Relevant bibliographies by topics / Polyphasic taxonomy

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Academic literature on the topic 'Polyphasic taxonomy'

Author: Grafiati
Published: 4 June 2021
Last updated: 13 June 2025

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Journal articles on the topic "Polyphasic taxonomy"

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UILENBERG, GERRIT, and WILL L. GOFF. "Polyphasic Taxonomy." Annals of the New York Academy of Sciences 1081, no. 1 (2006): 492–97. http://dx.doi.org/10.1196/annals.1373.073.

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Mota, R. R., M. C. Marquez, D. R. Arahal, E. Mellado, and A. Ventosa. "Polyphasic Taxonomy of Nesterenkonia halobia." International Journal of Systematic Bacteriology 47, no. 4 (1997): 1231–35. http://dx.doi.org/10.1099/00207713-47-4-1231.

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Vandamme, Peter, and Charlotte Peeters. "Time to revisit polyphasic taxonomy." Antonie van Leeuwenhoek 106, no. 1 (2014): 57–65. http://dx.doi.org/10.1007/s10482-014-0148-x.

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Varga, János, Jens C. Frisvad, and Robert A. Samson. "Polyphasic taxonomy of Aspergillus section Sparsi." IMA Fungus 1, no. 2 (2010): 187–95. http://dx.doi.org/10.5598/imafungus.2010.01.02.12.

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Yilmaz, N., C. M. Visagie, J. Houbraken, J. C. Frisvad, and R. A. Samson. "Polyphasic taxonomy of the genus Talaromyces." Studies in Mycology 78 (June 2014): 175–341. http://dx.doi.org/10.1016/j.simyco.2014.08.001.

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Chen, A. J., J. Varga, J. C. Frisvad, X. Z. Jiang, and R. A. Samson. "Polyphasic taxonomy of Aspergillus section Cervini." Studies in Mycology 85 (September 2016): 65–89. http://dx.doi.org/10.1016/j.simyco.2016.11.001.

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Hong, Seung-Beom, Seung-Joo Go, Hyeon-Dong Shin, Jens C. Frisvad, and Robert A. Samson. "Polyphasic taxonomy ofAspergillus fumigatusand related species." Mycologia 97, no. 6 (2005): 1316–29. http://dx.doi.org/10.1080/15572536.2006.11832738.

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Houbraken, J., M. Due, J. Varga, M. Meijer, J. C. Frisvad, and R. A. Samson. "Polyphasic taxonomy of Aspergillus section Usti." Studies in Mycology 59 (2007): 107–28. http://dx.doi.org/10.3114/sim.2007.59.12.

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Ramasamy, Dhamodharan, Ajay Kumar Mishra, Jean-Christophe Lagier, et al. "A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species." International Journal of Systematic and Evolutionary Microbiology 64, Pt_2 (2014): 384–91. http://dx.doi.org/10.1099/ijs.0.057091-0.

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Currently, bacterial taxonomy relies on a polyphasic approach based on the combination of phenotypic and genotypic characteristics. However, the current situation is paradoxical in that the genetic criteria that are used, including DNA–DNA hybridization, 16S rRNA gene sequence nucleotide similarity and phylogeny, and DNA G+C content, have significant limitations, but genome sequences that contain the whole genetic information of bacterial strains are not used for taxonomic purposes, despite the decreasing costs of sequencing and the increasing number of available genomes. Recently, we diversified bacterial culture conditions with the aim of isolating uncultivated bacteria. To classify the putative novel species that we cultivated, we used a polyphasic strategy that included phenotypic as well as genomic criteria (genome characteristics as well as genomic sequence similarity). Herein, we review the pros and cons of genome sequencing for taxonomy and propose that the incorporation of genome sequences in taxonomic studies has the advantage of using reliable and reproducible data. This strategy, which we name taxono-genomics, may contribute to the taxonomic classification of bacteria.
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Stadler, Marc, Thomas Læssøe, Jacques Fournier, et al. "A polyphasic taxonomy of Daldinia (Xylariaceae)1." Studies in Mycology 77 (March 2014): 1–143. http://dx.doi.org/10.3114/sim0016.

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Dissertations / Theses on the topic "Polyphasic taxonomy"

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Kim, Bongcheol. "Polyphasic taxonomy of thermophilic actinomycetes." Thesis, University of Newcastle Upon Tyne, 1999. http://hdl.handle.net/10443/1757.

