Bioprospection of Basidiomycetes and molecular phylogenetic analysis using internal transcribed spacer (ITS) and 5.8S rRNA gene sequence

A Gram-negative, motile, denitrifying bacterium (strain AcBE2-1T) was isolated from activated sludge of a municipal wastewater treatment plant using 17β-oestradiol (E2) as sole source of carbon and energy. Cells were curved rods, 0.4–0.8×0.8–2.0 μm in size, non-fermentative, non-spore-forming, oxidase-positive and catalase-negative. E2 was oxidized completely to carbon dioxide and water by reduction of nitrate to a mixture of dinitrogen monoxide and dinitrogen, with the intermediate accumulation of nitrite. Electron recoveries were between 90 and 100 %, taking assimilated E2 into account. With nitrate as the electron acceptor, the bacterium also grew on fatty acids (C2 to C6), isobutyrate, crotonate, dl-lactate, pyruvate, fumarate and succinate. Phylogenetic analysis of its 16S rRNA gene sequence revealed that strain AcBE2-1T represents a separate line of descent within the family Rhodocyclaceae (Betaproteobacteria). The closest relatives are the cholesterol-degrading, denitrifying bacteria Sterolibacterium denitrificans DSM 13999T and strain 72Chol (=DSM 12783), with <93.9 % sequence similarity. The G+C content of the DNA was 61.4 mol%. Detection of a quinone system with ubiquinone Q-8 as the predominant compound and a fatty acid profile that included high concentrations of C16 : 1 ω7c/iso-C15 : 0 2-OH and C16 : 0, in addition to C18 : 1 ω7c and small amounts of C8 : 0 3-OH, supported the results of the phylogenetic analysis. On the basis of 16S rRNA gene sequence data in combination with chemotaxonomic and physiological data, strain AcBE2-1T (=DSM 16959T=JCM 12830T) is placed in a new genus Denitratisoma gen. nov. as the type strain of the type species Denitratisoma oestradiolicum gen. nov., sp. nov.

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Molecular phylogeny of the heterocystous cyanobacteria (subsections IV and V) based on nifD

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02821-0 ◽

2004 ◽

Vol 54 (2) ◽

pp. 493-497 ◽

Cited By ~ 60

Author(s):

Brian J. Henson ◽

Sharon M. Hesselbrock ◽

Linda E. Watson ◽

Susan R. Barnum

Keyword(s):

Phylogenetic Analysis ◽

Gene Sequence ◽

Sequence Data ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Cellular Division ◽

Heterocystous Cyanobacteria ◽

Nitrogen Fixation Gene ◽

True Branching ◽

Gene Sequence Data

The heterocystous cyanobacteria are currently placed in subsections IV and V, which are distinguished by cellular division in one plane (false branching) and in more than one plane (true branching), respectively. Published phylogenies of 16S rRNA gene sequence data support the monophyly of the heterocystous cyanobacteria, with members of subsection V embedded within subsection IV. It has been postulated that members of subsection V arose from within subsection IV. Therefore, phylogenetic analysis of nucleotide sequences of the nitrogen-fixation gene nifD from representatives of subsections IV and V was performed by using maximum-likelihood criteria. The heterocystous cyanobacteria are supported as being monophyletic, with the non-heterocystous cyanobacteria as their closest relative. However, neither subsection IV nor subsection V is monophyletic, with representatives of both subsections intermixed in two sister clades. Analysis of nifD does not support recognition of two distinct subsections.

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Sphingobium qiguonii sp. nov., a carbaryl-degrading bacterium isolated from a wastewater treatment system

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.020362-0 ◽

2010 ◽

Vol 60 (12) ◽

pp. 2724-2728 ◽

Cited By ~ 26

Author(s):

Qiu-Xiang Yan ◽

Yong-Xia Wang ◽

Shun-Peng Li ◽

Wen-Jun Li ◽

Qing Hong

Keyword(s):

Phylogenetic Analysis ◽

Wastewater Treatment ◽

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Gene Sequence ◽

Treatment System ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence

A Gram-staining-negative, catalase-positive, carbaryl-degrading, non-spore-forming, non-motile, rod-shaped bacterium, designated strain X23T, was isolated from a wastewater treatment system. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain belongs to the genus Sphingobium. The highest 16S rRNA gene sequence similarity observed for the isolate was 96.6 % with the type strain of Sphingobium amiense. Chemotaxonomic data [major ubiquinone: Q-10; major polar lipids: diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, sphingoglycolipid, phosphatidylethanolamine and unknown aminolipids and phospholipids; major fatty acids: summed feature 7 (C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t), C16 : 1 ω5c, C14 : 0 2-OH and C16 : 0 2-OH] as well as the inability to reduce nitrate and the presence of spermidine as the major polyamine supported the affiliation of the strain to the genus Sphingobium. Based on the phylogenetic analysis, whole-cell fatty acid composition and biochemical characteristics, the strain could be separated from all recognized species of the genus Sphingobium. Strain X23T should be classified as a novel species of the genus Sphingobium, for which the name Sphingobium qiguonii sp. nov. is proposed, with strain X23T (=CCTCC AB 208221T =DSM 21541T) as the type strain.

