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Vitorino IR, Klimek D, Calusinska M, Lobo-da-Cunha A, Vasconcelos V, Lage OM. Stieleria sedimenti sp. nov., a Novel Member of the Family Pirellulaceae with Antimicrobial Activity Isolated in Portugal from Brackish Sediments. Microorganisms 2022; 10:2151. [PMID: 36363743 PMCID: PMC9692418 DOI: 10.3390/microorganisms10112151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 09/23/2023] Open
Abstract
The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleriaisolate designated as strain ICT_E10.1T, obtained from sediments collected in the Tagus estuary (Portugal). Strain ICT_E10.1T is pink-pigmented, spherical to ovoid in shape, and 1.7 µm ± 0.3 × 1.4 µm ± 0.3 in size. Cells cluster strongly in aggregates or small chains, divide by budding, and have prominent fimbriae. Strain ICT_E10.1T is heterotrophic and aerobic. Growth occurs from 20 to 30 °C, from 0.5 to 3% (w/v) NaCl, and from pH 6.5 to 11.0. The analysis of the 16S rRNA gene sequence placed strain ICT_E10.1T into the genus Stieleria with Stieleria neptunia Enr13T as the closest validly described relative. The genome size is 9,813,311 bp and the DNA G+C content is 58.8 mol%. Morphological, physiological, and genomic analyses support the separation of this strain into a novel species, for which we propose the name Stieleria sedimenti represented by strain ICT_E10.1T as the type of strain (=CECT 30514T= DSM 113784T). Furthermore, this isolate showed biotechnological potential by displaying relevant biosynthetic gene clusters and potent activity against Staphylococcus aureus.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Dominika Klimek
- The Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 2 Avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Magdalena Calusinska
- The Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg
| | - Alexandre Lobo-da-Cunha
- Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Vasconcelos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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Anatilimnocola floriformis sp. nov., a novel member of the family Pirellulaceae from a boreal lake, and emended description of the genus Anatilimnocola. Antonie Van Leeuwenhoek 2022; 115:1253-1264. [DOI: 10.1007/s10482-022-01769-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
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Perez-Mon C, Stierli B, Plötze M, Frey B. Fast and persistent responses of alpine permafrost microbial communities to in situ warming. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150720. [PMID: 34610405 DOI: 10.1016/j.scitotenv.2021.150720] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Global warming in mid-latitude alpine regions results in permafrost thawing, together with greater availability of carbon and nutrients in soils and frequent freeze-thaw cycles. Yet it is unclear how these multifactorial changes will shape the 1 m-deep permafrost microbiome in the future, and how this will in turn modulate microbially-mediated feedbacks between mountain soils and climate (e.g. soil CO2 emissions). To unravel the responses of the alpine permafrost microbiome to in situ warming, we established a three-year experiment in a permafrost monitoring summit in the Alps. Specifically, we simulated conditions of warming by transplanting permafrost soils from a depth of 160 cm either to the active-layer topsoils in the north-facing slope or in the warmer south-facing slope, near the summit. qPCR-based and amplicon sequencing analyses indicated an augmented microbial abundance in the transplanted permafrost, driven by the increase in copiotrophic prokaryotic taxa (e.g. Noviherbaspirillum and Massilia) and metabolically versatile psychrotrophs (e.g. Tundrisphaera and Granulicella); which acclimatized to the changing environment and potentially benefited from substrates released upon thawing. Metabolically restricted Patescibacteria lineages vastly decreased with warming, as reflected in the loss of α-diversity in the transplanted soils. Ascomycetous sapro-pathotrophs (e.g. Tetracladium) and a few lichenized fungi (e.g. Aspicilia) expanded in the transplanted permafrost, particularly in soils transplanted to the warmer south-facing slope, replacing basidiomycetous yeasts (e.g. Glaciozyma). The transplantation-induced loosening of microbial association networks in the permafrost could potentially indicate lesser cooperative interactions between neighboring microorganisms. Broader substrate-use microbial activities measured in the transplanted permafrost could relate to altered soil C dynamics. The three-year simulated warming did not, however, enhance heterotrophic respiration, which was limited by the carbon-depleted permafrost conditions. Collectively, our quantitative findings suggest the vulnerability of the alpine permafrost microbiome to warming, which might improve predictions on microbially-modulated transformations of mountain soil ecosystems under the future climate.