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Molecular systematic methods were applied in a series of studies designed to resolve the taxonomic relationships of thermophilic actinomycetes known to be difficult to classify using standard taxonomic procedures. The test strains included representatives of clusters defined in an extensiven umerical phenetic survey of thermophilic streptomycetesa nd twelve marker strains. The resultant genotypic data together with the results of corresponding phenotypic studies were used to highlight novel taxa and to improve the circumscription of validly described species. The most comprehensive study was undertaken to clarify relationships within and between representative alkalitolerant, thermophilic and neutrophilic, thermophilic streptomycetes isolated from soil and appropriate marker strains. The resultant data, notably those from DNA: DNA relatedness studies, supported the taxonomic integrity of the validly described species Streptomyces thermodiastaticus, Streptomyces thermoviolaceus and Streptomyces thermovulgaris. However, the genotypic and phenotypic data clearly show that Streptomyces thermonitrificans Desai and Dhala 1967 and Streptomyces thermovulgaris (Henssen 1957) Goodfellow et al. 1987 represent a single species. On the basis of the priority, Streptomyces thermonitrificans is a later subjective synonym of Streptomyces thermovulgaris. Similarly, eight out of eleven representative alkalitolerant, thermophilic isolates and three out of sixteen representative neutrophilic, thermophilic isolates had a combination of properties consistent with their classification as Streptomyces thermovulgaris. One of the remaining alkalitolerant, thermophilic isolate, Streptomyces strain TA56, merited species status. The name Streptomyces thermoalcalitolerans sp. nov. is proposed for this strain. A neutrophilic, thermophilic isolate, Streptomyces strain NAR85, was identified as Streptomyces thermodiastaticus. Four other neutrophilic thermophilic isolates assigned to a numerical phenetic cluster and a thermophilic isolates from poultry faeces were also considered to warrant species status; the names Streptomyces eurythermophilus sp. nov. and Streptomyces thermocoprophilus sp. nov. are proposed to accommodate these strains. It was also concluded that additional comparative taxonomic studies are required to clarify the relationships between additional thermophilic streptomycete strains included in the present investigation. A corresponding polyphasic approach was used to clarify the taxonomy of six thermophilic isolates provisionally assigned to either the genera Amycolatopsis or Excellospora. Two of the isolates, strain NT202 and NT303, had properties consistent with their classification in the genus Amycolatopsis. However, the genotypic and phenotypic data also showed that these strains formed a new centre of taxonomic variation for which the name Amycolatopsis eurythermus sp. nov. is proposed. Similarly, the four remaining strains formed two new centre of taxonomic variation within the genus Excellospora. It is proposed that isolates TA113 and TA114 be designated Excellospora alcalithermophilus sp. nov. Similarly, the name Excellospora thermoalcalitolerans sp. nov. is proposed for strains TA86 and TA111. An emended description is also given for the genus Excellospora.
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Mheen, Hye Sook. "Computer program for polyphasic taxonomy." Thesis, University of Newcastle Upon Tyne, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299419.

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Maldonado, Luis Angel. "Polyphasic taxonomy of members of the genus Nocardia." Thesis, University of Newcastle Upon Tyne, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.246690.

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Sukhoom, Ampaitip. "Selective isolation and characterisation of rhodococci for use in bioremediation." Thesis, University of Newcastle Upon Tyne, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299635.

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Rodriguez-Diaz, Marina. "Application of miniaturized identification systems to the polyphasic taxonomy of Bacillus and relatives." Thesis, Glasgow Caledonian University, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414866.

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Visagie, Cobus Meyer. "The polyphasic taxonomy of penicillium and talaromyces spp. isolated from the diverse Fynbos biome." Thesis, Stellenbosch : Stellenbosch University, 2012. http://hdl.handle.net/10019.1/71947.

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Espinoza, dela Cruz Thomas Edison. "Marine Dendryphiella species from different geographical locations an integrated, polyphasic approach to its taxonomy and physioecology /." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=980409624.

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Abreu, Filho Benicio Alves de. "Caracterização taxonomica de linhagens de Alicyclobacillus ssp. isolados na industria de suco concentrado de laranja." [s.n.], 2005. http://repositorio.unicamp.br/jspui/handle/REPOSIP/256662.

