Morphological and molecular characterisation of populations of Longidorus longicaudatus Siddiqi, 1962 and L. americanus Handoo, Carta, Skantar, Ye, Robbins, Subbotin, Fraedrich & Cram, 2005 from Florida, USA

Nematology ◽  
2020 ◽  
pp. 1-17
Author(s):  
Renato N. Inserra ◽  
Alberto Troccoli ◽  
Silvia Vau ◽  
Sergei A. Subbotin
Keyword(s):  
Gene Sequence ◽  
Original Description ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Pine Needle ◽  
Type Specimens ◽  
Gene Sequence Analysis ◽  
Amphidial Fovea ◽  
Two Populations

Summary Two populations of needle nematode, Longidorus longicaudatus Siddiqi, 1962, are described from Quercus hemisphaerica, Q. nigra and Q. virginiana from north Florida, USA. These populations are characterised morphologically by females having a body shorter than 3800 μm, a rounded or slightly flattened lip region, an amphidial fovea pouch-like often with two symmetrical lobes, an odontostyle 99-110 μm long, a conoid tail ending in a bluntly pointed terminus, ranging values of ratio c′ greater than 2, and males very rare. The polytomous code for these populations is A34, B23, C2, D23, E2, F12, G12, H6, I12, J1, K6. Although the morphology and morphometrics of these two populations fit the original description of Longidorus longicaudatus, Florida specimens have greater diameters of lip region, mid and anal body than those of the five type specimens used for the description of this species. The Florida L. longicaudatus is similar to L. paralongicaudatus, but differs from the paratypes of this species in having smaller and greater values of ratios c (53.8 (43.8-64.5) vs 79.2 (61.9-103.5)) and c′ (2.4 (2.1-2.9) vs 1.8 (1.5-2.0)), respectively, and longer tail (60 (53-67) vs 46 (36-53) μm). Molecular characterisation of one of the two Florida L. longicaudatus populations was made based on the D2-D3 of 28S rRNA, ITS1 rRNA and COI gene sequences. The results of the ITS1 rRNA gene sequence analysis indicated that it is genetically different from L. paralongicaudatus. A few specimens of a needle nematode associated with L. longicaudatus were identified morphologically and molecularly as the pine needle nematode, L. americanus. This detection is a new record of the occurrence of the pine needle nematode in Florida.

scholarly journals Identification of Scopulariopsis Species by Partial 28S rRNA Gene Sequence Analysis

2013 ◽  
Vol 62 (3) ◽  
pp. 303-306 ◽  
Author(s):  
TOMASZ JAGIELSKI ◽  
KINGA KOSIM ◽  
MAGDALENA SKÓRA ◽  
ANNA BARBARA MACURA ◽  
JACEK BIELECKI
Keyword(s):  
Sequence Analysis ◽  
Gene Sequence ◽  
Systemic Disease ◽  
Molecular Diagnostic ◽  
Rrna Gene ◽  
28S Rrna ◽  
Opportunistic Pathogens ◽  
Deep Tissue ◽  
28S Rrna Gene ◽  
Gene Sequence Analysis

The genus Scopulariopsis contains over 30 species of mitosporic moulds, which although usually saprophytic may also act as opportunistic pathogens in humans. They have mainly been associated with onychomycosis, and only sporadically reported as a cause of deep tissue infections or systemic disease. Identification of Scopulariopsis species still largely relies on phenotype-based methods. There is a need for a molecular diagnostic approach, that would allow to reliably discriminate between different Scopulariopsis species. The aim of this study was to apply sequence analysis of partial 28S rRNA gene for species identification of Scopulariopsis clinical isolates. Although the method employed did reveal some genetic polymorphism among Scopulariopsis isolates tested, it was not enough for species delineation. For this to be achieved, other genetic loci, within and beyond the rDNA operon, need to be investigated.

Molecular characterisation of two known species of Paratylenchus Micoletzky, 1922 from Iran with notes on the validity of Paratylenchus audriellus Brown, 1959

Nematology ◽  
2016 ◽  
Vol 18 (5) ◽  
pp. 591-604 ◽  
Author(s):  
Mehrab Esmaeili ◽  
Ramin Heydari ◽  
Pablo Castillo ◽  
Mozhgan Ziaie Bidhendi ◽  
Juan E. Palomares-Rius
Keyword(s):  
18S Rrna ◽  
First Record ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Female Tail ◽  
Valid Taxon ◽  
Two Populations ◽  
Partial 18S

During a survey on pin nematodes in western Iran, two populations of Paratylenchus audriellus and Paratylenchus tenuicaudatus were collected and subsequently analysed morphologically and molecularly. Paratylenchus audriellus is characterised by the long stylet (48-61 μm) and the typical female tail with a characteristic claw-like process with sharply pointed terminus. To our knowledge, the Iranian population of P. tenuicaudatus is the first record from Iran. The molecular characterisation of P. audriellus nematodes using the D2-D3 of 28S rRNA and the partial 18S rRNA gene sequences revealed that this species is clearly separated from P. straeleni and should be considered as a valid taxon.