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Lactobacillus farraginis sp. nov. and Lactobacillus parafarraginis sp. nov., heterofermentative lactobacilli isolated from a compost of distilled shochu residue

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64618-0 ◽

2007 ◽

Vol 57 (4) ◽

pp. 708-712 ◽

Cited By ~ 31

Author(s):

Akihito Endo ◽

Sanae Okada

Keyword(s):

Phylogenetic Analysis ◽

Type Strain ◽

Gene Sequence ◽

Novel Species ◽

Sequence Similarity ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Dna Relatedness ◽

Clear Separation ◽

Micro Organisms

Five strains of lactic acid bacteria were isolated from a compost of distilled shochu residue in Japan. The isolates were separated into two groups on the basis of 16S rRNA gene sequence similarity, and two subclusters were formed that comprised micro-organisms closely related to Lactobacillus buchneri, L. diolivorans, L. hilgardii, L. kefiri, L. parabuchneri and L. parakefiri. DNA–DNA relatedness results revealed that the isolates could be separated into two groups, and these groups correlated well with the subclusters generated using the phylogenetic analysis. Moreover, the levels of DNA–DNA relatedness showed clear separation of the two groups from their phylogenetic relatives. Therefore, the two groups represent two novel species, for which the names Lactobacillus farraginis sp. nov. (type strain NRIC 0676T=JCM 14108T=DSM 18382T) and Lactobacillus parafarraginis sp. nov. (type strain NRIC 0677T=JCM 14109T=DSM 18390T) are proposed.

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Solimonas soli gen. nov., sp. nov., isolated from soil of a ginseng field

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64938-0 ◽

2007 ◽

Vol 57 (11) ◽

pp. 2591-2594 ◽

Cited By ~ 17

Author(s):

Myung Kyum Kim ◽

Yu-Jin Kim ◽

Dong-Ha Cho ◽

Tae-Hoo Yi ◽

Nak-Kyun Soung ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Phylogenetic Analysis ◽

Type Strain ◽

Gene Sequence ◽

Taxonomic Status ◽

Rrna Gene ◽

The Novel ◽

Rrna Gene Sequence ◽

Gram Negative ◽

The 16S Rrna Gene

A micro-organism, DCY12T, comprising Gram-negative, non-motile, pale-yellow rods was isolated from soil from a ginseng field in South Korea and was investigated to determine its taxonomic status. It grew optimally at 30 °C and at pH 7.0, the G+C content of its DNA was 40.5 mol%, the major components of the fatty acid profile were C16 : 0 and C18 : 1 and the major ubiquinone was Q-8. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate was most closely related to Hydrocarboniphaga effusa AP103T (89.2 %), Nevskia ramosa Soe1 (88.8 %) and Pseudomonas aeruginosa ATCC 10145T (83.2 %). The phenotypic, physiological, metabolic and phylogenetic properties of DCY12T suggest that it represents a novel genus (class Gammaproteobacteria) and species, for which the name Solimonas soli gen. nov., sp. nov. is proposed. The type strain of Solimonas soli is DCY12T (=KCTC 12834T =LMG 24014T).

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Infundibulicybe macrospora sp. nov., a new and noteworthy species from Himalayan moist temperate forests of Pakistan

Phytotaxa ◽

10.11646/phytotaxa.452.4.2 ◽

2020 ◽

Vol 452 (4) ◽

pp. 268-277

Author(s):

MUHAMMAD ALI ◽

JUNAID KHAN ◽

HIRA BASHIR ◽

ABDUL REHMAN NIAZI ◽

HASSAN SHER ◽

...

Keyword(s):

Phylogenetic Analysis ◽

New Species ◽

Internal Transcribed Spacer ◽

Temperate Forests ◽

Its Region ◽

Molecular Phylogenetic Analysis ◽

Molecular Phylogenetic ◽

A New Species ◽

Reddish Orange ◽

Light Orange

Infundibulicybe macrospora, a new species, is described and illustrated from the Himalayan moist temperate forests of Pakistan. The new species can be differentiated from close allies by its reddish orange to light orange pileus, whitish lamellae and stipe, and larger and broader basidiospores. The new species is also supported by molecular phylogenetic analysis inferred from internal transcribed spacer (ITS) region.

