Description of Stenomitos kolaenensis and S. hiloensis sp. nov. (Leptolyngbyaceae, Cyanobacteria) with an emendation of the genus

Stenomitos is a recently established cyanobacterial genus, some species of which appear to be cryptic. Here we describe two new species in this genus, Stenomitos kolaensis sp. nov. isolated from the Al-Fe humic podzols of a boreal forest near Nikel town, Murmansk region, Russia and S. hiloensis sp. nov. isolated from a basaltic seep wall on Akeola Road, Hilo, Hawaii, USA. Phylogenetic analyses were conducted on the 16S and 16S-23S ITS rRNA gene regions using Bayesian Inference, and Maximum Likelihood. Phylogenetic analysis of the 16S-23S ITS rRNA region resulted in both S. kolaensis and S. hiloensis forming separate clades from other Stenomitos lineages. Antarctic strains of Stenomitos frigidus (previously reported as “Leptolyngbya frigida”) show that species to be polyphyletic and in need of revision. The structure of the conserved ITS regions (Box-B, D1-D1ʹ, V2 and V3 helices) provided support for separation of the species, and the p-distances among aligned ITS regions further confirmed that a number of species exist within the genus. S. kolaensis and S. hiloensis can be distinguished from other described Stenomitos species (S. rutilans and S. tremulus) by their geographical distribution, habitat preference, 16S rRNA phylogeny, and differences in the secondary structure of the 16S-23S ITS region.

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New cyanobacterium Nodosilinea svalbardensis sp. nov. (Prochlorotrichaceae, Synechococcales) isolated from alluvium in Mimer river valley of the Svalbard archipelago

Phytotaxa ◽

10.11646/phytotaxa.442.2.2 ◽

2020 ◽

Vol 442 (2) ◽

pp. 61-79 ◽

Cited By ~ 1

Author(s):

DENIS DAVYDOV ◽

SERGEI SHALYGIN ◽

ANNA VILNET

Keyword(s):

Phylogenetic Analyses ◽

Natural Populations ◽

Its Region ◽

Total Evidence ◽

Rrna Gene ◽

New Taxon ◽

Cyanobacterial Strain ◽

Svalbard Archipelago ◽

Molecular Approaches ◽

The 16S Rrna Gene

A cyanobacterial strain isolated from the Svalbard archipelago was studied using morphological, ecological, and molecular approaches. The morphology of natural populations fit well the description of the Leptolyngbya s.l. however, in culture, they formed specific nodules that prevented affiliation to this genus. Further phylogenetic analyses including the 16S rRNA gene and 16S-23S ITS region revealed that the strain corresponds to the genus Nodosilinea. Based on this total evidence approach, we provide here a description of the new taxon Nodosilinea svalbardensis sp. nov.

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Phylogenetic analysis of Streptomyces spp. isolated from potato scab lesions in Korea on the basis of 16S rRNA gene and 16S–23S rDNA internally transcribed spacer sequences

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02624-0 ◽

2004 ◽

Vol 54 (1) ◽

pp. 203-209 ◽

Cited By ~ 51

Author(s):

Jaekyeong Song ◽

Seong-Chan Lee ◽

Jun-Won Kang ◽

Hyung-Jin Baek ◽

Joo-Won Suh

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Its Region ◽

Potato Scab ◽

Rrna Gene ◽

16S Rrna Gene Sequences ◽

Its Regions ◽

Streptomyces Scabiei ◽

Internally Transcribed Spacer

The 16S rRNA gene sequences for 34 strains, including 11 isolates, were determined to classify scab-causing Streptomyces spp. and relatives isolated from potato scab lesions collected in Jeju, Korea. The 16S–23S rDNA internally transcribed spacer (ITS) sequences were determined to investigate whether the 16S–23S ITS region is useful for analysing intra- and interspecific relationships in these bacteria. On the basis of phylogenetic analysis of 16S rRNA gene sequences, most of the isolates were classified as Streptomyces scabiei and Streptomyces acidiscabies. Isolate KJO61 was placed in an ambiguous taxonomic position between Streptomyces reticuliscabiei and Streptomyces turgidiscabies. 16S–23S ITS region sequence analysis showed that tRNA genes were not found in this region of Streptomyces spp. The 16S–23S ITS regions of Streptomyces spp. exhibited various lengths and highly variable sequence similarities (35–100 %) within strains as well as intra- and interspecies. It was revealed that Streptomyces europaeiscabiei could be clearly differentiated from Streptomyces scabiei. However, it was clarified that ITS regions are not useful in phylogenetic analysis of Streptomyces spp.