Molecular and morphological characterisation of Paralongidorus iranicus n. sp. and P. bikanerensis (Lal & Mathur, 1987) Siddiqi, Baujard & Mounport, 1993 (Nematoda: Longidoridae) from Iran

Nematology ◽  
2012 ◽  
Vol 14 (4) ◽  
pp. 427-443 ◽  
Author(s):  
Majid Pedram ◽  
Ebrahim Pourjam ◽  
Somayeh Namjou ◽  
Mohammad Reza Atighi ◽  
Carolina Cantalapiedra-Navarrete ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Large Body ◽  
Original Description ◽  
Phoenix Dactylifera ◽  
Rrna Gene ◽  
28S Rrna ◽  
Northern Iran ◽  
Data Set ◽  
Eastern Iran ◽  
Amphidial Fovea

Paralongidorus iranicus n. sp., a new bisexual species of the genus, is described and illustrated by light microscopy, scanning electron microscopy and molecular studies from specimens collected in the rhizosphere of Scots pine (Pinus sylvestris) from the Caspian (Khazar) seashore, Nour, northern Iran. Paralongidorus iranicus n. sp. is characterised by the large body size (7.8-11.4 mm), a rounded lip region, clearly set off by a collar-like constriction at level of, or slightly posterior to, the amphidial aperture, and bearing a very large, stirrup-shaped, amphidial fovea, with conspicuous slit-like aperture, a very long and flexible odontostyle ca 170 μm long, guiding ring located at 34 μm from anterior end and males with spicules ca 80 μm long. In addition, data from an Iranian population of P. bikanerensis recovered from the rhizosphere of palm (Phoenix dactylifera L.) in Bam, Kerman province, south-eastern Iran, agree very well and are very close to the original description of the species from India. The D2 and D3 expansion regions of 28S rRNA gene, ITS1, and 18S rRNA sequences were obtained for P. iranicus n. sp. and P. bikanerensis. Phylogenetic analyses of P. iranicus n. sp. and P. bikanerensis rRNA gene sequences and of Longidorus spp. sequences published in GenBank were done using Maximum Likelihood and Bayesian inference. Paralongidorus species (including P. iranicus n. sp.) clustered together; however, P. bikanerensis clustered within Longidorus spp. and was clearly separated from all other Paralongidorus spp. in trees generated from the D2-D3 expansion segments of 28S and partial 18S data set, respectively.

scholarly journals Microbial Diversity of Septic Tank Effluent and a Soil Biomat

2009 ◽  
Vol 75 (10) ◽  
pp. 3348-3351 ◽  
Author(s):  
Jill Tomaras ◽  
Jason W. Sahl ◽  
Robert L. Siegrist ◽  
John R. Spear
Keyword(s):  
Sequence Analysis ◽  
Microbial Diversity ◽  
Gene Sequence ◽  
Septic Tank ◽  
Rrna Gene ◽  
Control Soil ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Site Water ◽  
Septic Tank Effluent

ABSTRACT Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

scholarly journals Actinocorallia cavernae sp. nov., isolated from a natural cave in Jeju, Korea

2006 ◽  
Vol 56 (5) ◽  
pp. 1085-1088 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Dilution Method ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Properties ◽  
Polar Lipid Profile ◽  
Phylogenetic Cluster ◽  
Gene Sequence Analysis ◽  
Actinomycete Strain

A novel actinomycete, strain N3-7T, was isolated from a natural cave in Jeju, Republic of Korea, using a dilution method and was subjected to characterization using polyphasic taxonomy. A 16S rRNA gene sequence analysis revealed that the organism belonged to the phylogenetic cluster of the genus Actinocorallia and was most closely related to Actinocorallia glomerata and Actinocorallia longicatena (97.6 and 97.5 % similarity, respectively). The main chemotaxonomic properties of strain N3-7T, such as the principal amino acid of the peptidoglycan, the predominant menaquinone and the polar lipid profile, supported classification in the genus Actinocorallia. The organism was readily differentiated from Actinocorallia species with validly published names on the basis of a broad range of phenotypic properties. Thus the isolate represents a novel species of the genus Actinocorallia, for which the name Actinocorallia cavernae sp. nov. is proposed. The type strain is strain N3-7T (=JCM 13278T=NRRL B-24429T).

scholarly journals Kaistia terrae sp. nov., isolated from a wetland in Korea

2010 ◽  
Vol 60 (4) ◽  
pp. 949-952 ◽  
Author(s):  
Soo-Jin Kim ◽  
Hang-Yeon Weon ◽  
Yi-Seul Kim ◽  
Rangasamy Anandham ◽  
Seung-Hee Yoo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