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Affiliation(s)
- Carla Perez-Mon
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Michael Plötze
- Institute for Geotechnical Engineering, ETH Zurich, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
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Vitorino IR, Lage OM. The Planctomycetia: an overview of the currently largest class within the phylum Planctomycetes. Antonie van Leeuwenhoek 2022; 115:169-201. [PMID: 35037113 DOI: 10.1007/s10482-021-01699-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 01/21/2023]
Abstract
The phylum Planctomycetes comprises bacteria with uncommon features among prokaryotes, such as cell division by budding, absence of the bacterial tubulin-homolog cell division protein FtsZ and complex cell plans with invaginations of the cytoplasmic membrane. Although planctomycetes are ubiquitous, the number of described species and isolated strains available as axenic cultures is still low compared to the diversity observed in metagenomes or environmental studies. An increasing interest in planctomycetes is reflected by the recent description of a large number of new species and their increasing accessibility in terms of pure cultures. In this review, data from all taxonomically described species belonging to Planctomycetia, the class with the currently highest number of characterized members within the phylum Planctomycetes, is summarized. Phylogeny, morphology, physiology, ecology and genomic traits of its members are discussed. This comprehensive overview will help to acknowledge several aspects of the biology of these fascinating bacteria.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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Phylo-taxogenomics of the genus Tautonia with descriptions of Tautonia marina sp. nov., Tautonia rosea sp. nov., and emended description of the genus. Syst Appl Microbiol 2021; 44:126229. [PMID: 34273679 DOI: 10.1016/j.syapm.2021.126229] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 12/21/2022]
Abstract
Four strains of Planctomycetes, (JC636, JC649, JC650T, JC657T) which are all salt and alkali tolerant, pink coloured, with spherical to oval shaped, Gram-stain-negative, non-motile cells were isolated from different regions of Chilika lagoon, India. All strains have obligate requirement for N-acetylglucosamine (NAG) and share highest 16S rRNA gene sequence identity with members of the genus Tautonia (<95%) of the family Isosphaeraceae. The 16S rRNA gene sequence identity between strains was >99.5%. Respiratory quinone for all the strains was MK6. Major fatty acids of all the strains were C18:1ω9c, C16:0 and C18:0. Major polar lipid of the strain JC650T was phosphatidylethanolamine, while, phosphatidylcholine and phosphatidylglycerol for strain JC657T. Spermidine was the only common polyamine for all the four strains. Strains JC657T, JC636 and JC649 shared highest phenotypic similarity along with 100% 16S rRNA gene sequence identity. Strains JC657T, JC636 and JC649 differed from strain JC650T phenotypically, chemotaxonomically and genotypically, thus belong to a different species. The genomic size of strain JC650T and JC657T are 7.06 Mb and 6.96 Mb with DNA G + C content of 63.9 and 62.7 mol%, respectively. Based on phylogenetic, genomic (ANI, AAI, POCP, dDDH), chemotaxonomic, physiological and biochemical characteristics, we conclude that strains JC650T and JC657T (together with strains JC636, JC649) belong to the genus Tautonia and constitute two novel species for which we propose the names Tautonia marina sp. nov., and Tautonia rosea sp. nov., respectively. These two novel species are represented by the type strains JC650T (=KCTC 72177T = NBRC 113885T) and JC657T (=KCTC 72597T = NBRC 113883T) respectively.
