scholarly journals Characterization by 16S rRNA Sequence Analysis of Pseudomonads Causing Blotch Disease of Cultivated Agaricus bisporus

2001 ◽  
Vol 67 (9) ◽  
pp. 4316-4323 ◽  
Author(s):  
S. A. C. Godfrey ◽  
S. A. Harrow ◽  
J. W. Marshall ◽  
J. D. Klena
Keyword(s):  
16S Rrna ◽  
Agaricus Bisporus ◽  
Biochemical Analysis ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Brown Blotch ◽  
Repetitive Extragenic Palindromic Pcr

ABSTRACT Bacterial blotch of Agaricus bisporus has typically been identified as being caused by either Pseudomonas tolaasii (brown blotch) or Pseudomonas gingeri(ginger blotch). To address the relatedness of pseudomonads able to induce blotch, a pilot study was initiated in which pseudomonads were selectively isolated from mushroom farms throughout New Zealand. Thirty-three pseudomonad isolates were identified as being capable of causing different degrees of discoloration (separable into nine categories) of A. bisporus tissue in a bioassay. These isolates were also identified as unique using repetitive extragenic palindromic PCR and biochemical analysis. Relationships between these 33 blotch-causing organisms (BCO) and a further 22 selected pseudomonad species were inferred by phylogenetic analyses of near-full-length 16S rRNA gene nucleotide sequences. The 33 BCO isolates were observed to be distributed throughout thePseudomonas fluorescens intrageneric cluster. These results show that in addition to known BCO (P. tolaasii, P. gingeri, and Pseudomonas reactans), a number of diverse pseudomonad species also have the ability to cause blotch diseases with various discolorations. Furthermore, observation of ginger blotch discoloration of A. bisporus being independently caused by many different pseudomonad species impacts on the homogeneity and classification of the previously described P. gingeri.

scholarly journals Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand

2007 ◽  
Vol 57 (5) ◽  
pp. 954-958 ◽  
Author(s):  
Soon-Wo Kwon ◽  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Youn-Kyung Baek ◽  
Seung-Joo Go
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Curved Rods ◽  
Taxonomic Approach ◽  
Seashore Sand ◽  
Sequence Similarities

A Gram-negative, aerobic bacterium, designated strain HO3-R19T, which was isolated from seashore sand in Pohang city, Korea, was characterized on the basis of a polyphasic taxonomic approach. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain HO3-R19T represents a new lineage within the Gammaproteobacteria; sequence similarities between strain HO3-R19T and members of other related genera were less than 93.5 %. Strain HO3-R19T was also distinguished from related genera based on differences in several phenotypic characteristics. Cells were straight or slightly curved rods and formed white colonies on R2A agar. The major isoprenoid quinone was ubiquinone 8 (Q-8), and predominant cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c. The DNA G+C content of strain HO3-R19T was 65.0 mol%. Based on physiological, biochemical and chemotaxonomic traits together with results of comparative 16S rRNA sequence analysis, strain HO3-R19T is considered to represent a novel species in a new genus, for which the name Arenimonas donghaensis gen. nov., sp. nov. is proposed. The type strain of Arenimonas donghaensis is HO3-R19T (=KACC 11381T=DSM 18148T).

Phylogenetic studies on uncultured Frankia populations in nodules of Datisca cannabina

1994 ◽  
Vol 40 (4) ◽  
pp. 313-318 ◽  
Author(s):  
M. Sajjad Mirza ◽  
Dittmar Hahn ◽  
Svetlana V. Dobritsa ◽  
Antoon D. L. Akkermans
Keyword(s):  
16S Rrna ◽  
Root Nodules ◽  
Alnus Glutinosa ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Phylogenetic Studies ◽  
Close Relationship ◽  
16S Rrna Sequence Analysis ◽  
Relationship Of ◽  
The 16S Rrna Gene