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Establishment of a New Filamentous Cyanobacterial Genus, Microcoleusiopsis gen. nov. (Microcoleaceae, Cyanobacteria), from Benthic Mats in Open Channel, Jiangxi Province, China

Diversity ◽

10.3390/d13110548 ◽

2021 ◽

Vol 13 (11) ◽

pp. 548

Author(s):

Ruozhen Geng ◽

Wenke Li ◽

Aimin Chao ◽

Xiaoyu Guo ◽

Hua Li ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Phylogenetic Analyses ◽

Secondary Structures ◽

16S Rrna Gene Sequence ◽

Jiangxi Province ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Cyanobacterial Genus

Cyanobacterial taxonomic studies performed by using the modern approaches always lead to creation of many new genera and species. During the field survey for cyanobacterial resources in China, a filamentous cyanobacterial strain was successfully isolated from a microbial mat attached to rock surfaces of the Ganfu Channel, Jiangxi Province, China. This strain was morphologically similar to the cyanobacterial taxa belonging to the genera Microcoleus and Phormidium. The phylogenetic analyses based on 16S rRNA gene sequences showed that this strain formed a well-supported clade, close to the filamentous genera Microcoleus, Tychonema, and Kamptonema. The maximum similarity of 16S rRNA gene sequence of this strain with the related genera was 95.04%, less than the threshold for distinguishing bacterial genus. The ITS secondary structures also distinguish this strain from the related cyanobacterial genera. Therefore, combined with morphology, 16S rRNA gene sequence, and ITS secondary structures, a novel cyanobacterial genus here as Microcoleusiopsis was established, with the species type as Microcoleusiopsis ganfuensis.

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Aerofilum fasciculatum gen. nov., sp. nov. (Oculatellaceae) and Euryhalinema pallustris sp. nov. (Prochlorotrichaceae) isolated from an Indian mangrove forest

Phytotaxa ◽

10.11646/phytotaxa.522.3.1 ◽

2021 ◽

Vol 522 (3) ◽

pp. 165-186

Author(s):

SANDEEP CHAKRABORTY ◽

VEERABADHRAN MARUTHANAYAGAM ◽

ANUSHREE ACHARI ◽

ARNAB PRAMANIK ◽

PARASURAMAN JAISANKAR ◽

...

Keyword(s):

16S Rrna ◽

Reference Strain ◽

Its Region ◽

Rrna Gene ◽

The Novel ◽

Diagnostic Features ◽

Species Relationship ◽

Distinct Lineage ◽

Rrna Phylogeny ◽

Reference Strains

Two novel cyanobacteria (AP3 and AP3b) with thin cells and simple morphology were isolated from two islands of the Indian Sundarbans. The 16S rRNA phylogeny data revealed the distinct lineage of AP3b which was nearest to the clade incorporating the genus Oculatella and Tildeniella. Strain AP3 shared a common ancestor with the species Euryhalinema mangrovii. Additionally, the novel 16S rRNA gene sequences of strains AP3 and AP3b showed similarities about 98% and 93% respectively compared to those of established genera or species to which they were phylogenetically related. Furthermore, the folding patterns of semi-conservative structures like D1-D1’, Box-B and V2 helices of 16S-23S ITS region for both strains AP3 and AP3b displayed significant variations and uniqueness when compared with their respective reference strains (Euryhalinema mangrovii for AP3 and all the genera of Oculatellaceae for AP3b). Strain AP3 shared similar morphological features with its reference strain which confirmed its inter-species relationship. The diagnostic features of AP3b including the presence of necridic cells, aerotopes and a cluster-like growth pattern were found to be very contrasting. Altogether, these results substantiated the establishment of strain AP3b as a novel mono-specific genus named Aerofilum fasciculatum and strain AP3 as the second novel species under the genus Euryhalinema, referred to as Euryhalinema pallustris.

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Zygotorulaspora dagestanica sp. nov., a novel ascomycetous yeast species associated with the Georgian honeysuckle (Lonicera iberica M. Bieb.)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004785 ◽

2021 ◽

Vol 71 (4) ◽

Author(s):

Aleksey V. Kachalkin ◽

Dinakhanum A. Abdullabekova ◽

Elena S. Magomedova ◽

Andrey M. Yurkov

Keyword(s):

New Species ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Its Region ◽

Rrna Gene ◽

Ascomycetous Yeast ◽

Wild Fruit ◽

Large Subunit Rrna ◽

A New Species ◽

Basal Position

During an investigation of the yeast communities associated with wild fruit shrubs in Dagestan (Caucasus, Russia), four fermenting ascospore-producing yeast strains were isolated from leaves of the Georgian honeysuckle (Lonicera iberica M. Bieb.) and from soil underneath this plant. Phylogenetic analyses based on concatenated sequences of the ITS region and D1/D2 domains of the large subunit rRNA gene and concatenated sequences of the ribosomal DNA cystron, RPB2 and TEF1 genes showed that the isolated strains represented a new species of the genus Zygotorulaspora. The new species was placed in the basal position to other species of the clade and close to Zygotorulaspora mrakii. Based on the results of phylogenetic analyses and the phenotypic characteristics of the four studied strains, a novel species is described, for which the name Zygotorulaspora dagestanica sp. nov. is proposed. The holotype is KBP Y-4591T, three metabolically inactive cryopreserved isotype cultures are DSM 100088, VKM Y-3060 and VKPM Y-4318. The MycoBank number is MB 838285.

