scholarly journals Morphology and molecular evaluation of Iphinoe spelaeobios gen. nov., sp. nov. and Loriellopsis cavernicola gen. nov., sp. nov., two stigonematalean cyanobacteria from Greek and Spanish caves

2011 ◽  
Vol 61 (12) ◽  
pp. 2907-2915 ◽  
Author(s):  
V. Lamprinou ◽  
M. Hernández-Mariné ◽  
T. Canals ◽  
K. Kormas ◽  
A. Economou-Amilli ◽  
...  
Keyword(s):  
Morphological Characteristics ◽  
Molecular Data ◽  
Rrna Gene ◽  
Genetic Traits ◽  
Transmission Electron ◽  
Different Strains ◽  
Taxonomic Groups ◽  
Type V ◽  
Micro Organisms

Caves have generally been found to host phototrophic micro-organisms from various taxonomic groups, with cyanobacteria comprising an important group that have adapted to these stable and highly specific environments. A polyphasic study based on aspects of classical morphology and molecular data revealed two new monospecific genera from fresh material of Greek and Spanish caves. Both taxa are characterized by obligatory true branching (T-type, V-type and false branching), the presence of heterocysts, and reproduction by hormocysts and akinetes. They shared some similarities in their morphological characteristics as revealed by light, scanning electron and transmission electron microscopy, but phylogenetic analysis based on 16S rRNA gene sequences showed that the two phylotypes were different (89.8 % similarity); this represents an example of shared morphology in genetically different strains of cave-adapted species. Phenotypic and genetic traits strongly support classification of the phylotypes as independent taxa in the order Stigonematales (the most differentiated and complicated group of cyanobacteria), family Loriellaceae Geitl 1925. Hence, the names Iphinoe spelaeobios Lamprinou and Pantazidou gen. nov., sp. nov. and Loriellopsis cavernicola Hernández-Mariné and Canals gen. nov., sp. nov. are proposed.

Pinocchia daecheonga sp. nov. (Synechococcales, Cyanobacteria) isolated from a Daecheong Lake in Geum River, Republic of Korea

Phytotaxa ◽  
2021 ◽  
Vol 510 (2) ◽  
Author(s):  
DO-HYUN KIM ◽  
HYE JEONG CHOI ◽  
JANG-SEU KI ◽  
OK-MIN LEE
Keyword(s):  
16S Rrna ◽  
Its Region ◽  
Molecular Data ◽  
23S Rrna ◽  
Rrna Gene ◽  
Genetic Traits ◽  
Sequence Composition ◽  
Transmission Electron ◽  
Sister Clade ◽  
23S Rrna Gene

The collection of Pinocchia daecheonga sp. nov. was performed at the Daecheong Lake in Korea, five strains of which with four clones were investigated through light microscopy, transmission electron microscopy and molecular data comprising the 16S rRNA to 23S rRNA gene. P. daecheonga differed from type species P. polymorpha by absence of the polar aerotopes. Investigated stains and four clones of P. daecheonga turned out to be a sister clade to the P. polymorpha according to the phylogenetic analysis of 16S rRNA gene. In addition, the Pinocchia was clustered with the family Leptolyngbyaceae members, genera Leptothoe and Leptoelongatus. 16S–23S rRNA intergenic transcribed spacer (ITS) region of P. daecheonga was found to be substantially distinct to P. polymorpha in terms of the secondary structure and nucleotide sequence composition, which concludes that the Pinocchia daecheonga isolated from the Daecheong Lake is a unique species due to differences in morphology and genetic traits compared to the relative P. polymorpha.

scholarly journals Four new species in the Tremella fibulifera complex (Tremellales, Basidiomycota)

MycoKeys ◽  
2021 ◽  
Vol 82 ◽  
pp. 33-56
Author(s):  
Long-Fei Fan ◽  
Renato Lúcio Mendes Alvarenga ◽  
Tatiana Baptista Gibertoni ◽  
Fang Wu ◽  
Yu-Cheng Dai
Keyword(s):  
New Species ◽  
Rna Polymerase Ii ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Small Subunit ◽  
Molecular Evidence ◽  
Rrna Gene