Part of the 16S rRNA gene was amplified directly from uncultured endophyte populations within the root nodules of Datisca cannabina and three strains isolated from nodules of Alnus glutinosa (AgKG′84/4), Coriaria nepalensis (Cn3), and D. cannabina (Dc2). Sequence comparison based on 930 nucleotides indicated that the endophyte of D. cannabina nodules belongs to the genus Frankia and is highly related to the endophyte of C. nepalensis root nodules. The relatedness of the endophytes of C. nepalensis and D. cannabina nodules was also reflected by closely related nifH sequences amplified from the nodules. 16S rRNA sequence analysis of the noninfective strains obtained from both D. cannabina (Dc2) and C. nepalensis (Cn3) nodules also revealed the close relationship of these strains to the genus Frankia.Key words: nitrogen fixation, Frankia, 16S rRNA, nifH.

scholarly journals A rare case of equine Haemotropic Mycoplasma infection in Nigeria

2021 ◽  
Vol 41 (3) ◽  
pp. 274-286
Author(s):  
A.N Happi ◽  
P.E Oluniyi
Keyword(s):  
16S Rrna ◽  
Bacterial Infections ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Clinical Findings ◽  
Epidemiological Surveillance ◽  
Response To Treatment ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
16S Rrna Sequence

Equine haemotropic mycoplasmosis (EHM) is a condition rarely reported worldwide. A horse presented with unspecific clinical findings and non-response to treatment to the common and endemic haemoparasitic and bacterial infections, warranted a thorough molecular investigation of suspected haemoparasitic infection given the fluctuating parasitaemia and the low sensitivity and specificity of Light Microscopy (LM) detection of haemoparasitic infections. Blood collected from an adult horse, domiciled at the University of Ibadan Veterinary Teaching Hospital, Ibadan, Nigeria was screened by LM and PCR techniques for haemo-parasites. The 16S rRNA gene of pan-Hemoplasma spp was targeted amplified and sequenced using Sanger automatic sequencing techniques. This case shows the very first molecular evidence of EHM in Africa and Nigeria, and the third case in the World. Microscopic examination of the horse’s blood smear presented with signs of lethargy, inactivity, anorexia and moderate emaciation, showed numerous coccoid-shaped epierythrocytic parasites. Subsequent 16S rRNA sequence data and phylogenetic analyses confirmed the presence of a haemotropic mycoplasma (‘Candidatus M. haemocervae’–like) in the horse. The hemoplasma sequence obtained falls in the same clade with some Candidatus Mycoplasma haemocervae sequences with which it shared more than 98.7% homology. This finding suggests that horses in this geographical region may also be suffering from EHM and calls for the need of epidemiological surveillance of equine hemoplasmosis with emphasis on their clinical, economic, performance and zoonotic implications in the sub-region. Keywords: Nigeria, Horse, Haemotropic mycoplasma, ‘Candidatus M. haemocervae’–like

Halomonas titanicae sp. nov., a halophilic bacterium isolated from the RMS Titanic

2010 ◽  
Vol 60 (12) ◽  
pp. 2768-2774 ◽  
Author(s):  
Cristina Sánchez-Porro ◽  
Bhavleen Kaur ◽  
Henrietta Mann ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Halophilic Bacterium ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Closely Related Species ◽  
Micro Organisms ◽  
Type Strains

