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Wang Y, Jia N, Geng R, Yu G, Li R. Phylogenetic insights into chroococcus-like taxa (Chroococcales, Cyanobacteria), describing Cryptochroococcus tibeticus gen. nov. sp. nov. and Limnococcus fonticola sp. nov. from Qinghai-Tibet plateau. J Phycol 2021; 57:1739-1748. [PMID: 34370871 DOI: 10.1111/jpy.13205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 05/13/2021] [Accepted: 05/13/2021] [Indexed: 06/13/2023]
Abstract
Several coccoid cyanobacterial strains, morphologically similar to typical characteristics of Chroococcus, from the Qinghai-Tibet Plateau were isolated and characterized using a polyphasic approach including morphological and molecular information. Morphological characteristics, the phylogeny based on 16S rRNA gene, and 16S-23S internal transcribed spacer secondary structures support establishing a novel Chroococcus-like genus, Cryptochroococcus gen. nov., as well as Limnococcus fonticola sp. nov. Limnococcus is phylogenetically included in Chroococcaceae and has irregularly arranged thylakoids. Therefore, it should no longer be a member of Merismopediaceae (Synechococcales). The phylogeny based on the 16S rRNA gene revealed that Chroococcus-associated genera were monophyletic.
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Affiliation(s)
- Yilang Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nannan Jia
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruozhen Geng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gongliang Yu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Renhui Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, China
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2
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Shalygin S, Huang IS, Allen EH, Burkholder JM, Zimba PV. Odorella benthonica gen. & sp. nov. (Pleurocapsales, Cyanobacteria): an odor and prolific toxin producer isolated from a California aqueduct. J Phycol 2019; 55:509-520. [PMID: 30637743 DOI: 10.1111/jpy.12834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/28/2018] [Indexed: 06/09/2023]
Abstract
Pleurocapsales are one of the least understood groups of cyanobacteria in terms of molecular systematics and biochemistry. Considering the high number of cryptic taxa within the Synechococcales and Oscillatoriales, it is likely that such taxa also occur in the Pleurocapsales. The new genus described in our research is the first known pleurocapsalean cryptic taxon. It produces off-flavor and a large number of bioactive metabolites (n = 38) some of which can be toxic including four known microcystins. Using a polyphasic approach, we propose the establishment of the genus Odorella with the new species O. benthonica from material originally isolated from the California Aqueduct near Los Angeles.
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Affiliation(s)
- Sergei Shalygin
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, Texas, 78412, USA
| | - I-Shuo Huang
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, Texas, 78412, USA
| | - Elle H Allen
- Center for Applied Aquatic Ecology, North Carolina State University, 620 Hutton Street Suite 104, Raleigh, North Carolina, 27606, USA
| | - JoAnn M Burkholder
- Center for Applied Aquatic Ecology, North Carolina State University, 620 Hutton Street Suite 104, Raleigh, North Carolina, 27606, USA
| | - Paul V Zimba
- Center for Coastal Studies, Texas A&M University Corpus Christi, 6300 Ocean Drive, Corpus Christi, Texas, 78412, USA
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3
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de Alvarenga LV, Vaz MGMV, Genuário DB, Esteves-Ferreira AA, Almeida AVM, de Castro NV, Lizieri C, Souza JJLL, Schaefer CEGR, Nunes-Nesi A, Araújo WL. Extending the ecological distribution of Desmonostoc genus: proposal of Desmonostoc salinum sp. nov., a novel Cyanobacteria from a saline-alkaline lake. Int J Syst Evol Microbiol 2018; 68:2770-2782. [PMID: 29985124 DOI: 10.1099/ijsem.0.002878] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cyanobacteria is an ancient phylum of oxygenic photosynthetic microorganisms found in almost all environments of Earth. In recent years, the taxonomic placement of some cyanobacterial strains, including those belonging to the genus Nostocsensu lato, have been reevaluated by means of a polyphasic approach. Thus, 16S rRNA gene phylogeny and 16S-23S internal transcribed spacer (ITS) secondary structures coupled with morphological, ecological and physiological data are considered powerful tools for a better taxonomic and systematics resolution, leading to the description of novel genera and species. Additionally, underexplored and harsh environments, such as saline-alkaline lakes, have received special attention given they can be a source of novel cyanobacterial taxa. Here, a filamentous heterocytous strain, Nostocaceae CCM-UFV059, isolated from Laguna Amarga, Chile, was characterized applying the polyphasic approach; its fatty acid profile and physiological responses to salt (NaCl) were also determined. Morphologically, this strain was related to morphotypes of the Nostocsensu lato group, being phylogenetically placed into the typical cluster of the genus Desmonostoc. CCM-UFV059 showed identity of the 16S rRNA gene as well as 16S-23S secondary structures that did not match those from known described species of the genus Desmonostoc, as well as distinct ecological and physiological traits. Taken together, these data allowed the description of the first strain of a member of the genus Desmonostoc from a saline-alkaline lake, named Desmonostoc salinum sp. nov., under the provisions of the International Code of Nomenclature for algae, fungi and plants. This finding extends the ecological coverage of the genus Desmonostoc, contributing to a better understanding of cyanobacterial diversity and systematics.