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Orientadores: Gilson Paulo Manfio, Valeria Maia de Oliveira
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos
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Resumo: Trinta linhagens de bactérias acidotermofílicas isoladas do processamento industrial de suco de laranja concentrado congelado (Frozen Concentrated Orange Juice, FCOJ) em diferentes regiões do estado de São Paulo foram estudadas, utilizando-se uma abordagem polifásica, a fim de se determinar a diversidade e potencial deteriogênico destas em processos de produção de FCOJ no país. A caracterização dos isolados envolveu a determinação da capacidade de crescimento e produção de odor em suco reconstituído, análises fenotípicas (padrão de utilização de carboidratos, sistema API 50 CH), quimiotaxonômicas (perfil de FAMES, sistema MIDI) e de caracterização molecular (ARDRA de região espaçadora DNAr 16S-23S com Hae III, Hha I e Msp I, e análise filogenética de DNAr 16S). Todos os isolados foram identificados como pertencentes ao gênero Alicyclobacillus pelos padrões característicos de ácidos graxos. Diferentemente de relatos de literatura, foi confirmada a presença de omega-ciclohexil-C17:0 e omega-ciclohexil-C19:0 em amostras identificadas como A. pomorum. Das 30 amostras ambientais de aliciclobacilos analisadas, 21 foram capazes de se multiplicar em suco de laranja reconstituído após 24 ou 48 h de incubação a 45 °C, mas apenas 10 produziram odor característico de biodeterioração. Seis ribotipos de ARDRA foram obtidos para os isolados, permitindo a alocação destes nas espécies A. acidocaldarius e A. acidoterrestris, e em grupos relacionados a espécies válidas designados como A. acidocaldarius-like e A. pomorum-like
Abstract: Thirty strains isolated from industrial processing of frozen concentrated orange juice (FCOJ) in different regions of the state of São Paulo were studied using a polyphasic approach with the goal of determining the diversity and deteriogenic potential of isolates from FCOJ production in Brazil. Characterization of isolates involved determining their ability to grow and produce odor in reconstituted orange juice, and phenotypic (carbohydrate utilization, API 50 CH), chemotaxonomic (FAMES, MIDI system) and molecular analyses (ARDRA of 16S-23S rDNA spacer region, Hae III, Hha I and Msp I, and 16S rDNA phylogenetic analysis). All isolates were identified as Alicyclobacillus spp. according to the characteristic fatty acid patterns. Contrary to literature data, omega-cyclohexyl-C17:0 and omega-cyclohexyl-C19:0 were confirmed in samples identified as A. pomorum. From the 30 environmental alicyclobacili samples analyzed, 21 were able to grow in reconstituted orange juice after 24 or 48 hs incubation at 45 °C, but only 10 isolates yielded a characteristic biodeterioration odor. Six ARDRA patterns were obtained for the isolates analyzed, enabling them to be assigned to A. acidocaldarius and A. acidoterrestris, and to groups related to valid species named A. acidocaldarius-like and A. pomorum-like
Doutorado
Doutor em Ciência de Alimentos
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Passarini, Michel Rodrigo Zambrano 1979. "Caracterização da diversidade de fungos filamentosos associados a esponjas marinhas e avaliação da produção de lacase = Diversity of filamentous fungi associated with marine sponges and evaluation of laccase production." [s.n.], 2012. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316911.