A Gram-negative, heterotrophic, aerobic, non-endospore-forming, peritrichously flagellated and motile bacterial strain, designated BH1T, was isolated from samples of rusticles, which are formed in part by a consortium of micro-organisms, collected from the RMS Titanic wreck site. The strain grew optimally at 30–37 °C, pH 7.0–7.5 and in the presence of 2–8 % (w/v) NaCl. We carried out a polyphasic taxonomic study in order to characterize the strain in detail. Phylogenetic analyses based on 16S rRNA gene sequence comparison indicated that strain BH1T clustered within the branch consisting of species of Halomonas. The most closely related type strains were Halomonas neptunia (98.6 % 16S rRNA sequence similarity), Halomonas variabilis (98.4 %), Halomonas boliviensis (98.3 %) and Halomonas sulfidaeris (97.5 %). Other closely related species were Halomonas alkaliphila (96.5 % sequence similarity), Halomonas hydrothermalis (96.3 %), Halomonas gomseomensis (96.3 %), Halomonas venusta (96.3 %) and Halomonas meridiana (96.2 %). The major fatty acids of strain BH1T were C18 : 1 ω7c (36.3 %), C16 : 0 (18.4 %) and C19 : 0 cyclo ω8c (17.9 %). The DNA G+C content was 60.0 mol% (T m). Ubiquinone 9 (Q-9) was the major lipoquinone. The phenotypic features, fatty acid profile and DNA G+C content further supported the placement of strain BH1T in the genus Halomonas. DNA–DNA hybridization values between strain BH1T and H. neptunia CECT 5815T, H. variabilis DSM 3051T, H. boliviensis DSM 15516T and H. sulfidaeris CECT 5817T were 19, 17, 30 and 29 %, respectively, supporting the differential taxonomic status of BH1T. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain BH1T is considered to represent a novel species, for which the name Halomonas titanicae sp. nov. is proposed. The type strain is BH1T (=ATCC BAA-1257T =CECT 7585T =JCM 16411T =LMG 25388T).

scholarly journals Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria)

2005 ◽  
Vol 55 (1) ◽  
pp. 11-26 ◽  
Author(s):  
Pirjo Rajaniemi ◽  
Pavel Hrouzek ◽  
Klára Kaštovská ◽  
Raphaël Willame ◽  
Anne Rantala ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Data ◽  
Morphological Changes ◽  
Phylogenetic Analyses ◽  
Phylogenetic Study ◽  
Rrna Gene ◽  
Monophyletic Cluster ◽  
Morphological Studies

The heterocytous cyanobacteria form a monophyletic group according to 16S rRNA gene sequence data. Within this group, phylogenetic and morphological studies have shown that genera such as Anabaena and Aphanizomenon are intermixed. Moreover, the phylogeny of the genus Trichormus, which was recently separated from Anabaena, has not been investigated. The aim was to study the taxonomy of the genera Anabaena, Aphanizomenon, Nostoc and Trichormus belonging to the family Nostocaceae (subsection IV.I) by morphological and phylogenetic analyses of 16S rRNA gene, rpoB and rbcLX sequences. New strains were isolated to avoid identification problems caused by morphological changes of strains during cultivation. Morphological and phylogenetic data showed that benthic and planktic Anabaena strains were intermixed. In addition, the present study confirmed that Anabaena and Aphanizomenon strains were not monophyletic, as previously demonstrated. The evolutionary distances between the strains indicated that the planktic Anabaena and Aphanizomenon strains as well as five benthic Anabaena strains in cluster 1 could be assigned to a single genus. On the basis of the 16S rRNA, rpoB and rbcLX gene sequences, the Anabaena/Aphanizomenon strains (cluster 1) were divided into nine supported subclusters which could also be separated morphologically, and which therefore might represent different species. Trichormus strains were morphologically and phylogenetically heterogeneous and did not form a monophyletic cluster. These Trichormus strains, which were representatives of three distinct species, might actually belong to three genera according to the evolutionary distances. Nostoc strains were also heterogeneous and seemed to form a monophyletic cluster, which may contain more than one genus. It was found that certain morphological features were stable and could be used to separate different phylogenetic clusters. For example, the width and the length of akinetes were useful features for classification of the Anabaena/Aphanizomenon strains in cluster 1. This morphological and phylogenetic study with fresh isolates showed that the current classification of these anabaenoid genera needs to be revised.

