 10.3389/fmicb.2017.00882] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
Spatial and temporal patterns in microbial biodiversity across the Amazon river-ocean continuum were investigated along ∼675 km of the lower Amazon River mainstem, in the Tapajós River tributary, and in the plume and coastal ocean during low and high river discharge using amplicon sequencing of 16S rRNA genes in whole water and size-fractionated samples (0.2–2.0 μm and >2.0 μm). River communities varied among tributaries, but mainstem communities were spatially homogeneous and tracked seasonal changes in river discharge and co-varying factors. Co-occurrence network analysis identified strongly interconnected river assemblages during high (May) and low (December) discharge periods, and weakly interconnected transitional assemblages in September, suggesting that this system supports two seasonal microbial communities linked to river discharge. In contrast, plume communities showed little seasonal differences and instead varied spatially tracking salinity. However, salinity explained only a small fraction of community variability, and plume communities in blooms of diatom-diazotroph assemblages were strikingly different than those in other high salinity plume samples. This suggests that while salinity physically structures plumes through buoyancy and mixing, the composition of plume-specific communities is controlled by other factors including nutrients, phytoplankton community composition, and dissolved organic matter chemistry. Co-occurrence networks identified interconnected assemblages associated with the highly productive low salinity near-shore region, diatom-diazotroph blooms, and the plume edge region, and weakly interconnected assemblages in high salinity regions. This suggests that the plume supports a transitional community influenced by immigration of ocean bacteria from the plume edge, and by species sorting as these communities adapt to local environmental conditions. Few studies have explored patterns of microbial diversity in tropical rivers and coastal oceans. Comparison of Amazon continuum microbial communities to those from temperate and arctic systems suggest that river discharge and salinity are master variables structuring a range of environmental conditions that control bacterial communities across the river-ocean continuum.
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Affiliation(s)
- Mary Doherty
- Horn Point Laboratory, University of Maryland Center for Environmental Science, CambridgeMD, United States
| | - Patricia L Yager
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Victoria J Coles
- Horn Point Laboratory, University of Maryland Center for Environmental Science, CambridgeMD, United States
| | - Caroline S Fortunato
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods HoleMA, United States
| | - Alex V Krusche
- Center of Nuclear Energy in Agriculture, University of São PauloPiracicaba, Brazil
| | - Patricia M Medeiros
- Department of Marine Sciences, University of Georgia, AthensGA, United States
| | - Jérôme P Payet
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, CorvallisOR, United States
| | - Jeffrey E Richey
- School of Oceanography, University of Washington, SeattleWA, United States
| | | | - Henrique O Sawakuchi
- Center of Nuclear Energy in Agriculture, University of São PauloPiracicaba, Brazil
| | - Nicholas D Ward
- Marine Sciences Laboratory, Pacific Northwest National Laboratory, SequimWA, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, CorvallisOR, United States
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Lin SY, Hameed A, Liu YC, Hsu YH, Hung MH, Lai WA, Young CC. Ruficoccus amylovorans gen. nov., sp. nov., an amylolytic and nitrate-reducing diazotroph of the family Puniceicoccaceae. Int J Syst Evol Microbiol 2017; 67:956-962. [DOI: 10.1099/ijsem.0.001723] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Shih-Yao Lin
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Asif Hameed
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - You-Cheng Liu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Yi-Han Hsu
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Mei-Hua Hung
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Wei-An Lai
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Chiu-Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
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Rast P, Glöckner I, Boedeker C, Jeske O, Wiegand S, Reinhardt R, Schumann P, Rohde M, Spring S, Glöckner FO, Jogler C, Jogler M. Three Novel Species with Peptidoglycan Cell Walls form the New Genus Lacunisphaera gen. nov. in the Family Opitutaceae of the Verrucomicrobial Subdivision 4. Front Microbiol 2017; 8:202. [PMID: 28243229 PMCID: PMC5303756 DOI: 10.3389/fmicb.2017.00202] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/27/2017] [Indexed: 11/13/2022] Open
Abstract