Samples of species close to Tremella fibulifera from China and Brazil are studied, and T. fibulifera is confirmed as a species complex including nine species. Five known species (T. cheejenii, T. fibulifera s.s., T. “neofibulifera”, T. lloydiae-candidae and T. olens) and four new species (T. australe, T. guangxiensis, T. latispora and T. subfibulifera) in the complex are recognized based on morphological characteristics, molecular evidence, and geographic distribution. Sequences of eight species of the complex were included in the phylogenetic analyses because T. olens lacks molecular data. The phylogenetic analyses were performed by a combined sequence dataset of the internal transcribed spacer (ITS) and the partial nuclear large subunit rDNA (nLSU), and a combined sequence dataset of the ITS, partial nLSU, the small subunit mitochondrial rRNA gene (mtSSU), the translation elongation factor 1-α (TEF1), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2). The eight species formed eight independent lineages with robust support in phylogenies based on both datasets. Illustrated description of the six species including Tremella fibulifera s.s., T. “neofibulifera” and four new species, and discussions with their related species, are provided. A table of the comparison of the important characteristics of nine species in the T. fibulifera complex and a key to the whitish species in Tremella s.s. are provided.

A new predatory leech from Vietnam (Hirudinida : Arhynchobdellida : Salifidae): its phylogenetic position with comments on the classification of the family

2015 ◽  
Vol 29 (5) ◽  
pp. 473 ◽  
Author(s):  
Takafumi Nakano ◽  
Son Truong Nguyen
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
The Family ◽  
Morphological And Molecular Data ◽  
First Time

The family Salifidae is a predaceous leech taxon in the suborder Erpobdelliformes. Although Salifidae is widely distributed in the African, Oriental, Indo-Malayan, Sino-Japanese and Australasian regions, the phylogenetic relationships of the family Salifidae have never been tested using molecular data obtained from leeches collected from the family distributional range. A salifid species was collected for the first time in Vietnam, and relevant morphological and molecular data are presented here. Because the Vietnamese salifid species possesses unique morphological characteristics among the known salifid species, this species is herein described as a new species, Salifa motokawai, sp. nov. Phylogenetic analyses based on nuclear 18S rRNA and histone H3, as well as mitochondrial cytochrome c oxidase subunit I, tRNACys, tRNAMet, 12S rRNA, tRNAVal, 16S rRNA, tRNALeu and NADH dehydrogenase subunit 1 markers demonstrate that the Vietnamese salifid species is a close congener with the African Salifa perspicax and the Malagasy Linta be. Furthermore, molecular data revealed non-monophyly of the Asian salifid leeches. According to the observed phylogenetic relationships and morphological characteristics of the Vietnamese Salifa motokawai, sp. nov., the current classification of salifid taxa should be revised.

scholarly journals Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia

2007 ◽  
Vol 57 (10) ◽  
pp. 2299-2306 ◽  
Author(s):  
Takeshi Yamada ◽  
Hiroyuki Imachi ◽  
Akiyoshi Ohashi ◽  
Hideki Harada ◽  
Satoshi Hanada ◽  
...  
Keyword(s):  
Yeast Extract ◽  
Rice Paddy ◽  
Limited Range ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Optimum Growth ◽  
Cell Width ◽  
Genetic Traits ◽  
Ph Range ◽  
Micro Organisms

Thermophilic (strain GOMI-1T) and mesophilic (strain KOME-1T) strains were isolated from two different cultures of propionate-degrading consortia obtained from thermophilic digester sludge and rice paddy soil, respectively. The two strains were non-spore-forming, non-motile and Gram-negative. Both strains were obligately anaerobic micro-organisms, showing multicellular filamentous morphotypes more than 100 μm in length. The cell width for strain GOMI-1T was 0.2–0.4 μm and that of strain KOME-1T was 0.4–0.6 μm. Strain GOMI-1T could grow at 45–65 °C with a pH range of 6.0–7.5 (optimum growth at 55 °C, pH 7.0). The temperature range for growth of strain KOME-1T was 30–40 °C and the pH range was pH 5.0–8.5 (optimum growth around 37 °C, pH 7.0). Yeast extract was required for growth of both strains. Strain GOMI-1T was able to grow with a number of carbohydrates in the presence of yeast extract. In yeast extract-containing medium, strain KOME-1T could utilize proteins and a limited range of sugars for growth. The G+C contents of the DNA of strains GOMI-1T and KOME-1T were respectively 54.7 and 57.6 mol%. Major fatty acids of strain GOMI-1T were C16 : 0, C14 : 0 and iso-C15 : 0, whereas those of strain KOME-1T were iso-C15 : 0, anteiso-C15 : 0 and C14 : 0. Based on comparative analysis of 16S rRNA gene sequences of strains GOMI-1T and KOME-1T, the strains were placed in different phylogenetic positions in the class Anaerolineae of the bacterial phylum Chloroflexi. Their phenotypic and genetic traits strongly supported the conclusion that the strains should be described as two independent taxa in the class Anaerolineae. Hence, we propose the names Bellilinea caldifistulae gen. nov., sp. nov., and Longilinea arvoryzae gen. nov., sp. nov., for strains GOMI-1T and KOME-1T. The type strains of Bellilinea caldifistulae and Longilinea arvoryzae are respectively GOMI-1T (=JCM 13669T =DSM 17877T) and KOME-1T (=JCM 13670T =KTCC 5380T).