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Description of Anaerobacterium chartisolvens gen. nov., sp. nov., an obligately anaerobic bacterium from Clostridium rRNA cluster III isolated from soil of a Japanese rice field, and reclassification of Bacteroides cellulosolvens Murray et al. 1984 as Pseudobacteroides cellulosolvens gen. nov., comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.059378-0 ◽

2014 ◽

Vol 64 (Pt_4) ◽

pp. 1296-1303 ◽

Cited By ~ 33

Author(s):

Haruka Horino ◽

Takashi Fujita ◽

Akio Tonouchi

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Type Species ◽

Gene Sequence ◽

Rice Field ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Content Type

An obligately anaerobic bacterial strain designated T-1-35T was isolated as a dominant cultivable cellulose-degrading bacterium from soil of a Japanese rice field as an anaerobic filter-paper degrader. Cells of strain T-1-35T stained Gram-positive and were non-spore-forming rods with rounded ends, 0.8–1.0×3.5–15.0 µm, and motile by means of two to four polar flagella. Cells of strain T-1-35T exhibited pleomorphism: in aged cultures (over 90 days of incubation), almost all cells were irregularly shaped. Although no spore formation was observed, cells tolerated high temperatures, up to 90 °C for 10 min. The temperature range for growth was 15–40 °C, with an optimum at 35 °C. The pH range for growth was 5.5–9.0, with an optimum at pH 8.0–8.5 (slightly alkaliphilic). Strain T-1-35T fermented some carbohydrates to produce ethanol and lactate as the major products. Major cellular fatty acids were iso-C16 : 0 and iso-C13 : 0 3-OH. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain T-1-35T belonged to Clostridium rRNA cluster III. The closest relative of strain T-1-35T was Bacteroides cellulosolvens WM2T, with 16S rRNA gene sequence similarity of 93.4 %. Phenotypic, physiological and molecular genetic methods demonstrated that strain T-1-35T was distinct from its phylogenetic relatives (members of Clostridium rRNA cluster III) because it predominantly produced ethanol, iso-C13 : 0 3-OH was a major cellular fatty acid and it always exhibited pleomorphism. On the basis of the results of a polyphasic taxonomic study, strain T-1-35T is considered to represent a novel genus and species, Anaerobacterium chartisolvens gen. nov., sp. nov. The type strain of Anaerobacterium chartisolvens is T-1-35T ( = DSM 27016T = NBRC 109520T). In addition, from the results of our phylogenetic analysis and its phenotypic features, the species Bacteroides cellulosolvens Murray et al. 1984 is proposed to be reclassified in the new genus Pseudobacteroides as Pseudobacteroides cellulosolvens gen. nov., comb. nov., with the type strain WM2T ( = ATCC 35603T = DSM 2933T = NRCC 2944T).

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Molecular phylogenetic study of rare weed-field species of the genus Avena L.

Проблемы ботаники Южной Сибири и Монголии ◽

10.14258/pbssm.2021022 ◽

2021 ◽

Vol 20 (1) ◽

pp. 108-111

Author(s):

A. A. Gnutikov ◽

N. N. Nosov ◽

I. G. Loskutov ◽

E. V. Blinova ◽

A. V. Rodionov

Keyword(s):

Phylogenetic Study ◽

Rrna Gene ◽

Its1 Sequence ◽

5.8S Rrna Gene ◽

Molecular Phylogenetic Study ◽

5.8S Rrna ◽

C Genome ◽

Molecular Phylogenetic ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

A molecular phylogenetic study of weed-field species of the genus Avena L. using marker sequences ITS1–5.8S rRNA gene–ITS2 was undertaken. In addition, next-generation sequencing (NGS) was performed on the Illuminaplatform for the ITS1 sequence and the beginning of the gene 5.8S rRNA. Sanger sequencing results revealed the separateclade of microspecies with a good level of support and small level of difference between themselves. According to NGSsequencing data, the two most abundant subgenomes in terms of the number of sequences were identified. Among thecommon sequences of hexaploids, those associated with the C-genome were not found. The presence of unique ribotypeswas shown for A. persica and A. georgica.

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Sphingomonas xinjiangensis sp. nov., isolated from desert sand

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.021147-0 ◽

2011 ◽

Vol 61 (8) ◽

pp. 1865-1869 ◽

Cited By ~ 17

Author(s):

Hongli An ◽

Mengbo Xu ◽

Jun Dai ◽

Yang Wang ◽

Feng Cai ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Biochemical Characterization ◽

Sequence Similarity ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Sand Sample ◽

Rrna Gene Sequence

A Gram-negative, aerobic, motile, Sphingomonas-like rod, strain 10-1-84T, was isolated from a sand sample collected from the desert of Xinjiang, China. The isolate contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, C16 : 0, C16 : 1ω7c and C14 : 0 2-OH as the major fatty acids. The polyamine pattern contained predominantly sym-homospermidine. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine and an unknown polar lipid. The DNA G+C content was 63.3 mol%. 16S rRNA gene sequence similarity between strain 10-1-84T and the type strains of species of the genus Sphingomonas ranged from 91.11 to 96.54 %. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain 10-1-84T belonged to the genus Sphingomonas. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain 10-1-84T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas xinjiangensis sp. nov. is proposed. The type strain is 10-1-84T ( = CCTCC AB 208035T = NRRL B-51332T).

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