scholarly journals Pedobacter terrae sp. nov., isolated from soil

2007 ◽  
Vol 57 (11) ◽  
pp. 2462-2466 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Dna Relatedness ◽  
The Family ◽  
Type Strains

A Gram-negative, non-motile, rod-shaped bacterial strain, DS-57T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated using a polyphasic approach. It grew optimally at 25 °C and in trypticase soy broth without NaCl and trypticase soy broth with 0.5 % NaCl. Strain DS-57T contained MK-7 as the predominant menaquinone and iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and iso-C17 : 0 3-OH as the major fatty acids. The DNA G+C content was 39.7 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DS-57T was most closely related to the genus Pedobacter of the family Sphingobacteriaceae, clustering coherently with Pedobacter suwonensis, Pedobacter roseus and Pedobacter sandarakinus. Strain DS-57T exhibited 16S rRNA gene sequence similarity values of 99.2, 97.9 and 97.2 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively, and values less than 95.6 % with respect to the type strains of other Pedobacter species. Strain DS-57T exhibited levels of DNA–DNA relatedness of 45, 17 and 15 % with respect to the type strains of P. suwonensis, P. roseus and P. sandarakinus, respectively. Differential phenotypic properties, together with the phylogenetic distinctiveness and the DNA–DNA relatedness data, were sufficient to allow the classification of strain DS-57T as a species that is separate from recognized Pedobacter species. On the basis of phenotypic properties and phylogenetic distinctiveness, therefore, strain DS-57T represents a novel species of the genus Pedobacter, for which the name Pedobacter terrae sp. nov. is proposed. The type strain is DS-57T (=KCTC 12762T=DSM 17933T).

scholarly journals Hymenobacter Humicola sp. nov., Isolated from Soil in South Korea.

2021 ◽  
Author(s):  
Tuvshinzaya Damdintogtokh ◽  
Jaewoo Bai ◽  
Myung Kyum Kim
Keyword(s):  
16S Rrna ◽  
South Korea ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
16S Rrna Sequence Analysis ◽  
Gene Similarity

Abstract Two novel bacterial strains, designated as BT186T and BT505, were isolated from a soil sample collected in South Korea and characterized. Both strains were Gram-stain-negative, rod-shaped, aerobic, circular, convex, and had red-colored colonies. 16S rRNA sequence analysis indicated that strains BT186T and BT505 belong to a distinct lineage within the genus Hymenobacter (family Hymenobacteraceae, order Cytophagales, class Cytophagia, phylum Bacteroidetes, kingdom Bacteria). Both strains were closely related to Hymenobacter norwichensis DSM 15439T (98.3% 16S rRNA gene similarity), Hymenobacter aquaticus JCM 31653T (96.8%), and Hymenobacter perfusus LMG26000T (96.5%). The strain BT186T was found to have the MK-7 as the major respiratory quinone. The major polar lipid of strain BT186T was identified to be phosphatidylethanolamine (PE). The major cellular fatty acid profiles of strain BT186T were C16:1 ω5c (24.3%), iso-C15:0 (20.3%) and summed feature 3 (C16:1 ω6c / C16:1 ω7c) (19.9%). Characterization based on polyphasic analysis indicated that strains BT186T and BT505 represent novel species of the genus Hymenobacter and the name Hymenobacter humicola sp. nov. is proposed. The type strain of Hymenobacter humicola is BT186T (= KCTC 72338T= NBRC 114968T).

scholarly journals The Genus Caedibacter Comprises Endosymbionts of Paramecium spp. Related to the Rickettsiales (Alphaproteobacteria) and to Francisella tularensis (Gammaproteobacteria)

2002 ◽  
Vol 68 (12) ◽  
pp. 6043-6050 ◽  
Author(s):  
Cora L. Beier ◽  
Matthias Horn ◽  
Rolf Michel ◽  
Michael Schweikert ◽  
Hans-Dieter Görtz ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Bacterial Species ◽  
Sister Group ◽  
Rrna Gene ◽  
Paramecium Tetraurelia ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Bacterial Endosymbionts