Toxopsis calypsus gen. nov., sp. nov. (Cyanobacteria, Nostocales) from cave ‘Francthi’, Peloponnese, Greece: a morphological and molecular evaluation

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2870-2877 ◽  
Author(s):  
V. Lamprinou ◽  
K. Skaraki ◽  
G. Kotoulas ◽  
A. Economou-Amilli ◽  
A. Pantazidou
Keyword(s):  
16S Rrna ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Rrna Gene ◽  
New Taxon ◽  
Ecological Data ◽  
16S Rrna Sequence ◽  
Transmission Microscopy ◽  
Genetic Traits ◽  
Fresh Material

Representatives of a new cyanobacterial genus, Toxopsis Lamprinou & Pantazidou gen. nov., were found in fresh material from Cave ‘Francthi’ (Peloponnese, Greece) and isolated in cultures. Ecological data relating to the environmental parameters of the sampling sites are provided, such as the photosynthetically active radiation (PAR), temperature and relative humidity. Morphological characteristics and the life cycle of the type species Toxopsis calypsus Lamprinou & Pantazidou sp. nov. were studied using light microscopy and scanning and transmission microscopy. Molecular analysis based on the 16S rRNA gene sequence was also conducted. Toxopsis calypsus sp. nov. is a false-branched nostocalean cyanobacterium with both isopolar and heteropolar filaments bearing mono-pored and bi-pored heterocysts, and also hormogonia and akinetes. Isopolar filaments adhere by the centre to the substrate and are found mainly in fresh material and in young cultures; heteropolar filaments bearing a basic mono-pore heterocyst are dominant in aged (more than one-year-old) cultures. According to the revised taxonomic classification system of Komárek & Anagnostidis (1989) [Komárek, J. & Anagnostidis, K. (1989). Algol Stud, 56, 247–345] based mainly on morphological data, the new genus described here shares morphological characters with both nostocalean families Scytonemataceae and Microchaetaceae, showing similarities in particular to Scytonematopsis contorta [Vaccarino, M. A. & Johansen, J. R. (2011). Fottea 11, 149–161], Microchaetaceae. Molecular data from the 16S rRNA sequence determined in this paper showed that Toxopsis calypsus sp. nov. is more related to the family Microchaetaceae, and the five phylotypes analysed by PCR showed that the closest nostocalean relatives are Tolypothrix distorta SAG 93.79 (GenBank accession no. GQ287651) and Coleodesmium sp. ANT.L52B.5 (AY493596) with 95–96 % and 96 % similarity, respectively. In contrast, the five phylotypes showed a distant similarity to Scytonematopsis contorta (<91 %). The phenotypic and genetic traits strongly supported the classification of the five phylotypes as a new taxon for which the name Toxopsis calypsus Lamprinou & Pantazidou gen. nov., sp. nov. is proposed.

Mitochondrial Cytochrome oxidase 1 phylogeny supports alternative taxonomic scheme for the marine Haplosclerida

2007 ◽  
Vol 87 (6) ◽  
pp. 1577-1584 ◽  
Author(s):  
Jean Raleigh ◽  
Niamh E. Redmond ◽  
Emma Delahan ◽  
Seamus Torpey ◽  
Rob W.M. van Soest ◽  
...  
Keyword(s):  
Cytochrome Oxidase ◽  
Phylogenetic Signal ◽  
Molecular Data ◽  
Rrna Gene ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Freshwater Sponges ◽  
Cytochrome Oxidase 1 ◽  
Mitochondrial Cytochrome Oxidase

Recent molecular studies have shown that the sponge order Haploslcerida is polyphyletic as the freshwater sponges appear to be more closely related to other demosponges than they are to the marine haplosclerids. Within the marine haplosclerid clade relationships viewed via 18S and 28S rRNA gene phylogenies suggest that the suborders and many families and genera are also polyphyletic. However, both of these genes are on the same locus and do not evolve completely independently. We have analysed mitochondrial Cytochrome oxidase 1 gene fragments from 44 species of marine Haplosclerida and show conclusively that the classification of this group needs complete revision. Molecular data show a very complicated phylogeny supporting very few morphological hypotheses and little geographical pattern. However, the molecular data contain a great deal of phylogenetic signal at many taxonomic levels and support phylogenies drawn from the other genes.

