scholarly journals Biometrical, Biochemical, and Molecular Diagnosis of Portuguese Meloidogyne hispanica Isolates

Plant Disease ◽  
2012 ◽  
Vol 96 (6) ◽  
pp. 865-874 ◽  
Author(s):  
Carla M. Maleita ◽  
Maria José Simões ◽  
Conceição Egas ◽  
Rosane H. C. Curtis ◽  
Isabel M. de O. Abrantes
Keyword(s):  
Original Description ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Characteristics ◽  
Species Differentiation ◽  
Polymorphism Analysis ◽  
Accurate Identification ◽  
Restriction Sites ◽  
Meloidogyne Spp ◽  
Enzyme Pattern

Meloidogyne hispanica infects many economically important crops worldwide. The accurate identification of this pathogen is essential for the establishment of efficient and sustainable integrated pest management programs. Portuguese M. hispanica isolates were studied by biometrical, biochemical, and molecular characteristics. Biometrical characteristics of M. hispanica females, males, and second-stage juveniles were similar to the original description. Biochemical studies revealed a unique enzyme pattern (Hi4) for M. hispanica esterases that allowed for species differentiation. Molecular analysis of the mtDNA region from COII and 16S rRNA genes resulted in amplification products (1,800 bp) similar to M. hispanica, M. ethiopica, and M. javanica, and the described HinfI was unable to discriminate M. hispanica from the other two species. Analysis of the mtDNA sequences revealed altered nucleotides among the isolates that created new restriction sites for AluI and DraIII. The resulting restriction patterns successfully discriminated between the three species, providing a new tool for Meloidogyne identification. Finally, the phylogenetic relationship between M. hispanica and several Meloidogyne spp. sequences was analyzed using mtDNA, confirming the divergence between meiotic and mitotic species and revealing the proximity of M. hispanica to closely related species. Based on the studies conducted, the application of isozyme or polymerase chain reaction restriction fragment length polymorphism analysis would be a useful and efficient methodology for M. hispanica identification.

scholarly journals Morphological, Biometrical, Biochemical, and Molecular Characterization of the Coffee Root-Knot Nematode Meloidogyne megadora

Plant Disease ◽  
2016 ◽  
Vol 100 (8) ◽  
pp. 1725-1734 ◽  
Author(s):  
Carla M. Maleita ◽  
Ana M. S. F. de Almeida ◽  
Nicola Vovlas ◽  
Isabel Abrantes
Keyword(s):  
Random Amplified Polymorphic Dna ◽  
Its Region ◽  
Nematode Species ◽  
Molecular Characteristics ◽  
Species Differentiation ◽  
Root Knot Nematode ◽  
Accurate Identification ◽  
Specific Sequence ◽  
Second Stage ◽  
Meloidogyne Spp

Meloidogyne megadora infects coffee trees, an economically important crop worldwide. The accurate identification of M. megadora is essential for the development of preventive measures to avoid the dispersion of this pathogen and establishment of efficient and sustainable integrated pest management programs. One M. megadora isolate was studied by biometrical, biochemical, and molecular characteristics (random amplified polymorphic DNA [RAPD] and PCR of internal transcribed spacer [ITS] region). Biometrical characteristics of M. megadora females, males, and second-stage juveniles were similar to the original description. Biochemical studies revealed a unique enzyme pattern for M. megadora esterases (Me3) that allowed for species differentiation. Three RAPD primers (OPG-4, OPG-5, and OPG-6) produced specific bands to all Meloidogyne spp. studied: M. megadora, M. arenaria, M. incognita, and M. javanica. Molecular analysis of the ITS region resulted in an amplification product of 700 bp. The phylogenetic relationship between M. megadora and several Meloidogyne spp. sequences was analyzed, revealing that M. megadora clearly differs from the most common root-knot nematode species. Based on the studies conducted, isozyme analysis remains a useful and efficient methodology for M. megadora identification when females are available. Further studies will be needed to convert the M. megadora differential DNA fragment obtained by RAPD and develop a species-specific sequence-characterized amplified region PCR assay for its diagnosis based on second-stage juveniles.

scholarly journals Unraveling the Etiology of North American Grapevine Yellows (NAGY): Novel NAGY Phytoplasma Sequevars Related to ‘Candidatus Phytoplasma pruni’

