the Pv-KDL from P. kumamotoensis (GenBank accession: KT175521.1) clearly with a very low 86.22% similarity. Phylogenetic analysis of the rDNA ITS and LSU regions combined suggested the nematodes from the two fields belong to one population (Fig. 2) and are isolated from the rest of the previous populations from other geographic regions (Table 2).
GenBank sequence deposit information of multiple gene regions of P. vulnus Taiwan isolates from strawberry fields GS and KDL.
Journal of Nematology , 1–5
on data. Alignments of Hsp90 intron regions were adjusted further using Geneious Alignment with free end gaps and identity (1.0/0.0) cost matrix and inspected visually to ensure preservation of exon boundaries and reading frames. Phylogenetic analysis using Bayesian inference (Huelsenbeck and Ronquist, 2001) was performed via the CIPRES Gateway (Miller et al., 2010), except where noted otherwise. The model of nucleotide evolution was determined by jModelTest 2.1.3 (Darriba et al., 2012), with the
Andrea M. Skantar,
Zafar A. Handoo,
Mihail R. Kantor,
Lynn K. Carta,
Journal of Nematology , 1–8
A bacterial isolate MR-CH-I2 [KC809939] isolated from soil contaminated mainly by high nickel concentrations in southwest Slovakia was previously found carrying nccA-like heavy-metal resistance determinant, marked as MR-CH-I2-HMR [KF218096]. According to phylogenetic analysis of short (696 bp) 16S rDNA (16S rRNA) sequences this bacterium was tentatively assigned to Uncultured beta proteobacterium clone GC0AA7ZA05PP1 [JQ913301]. nccA-like gene product was on the same base of its partial (581 bp
Polish Journal of Microbiology , ISSUE 2, 191–201
using gene-specific primers and sent for sequencing by using forward and reverse M13 primers. The forward and reverse sequences were manually edited for quality, aligned using ClustalW, and a consensus sequence was generated using BioEdit v.7.2.6 (Tom Hall, NCSU, USA). The phylogenetic analysis of the ITS and 28S D2/D3 sequences were carried out as described (Ye et al., 2018). In brief, the new and previously published sequences for each gene were aligned using ClustalW in MEGAX (Kumar et al., 2018
Vishal S. Somvanshi,
Journal of Nematology , 1–11
The objective of the present study was to describe the molecular characteristics of enteroviruses associated with hand, food, and mouth disease (HFMD) in Poland. Clinical material from HFMD cases, that occurred during 2013–2016 were examined. It has been showed that coxsackievirus A6 (CVA6), CVA10 and CVA16 were circulating in the country. Phylogenetic analysis showed that Polish CVA6 strains were divided into two distinct clusters suggesting two independent introductions. This is the
Polish Journal of Microbiology , ISSUE 3, 405–409
slender, slightly curved and 17.5 to 18.9 µm long. In the phylogenetic analysis based on 18S, D2-D3 of 28S and ITS regions of rDNA, the new species is clustered with Paratylenchid species having longer stylet length. Morphologically, the new species belongs to Group 9 of Paratylenchus sensu lato and is most similar to G. latescens.
Thomas O. Powers,
Journal of Nematology , ISSUE 4, 611–622
of the following rDNA regions: ITS1, ITS2, 5.8S, 28S rDNA, LSU and β-tubulin were carried out for the isolates studied. A high level of similarity was found between sequences from certain rDNA regions, i.e. ITS1-5.8S-ITS2 and LSU, what confirmed the classification of the isolates to the species A. penicillioides. The classification of our isolates to A. penicillioides species was confirmed also by the phylogenetic analysis.
EWA DOROTA ZALEWSKA
Polish Journal of Microbiology , ISSUE 4, 407–416
with ABI 3730 (Suzhou Genewiz Biotechnology Co., Ltd., Tianjin, China). Sequences were aligned using Clustalw with the default settings in MEGA X software package (Kumar et al., 2018). Sequences were visually proofread, edited, and assembled into contigs in Bioedit v7.1.7 (Hall, 2012). The resulting sequences were submitted to GenBank. Sequences of mermithid from Genbank were searched and involved into the phylogenetic analysis. Pairwise distances and neighbor-joining (NJ) (Saitou and Nei, 1987
Journal of Nematology , 1–7
at 94°C, 45 s at 55°C, and 1 min at 72°C and final extension of 10 min at 72°C. PCR products were sequenced in both directions at BIONNER Korea.
Consensus sequences were edited using the software Geneious (Kearse et al., 2012) and BLAST (Basic Local Alignment Search Tool) at NCBI (National Center for Biotechnology Information) was used to confirm the species’ identity of the sequences. To estimate the phylogenetic history of Helicotylenchus, D2 to D3 sequences of others
Ana Teresa Mosquera-Espinosa,
Francia Varón De Agudelo,
Claudio Marcelo Gonçalves de Oliveira,
Jaime Eduardo Muñoz-Florez
Journal of Nematology , 1–19
, Samastipur grouped with M. oryzae and M. graminis. Molecular phylogenetic analysis using internal transcribed spacer (ITS) suggested that in spite of morphological differences, these populations belonged to M. graminicola.