scholarly journals Biodiversity of Magnetotactic Bacteria in the Freshwater Lake Beloe Bordukovskoe, Russia

2019 ◽  
Author(s):  
V. V. Koziaeva ◽  
L. M. Alekseeva ◽  
M. M. Uzun ◽  
P. Leão ◽  
M. V. Sukhacheva ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Marker Gene ◽  
Magnetotactic Bacteria ◽  
Freshwater Lake ◽  
Rrna Gene ◽  
Specific Marker ◽  
Transmission Electron ◽  
Taxonomic Groups

AbstractAccording to 16S rRNA gene- or genome-based phylogeny, magnetotactic bacteria (MTB) belong to diverse taxonomic groups. Here we analyzed the diversity of MTB in a sample taken from the freshwater lake Beloe Bordukovskoe near Moscow, Russia, by using molecular identification based on sequencing of the 16S rRNA gene andmamK, a specific marker gene for these bacteria. A protein encoded by themamKgene is involved in magnetosome chain arrangement inside the cell. As a result, six operational taxonomic units (OTUs) of MTB were identified. Among them, OTUs affiliated with the phylumNitrospiraewere predominant. ‘Ca. Etaproteobacteria’ andAlphaproteobacteriarepresented the minor groups of MTB. We also identified a novel MTB belonging to the familySyntrophaceaeof theDeltaproteobacteriaclass. Using a combination of fluorescence and transmission electron microscopy, the bacteria belonging to these new MTB groups were visualized. Electron microscopy revealed thatSyntrophaceaeMTB were rod-shaped and synthesized elongated magnetosomes, arranged as a disorganized cluster. Among theNitrospiraegroup, two groups with vibrioid cell shape and one group of ovoid-shaped bacteria were identified, all of which had elongated magnetosome crystals consisting of magnetite.

Phylogenetic relationships among the genera of the Penaeidae (Crustacea: Decapoda) revealed by mitochondrial 16S rRNA gene sequences

Zootaxa ◽  
2008 ◽  
Vol 1694 (1) ◽  
pp. 38 ◽  
Author(s):  
TIN-YAM CHAN ◽  
JINGOU TONG ◽  
YAN KIT TAM ◽  
KA HOU CHU
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Relationships ◽  
Molecular Data ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Mitochondrial 16S Rrna Gene

The phylogenetic relationships within the family Penaeidae are examined based on mitochondrial 16S rRNA gene sequence analysis of 30 species from 20 genera. The analysis generally supports the three-tribe scheme proposed by Burkenroad (1983) but it is not consistent with the five-group classification of Kubo (1949). Three clades are resolved: (Penaeus sensu stricto + Fenneropenaeus + Litopenaeus + Farfantepenaeus + Marsupenaeus + Melicertus + Funchalia + Heteropenaeus), (Metapenaeus + Parapenaeopsis + Xiphopenaeus + Rimapenaeus + Megokris + Trachysalambria) and (Metapenaeopsis + Penaeopsis + Parapenaeus), corresponding to the Penaeini, Trachypenaeini and Parapenaeini respectively, while the affinities of Atypopenaeus and Trachypenaeopsis are obscure. The molecular data support that Miyadiella represents the juvenile stage of Atypopenaeus. Within the Trachypenaeini, Trachypenaeus sensu lato is clearly paraphyletic, while the monophyly of Penaeus sensu lato in the Penaeini is questionable.

scholarly journals Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi

2006 ◽  
Vol 56 (6) ◽  
pp. 1331-1340 ◽  
Author(s):  
Takeshi Yamada ◽  
Yuji Sekiguchi ◽  
Satoshi Hanada ◽  
Hiroyuki Imachi ◽  
Akiyoshi Ohashi ◽  
...  
Keyword(s):  
Yeast Extract ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Genetic Traits ◽  
Class Level ◽  
Long Time ◽  
Micro Organisms