The cell wall of free-living bacteria consists of peptidoglycan (PG) and is critical for maintenance of shape as dissolved solutes cause osmotic pressure and challenge cell integrity. Surprisingly, the subdivision 4 of the phylum Verrucomicrobia appears to be exceptional in this respect. Organisms of this subdivision are described to be devoid of muramic or diaminopimelic acid (DAP), usually found as components of PG in bacterial cell walls. Here we describe three novel bacterial strains from a freshwater lake, IG15T, IG16bT, and IG31T, belonging to a new genus in the subdivision 4 of Verrucomicrobia which we found to possess PG as part of their cell walls. Biochemical analysis revealed the presence of DAP not only in these novel strains, but also in Opitutus terrae PB90-1T, the closest described relative of strains IG15T, IG16bT, and IG31T. Furthermore, we found that nearly all genes necessary for peptidoglycan synthesis are present in genomes of subdivision 4 members, as well as in the complete genome sequence of strain IG16bT. In addition, we isolated and visualized PG-sacculi for strain IG16bT. Thus, our results challenge the concept of peptidoglycan-less free-living bacteria. Our polyphasic taxonomy approach places the novel strains in a new genus within the family Opitutaceae, for which the name Lacunisphaera gen. nov. is proposed. Strain designations for IG15T, IG16bT and IG31T are Lacunisphaera parvula sp. nov. (=DSM 26814 = LMG 29468), L. limnophila sp. nov. (=DSM 26815 = LMG 29469) and L. anatis sp. nov. (=DSM 103142 = LMG 29578) respectively, with L. limnophila IG16bT being the type species of the genus.
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Affiliation(s)
- Patrick Rast
- Microbial Cell Biology and Genetics, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany
| | - Ines Glöckner
- Institute for Pharmacology, Toxicology and Clinical Pharmacy, University of Technology Braunschweig, Germany
| | - Christian Boedeker
- Microbial Cell Biology and Genetics, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany
| | - Olga Jeske
- Microbial Cell Biology and Genetics, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany
| | - Sandra Wiegand
- Microbial Cell Biology and Genetics, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany
| | - Richard Reinhardt
- Max Planck Genome Center, Max Planck Institute for Plant Breeding Research Köln, Germany
| | - Peter Schumann
- Department of Central Services, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research Braunschweig, Germany
| | - Stefan Spring
- Department Microorganisms, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany
| | - Frank O Glöckner
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Christian Jogler
- Microbial Cell Biology and Genetics, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHBraunschweig, Germany; Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud UniversityNijmegen, Netherlands
| | - Mareike Jogler
- Microbial Cell Biology and Genetics, Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Braunschweig, Germany
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Lin JY, Russell JA, Sanders JG, Wertz JT. Cephaloticoccus gen. nov., a new genus of 'Verrucomicrobia' containing two novel species isolated from Cephalotes ant guts. Int J Syst Evol Microbiol 2016; 66:3034-3040. [PMID: 27154284 DOI: 10.1099/ijsem.0.001141] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Two novel members of the bacterial phylum 'Verrucomicrobia', strains CAG34T and CV41T, were isolated from the guts of Cephalotes rohweri and Cephalotes varians ants, respectively. Strains CAG34T and CV41T were coccoid, Gram-stain-negative, non-motile, and formed cream-coloured colonies on trypticase soy agar. Optimum growth occurred under an atmosphere of 12-20 % O2 and 1 % CO2 for both strains, although strain CV41T could not grow without supplemental CO2. Growth was possible under NaCl concentrations of 0.5-1.5 % (w/v) and temperatures of 23-37 °C for both strains, and pH values of 6.9-7.7 for strain CAG34T and 6.9-7.3 for strain CV41T. The G+C content of the genomic DNA was 60.7 mol% for strain CAG34T and 60.5 mol% for strain CV41T. The major fatty acids for both strains were anteiso-C15 : 0, iso-C14 : 0, C16 : 0, and C16 : 1ω5c. Based on the phylogenetic analysis of 16S rRNA gene sequences, the closest cultivated relative for both strains was the type strain of Opitutus terrae (91.8 % similarity). Hence, strains CAG34T and CV41T are considered to represent a new genus within the 'Verrucomicrobia' family Opitutaceae, for which we propose the name Cephaloticoccus gen. nov. Given that strains CAG34T and CV41T share 97.7 % 16S rRNA gene sequence similarity with each other and are physiologically distinct, we propose to classify the isolates as representing two novel species, Cephaloticoccus primus sp. nov. for strain CAG34T (=NCIMB 15004T =ATCC TSD-38T) and Cephaloticoccus capnophilus sp. nov. for strain CV41T (=NCIMB 15005T =ATCC TSD-39T =DSM 100879T).
