• ALGAE
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• v.21 no.4
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• pp.349-375
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• 2006

The application of modern ecological, ultrastructural and molecular methods, aided by the cultivation of numerous cyanobacterial morphotypes, has substantially changed our knowledge of these organisms. It has led to major advances in cyanobacterial taxonomy and criteria for their phylogenetic classification. Molecular data provide basic criteria for cyanobacterial taxonomy; however, a correct phylogenetic system cannot be constructed without combining genetic data with knowledge from the previous 150 years research of cyanobacterial diversity. Thus, studies of morphological variation in nature, and modern morphological, ultrastructural, ecophysiological and biochemical characters need to be combined in a “polyphasic” approach. Taxonomic concepts for generic and infrageneric ranks are re-evaluated in light of combined phenotypic and molecular criteria. Despite their usefulness in experimental studies, the limitations of using strains from culture collections for systematic and nomenclatural purposes is highlighted. The need for a continual revision of strain identification and proper nomenclatural practice associated with either the bacteriological or botanical codes is emphasized. Recent advances in taxonomy are highlighted in the context of prospects for understanding cyanobacterial diversity from natural habitats, and the evolutionary and adaptational processes that cyanobacteria undergo.

• ALGAE
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• v.37 no.1
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• pp.1-14
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• 2022

Cyanobacteria are distributed worldwide, and many new cyanobacterial species are discovered in tropical region. The Nostoc-like genus Amazonocrinis has been separated from the genus Nostoc based on polyphasic methods. However, species diversity within this genus remains poorly understood systematically because only one species (Amazonocrinis nigriterrae) has been described. In this study, two novel strains (NUACC02 and NUACC03) were isolated from moist rice field soil in Thailand. These two strains were characterized using a polyphasic approach, based on morphology, 16S rRNA phylogenetic analysis, internal transcribed spacer secondary structure and ecology. Phylogenetic analyses based on 16S rRNA gene sequences confirmed that the two novel strains formed a monophyletic clade related to the genus Amazonocrinis and were distant from the type species A. nigriterrae. The 16S rRNA gene sequence similarity (<98.1%) between novel strains and all other closely related taxa including the Amazonocrinis members exceeded the cutoff for species delimitation in bacteriology, reinforcing the presence of a new Amazonocrinis species. Furthermore, the novel strains possessed unique phenotypic characteristics such as the presence of the sheath, necridia-like cells, larger cell dimension and akinete cell arrangement in long-chains and the singularity of D1-D1', Box-B, V2, and V3 secondary structures that distinguished them from other Amazonocrinis members. Considering all the results, we described our two strains as Amazonocrinis thailandica sp. nov. in accordance with the International Code of Nomenclature for Algae, Fungi and Plants.

• ALGAE
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• v.36 no.2
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• pp.111-121
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• 2021

Two cyanobacterial morphotypes isolated from Signy Island, South Orkney Islands, maritime Antarctica were characterised using a polyphasic approach combining morphological, cytological and molecular analyses. These analyses showed that the strains grouped with members of the genus Wilmottia. This genus currently includes three species, W. murrayi, W. stricta, and W. koreana. Both morphotypes analysed in this study were placed within the clade of W. murrayi. This clade showed a well-supported separation from Antarctic and New Zealand strains, as well as strains from other regions. W. murrayi was first described from Antarctica and is now known from several Antarctic regions. Confirmation of the occurrence of W. murrayi at Signy Island significantly extends its known distribution in Antarctica. In addition, a new combination, W. arthurensis, is suggested for Phormidium arthurensis.

• ALGAE
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• v.38 no.2
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• pp.93-110
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• 2023

Progress in phylogenomic analysis has led to a considerable re-evaluation of former cyanobacterial system, with many new taxa being established at different nomenclatural levels. The family Geminocystaceae is among cyanobacterial taxa recently described on the basis of polyphasic approach. Within this family, there are six genera: Geminocystis, Cyanobacterium, Geminobacterium, Annamia, Picocyanobacterium, and Microcrocis. The genus Geminocystis previously encompassed two species: G. herdmanii and G. papuanica. Herein, a new species G. urbisnovae was proposed under the provision of the International Code of Nomenclature for algae, fungi, and plants (ICN). Polyphasic analysis was performed for five strains from the CALU culture collection (St. Petersburg State University, Russian Federation), and they were assigned to the genus Geminocystis in accordance with high 16S rRNA gene similarity to existing species, as well as because of proximity to these species on the phylogenetic trees reconstructed with RaxML and Bayes methods. Plausibility of their assignment to a separate species of the genus Geminocystis was substantiated with smaller cell size; stenohaline freshwater ecotype; capability to complementary chromatic adaptation of second type (CA2); distinct 16S rRNA gene clustering; sequences and folding of D1-D1' and B box domains of the 16S-23S internal transcribed spacer region. The second objective pursued by this communication was to provide a survey of the family Geminocystaceae. The overall assessment was that, despite attention of many researchers, this cyanobacterial family has been understudied and, especially in the case of the crucially important genus Cyanobacterium, taxonomically problematic.