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Trimethylornithine Membrane Lipids: Discovered in Planctomycetes and Identified in Diverse Environments. Metabolites 2021; 11:metabo11010049. [PMID: 33445571 PMCID: PMC7828035 DOI: 10.3390/metabo11010049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
Intact polar membrane lipids (IPLs) are the building blocks of all cell membranes. There is a wide range of phosphorus-free IPL structures, including amino acid containing IPLs, that can be taxonomically specific. Trimethylornithine membrane lipids (TMOs) were discovered in northern wetland Planctomycete species that were isolated and described in the last decade. The trimethylated terminal nitrogen moiety of the ornithine amino acid in the TMO structure gives the lipid a charged polar head group, similar to certain phospholipids. Since their discovery, TMOs have been identified in various other recently described northern latitude Planctomycete species, and in diverse environments including tundra soil, a boreal eutrophic lake, meso-oligotrophic lakes, and hot springs. The majority of environments or enrichment cultures in which TMOs have been observed include predominately heterotrophic microbial communities involved in the degradation of recalcitrant material and/or low oxygen methanogenic conditions at primarily northern latitudes. Other ecosystems occupied with microbial communities that possess similar metabolic pathways, such as tropical peatlands or coastal salt marshes, may include TMO producing Planctomycetes as well, further allowing these lipids to potentially be used to understand microbial community responses to environmental change in a wide range of systems. The occurrence of TMOs in hot springs indicates that these unique lipids could have broad environmental distribution with different specialized functions. Opportunities also exist to investigate the application of TMOs in microbiome studies, including forensic necrobiomes. Further environmental and microbiome lipidomics research involving TMOs will help reveal the evolution, functions, and applications of these unique membrane lipids.
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Jogler C, Wiegand S, Boedeker C, Heuer A, Peeters SH, Jogler M, Jetten MSM, Rohde M, Kallscheuer N. Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago. Antonie Van Leeuwenhoek 2020; 113:1889-1900. [PMID: 32399714 PMCID: PMC7716859 DOI: 10.1007/s10482-020-01424-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023]
Abstract
A novel planctomycetal strain, designated ElPT, was isolated from an alga in the shallow hydrothermal vent system close to Panarea Island in the Tyrrhenian Sea. Cells of strain ElPT are spherical, form pink colonies and display typical planctomycetal characteristics including division by budding and presence of crateriform structures. Strain ElPT has a mesophilic (optimum at 30 °C) and neutrophilic (optimum at pH 7.5) growth profile, is aerobic and heterotrophic. It reaches a generation time of 29 h (µmax = 0.024 h-1). The strain has a genome size of 9.40 Mb with a G + C content of 71.1% and harbours five plasmids, the highest number observed in the phylum Planctomycetes thus far. Phylogenetically, the strain represents a novel species of the recently described genus Tautonia in the family Isosphaeraceae. A characteristic feature of the strain is its tendency to attach strongly to a range of plastic surfaces. We thus propose the name Tautonia plasticadhaerens sp. nov. for the novel species, represented by the type strain ElPT (DSM 101012T = LMG 29141T).
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Affiliation(s)
- Christian Jogler
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
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Kaboré OD, Godreuil S, Drancourt M. Planctomycetes as Host-Associated Bacteria: A Perspective That Holds Promise for Their Future Isolations, by Mimicking Their Native Environmental Niches in Clinical Microbiology Laboratories. Front Cell Infect Microbiol 2020; 10:519301. [PMID: 33330115 PMCID: PMC7734314 DOI: 10.3389/fcimb.2020.519301] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Traditionally recognized as environmental bacteria, Planctomycetes have just been linked recently to human pathology as opportunistic pathogens, arousing a great interest for clinical microbiologists. However, the lack of appropriate culture media limits our future investigations as no Planctomycetes have ever been isolated from patients' specimens despite several attempts. Several Planctomycetes have no cultivable members and are only recognized by 16S rRNA gene sequence detection and analysis. The cultured representatives are slow-growing fastidious bacteria and mostly difficult to culture on synthetic media. Accordingly, the provision of environmental and nutritional conditions like those existing in the natural habitat where yet uncultured/refractory bacteria can be detected might be an option for their potential isolation. Hence, we systematically reviewed the various natural habitats of Planctomycetes, to review their nutritional requirements, the physicochemical characteristics of their natural ecological niches, current methods of cultivation of the Planctomycetes and gaps, from a perspective of collecting data in order to optimize conditions and the protocols of cultivation of these fastidious bacteria. Planctomycetes are widespread in freshwater, seawater, and terrestrial environments, essentially associated to particles or organisms like macroalgae, marine sponges, and lichens, depending on the species and metabolizable polysaccharides by their sulfatases. Most Planctomycetes grow in nutrient-poor oligotrophic environments with pH ranging from 3.4 to 11, but a few strains can also grow in quite nutrient rich media like M600/M14. Also, a seasonality variation of abundance is observed, and bloom occurs in summer-early autumn, correlating with the strong growth of algae in the marine environments. Most Planctomycetes are mesophilic, but with a few Planctomycetes being thermophilic (50°C to 60°C). Commonly added nutrients are N-acetyl-glucosamine, yeast-extracts, peptone, and some oligo and macro-elements. A biphasic host-associated extract (macroalgae, sponge extract) conjugated with a diluted basal medium should provide favorable results for the success of isolation in pure culture.