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Affiliation(s)
- Jonathan Y Lin
- Department of Biology, Calvin College, Grand Rapids, MI, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, PA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - John T Wertz
- Department of Biology, Calvin College, Grand Rapids, MI, USA
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Genomic and physiological characterization of the Verrucomicrobia isolate Geminisphaera colitermitum gen. nov., sp. nov., reveals microaerophily and nitrogen fixation genes. Appl Environ Microbiol 2011; 78:1544-55. [PMID: 22194293 DOI: 10.1128/aem.06466-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previously we reported the cultivation of novel verrucomicrobia, including strain TAV2 (93% 16S rRNA gene identity to its nearest cultivated representative, Opitutus terreae PB90-1) from the gut of the termite Reticulitermes flavipes. To gain better insight into the Verrucomicrobia as a whole and understand the role of verrucomicrobia within the termite gut ecosystem, we analyzed a draft genome and undertook a physiological characterization of TAV2. Strain TAV2 is an autochthonous member of the R. flavipes gut microbiota and groups phylogenetically among diverse Verrucomicrobia from R. flavipes and other termites that are represented by 16S rRNA gene sequences alone. TAV2 is a microaerophile, possessing a high-affinity cbb(3)-type terminal oxidase-encoding gene and exhibiting an optimum growth rate between 2 and 8% (vol/vol) oxygen. It has the genetic potential to degrade cellulose, an important function within termite guts, but its in vitro substrate utilization spectrum was limited to starch and a few mono- and disaccharides. Growth occurred on nitrogen-free medium, and genomic screening revealed genes for dinitrogenases, heretofore detected in only a few members of the Verrucomicrobia. This represents the first (i) characterization of a verrucomicrobial species from the termite gut, (ii) report of nif and anf genes in a nonacidophilic verrucomicrobial species, and (iii) description of a microaerophilic genotype and phenotype in this phylum of bacteria. The genetic and physiological distinctiveness of TAV2 supports its recognition as the type strain of a new genus and species, for which the name Geminisphaera colitermitum gen. nov., sp. nov., is proposed.
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Domman DB, Steven BT, Ward NL. Random transposon mutagenesis of Verrucomicrobium spinosum DSM 4136(T). Arch Microbiol 2010; 193:307-12. [PMID: 21184215 DOI: 10.1007/s00203-010-0666-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/01/2010] [Accepted: 12/06/2010] [Indexed: 01/09/2023]
Abstract
The Verrucomicrobia are a bacterial group of growing interest due to their environmental ubiquity as free-living and host-associated microbes. They also exhibit an unusual compartmentalized cell plan, shared with members of neighboring phyla that include the Planctomycete bacteria. However, Verrucomicrobia are currently difficult to study, due to a lack of available genetic tools that would permit robust testing of hypotheses formulated from ecological and genomic data. To our knowledge, there are no published studies describing the transformation of exogenous DNA into any members of the Verrucomicrobia (or the neighboring phylum containing Planctomycetes). Here, we present a procedure for the transformation of DNA into Verrucomicrobium spinosum DSM 4136(T) via electroporation and the first description of a random transposon mutant library in this organism. We anticipate that this approach could be applied successfully to other Verrucomicrobia, providing opportunities to test the role of predicted gene function in ecological interactions and identify genes associated with the distinctive Planctomycete-Verrucomicrobial cell plan.