Plant Disease ◽  
2015 ◽  
Vol 99 (8) ◽  
pp. 1087-1097 ◽  
Author(s):  
Robert E. Davis ◽  
Ellen L. Dally ◽  
Yan Zhao ◽  
Ing-Ming Lee ◽  
Wei Wei ◽  
...  
Keyword(s):  
16S Rdna ◽  
North American ◽  
Phylogenetic Analyses ◽  
New York State ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Vitis Vinifera L ◽  
Polymorphism Analysis ◽  
Ribosomal Protein Genes ◽  
Grapevine Yellows

North American grapevine yellows (NAGY) disease has sometimes been attributed to infection of Vitis vinifera L. by Prunus X-disease phytoplasma (‘Candidatus Phytoplasma pruni’) but this attribution may not be fully adequate. In this study, phytoplasma strains related to ‘Ca. Phytoplasma pruni’ were found in NAGY-diseased grapevines in Maryland, Pennsylvania, Virginia, Ohio, Missouri, and New York State. Based on restriction fragment length polymorphism analysis of 16S ribosomal RNA gene (16S rDNA) sequences, the strains (termed NAGYIII strains) were classified in group 16SrIII (X-disease group) but they contained a recognition site for the restriction endonuclease MseI that is not present in the 16S rDNA of ‘Ca. Phytoplasma pruni’. The 16S rDNA of the strains differed by three or four nucleotides from that of ‘Ca. Phytoplasma pruni’, indicating that they belonged to two novel 16S rDNA sequevars, designated NAGYIIIα and NAGYIIIβ. Both sequevars differed from ‘Ca. Phytoplasma pruni’ by a single base in each of three regions corresponding to species-unique (signature) sequences described for ‘Ca. Phytoplasma pruni’. Phylogenetic analyses of 16S rRNA genes and SecY proteins, and single-nucleotide polymorphism analyses of secY and ribosomal protein genes, further distinguished the two grapevine sequevar lineages from one another and from ‘Ca. Phytoplasma pruni’. The NAGYIIIα and NAGYIIIβ sequevars also differed from ‘Ca. Phytoplasma pruni’ in regions of the folded SecY protein that are predicted to be near or exposed at the outer surface of the phytoplasma membrane. No evidence indicated that diseased grapevines contained any phytoplasma strain conforming to ‘Ca. Phytoplasma pruni’ sensu stricto. Because the NAGYIII sequevars have not been reported in X-disease, a question is raised as to whether NAGYIII and Prunus X-disease are caused by different phytoplasma genotypes.

Composition of the archaeal community involved in methane production during the decomposition of Microcystis blooms in the laboratory

2012 ◽  
Vol 58 (10) ◽  
pp. 1153-1158 ◽  
Author(s):  
Peng Xing ◽  
Huabing Li ◽  
Qing Liu ◽  
Jiuwen Zheng
Keyword(s):  
Lake Taihu ◽  
Archaeal Community ◽  
Oxygen Depletion ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Methanogenic Community ◽  
Controlled Systems ◽  
Microcystis Blooms ◽  
Different Temperatures

We investigated the microbial processes involved in methane (CH4) production from Microcystis bloom scums at different temperatures. A Microcystis slurry was collected from Lake Taihu and incubated in airtight bottles at 15, 25, and 35 °C. The production of CH4 was monitored, and the emission rate was calculated. The dynamics of the methanogenic community were analyzed by terminal restriction fragment length polymorphism analysis of archaeal 16S rRNA genes. Phylogenetic information for the methanogens was obtained by cloning and sequencing selected samples. Significant CH4 emission from the Microcystis scums was delayed by approximately 12 days by the natural oxygen depletion process, and CH4 production was enhanced at higher temperatures. Phylogenetic analysis indicated that the archaeal community was composed of Methanomicrobiales, Methanobacteriaceae, and a novel cluster of Archaea. An apparent succession of the methanogenic community was demonstrated, with a predominance of Methanobacteriaceae at higher temperatures. Higher temperatures enhanced the methanogenic transformation of the Microcystis biomass and the phylogenetic dominance of hydrogenotrophic methanogens, suggesting that H2 and CO2 might be the primary substrates for CH4 production during Microcystis decomposition without the participation of lake sediment. This work provides insight into the microbial components involved in Microcystis biomass fermentation in controlled systems.