An ivory-coloured bacterium, designated strain 5YN7-3T, was isolated from a wetland, Yongneup, Korea. Cells of the strain were aerobic, Gram-stain-negative, non-motile and short rods. 16S rRNA gene sequence analysis demonstrated that strain 5YN7-3T belongs to the order Rhizobiales of the class Alphaproteobacteria and is closely related to Kaistia soli 5YN9-8T (97.8 %), Kaistia granuli Ko04T (97.6 %) and Kaistia adipata Chj404T (97.4 %). Strain 5YN7-3T showed DNA–DNA hybridization values of 28, 22 and 35 % with K. granuli Ko04T, K. soli 5YN9-8T and K. adipata Chj404T, respectively. The major fatty acids were C18 : 1 ω7c (51.2 %), C19 : 0 cyclo ω8c (25.0 %), C18 : 0 (12.9 %) and C16 : 0 (10.8 %) (>10 % of total fatty acids). Ubiquinone-10 was the major isoprenoid quinone and the DNA G+C content was 66.5 mol%. The phenotypic characteristics in combination with 16S rRNA gene sequence analysis and DNA–DNA hybridization data clearly define strain 5YN7-3T as a novel species of the genus Kaistia, for which the name Kaistia terrae sp. nov. is proposed. The type strain is 5YN7-3T (=KACC 12910T =DSM 21341T).

Patulibacter medicamentivorans sp. nov., isolated from activated sludge of a wastewater treatment plant

2013 ◽  
Vol 63 (Pt_7) ◽  
pp. 2588-2593 ◽  
Author(s):  
Bárbara Almeida ◽  
Ivone Vaz-Moreira ◽  
Peter Schumann ◽  
Olga C. Nunes ◽  
Gilda Carvalho ◽  
...  
Keyword(s):  
Wastewater Treatment ◽  
Sequence Analysis ◽  
Type Species ◽  
Gene Sequence ◽  
Treatment Plant ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis

A Gram-positive, aerobic, non-motile, non-endospore-forming rod-shaped bacterium with ibuprofen-degrading capacity, designated strain I11T, was isolated from activated sludge from a wastewater treatment plant. The major respiratory quinone was demethylmenaquinone DMK-7, C18 : 1 cis9 was the predominant fatty acid, phosphatidylglycerol was the predominant polar lipid, the cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the G+C content of the genomic DNA was 74.1 mol%. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours of strain I11T were Patulibacter ginsengiterrae CECT 7603T (96.8 % similarity), Patulibacter minatonensis DSM 18081T (96.6 %) and Patulibacter americanus DSM 16676T (96.6 %). Phenotypic characterization supports the inclusion of strain I11T within the genus Patulibacter (phylum Actinobacteria) . However, distinctive features and 16S rRNA gene sequence analysis suggest that is represents a novel species, for which the name Patulibacter medicamentivorans sp. nov. is proposed. The type strain is I11T ( = DSM 25962T = CECT 8141T).

scholarly journals Parabacteroides johnsonii sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (2) ◽  
pp. 293-296 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Maki Kitahara ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Gene Sequence Analysis

A bacterial strain isolated from human faeces, M-165T, was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile, menaquinone profile and phylogenetic position (based on 16S rRNA gene sequence analysis). A 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Parabacteroides. Strain M-165T was closely related to Parabacteroides merdae strains, showing 98 % sequence similarity. The strain was obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative, rod-shaped and was able to grow on media containing 20 % bile. Although the phenotypic characteristics of the strain M-165T were similar to those of P. merdae, the isolate could be differentiated from P. merdae by means of API 20A tests for l-arabinose and l-rhamnose fermentation. DNA–DNA hybridization experiments revealed the genomic distinctiveness of the novel strain with respect to P. merdae JCM 9497T (⩽60 % DNA–DNA relatedness). The DNA G+C content of the strain is 47.6 mol%. On the basis of these data, strain M-165T represents a novel species of the genus Parabacteroides, for which the name Parabacteroides johnsonii sp. nov. is proposed. The type strain is M-165T (=JCM 13406T=DSM 18315T).

scholarly journals Winogradskyella thalassocola gen. nov., sp. nov., Winogradskyella epiphytica sp. nov. and Winogradskyella eximia sp. nov., marine bacteria of the family Flavobacteriaceae

2005 ◽  
Vol 55 (1) ◽  
pp. 49-55 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Suk Kyun Han ◽  
Cindy Snauwaert ◽  
Marc Vancanneyt ◽  
...  
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Peter The Great ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Major Respiratory Quinone

Three novel heterotrophic, Gram-negative, yellow-pigmented, aerobic, gliding, oxidase- and catalase-positive bacteria were isolated from algae collected in the Gulf of Peter the Great, Sea of Japan. 16S rRNA gene sequence analysis revealed that the strains studied represented members of the family Flavobacteriaceae and showed 93·5–93·8 % similarity with their closest relative, Psychroserpens burtonensis. The DNA G+C content of the strains was 34–37 mol%. The major respiratory quinone was MK-6. The predominant fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C15 : 1, iso-C16 : 0-3OH and iso-C17 : 0-3OH. On the basis of their phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the newly described bacteria have been assigned to the new genus Winogradskyella gen. nov., as Winogradskyella thalassocola sp. nov. (type strain, KMM 3907T=KCTC 12221T=LMG 22492T=DSM 15363T), Winogradskyella epiphytica sp. nov. (type strain, KMM 3906T=KCTC 12220T=LMG 22491T=CCUG 47091T) and Winogradskyella eximia sp. nov. (type strain, KMM 3944T (=KCTC 12219T=LMG 22474T).

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