ABSTRACT Obligate bacterial endosymbionts of paramecia able to form refractile inclusion bodies (R bodies), thereby conferring a killer trait upon their ciliate hosts, have traditionally been grouped into the genus Caedibacter. Of the six species described to date, only the Paramecium caudatum symbiont Caedibacter caryophilus has been phylogenetically characterized by its 16S rRNA gene sequence, and it was found to be a member of the Alphaproteobacteria related to the Rickettsiales. In this study, the Caedibacter taeniospiralis type strain, an R-body-producing cytoplasmatic symbiont of Paramecium tetraurelia strain 51k, was investigated by comparative 16S rRNA sequence analysis and fluorescence in situ hybridization with specific oligonucleotide probes. C. taeniospiralis is not closely related to C. caryophilus (80% 16S rRNA sequence similarity) but forms a novel evolutionary lineage within the Gammaproteobacteria with the family Francisellaceae as a sister group (87% 16S rRNA sequence similarity). These findings demonstrate that the genus Caedibacter is polyphyletic and comprises at least two phylogenetically different bacterial species belonging to two different classes of the Proteobacteria. Comparative phylogenetic analysis of C. caryophilus, five closely related Acanthamoeba endosymbionts (including one previously uncharacterized amoebal symbiont identified in this study), and their hosts suggests that the progenitor of the alphaproteobacterial C. caryophilus lived within acanthamoebae prior to the infection of paramecia.

scholarly journals Parapedobacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 129-134 ◽  
Author(s):  
Roshan Kumar ◽  
Vatsala Dwivedi ◽  
Namita Nayyar ◽  
Helianthous Verma ◽  
Amit Kumar Singh ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Gene Sequence Analysis ◽  
16S Rrna Sequence Analysis

Strain RK1T, a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium was isolated from a hexachlorocyclohexane (HCH) dumpsite, Lucknow, India. 16S rRNA gene sequence analysis revealed that strain RK1T belongs to the family Sphingobacteriaceae and showed highest sequence similarity to Parapedobacter koreensis Jip14T (95.63 %). The major cellular fatty acids of strain RK1T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c), iso-C15 : 0 3-OH and C16 : 0. The major respiratory pigment and polyamine of RK1T were menaquinone (MK-7) and homospermidine, respectively. The main polar lipids were phosphatidylethanolamine and sphingolipid. The G+C content of the DNA was 44.5 mol%. The results of physiological and biochemical tests and 16S rRNA sequence analysis clearly demonstrated that strain RK1T represents a novel species of the genus Parapedobacter , for which the name Parapedobacter indicus sp. nov. is proposed. The type strain is RK1T ( = DSM 28470T = MCC 2546T).

scholarly journals Pseudomonas eucalypticola sp. nov., a producer of antifungal agents isolated from Eucalyptus dunnii leaves

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yujing Liu ◽  
Zhang Song ◽  
Hualong Zeng ◽  
Meng Lu ◽  
Weiyao Zhu ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Antifungal Agents ◽  
Novel Species ◽  
Phytopathogenic Fungi ◽  
Strictly Aerobic ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Eucalyptus Dunnii ◽  
16S Rrna Sequence Analysis

AbstractPseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1 T, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against five tested phytopathogenic fungi. The strain is a Gram-negative rod-shaped bacterium containing a single polar flagellum. It is strictly aerobic, grows at 4–37 °C, 2–5% NaCl, and pH 3–7. The 16S rRNA sequence analysis showed that NP-1 T belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 T belongs to Pseudomonas fluorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 T genome is 63.96, and the differences between NP-1 T and related species are larger than 1. The digital DNA-DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 T from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confirmed its differentiation from related taxa. The results from this polyphasic approach support the classification of NP-1 T as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 T (= CCTCC M2018494T = JCM 33572 T).

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