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Affiliation(s)
- Daryl B Domman
- Department of Molecular Biology, University of Wyoming, Dept 3944, 1000 E. University Ave, Laramie, WY 82071, USA
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11
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Yoon J, Matsuo Y, Matsuda S, Kasai H, Yokota A. Cerasicoccus maritimus sp. nov. and Cerasicoccus frondis sp. nov., two peptidoglycan-less marine verrucomicrobial species, and description of Verrucomicrobia phyl. nov., nom. rev. J GEN APPL MICROBIOL 2010; 56:213-22. [PMID: 20647678 DOI: 10.2323/jgam.56.213] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Three Gram-negative, pale-pink-pigmented, spherical, chemoheterotrophic bacteria were isolated from seawater and a dystrophic leaf in the Republic of Palau. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel isolates YM31-114(T), YM31-066(T) and YM31-067 shared approximately 97-100% sequence similarity with members of the genus Cerasicoccus of the family Puniceicoccaceae within the phylum 'Verrucomicrobia.' The hybridization values for DNA-DNA relatedness between the novel isolates and Cerasicoccus arenae YM26-026(T) were less than 70%, which is accepted as a phylogenetic definition of a species. beta-Lactam antibiotic susceptibility test and amino acid analysis of cell-wall hydrolysates revealed that the novel isolates did not contain muramic acid or diaminopimelic acid in their cell walls, suggesting that these strains lack peptidoglycan. The DNA G+C contents of the three strains were 55-56 mol%; MK-7 was the major menaquinone. The presence of C14:0 and C18:1omega9c as the major cellular fatty acids supported the identification of the novel isolates as members of the genus Cerasicoccus. On the basis of polyphasic taxonomic evidence, it was concluded that these strains should be classified as representing two novel, separate species in the genus Cerasicoccus within the phylum 'Verrucomicrobia,' for which the names Cerasicoccus maritimus sp. nov. (type strain YM31-114(T)=MBIC24844(T)) and Cerasicoccus frondis sp. nov. (type strain YM31-066(T)=MBIC24796(T)) are proposed. Proposal for designation of the Verrucomicrobia phyl. nov., nom. rev. is also presented.
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Affiliation(s)
- Jaewoo Yoon
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
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12
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Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Woyke T, Goodwin L, Pitluck S, Held B, Brettin T, Tapia R, Ivanova N, Mikhailova N, Pati A, Liolios K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC. Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24). Stand Genomic Sci 2010; 2:290-9. [PMID: 21304713 PMCID: PMC3035286 DOI: 10.4056/sigs.952166] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coraliomargarita akajimensis Yoon et al. 2007 is the type species of the genus Coraliomargarita. C. akajimensis is an obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium that was isolated from seawater surrounding the hard coral Galaxea fascicularis. C. akajimensis is of special interest because of its phylogenetic position in a genomically under-studied area of the bacterial diversity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Puniceicoccaceae. The 3,750,771 bp long genome with its 3,137 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Matsuzawa H, Tanaka Y, Tamaki H, Kamagata Y, Mori K. Culture-Dependent and Independent Analyses of the Microbial Communities Inhabiting the Giant Duckweed (Spirodela polyrrhiza) Rhizoplane and Isolation of a Variety of Rarely Cultivated Organisms within the Phylum Verrucomicrobia. Microbes Environ 2010; 25:302-8. [DOI: 10.1264/jsme2.me10144] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hiroaki Matsuzawa
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
| | - Yasuhiro Tanaka
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoichi Kamagata
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
- Research Faculty of Agriculture, Hokkaido University
| | - Kazuhiro Mori
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
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Kielak A, Rodrigues JL, Kuramae EE, Chain PS, Van Veen JA, Kowalchuk GA. Phylogenetic and metagenomic analysis of Verrucomicrobiaâin former âagricultural grassland soil. FEMS Microbiol Ecol 2010; 71:23-33. [DOI: 10.1111/j.1574-6941.2009.00785.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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