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Orientador: Lara Durães Sette
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: O oceano representa um habitat promissor na busca por novos micro-organismos, os quais podem apresentar capacidade de produzir enzimas de interesse industrial diferentes das produzidas por seus parceiros terrestres. Neste contexto, duas amostras da esponja marinha Dragmacidon reticulatum foram coletadas no litoral Norte do Estado de São Paulo, objetivando a caracterização da diversidade fúngica por métodos dependentes e independentes de cultivo, bem como a avaliação da produção, expressão da enzima e caracterização do gene da lacase. Com relação à parcela cultivada das amostras, 108 fungos filamentosos foram isolados. Destes, 64 ribotipos distintos foram submetidos aos experimentos de taxonomia polifásica e aos relacionados com a lacase. Análises macro- e microscópicas, moleculares (genes ribossomais ITS/28S) e pela técnica de MALDI TOF ICMS, resultaram na caracterização de 38 isolados distribuídos em 23 gêneros pertencentes ao Filo Ascomycota e um ao Filo Zygomycota. Este foram posteriormente depositados na Coleção Brasileira de Micro-organismos de Ambiente e Indústria (CBMAI). Dentre os isolados obtidos, uma potencial espécie nova de Penicillium foi identificada. Os resultados da triagem enzimática permitiram a seleção de dois isolados identificados como Nigrospora sp. CBMAI 1328 (0,30 U L-1) e Arthorpyrenia sp. CBMAI 1330 (0,40 U L-1), os quais foram submetidos à uma nova avaliação da atividade e expressão (RT-PCR) com indução de íons cobre e caracterização do genes da lacase. A adição de íons cobre na concentração de 5 mM, proporcionou aumento das atividades enzimáticas dos isolados CBMAI 1328 e CBMAI 1330 em 3,9X (25,2 U L-1) e 1,2X (9,0 U L-1) após 120 h, respectivamente. Os resultados da expressão dos genes da lacase para o isolado CBMAI 1328 foram os mesmos encontrados pela indução com cobre (maior expressão em 5 mM após 120 h), entretanto para o isolado CBMAI 1330, a maior expressão foi após 96 h sem adição de cobre. Os resultados da caracterização dos genes da lacase revelaram a possivel existência de 3 novos putativos genes de lacases marinhas. Com relação à parcela não cultivada, foi possível a identificação de 7 gêneros e de um fungo não cultivado (uncultured fungi) do Filo Ascomycota bem como 3 gêneros e um fungo não cultivado (uncultured fungi) do Filo Basidiomycota a partir da técnica de DGGE e do sequenciamento direto do gene RNAr ITS e do gene 18S. Em ambas as abordagens utilizadas, a maior diversidade foi encontrada na amostra DR9. Os dados derivados do presente trabalho, ressaltam a importância em se utilizar a taxonomia polifásica, bem como empregar metodologias dependente e independente de cultivo (em paralelo) para um melhor e maior conhecimento da real diversidade em amostras ambientais. Estes resultados ampliam o conhecimento dos fungos filamentosos recuperados de esponjas marinhas e demonstram o potencial biotecnológico destes micro-organismos
Abstract: The ocean represents a promissing habitat in the search for new microorganisms, which may have the ability to produce enzymes of industrial interests different from that produced by their terrestrial counterparts. In this context, two samples of the marine sponge Dragmacidon reticulatum were collected on northern coast of São Paulo State, aiming at the characterization of fungal diversity by cultureddependent and -independent approaches as well as the evaluation of the production, characterization and expression of laccase enzyme gene. Regarding the cultivated portion of the samples, around 108 filamentous fungi were isolated, belonging to 64 different taxonomic groups (ribotypes), which were subjected to enzymatic activity assays. Polyphasic taxonomy approaches (macro- and microscopic, molecular - ITS/28S ribosomal genes - and MALDI TOF ICMS analyses) resulted in the characterization of 38 isolates distributed in 23 genera belonging to the phylum Ascomycota and one to the phylum Zygomycota, which were deposited in the Brazilian Collection of Micro-organisms from Environment and Industry (CBMAI). Among the isolates recovered one possible new species of Penicillium was identified. Enzymatic screening allowed the selection of two isolates identified as Nigrospora sp. CBMAI 1328 (0,30 U L-1) and Arthorpyrenia sp. CBMAI 1330 (0,40 U L-1), which were subjected to a new activity evaluation and expression (RT-PCR) with the induction of copper ions and the laccase genes characterization. The addition of copper ions in a concentration of 5 mM resulted in an increase in the enzymatic activities of CBMAI 1328 and CBMAI 1330 strains in 3,9X (25,2 U L-1) and 1,2X (9,0 U L-1) after 120h, respectively. The results of the expression of the laccase genes for CBMAI 1328 strain were the same found by induction with copper (expression increased in 5 mM after 120 h), however for CBMAI 1330 the higher expression was after 96 h without addition of copper. Results of laccase genes characterization revealed the existence of three possible putative new marine laccase genes. Regarding to the uncultured portion of the samples, from the DGGE and direct sequencing of the ITS rRNA gene and 18S gene approaches, was possible to identify seven species of fungi and one uncultured fungus from phylum Ascomycota and three species and one uncultured fungus from phylum Basidiomycota. For both approaches used the greatest diversity was achieved in the DR9 sample. Data derived from the present work highlight the importance of using polyphasic taxonomy as well as applying culturedependent and culture-independent methodologies (in parallel) in order to have a better and greater knowledge of the real diversity in environmental sample. These results expand the knowledge of fungi recovery from marine sponges and demonstrate the biotechnological potential of these micro-organisms
Doutorado
Genetica de Microorganismos
Doutor em Genetica e Biologia Molecular
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Andreote, Ana Paula Dini. "Filosfera da Mata Atlântica: isolamento e sistemática de cianobactérias, bioprospecção e caracterização da comunidade diazotrófica." Universidade de São Paulo, 2014. http://www.teses.usp.br/teses/disponiveis/64/64133/tde-17042014-104142/.