One thermophilic (strain IMO-1T) and two mesophilic (strains KIBI-1T and YMTK-2T) non-spore-forming, non-motile, Gram-negative, multicellular filamentous micro-organisms, which were previously isolated as members of the tentatively named class ‘Anaerolineae’ of the phylum Chloroflexi, were characterized. All isolates were strictly anaerobic micro-organisms. The length of the three filamentous isolates was greater than 100 μm and the width was 0.3–0.4 μm for strain IMO-1T, 0.4–0.5 μm for strain KIBI-1T and thinner than 0.2 μm for strain YMTK-2T. Strain IMO-1T could grow at pH 6.0–7.5 (optimum growth at pH 7.0). The optimal temperature for growth of strain IMO-1T was around 50 °C (growth occurred between 42 and 55 °C). Growth of the mesophilic strains KIBI-1T and YMTK-2T occurred at pH 6.0–7.2 with optimal growth at pH 7.0. Both of the mesophilic strains were able to grow in a temperature range of 25–50 °C with optimal growth at around 37 °C. Yeast extract was required for growth of all three strains. All the strains could grow with a number of carbohydrates in the presence of yeast extract. The G+C contents of the DNA of strains IMO-1T, KIBI-1T and YMTK-2T were respectively 53.3, 59.5 and 48.2 mol%. Major fatty acids for thermophilic strain IMO-1T were anteiso-C17 : 0, iso-C15 : 0, C16 : 0 and anteiso-C15 : 0, whereas those for mesophilic strains KIBI-1T and YMTK-2T were branched C14 : 0, iso-C15 : 0, C16 : 0 and branched C17 : 0, and branched C17 : 0, C16 : 0, C14 : 0 and C17 : 0, respectively. Detailed phylogenetic analyses based on their 16S rRNA gene sequences indicated that the isolates belong to the class-level taxon ‘Anaerolineae’ of the bacterial phylum Chloroflexi, which for a long time had been considered as a typical uncultured clone cluster. Their morphological, physiological, chemotaxonomic and genetic traits strongly support the conclusion that these strains should be described as three novel independent taxa in the phylum Chloroflexi. Here, Anaerolinea thermolimosa sp. nov. (type strain IMO-1T=JCM 12577T=DSM 16554T), Levilinea saccharolytica gen. nov., sp. nov. (type strain KIBI-1T=JCM 12578T=DSM 16555T) and Leptolinea tardivitalis gen. nov., sp. nov. (type strain YMTK-2T=JCM 12579T=DSM 16556T) are proposed. In addition, we formally propose to subdivide the tentative class-level taxon ‘Anaerolineae’ into Anaerolineae classis nov. and Caldilineae classis nov. We also propose the subordinate taxa Anaerolineales ord. nov., Caldilineales ord. nov., Anaerolineaceae fam. nov. and Caldilineaceae fam. nov.

scholarly journals Refinement of the Taxonomic Structure of 16SrXI and 16SrXIV Phytoplasmas of Gramineous Plants using Multilocus Sequence Typing

Plant Disease ◽  
2016 ◽  
Vol 100 (10) ◽  
pp. 2001-2010 ◽  
Author(s):  
Saman Abeysinghe ◽  
Pushpa Damayanthi Abeysinghe ◽  
Chamini Kanatiwela-de Silva ◽  
Preethi Udagama ◽  
Kanjana Warawichanee ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Distinct Group ◽  
Napier Grass ◽  
Southern India ◽  
Bermuda Grass ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Seca Gene ◽  
Taxonomic Groups

Phytoplasmas that infect gramineous plants, including Napier grass stunt, sugarcane whiteleaf, sugarcane grassy shoot, and Bermuda grass whiteleaf, have been classified into two closely related groups, 16SrXI and 16SrXIV, based on the 16S ribosomal RNA (rRNA) gene. Subsequently, phytoplasmas associated with coconut and Areca palm in southern India and Sri Lanka have been added into the 16SrXI group. However, the 16S rRNA gene gives relatively poor resolution between these phytoplasmas. In this study, a new set of universal phytoplasma primers that amplify approximately 1 kb of the leucyl transfer RNA synthetase (leuS) gene have been validated on a broad range of phytoplasma taxonomic groups. These have been used along with partial sequences of the secA gene to clarify the taxonomic classification of 16SrXI and 16SrXIV phytoplasmas. Based on this data, the sugarcane whiteleaf and grassy shoot phytoplasmas appear to be the same phytoplasma. The Napier grass stunt phytoplasma forms a distinct group from the Bermuda grass whiteleaf and sugarcane phytoplasmas, suggesting that Napier grass stunt should be in its own ‘Candidatus Phytoplasma sp.’. The phytoplasmas associated with coconut and arecanut in southern India and Sri Lanka, which are in the same 16SrXI group, appear in different groups based on secA analysis.

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