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A novel filamentous cyanobacterium Microseira minor sp. nov. (Oscillatoriaceae, Cyanobacteria) from the Ganfu Channel, Jiangxi, China

Phytotaxa ◽

10.11646/phytotaxa.524.3.2 ◽

2021 ◽

Vol 524 (3) ◽

pp. 178-190

Author(s):

RUOZHEN GENG ◽

QIANZHI WEN ◽

YILANG WANG ◽

PING YANG ◽

GUOFEI DAI ◽

...

Keyword(s):

16S Rrna ◽

Phylogenetic Analyses ◽

Its Region ◽

Jiangxi Province ◽

Species Differentiation ◽

Rrna Gene ◽

Filamentous Cyanobacterium ◽

Molecular Features ◽

Cyanobacterial Diversity ◽

The Difference

Two filamentous cyanobacterial strains were isolated from the mats attached to rock surfaces in the Ganfu Channel, Jiangxi Province, China. A polyphasic approach based on the combination of morphological and molecular features was used to characterize the two strains. Both strains showed the Lyngbya-like morphology under the light microscopy, and had the highest similarity range of 16S rRNA gene sequences as 95.00-96.01% to clones of Microseira wollei, exceeding the cutoff for species delimitation in cyanobacteria. Phylogenetic analyses based on both 16S rRNA and nifH genes and smaller sizes of trichomes in the two Lyngbya-like strains supported them to be proposed as a new species in the genus Microseira as Microseira minor, which is the second species of the genus Microseira. The difference of the 16S-23S ITS region between the two Microseira minor strains and its implication for the evaluation on cyanobacterial diversity and species differentiation were also discussed.

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DNA barcoding, phylogeny and phylogeography of the cyst nematode species of the Avenae group from the genus Heterodera (Tylenchida: Heteroderidae)

Nematology ◽

10.1163/15685411-00003170 ◽

2018 ◽

Vol 20 (7) ◽

pp. 671-702 ◽

Cited By ~ 5

Author(s):

Sergei A. Subbotin ◽

Fateh Toumi ◽

Ibrahim Halil Elekçioğlu ◽

Lieven Waeyenberge ◽

Zahra Tanha Maafi

Keyword(s):

Dna Barcoding ◽

Phylogenetic Analyses ◽

Nematode Species ◽

Cyst Nematode ◽

Rrna Gene ◽

Gene Sequences ◽

Cyst Nematodes ◽

Long Distance ◽

Its Rrna Gene ◽

Its Rrna

Summary Among the recognised species groups of Heterodera, the Avenae group is one of the largest with a total of 12 species. Ten of them, H. arenaria, H. aucklandica, H. australis, H. avenae, H. filipjevi, H. mani, H. pratensis, H. riparia, H. sturhani and H. ustinovi, are morphologically closely related and represent the H. avenae species complex, and the other two, H. hordecalis and H. latipons, are morphologically more distinct from this complex. In this study we provide comprehensive phylogenetic analyses of several hundred COI and ITS rRNA gene sequences from the Avenae group using Bayesian inference, maximum likelihood and statistical parsimony. Some 220 COI and 11 ITS rRNA new gene sequences from 147 nematode populations collected in 26 countries were obtained in this study. Our study showed that the COI gene is a powerful DNA barcoding marker for identification of populations and species from the Avenae group. A putatively new cyst nematode species related to H. latipons was revealed from the analysis of COI and ITS rRNA gene datasets. COI gene sequences allow distinguishing H. arenaria, H. australis and H. sturhani from each other and other species. Problems of species delimiting of these species are discussed. The results of the analysis showed that COI haplotypes corresponded to certain pathotypes of the cereal cyst nematodes. It is recommended that information on COI haplotypes of studied populations be included in research with these nematodes. Based on the results of phylogeographical analysis and age estimation of clades with a molecular clock approach, it was hypothesised that several species of the Avenae group primarily originated and diversified in the Irano-Anatolian hotspot during the Pleistocene and Holocene periods and then dispersed from this region across the world. Different geographic barriers, centres and times of origin might explain current known distribution patterns for species of the Avenae group. Possible pathways, including a long distance trans-Atlantic dispersal, and secondary centres of diversification are proposed and discussed.