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Affiliation(s)
- Luna Viggiano de Alvarenga
- 1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,2Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Marcelo Gomes Marçal Vieira Vaz
- 1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,2Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Diego Bonaldo Genuário
- 3Laboratório de Microbiologia Ambiental, EMBRAPA Meio Ambiente, 13820-000, Jaguariúna, São Paulo, Brazil
| | - Alberto A Esteves-Ferreira
- 1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,2Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Allan V Martins Almeida
- 1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,2Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Naira Valle de Castro
- 1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,2Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Claudineia Lizieri
- 1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,‡Present address: Instituto de Engenharia e Tecnologia, Centro Universitário de Belo Horizonte, UniBH, 30455-610, Belo Horizonte, Minas Gerais, Brazil
| | - José João L L Souza
- 4Departamento de Solos, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,5Departamento de Geografia, Universidade Federal do Rio Grande do Norte, 59300-000, Caicó, Rio Grande do Norte, Brazil
| | | | - Adriano Nunes-Nesi
- 1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,2Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Wagner L Araújo
- 2Max Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil.,1Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
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Benevides L, Burman S, Martin R, Robert V, Thomas M, Miquel S, Chain F, Sokol H, Bermudez-Humaran LG, Morrison M, Langella P, Azevedo VA, Chatel JM, Soares S. New Insights into the Diversity of the Genus Faecalibacterium. Front Microbiol 2017; 8:1790. [PMID: 28970823 PMCID: PMC5609107 DOI: 10.3389/fmicb.2017.01790] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/05/2017] [Indexed: 01/01/2023] Open
Abstract
Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters—A, B, and C—composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the in silico classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to F. prausnitzii, but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.
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Affiliation(s)
- Leandro Benevides
- Department of General Biology, Federal University of Minas GeraisBelo Horizonte, Brazil.,Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Sriti Burman
- Faculty of Medicine, Translational Research Institute, University of Queensland Diamantina Institute, University of QueenslandSt. Lucia, QLD, Australia
| | - Rebeca Martin
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Véronique Robert
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Muriel Thomas
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Sylvie Miquel
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France.,UMR 6023 Laboratoire Microorganismes: Génome et Environnement, Centre National de la Recherche Scientifique, Université Clermont AuvergneClermont-Ferrand, France
| | - Florian Chain
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Harry Sokol
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France.,Faculté de Médecine Saint-Antoine, Institut National de la Santé et de la Recherche Médicale U1157/UMR7203, AVENIR Team Gut Microbiota and Immunity Equipe de Recherche Labélisée, Université Pierre et Marie CurieParis, France.,Service de Gastroentérologie, Hôpital Saint-Antoine, Assistance Publique-Hôpitaux de ParisParis, France
| | - Luis G Bermudez-Humaran
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Mark Morrison
- Faculty of Medicine, Translational Research Institute, University of Queensland Diamantina Institute, University of QueenslandSt. Lucia, QLD, Australia
| | - Philippe Langella
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Vasco A Azevedo
- Department of General Biology, Federal University of Minas GeraisBelo Horizonte, Brazil
| | - Jean-Marc Chatel
- Commensals and Probiotics-Host Interactions Laboratory, Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-SaclayJouy-en-Josas, France