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Affiliation(s)
- Odilon D. Kaboré
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Sylvain Godreuil
- Université de Montpellier UMR 1058 UMR MIVEGEC, UMR IRD 224-CNRS Inserm, Montpellier, France
| | - Michel Drancourt
- Aix Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
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Dedysh SN, Ivanova AA. Planctomycetes in boreal and subarctic wetlands: diversity patterns and potential ecological functions. FEMS Microbiol Ecol 2019; 95:5195516. [PMID: 30476049 DOI: 10.1093/femsec/fiy227] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/18/2018] [Indexed: 12/13/2022] Open
Abstract
Members of the phylum Planctomycetes are common inhabitants of boreal Sphagnum peat bogs and lichen-dominated tundra wetlands. These bacteria colonize both oxic and anoxic peat layers and reach the population size of 107 cells per gram of wet peat. The 16S rRNA gene sequences from planctomycetes comprise 5%-22% of total 16S rRNA gene reads retrieved from peat samples. Most abundant peat-inhabiting planctomycetes affiliate with the families Isosphaeraceae and Gemmataceae, and with as-yet-uncultured Phycisphaera-related group WD2101. The use of metatranscriptomics to assess the functional role of planctomycetes in peatlands suggested the presence of versatile hydrolytic capabilities in these bacteria. This evidence was further confirmed by the analysis of genome-encoded capabilities of isolates from wetlands. Large (up to 12 Mbp) genomes of planctomycetes encode wide repertoires of carbohydrate-active enzymes including many unclassified putative glycoside hydrolases, which suggests the presence of extremely high glycolytic potential in these bacteria. Experimental tests confirmed their ability to grow on xylan, pectin, starch, lichenan, cellulose, chitin and polysaccharides of microbial origin. These results provide an insight into the ecological roles of peat-inhabiting planctomycetes and suggest their participation in degradation of plant-derived polymers, exoskeletons of peat-inhabiting arthropods as well as exopolysaccharides produced by other bacteria.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Leninsky prospect 33-2, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Leninsky prospect 33-2, Russia
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Dedysh SN, Kulichevskaya IS, Beletsky AV, Ivanova AA, Rijpstra WIC, Damsté JSS, Mardanov AV, Ravin NV. Lacipirellula parvula gen. nov., sp. nov., representing a lineage of planctomycetes widespread in low-oxygen habitats, description of the family Lacipirellulaceae fam. nov. and proposal of the orders Pirellulales ord. nov., Gemmatales ord. nov. and Isosphaerales ord. nov. Syst Appl Microbiol 2019; 43:126050. [PMID: 31882205 PMCID: PMC6995999 DOI: 10.1016/j.syapm.2019.126050] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/10/2019] [Accepted: 12/11/2019] [Indexed: 11/07/2022]
Abstract
Pirellula-like planctomycetes are ubiquitous aquatic bacteria, which are often detected in anoxic or micro-oxic habitats. By contrast, the taxonomically described representatives of these bacteria, with very few exceptions, are strict aerobes. Here, we report the isolation and characterization of the facultatively anaerobic planctomycete, strain PX69T, which was isolated from a boreal lake. Its 16S rRNA gene sequence is affiliated with the Pirellula-related Pir4 clade, which is dominated by environmental sequences retrieved from a variety of low-oxygen habitats. Strain PX69T was represented by ellipsoidal cells that multiplied by budding and grew on sugars, some polysaccharides and glycerol. Anaerobic growth occurred by means of fermentation. Strain PX69T grew at pH 5.5–7.5 and at temperatures between 10 and 30 °C. The major fatty acids were C18:1ω9c, C16:0 and C16:1ω7c; the major intact polar lipid was dimethylphosphatidylethanolamine. The complete genome of strain PX69T was 6.92 Mb in size; DNA G + C content was 61.7 mol%. Among characterized planctomycetes, the highest 16S rRNA gene similarity (90.4%) was observed with ‘Bythopirellula goksoyri’ Pr1d, a planctomycete from deep-sea sediments. We propose to classify PX69T as a novel genus and species, Lacipirellula parvula gen. nov., sp. nov.; the type strain is strain PX69T (=KCTC 72398T = CECT 9826T = VKM B-3335T). This genus is placed in a novel family, Lacipirellulaceae fam. nov., which belongs to the order Pirellulales ord. nov. Based on the results of comparative genome analysis, we also suggest establishment of the orders Gemmatales ord. nov. and Isosphaerales ord. nov. as well as an emendation of the order Planctomycetales.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