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A filosfera da Mata Atlântica é um importante nicho de colonização por micro-organismos, cuja comunidade ainda é pouco conhecida. Algumas bactérias associadas à superfície das folhas possuem habilidade de fixar nitrogênio, mineralizar substratos orgânicos e também suprir as árvores com dióxido de carbono e fatores de crescimento. Este trabalho teve como objetivo gerar informações sobre a comunidade cianobacteriana que coloniza a filosfera de algumas plantas da Mata Atlântica e investigar a comunidade diazotrófica presente nesse habitat. Um total de 40 linhagens de cianobactérias da filosfera de Merostachys neesii (bambu), Euterpe edulis (palmeira Juçara), Guapira opposita e Garcinia gardneriana foram isoladas e cultivadas. Os isolados foram caracterizados por análises morfológicas e filogenia do gene 16S RNAr. Essa abordagem permitiu a identificação de uma linhagem do gênero Nostoc, sete Desmonostoc, seis Leptolyngbya, uma Oculatella, cinco Brasilonema, uma Pleurocapsa e duas Chroococcidiopsis. Dezessete linhagens (uma Microchaetaceae, dez Nostocaceae e seis Pseudanabaenaceae) não puderam ser identificadas ao nível de gênero. Vinte e seis linhagens (24 pertencentes às ordens Nostocales e duas à Pseudanabaenales) foram caracterizadas como diazotróficas pela amplificação, sequenciamento e filogenia do gene nifH. Além disso, caracterizou-se o perfil de fixação biológica de nitrogênio da linhagem Desmonostoc sp. CENA362. Com relação ao potencial biotecnológico dessas linhagens, treze isolados foram identificados como potenciais produtores de ácido indol acético (IAA) de acordo com o teste Salkowski. Diversas linhagens apresentaram genes associados à via biossintética do inibidor de protease microviridina, sendo que três delas codificam para novas variantes. Além disso, dez linhagens foram identificadas como potenciais produtoras aeruginosina, três de cianopeptolina e três de microcistina. A comunidade bacteriana diazotrófica avaliada por pirosequenciamento do gene nifH apresentou um perfil de variação espécie-específica para Proteobacteria e uma correlação positiva entre a riqueza e a fixação biológica de nitrogênio. Neste estudo, cianobactérias que habitam a filosfera da Mata Atlântica foram isoladas estão sendo mantidas em condições de cultivo. Novos táxons foram descobertos e vários gêneros conhecidos foram descritos pela primeira vez neste hábitat, o que contribuiu para o aprimoramento da sistemática de Cyanobacteria. As linhagens em cultivo e as informações geradas sobre os seus compostos metabólitos representam uma valiosa fonte para estudos posteriores. Além disso, informações sobre a comunidade bacteriana diazotrófica da filosfera pode auxiliar no entendimento da dinâmica do nitrogênio, elemento limitante e pouco disponível na Mata Atlântica
The phyllosphere of the Atlantic Forest is an important niche for colonization by microorganisms, whose community is still little known. Some bacteria associated with leaf surfaces may possess the ability to fix nitrogen, mineralize the organic substrates and also supply the trees with carbon dioxide and growth factors. Therefore, this study aimed to generate information about cyanobacterial community that colonize the phyllosphere of some plants of the Atlantic Forest and investigated the diazotrophic community in this habitat. A total of 40 strains of Cyanobacteria from the phyllosphere of Merostachys neesii (bamboo), Euterpe edulis (Juçara palm), Garcinia gardneriana and Guapira opposita was isolated and cultivated. The isolates were characterized by morphological analyses and phylogeny of the 16S rRNA gene. This approach allowed the identification of one strain of the genus Nostoc, seven Desmonostoc, six Leptolyngbya, one Oculatella, five Brasilonema, one Pleurocapsa and two Chroococcidiopsis. Seventeen strains (one Microchaetaceae, ten Nostocaceae and six Pseudanabaenaceae) could not be identified at the genus level. Twenty-six strains (24 belonging to Nostocales and two belonging to Pseudanabaenales) were characterized as diazotrophic by amplification, sequencing and phylogeny of nifH gene. Also, it was characterized the profile of biological nitrogen fixation for the strain Desmonostoc sp. CENA362. Regarding the biotechnological potential of these strains, thirteen strains were identified as potential producers of indole acetic acid (IAA) according to Salkowski test. Several strains presented genes involved in the biosynthetic pathway of the protease inhibitor microviridin, three of them encoding putative novel variants. Moreover, ten strains were identified as potential producers of aeruginosin, three of cyanopeptolin and three of microcystin. The diazotrophic bacterial community evaluated by pyrosequencing of the nifH gene showed a profile of variation plant species-specific for Proteobacteria, and a positive correlation between richness and biological nitrogen fixation. In this study, cyanobacteria that inhabiting Brazilian Atlantic Forest phyllosphere were isolated and are been maintained in culture conditions. New taxa were discovered and several known genera were described for the first time in this habitat, which contributed to improvement of the cyanobacterial systematic. The culturable strains and the information generated about their metabolites compounds represent a valuable source for further studies. In addition, information about the diazotrophic bacterial community inhabiting the phyllosphere may help in understanding the dynamics of nitrogen, a limiting and low available element in Atlantic Forest
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Books on the topic "Polyphasic taxonomy"