R. K. WALIA,
VISHAL SINGH SOMVANSHI,
Journal of Nematology , ISSUE 3, 254–267
During a screening of lactic acid bacteria producing bacteriocin from Cotija cheese, the strain QC38 was isolated. Based on the 16S rRNA gene nucleotide sequencing (516 pb accession no KJ210322) and phylogenetic analysis, the isolate was identified as Pediococcus acidilactici. Neutralized cell-free supernatant was tested for antimicrobial activity against 17 Gram-negative and Gram-positive pathogens. Growth inhibition was achieved against Listeria monocytogenes (supplier or indication or source
Aurea I. Morales-Estrada,
Enrico A. Ruiz,
Polish Journal of Microbiology , ISSUE 3, 279–285
M. L. Inácio,
L. C. Rusinque,
M. J. Camacho,
Journal of Nematology , 1–6
Rubzovinema. Based on the morphology and phylogenetic analysis, this nematode is described herein as Delatylus andersoni n. gen., n. sp. The new genus/species is characterized by the female body habitus ranging from nonobese to semiobese and from straight to dorsally curved when heat relaxed, cephalic framework with six unequal sized lip sectors, lateral fields having 10 to 12 lines, 4 to 5 guide rings on the stylet, excretory pore posterior to the nerve ring, spermatheca diminished or absent, vulvar
Journal of Nematology , ISSUE 1, 69–76
rounded terminus. Only two juvenile stages were available to study and no male was found. The polytomous identification codes for this new species are A1, B4, C2, D23, E1, F2, G2, H2, I2, J2, K?, L1 and it belongs to the morphospecies group 1. Phylogenetic analysis based on the 18S, ITS1 and 28S D2/D3 sequences of the new species showed close relationships with X. chambersi. Morphologically, the new species is similar to X. chambersi, X. hangzhouense, and X. winotoi but can be differentiated by
Journal of Nematology , ISSUE 3, 369–386
production, we isolated and characterized microorganisms from the fruiting body of A. bisporus. In total, 55 bacterial strains were isolated, among which nine isolates represented Actinomycetes. All the isolates were analyzed by 16S rRNA gene RFLP and sixteen representative strains by 16S rRNA gene sequencing. According to the phylogenetic analysis, eleven isolates represented the Gram-positive Bacillus, Lysinibacillus, Paenibacillus, Pandorea and Streptomyces genera, and five isolates belonged to the
Polish Journal of Microbiology , ISSUE 2, 201–207
the case of mitochondrial sequences and 5% in the case of 28S rDNA.
28S rDNA and mtCOI-based phylogenetic relationships of the investigated Hoplolaimidae species
Bayesian phylogenetic analysis of the 28S rDNA sequences derived from various Helicotylenchus species resulted in a tree topology (Fig. 4) that agrees with the phylogenetic data presented by Subbotin et al. (2015), Palomares-Rius et al. (2018), and Shokoohi et al. (2018). In total, 12 Helicotylenchus clades (I to XI, as defined in
Journal of Nematology , 1–17
Malorri R. Hughes,
Deborah A. Duffield,
Dana K. Howe,
Dee R. Denver
Journal of Nematology , 1–6
observations for drawings and morphometrics were conducted using live nematode material, which was handpicked from culture plates (Kanzaki et al., 2013).
Molecular characterization and phylogenetic analysis
A species phylogeny of the complete Pristionchus genus was reconstructed as described in Rödelsperger et al. (2018). In the following, we give a brief summary about the generation of the Pristionchus phylogeny (please see Rödelsperger et al., (2018) for full details). For all cultivable Pristionchus
Ralf J. Sommer
Journal of Nematology , 1–14
(Technelysium Pty Ltd, Helensvale, Australia) and aligned using ClustalW (http://workbench.sdsc.edu; Bioinformatics and Computational Biology Group, Department of Bioengineering, UC San Diego, CA). All available species of Deladenus and some other Hexatylina species from GenBank were also selected for phylogenetic analysis. Outgroup taxa for each data set was chosen according to previous published data (Esmaeili et al., 2016). The model of base substitution in the sequences data were evaluated using
Journal of Nematology , 1–10
Shahina, category of Aphelenchoides species. Phylogenetic analysis based on small subunit (SSU) and partial large subunit (LSU) sequences of rRNA supported themorphological results.
Journal of Nematology , ISSUE 1, 34–42
study. Molecular characterization based on 18SSU rDNA sequencing performed to confirm the taxonomic position of this species and to documents the morphological data. Sequence alignment detects a percent of identity up to 88.0% with other Heteroxynematidae species. Phylogenetic analysis showed that the present recorded is a putative sister taxon to A. tetraptera recorded in a previous study. The SSU rDNA sequence has been deposited in the GenBank under the accession no. MG019400.