| | - Irina S Kulichevskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Anastasia A Ivanova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - W Irene C Rijpstra
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands
| | - Jaap S Sinninghe Damsté
- NIOZ Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, and Utrecht University, P.O. Box 59, 1790 AB Den Burg, The Netherlands; Utrecht University, Faculty of Geosciences, Department of Earth Sciences, Geochemistry, Utrecht, The Netherlands
| | - Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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Lichenibacterium ramalinae gen. nov, sp. nov., Lichenibacterium minor sp. nov., the first endophytic, beta-carotene producing bacterial representatives from lichen thalli and the proposal of the new family Lichenibacteriaceae within the order Rhizobiales. Antonie van Leeuwenhoek 2019; 113:477-489. [PMID: 31741189 DOI: 10.1007/s10482-019-01357-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/06/2019] [Indexed: 12/19/2022]
Abstract
This study of lichens in the subarctic zone of the northern hemisphere has resulted in the detection of new representatives of the order Rhizobiales. The16S rRNA gene sequence phylogeny placed the strains as a separate branch inside the Rhizobiales clade. Strain RmlP001T exhibits 91.85% similarity to Roseiarcus fermentans strain Pf56T and 91.76% to Beijerinckia doebereinerae strain LMG 2819T, whilst strain RmlP026T is closely related to B. doebereinerae strain LMG 2819T (91.85%) and Microvirga pakistanensis strain NCCP-1258T (91.39%). A whole-genome phylogeny of the strains confirmed their taxonomic positions. The cells of both strains were observed to be Gram-negative, motile rods that multiplied by binary fission. The cells were found to contain poly-β-hydroxybutyrate and polyphosphate, to grow at pH 3.5-8.0 and 10-30 °C, and could not fix atmospheric nitrogen. Their major cellular fatty acid identified was C18:1ω7c (68-71%) and their DNA G + C contents determined to be 70.5-70.8%. Beta-carotene was identified as their major carotenoid pigment; Q-10 was the only ubiquinone detected. Strains RmlP001T and RmlP026T are distinguishable from related species by the presence of β-carotene, the absence of C1 metabolism and the ability to grow in the presence of 3.5% NaCl. Based on their phylogenetic, phenotypic and chemotaxonomic features, we propose a novel genus Lichenibacterium and two novel species, Lichenibacterium ramalinae (the type species of the genus) and Lichenibacterium minor, to accommodate these bacteria within the family Lichenibacteriaceae fam. nov. of the order Rhizobiales. The L. ramalinae type strain is RmlP001T (= KCTC 72076T = VKM B-3263T) and the L. minor type strain is RmlP026T (= KCTC 72077T = VKM B-3277T).
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Kovaleva OL, Elcheninov AG, Toshchakov SV, Novikov AA, Bonch-Osmolovskaya EA, Kublanov IV. Tautonia sociabilis gen. nov., sp. nov., a novel thermotolerant planctomycete, isolated from a 4000 m deep subterranean habitat. Int J Syst Evol Microbiol 2019; 69:2299-2304. [DOI: 10.1099/ijsem.0.003467] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Olga L. Kovaleva
- 1Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia
| | - Alexander G. Elcheninov
- 1Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia
| | - Stepan V. Toshchakov
- 1Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia
| | - Andrei A. Novikov
- 2Department of Physical Chemistry, Gubkin University, Moscow, Russia
| | | | - Ilya V. Kublanov
- 1Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS, Moscow, Russia
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13
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Wiegand S, Jogler M, Jogler C. On the maverick Planctomycetes. FEMS Microbiol Rev 2018; 42:739-760. [DOI: 10.1093/femsre/fuy029] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/22/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Sandra Wiegand
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen, The Netherlands
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