| | - Siomar Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo MineiroUberaba, Brazil
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Shalygin S, Shalygina R, Johansen JR, Pietrasiak N, Berrendero Gómez E, Bohunická M, Mareš J, Sheil CA. Cyanomargarita gen. nov. (Nostocales, Cyanobacteria): convergent evolution resulting in a cryptic genus. J Phycol 2017; 53:762-777. [PMID: 28403525 DOI: 10.1111/jpy.12542] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/04/2017] [Indexed: 05/25/2023]
Abstract
Two populations of Rivularia-like cyanobacteria were isolated from ecologically distinct and biogeographically distant sites. One population was from an unpolluted stream in the Kola Peninsula of Russia, whereas the other was from a wet wall in the Grand Staircase-Escalante National Monument, a desert park-land in Utah. Though both were virtually indistinguishable from Rivularia in field and cultured material, they were both phylogenetically distant from Rivularia and the Rivulariaceae based on both 16S rRNA and rbcLX phylogenies. We here name the new cryptic genus Cyanomargarita gen. nov., with type species C. melechinii sp. nov., and additional species C. calcarea sp. nov. We also name a new family for these taxa, the Cyanomargaritaceae.
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Affiliation(s)
- Sergei Shalygin
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Polar-Alpine Botanical Garden-Institute, Kola Science Center, Russian Academy of Science, Kirovsk-6, 184230, Russia
| | - Regina Shalygina
- Institute of Industrial Ecology Problems of the North, Kola Science Center, Russian Academy of Science, Akademgorodok 14a, Apatity, 184209, Russia
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Nicole Pietrasiak
- Department of Plant and Environmental Sciences, New Mexico State University, 945 College Drive, Las Cruces, New Mexico, 88003, USA
| | - Esther Berrendero Gómez
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
| | - Markéta Bohunická
- Institute of Botany of the Academy of Sciences of the Czech Republic, Dukelská 135, Třeboň, 379 82, Czech Republic
- Research and Breeding Institute of Pomology, Holovousy 129, Hořice, 508 01, Czech Republic
| | - Jan Mareš
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, 370 05, Czech Republic
- Institute of Botany of the Academy of Sciences of the Czech Republic, Dukelská 135, Třeboň, 379 82, Czech Republic
- Biology Centre of the Academy of Sciences of the Czech Republic, Institute of Hydrobiology, Na Sádkách 702/7, České Budějovice, 37005, Czech Republic
| | - Christopher A Sheil
- Department of Biology, John Carroll University, University Heights, Ohio, 44118, USA
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Korpole S, Sharma R, Verma D. Characterization and phylogenetic diversity of carboxymethyl cellulase producing bacillus species from a landfill ecosystem. Indian J Microbiol 2011; 51:531-5. [PMID: 23024419 DOI: 10.1007/s12088-011-0153-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 11/23/2009] [Indexed: 10/18/2022] Open
Abstract
Total population of cellulose degrading bacteria was studied in a landfill ecosystem as a part of microbial diversity study. Samples were obtained from 3 and 5 feet depth of a local landfill being operated for past 10 years. Among many isolates, 22 bacterial strains were selected based on their capability to decompose carboxymethyl cellulose (CMC). These isolates were cultivated on agar medium with CMC as the carbon source. All isolates were Gram positive, endospore forming and alkalophilic bacteria with optimum growth pH 9-10. They were grouped based on the phenotypic and chemotaxonomic characters and representative strains of different groups along with high carboxymethyl cellulase (CMCase) producing strains were included for further characterization. Analysis of 16S rRNA gene indicated that these strains belong to different species of the genus Bacillus. Maximum CMCase activity of 4.8 U/ml at 50°C was obtained by strain LFC15. Results in the present study indicated the potential of waste land ecosystems such as landfill are potential source for isolation of industrially important microorganisms.
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