• Journal of Microbiology and Biotechnology
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• v.17 no.6
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• pp.913-918
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• 2007

A Gram-positive, aerobic, rod-shaped, nonmotile, endospore-forming bacterium, designated Gsoil $349^T$, was isolated from soil of a ginseng field and characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that the strain Gsoil $349^T$ belongs to the family Paenibacillaceae, and the sequence showed closest similarity with Cohnella thermotolerans DSM $17683^T$ (94.1%) and Cohnella hongkongensis DSM $17642^T$ (93.6%). The strain showed less than 91.3% 16S rRNA gene sequence similarity with Paenibacillus species. In addition, the presence of MK-7 as the major menaquinone and $anteiso-C_{15:0},\;iso-C_{16:0},\;and\;C_{16:0}$ as major fatty acids suggested its affiliation to the genus Cohnella. The G+C content of the genomic DNA was 53.4 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil $349^T$ should be treated as a novel species within the genus Cohnella for which the name Cohnella panacarvi sp. nov. is proposed. The type strain is Gsoil $349^T\;(=KCTC\;13060^T=\;DSM\;18696^T)$.

• ALGAE
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• v.35 no.1
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• pp.1-15
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• 2020

Two strains isolated from a subtropical region in China, were morphologically identified as a Nostoc-like species, but its taxonomic identity was unknown. In this study, these two strains were taxonomically and phylogenetically characterized based on polyphasic approach combining morphological and genetic characteristics. Though both were virtually indistinguishable from Nostoc in field and cultured material, these two strains were phylogenetically distinct from Nostoc based on 16S rRNA phylogeny. The 16S-23S internal transcribed spacer rRNA secondary structure of these strains showed the unique pattern of D1-D1', Box-B, and V3 helix, which distinguished them from other Nostoc-like heterocytous genera. A unique cluster separated from Nostoc sensu stricto supports the establishment of Violetonostoc gen. nov. with the type species as Violetonostoc minutum sp. nov.

• Journal of Microbiology and Biotechnology
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• v.16 no.11
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• pp.1728-1733
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• 2006

A Gram-negative, strictly aerobic, nonmotile, and nonspore-forming bacterial strain, designated $T5-12^T$, was isolated from compost and characterized using a polyphasic taxonomical approach. The isolate was positive for catalase and oxidase tests. It could degrade DNA, but was negative for degradation of macromolecules such as casein, collagen, starch, chitin, cellulose, and xylan. The DNA G+C content was 36.0 mol%. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The major fatty acids were $iso-C_{15:0}$ (45.6%), $iso-C_{17:0}$ 3OH (17.2%), and summed feature 4 ($C_{16:0}\;{\omega}7c$ and/or $iso-C_{15:0}$ 2OH, 14.9%). Comparative 16S rRNA gene sequence analysis showed that strain $T5-12^T$ fell within the radiation of the cluster comprising members of the genus Sphingobacterium. Strain $T5-12^T$ exhibited lower than 94% of 16S rRNA gene sequence similarity with respect to the type strains of recognized Sphingobacterium species. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain $T5-12^T$ ($=KCTC\;12578^T=LMG\;23401^T=CCUG\;52467^T$) should be classified in the genus Sphingobacterium as the type strain of a novel species, for which the name Sphingobacterium composti sp. novo is proposed.