Saleh Al Quraishy,
Journal of Nematology , ISSUE 2, 117–132
®ZYM test were analyzed and genetic analysis made. Phylogenetic analysis of Streptomyces sp. 8812 revealed that its closest relative is Streptomyces capoamus JCM 4734 (98%), whereas sequence analysis for 16S rRNA gene using NCBI BLAST algorithm showed 100% homology between these two strains. Biosynthetic processes, mycelium growth and enzyme inhibitory activities of these two strains were also compared.
Polish Journal of Microbiology , ISSUE 1, 51–61
The endolithic environment is a ubiquitous habitat for microorganisms and a critical interface between biology and geology. In this study, a culture-based method and the phylogenetic analysis based on 16S rRNA and internal transcribed spacer (ITS) sequences were used to investigate the diversity of endolithic bacteria and fungi in two main types of carbonate rocks (namely dolomite and limestone) from Nanjiang Canyon in Guizhou karst area, China. The results of bacterial diversity indicated that
Polish Journal of Microbiology , ISSUE 4, 413–423
accession numbers indicated on the phylogenetic trees and in Table 1.
D2 to D3 segments, partial ITS1 rRNA, and partial CoxI sequences of different Xiphinema species belonging to the X. non-americanum group were obtained from GenBank and used for phylogenetic reconstruction. Outgroup taxa for each data set were chosen following previous published studies: Longidorus oleae (KT308871), Xiphinema americanum (KX263175); Longidorus caespiticola (KJ567469), Xiphinema duriense (KX244935
Juan E. Palomares-Rius,
Journal of Nematology , 1–21
phasmid (Castillo and Vovlas, 2007). Data on the morphometric measurements of the populations were analyzed using the bootstrap method. The same morphometric characters except b' were used for PCA analysis of P. hippeastri.
DNA extraction, PCR, and phylogenetic analysis
DNA extraction was done using the Chelex method (Straube and Juen, 2013). Five specimens of each species were hand-picked with a fine tip needle and transferred to a 1.5 ml Eppendorf tube containing 20 µl double distilled water. The
Phatu William Mashela,
Journal of Nematology , 1–26
cultures. The phylogenetic analysis of the 5’UTR and Npro region has revealed at least 21 distinct subtypes of BVDV-1 and 4 subtypes of BVDV-2. Genetic diversity of BVD viruses has serious clinical implications such as immune evasion, increase of virulence, host range alteration and also affects the efficacy of vaccination programmes and diagnostic methods.
Postępy Mikrobiologii - Advancements of Microbiology , ISSUE 4, 389–394
BPSAC70 isolated from root tissues showed highest percentage of inhibition (98.3 %) against Fusarium culmorum with significant activity against other tested fungal pathogens. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all seven strains shared 100 % similarity with the genus Streptomyces. In addition, the isolates were subjected to the amplification of antimicrobial genes encoding polyketide synthase type I (PKS-I) and nonribosomal peptide synthetase (NRPS) and found to be
Ajit Kumar Passari,
Vineet Kumar Mishra,
Vijai Kumar Gupta,
Bhim Pratap Singh
Polish Journal of Microbiology , ISSUE 3, 319–329
underwent phylogenetic analysis of 16S rRNA genes. The identification of PKS and NRPS genes in the strains investigated was demonstrated among the homologues the genes involved in the biosynthesis of antibiotics (bacillaene, difficidine, erythromycin, bacitracin, tridecaptin, and fusaricidin), biosurfactants (iturin, bacillomycin, plipastatin, fengycin, and surfactin) and antitumor agents (epothilone, calyculin, and briostatin). Bacillus spp. 9A and 2A strains showed the highest diversity of PKS and
Polish Journal of Microbiology , ISSUE 4, 501–516
://www.clustal.org/mbed.tgz. Results of multiple sequence alignment analysis were used to construct bootstrapped maximum composite likelihood neighbor-joining trees using Mega 7 software.
Phylogenetic analysis of petrol metabolizing bacteria.
Closest phylogenetic relative
Brevibacillus formosus strain NBRC 15716
Brevibacillus formosus strain NBRC 15716
Polish Journal of Microbiology , ISSUE 2, 193–201
serotypes of species B, CVB3 and CVB5 were more frequently detected than others, representing 40% of the characterized isolates, followed by CVB4 (16%), E4 (8%), and E11(8%). Phylogenetic analysis revealed that strains from Poland had the closest genetic relationship with isolates previously identified in Europe (France, Finland, Denmark, Moldova) but also in other parts of the world (Tunisia, China, USA), suggesting wide distribution of these lineages. The paper provides information about NPEV
Polish Journal of Microbiology , ISSUE 4, 443–450
species, raw sequences were checked and edited manually using BioEDIT, v. 7.2.5 (Hall, 1999). Consensus sequences obtained were compared with those deposited in the GenBank database using BLAST engine search for sequence homology. The newly obtained consensus sequences were submitted to the GenBank database under accession numbers KY773577 for D2–D3 of 28S gene and KY773578 for ITS rRNA.
To perform the phylogenetic analysis, D2–D3 LSU, ITS1-5.8S-ITS2 rDNA sequences obtained
Alemayehu W. Habteweld,
William T. Crow,
Journal of Nematology , 1–15