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Amadi, Emmanuel N. Micrococcus systematics: A polyphasic taxonomic study of the internal structure of the genus micrococcus and its suprageneric relationship to allied actinomycete taxa. 1986.

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Book chapters on the topic "Polyphasic taxonomy"

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Gillis, Monique, Peter Vandamme, Paul De Vos, Jean Swings, and Karel Kersters. "Polyphasic Taxonomy." In Bergey’s Manual® of Systematic Bacteriology. Springer New York, 2001. http://dx.doi.org/10.1007/978-0-387-21609-6_7.

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Gillis, Monique, Peter Vandamme, Paul De Vos, Jean Swings, and Karel Kersters. "Polyphasic Taxonomy." In Bergey’s Manual® of Systematic Bacteriology. Springer US, 2005. http://dx.doi.org/10.1007/0-387-28021-9_7.

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Komárek, Jiří. "Polyphasic (combined) approach to cyanobacterial taxonomy." In Süßwasserflora von Mitteleuropa, Bd. 19/3: Cyanoprokaryota. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-8274-2737-3_1.

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Göker, Markus. "What can genome analysis offer for bacteria?" In Trends in the systematics of bacteria and fungi. CABI, 2021. http://dx.doi.org/10.1079/9781789244984.0255.

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Abstract This book chapter is organized as follows: (i) the main approaches to the philosophy of taxonomic classification are recapitulated; (ii) the paradigm of polyphasic taxonomy is discussed in this context; (iii) the causes of conflict between previous classifications and genome-scale analyses are investigated, using examples from recent phylum-wide studies, with a discussion of how markers used in polyphasic taxonomy can be replaced by genome-derived ones; and (iv) the challenges in assigning taxonomic ranks using genome-scale or other data are revisited. The conclusion assesses the chances, or lack thereof, of reconciling taxonomic classifications. Phenetic and phylogenetic thinking still compete with each other on the classification of bacteria, with potentially conflicting and confusing results. Some causes of problematic taxonomic classifications are independent of the type and number of characters that can be used and can only be mitigated if, for example, taxon sampling and branch support are more appropriately taken into account. It may be possible to devise objective criteria for separating bacterial species, but the currently dominating approaches for microbial species delineation may be inadequate. It is even harder to delineate higher taxa; in contrast to claims in the literature, it may prove to be impossible to objectively assign taxonomic ranks above species level.
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Caballero-Mellado, J., T. Jiménez-Salgado, A. Tapia-Hernández, E. T. Wang, E. Martínez-Romero, and L. E. Fuentes-Ramírez. "Polyphasic Taxonomy of Nitrogen-Fixing Acetic Bacteria Isolated from the Rhizosphere of Coffee Plants." In Highlights of Nitrogen Fixation Research. Springer US, 1999. http://dx.doi.org/10.1007/978-1-4615-4795-2_55.