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.15-20
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• 2010

A Gram negative, aerobic, nonspore-forming, straight or curved rod-shaped bacterium, designated Gsoil $317^T$, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Cells were dimorphic, with stalk (or prostheca) and nonmotile or nonstalked and motile, by means of a single polar flagellum. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil $317^T$ was most closely related to Caulobacter mirabilis LMG $24261^T$ (97.2%), Caulobacter fusiformis ATCC $15257^T$ (97.1 %), Caulobacter segnis LMG $17158^T$ (97.0%), Caulobacter vibrioides DSM $9893^T$ (96.8%), and Caulobacter henricii ATCC $15253^T$ (96.7%). The sequence similarities to any other recognized species within Alphaproteobacteria were less than 96.0%. The detection of Q-10 as the major respiratory quinone and a fatty acid profile with summed feature 7 ($C_{18:1}\;{\omega}7c$ and/or $C_{18:1}\;{\omega}9t$ and/or $C_{18:1}\;{\omega}12t;$ 56.6%) and $C_{16:0}$ (15.9%) as the major fatty acids supported the affiliation of strain Gsoil $317^T$ to the genus Caulobacter. The G+C content of the genomic DNA was 65.5 mol%. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain Gsoil $317^T$ and its closest phylogenetic neighbors were below 11%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $317^T$ should be classified as representing a novel species in the genus Caulobacter, for which the name Caulobacter ginsengisoli sp. novo is proposed. The type strain is Gsoil $317^T$ (=KCTC $12788^T=DSM\;18695^T$).

• Journal of Microbiology and Biotechnology
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• v.22 no.3
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• pp.311-315
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• 2012

A novel ${\beta}$-proteobacterium, designated BXN5-$27^T$, was isolated from soil of a ginseng field of Baekdu Mountain in China, and was characterized using a polyphasic approach. The strain was Gram-staining-negative, aerobic, motile, non-spore-forming, and rod shaped. Strain BXN5-$27^T$ exhibited ${\beta}$-glucosidase activity that was responsible for its ability to transform ginsenoside $Rb_1$ (one of the dominant active components of ginseng) to compound Rd. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belonged to the family Comamonadaceae; it was most closely related to Ramlibacter henchirensis $TMB834^T$ and Ramlibacter tataouinensis$TTB310^T$ (96.4% and 96.3% similarity, respectively). The G+C content of the genomic DNA was 68.1%. The major menaquinone was Q-8. The major fatty acids were $C_{16:0}$, summed feature 4 (comprising $C_{16:1}$ ${\omega}7c$ and/or iso-$C_{15:0}$ 2OH), and $C_{17:0}$ cyclo. Genomic and chemotaxonomic data supported the affiliation of strain BXN5-$27^T$ to the genus Ramlibacter. However, physiological and biochemical tests differentiated it phenotypically from the other established species of Ramlibacter. Therefore, the isolate represents a novel species, for which the name Ramlibacter ginsenosidimutans sp. nov. is proposed, with the type strain being BXN5-$27^T$ (=DSM $23480^T$ = LMG $24525^T$ = KCTC $22276^T$).

• Journal of Microbiology and Biotechnology
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• v.20 no.10
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• pp.1386-1392
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• 2010

A bacterial strain designated GR5$^T$, previously isolated from a freshwater culture pond in Taiwan while screening for bacteria for antimicrobial compounds, was characterized using a polyphasic taxonomic approach. Strain GR5$^T$ was found to be Gram-negative, aerobic, greenish-yellow colored, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at $10-40^{\circ}C$ (optimum, $35^{\circ}C$), pH 7.0-8.0 (optimum pH 8.0), and with 0-2.0% NaCl (optimum, 0.5-1.0%). The major fatty acids were $C_{16:1}{\omega}7c$(36.3%), $C_{16:0}$(16.6%), $C_{12:0}$ 3-OH (12.5%), and $C_{18:1}{\omega}7c$(9.1%). The major respiratory quinone was Q-8, and the DNA G+C content of the genomic DNA was 51.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GR5$^T$ belongs to the genus Rheinheimera, where its most closely related neighbors are Rheinheimera texasensis A62-14B$^T$ and Rheinheimera tangshanensis JA3-B52$^T$ with sequence similarities of 98.1% and 97.5%, respectively, and the sequence similarities to any other recognized species within Gammaproteobacteria are less than 96.5%. The mean level of DNA-DNA relatedness between strain GR5$^T$ and R. texasensis A62-14B$^T$, the strain most closely related to the isolate, was $26.5{\pm}7.6%$. Therefore, based on the phylogenetic and phenotypic data, strain GR5$^T$ should be classified as a novel species, for which the name Rheinheimera aquatica sp. nov. is proposed. The type strain is GR5$^T$ (=BCRC 80081$^T$=LMG 25379$^T$).