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Nakazawaea Odontotermitis f.a., sp. nov., a Novel Yeast Isolated from the Gut of Odontotermes Horni in India.

10.21203/rs.3.rs-1113741/v1 ◽

2021 ◽

Author(s):

Snigdha Tiwari ◽

Bhaskar C. Behera ◽

Abhishek Baghela

Keyword(s):

New Species ◽

Type Strain ◽

Phylogenetic Analyses ◽

Large Subunit ◽

Its Region ◽

Small Subunit ◽

Rrna Gene ◽

Nucleotide Substitutions ◽

Ascomycetous Yeast ◽

Lsu Rrna Gene

Abstract Three strains SMT1.3, SMT1.10, and SMT2.2, representing a novel asexual ascomycetous yeast species, were isolated from the gut of a termite Odontotermes horni in Maharashtra, India. Phylogenetic analyses of the LSU, ITS and SSU sequences revealed that they belonged to the genus Nakazawaea, with N. siamensis as the closest relative. The new species differed from the type strain of N. siamensis (DMKU-RK467T) by 1.93% nucleotide substitutions in the D1/D2 region of the large subunit (LSU) rRNA gene, 0.53% nucleotide substitutions in the small subunit (SSU) rRNA gene and 12.6% nucleotide substitutions in the internal transcribed spacer (ITS) region. Notable physiological differences were also observed between N. siamensis and the new species. Hence, the species Nakazawaea odontotermitis f.a., sp. nov. is proposed. The type strain is SMT1.3T (MTCC 13105 = NFCCI 5011). The GenBank accession numbers of the LSU and ITS and SSU sequences of Nakazawaea odontotermitis f.a., sp. nov. are MZ234240, MZ234239 and OK384663. The MycoBank number is MB 841926.

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Nodosilinea chupicuarensis sp. nov. (Leptolyngbyaceae, Synechococcales) a subaerial cyanobacterium isolated from a stone monument in central Mexico

Phytotaxa ◽

10.11646/phytotaxa.334.2.6 ◽

2018 ◽

Vol 334 (2) ◽

pp. 167 ◽

Cited By ~ 13

Author(s):

JUAN VÁZQUEZ-MARTÍNEZ ◽

JUAN MANUEL GUTIERREZ-VILLAGOMEZ ◽

CITLALI FONSECA-GARCÍA ◽

ENRIQUE RAMÍREZ-CHÁVEZ ◽

MA. LOURDES MONDRAGÓN-SÁNCHEZ ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Its Region ◽

Molecular Data ◽

Central Mexico ◽

Rrna Gene ◽

North Central ◽

Stone Monuments ◽

Morphological And Molecular Data ◽

A New Species ◽

The 16S Rrna Gene

Microorganisms of subaerial biofilms, which develop on the surface of stone monuments, have been widely studied due to their impact on Cultural Heritage deterioration. Nevertheless, these extremophile microorganisms are poorly characterised. In this study, a cyanobacterial strain isolated from an archaeological zone in north-central Mexico was characterised through a polyphasic study based on ecological, morphological, and molecular data. Phylogenetic analyses were done using sequences of the 16S rRNA gene and the 16S-23S ITS region. Based on the polyphasic data, a new species corresponding to the genus Nodosilinea is described. This alkaliphilic species has optimum growth at pH of 9. Its fatty acid profile indicates that C18:1, 9E and C16:0 are its most abundant fatty acids. Extracellular polymeric substance production was verified on this strain. Only a few species of the genus Nodosilinea have been documented and described, and this is the first report of their presence in central Mexico. Hence the name Nodosilinea chupicuarensis sp. nov. is proposed.

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A mitochondrial 12S and 16S rRNA phylogeny of critical genera of Phoridae (Diptera) and related families of Aschiza

Zootaxa ◽

10.11646/zootaxa.593.1.1 ◽

2004 ◽

Vol 593 (1) ◽

pp. 1 ◽

Cited By ~ 11

Author(s):

CHARLES E. COOK ◽

JEREMY J. AUSTIN ◽

R. HENRY L. DISNEY

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Monophyletic Group ◽

Rrna Gene ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

16S Rrna Phylogeny ◽

Rrna Phylogeny

Phylogenetic analysis of mitochondrial 12S and 16S rRNA gene sequences supports the monophyly of the Phoridae. Within this family the Phorinae clade includes two aberrant termitophilous subfamilies, the Thaumatoxeninae and the Termitoxeniinae, which cluster with Dohrniphora and Diplonevra. These two genera include termitophiles and parasitoids of termites, so we hypothesize that these termitophilous phorids are a monophyletic group. While the data neither refute nor support the assumed monophyly of the Metopininae, the genera of this subfamily were not monophyletic in our analysis, but fell into two subclades that correspond with the tribes Metopinini and Gymnophorini.

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