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Managamuri, Ushakiranmayi, Muvva Vijayalakshmi, Sudhakar Poda, V. S. Rama Krishna Ganduri, and R. Satish Babu. "Bioactive Metabolites from Streptomyces nanhaiensis VSM-1: Polyphasic Taxonomy, Optimization, and Evaluation of Antimicrobial Metabolites by GC-MS Analysis." In Medicinal Plants: Biodiversity, Sustainable Utilization and Conservation. Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-1636-8_38.

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Wilmotte, Annick, H. Dail Laughinghouse IV, Camilla Capelli, Rosmarie Rippka, and Nico Salmaso. "Taxonomic Identification of Cyanobacteria by a Polyphasic Approach." In Molecular Tools for the Detection and Quantification of Toxigenic Cyanobacteria. John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781119332169.ch4.

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Zapomělová, Eliška, Olga Skácelová, Petr Pumann, Radovan Kopp, and Emil Janeček. "Biogeographically interesting planktonic Nostocales (Cyanobacteria) in the Czech Republic and their polyphasic evaluation resulting in taxonomic revisions of Anabaena bergii Ostenfeld 1908 (Chrysosporum gen. nov.) and A. tenericaulis Nygaard 1949 (Dolichospermum tenericaule comb. nova)." In Phytoplankton responses to human impacts at different scales. Springer Netherlands, 2012. http://dx.doi.org/10.1007/978-94-007-5790-5_25.

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A. Caires, Taiara, and Helen Michelle de J. Affe. "Brazilian Coast: A Significant Gap in the Knowledge of Cyanobacteria and Their Applications." In Cyanobacteria - Recent Advances in Taxonomy, Ecology and Applications [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97151.

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Abstract:
Brazil has 10.959 km of coastline which includes three ecoregions based on the biogeographic system, exhibiting a wide range of environments that favor the occurrence of numerous cyanobacterial morpho- and ecotypes. These organisms have a great adaptive capacity, which explains their occupancy in numerous environments and the high diversification of the group. Historically, the cyanobacteria have been classified only based on morphology, which makes their taxonomy quite challenging. There is usually little morphological variation between taxa, which makes it difficult to identify diacritical characteristics between some genera and species, making intergeneric and intraspecific delimitation tough. Thereby, the polyphasic approach based on different tools allows the identification of new taxa and the reassessment of those already established with more reliability, contributing to a better systematic resolution of the world ‘cyanoflora’, a term that we propose herein to describe the diversity of Cyanobacteria into Phycoflora area. However, the use of these tools is still not widely applied to most genera and species, especially those from tropical and subtropical environments, which has limited the real recognition of their biodiversity, as well as the knowledge about the cyanobacteria’s evolutionary history and biogeography. In Brazil, even with the great development of phycological studies, the knowledge about Cyanobacteria from marine benthic environments has not evolved to the same degree. This phylum has been neglected in floristic surveys, presenting only 46 benthic species reported to the long Brazilian coastline, evidencing the still incipient knowledge about the diversity and distribution of this microorganism’s group. Furthermore, biotechnological properties of Brazilian marine cyanobacteria are still almost completely unknown, with only three studies carried out to date, underestimating one of the most diverse groups and with promising potential for the possibility of isolating new biochemically active compounds. The ten new taxa related to the Brazilian coast in the last decade emphasizes the challenge of conducting further floristic surveys in the underexplored marine environments in order to fill an important lacune in the cyanoflora knowledge, as well as their biogeographic distribution and biotechnological potential. Besides, the recognition of the Brazilian cyanoflora makes an important contribution to the understanding of the functioning and monitoring of marine ecosystems and provide data for the construction of future public policies, which is a goal of the United Nations Decade for Ocean Science for Sustainable Development.
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Robles Montoya, Rosa Icela, Valeria Valenzuela Ruiz, Fannie Isela Parra Cota, Gustavo Santoyo, and Sergio de los Santos-Villalobos. "Description of a Polyphasic Taxonomic Approach for Plant Growth-Promoting Rhizobacteria (PGPR)." In Microbial Services in Restoration Ecology. Elsevier, 2020. http://dx.doi.org/10.1016/b978-0-12-819978-7.00017-8.

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