PCR-Ribotyping of Xenorhabdus andPhotorhabdus Isolates from the Caribbean Region in Relation to the Taxonomy and Geographic Distribution of Their Nematode Hosts

1998 ◽  
Vol 64 (11) ◽  
pp. 4246-4254 ◽  
Author(s):  
Marion Fischer-Le Saux ◽  
Hervé Mauléon ◽  
Philippe Constant ◽  
Brigitte Brunel ◽  
Noël Boemare
Keyword(s):  
Entomopathogenic Nematodes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Caribbean Region ◽  
Polymorphism Analysis ◽  
Caribbean Islands ◽  
Pcr Ribotyping ◽  
The Caribbean ◽  
And Cluster Analysis ◽  
Reference Strains

ABSTRACT The genetic diversity of symbiotic Xenorhabdus andPhotorhabdus bacteria associated with entomopathogenic nematodes was examined by a restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes (rDNAs). A total of 117 strains were studied, most of which were isolated from the Caribbean basin after an exhaustive soil sampling. The collection consisted of 77 isolates recovered from entomopathogenic nematodes in 14 Caribbean islands and of 40 reference strains belonging toXenorhabdus and Photorhabdus spp. collected at various localities worldwide. Thirty distinctive 16S rDNA genotypes were identified, and cluster analysis was used to distinguish the genus Xenorhabdus from the genusPhotorhabdus. The genus Xenorhabdusappears more diverse than the genusPhotorhabdus, and for both genera the bacterial genotype diversity is in congruence with the host-nematode taxonomy. The occurrence of symbiotic bacterial genotypes was related to the ecological distribution of host nematodes.

scholarly journals Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.

2007 ◽  
Vol 57 (3) ◽  
pp. 463-466 ◽  
Author(s):  
Kelly P. Nevin ◽  
Dawn E. Holmes ◽  
Trevor L. Woodard ◽  
Sean F. Covalla ◽  
Derek R. Lovley
Keyword(s):  
Type Strain ◽  
Original Description ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Temperature Optimum ◽  
Ph Optimum ◽  
Donor And Acceptor ◽  
The Family ◽  
Electron Donor And Acceptor

Reclassification of the species Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. is proposed on the basis of physiological traits and phylogenetic position. Characteristics additional to those provided in the original description revealed that the type strain (strain K1T=ATCC BAA-34T=JCM 14045T) has the ability to use Fe(III) as an electron acceptor for acetate oxidation and has an electron donor and acceptor profile typical of a Geobacter species, contains abundant c-type cytochromes, and has a temperature optimum of 30 °C and a pH optimum near pH 7.0; traits typical of members of the genus Geobacter. Phylogenetic analysis of nifD, recA, gyrB, rpoB, fusA and 16S rRNA genes further indicated that T. thiogenes falls within the Geobacter cluster of the family Geobacteraceae. Based on extensive phylogenetic evidence and the fact that T. thiogenes has the hallmark physiological characteristics of a Geobacter species, Trichlorobacter thiogenes should be reclassified as a member of the genus Geobacter.

scholarly journals Response of Endophytic Bacterial Communities in Potato Plants to Infection with Erwinia carotovora subsp. atroseptica

2002 ◽  
Vol 68 (5) ◽  
pp. 2261-2268 ◽  
Author(s):  
Birgit Reiter ◽  
Ulrike Pfeifer ◽  
Helmut Schwab ◽  
Angela Sessitsch
Keyword(s):  
Plant Stress ◽  
Erwinia Carotovora ◽  
Community Analysis ◽  
Antagonistic Activity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Blackleg Disease ◽  
Potato Plants

ABSTRACT The term endophyte refers to interior colonization of plants by microorganisms that do not have pathogenic effects on their hosts, and various endophytes have been found to play important roles in plant vitality. In this study, cultivation-independent terminal restriction fragment length polymorphism analysis of 16S ribosomal DNA directly amplified from plant tissue DNA was used in combination with molecular characterization of isolates to examine the influence of plant stress, achieved by infection with the blackleg pathogen Erwinia carotovora subsp. atroseptica, on the endophytic population in two different potato varieties. Community analysis clearly demonstrated increased bacterial diversity in infected plants compared to that in control plants. The results also indicated that the pathogen stress had a greater impact on the bacteria population than the plant genotype had. Partial sequencing of the 16S rRNA genes of isolated endophytes revealed a broad phylogenetic spectrum of bacteria, including members of the α, β, and γ subgroups of the Proteobacteria, high- and low-G+C-content gram-positive organisms, and microbes belonging to the Flexibacter-Cytophaga-Bacteroides group. Screening of the isolates for antagonistic activity against E. carotovora subsp. atroseptica revealed that 38% of the endophytes protected tissue culture plants from blackleg disease.

scholarly journals Response of Nursery Pigs to a Synbiotic Preparation of Starch and an Anti-Escherichia coli K88 Probiotic

2010 ◽  
Vol 76 (24) ◽  
pp. 8192-8200 ◽  
Author(s):  
D. O. Krause ◽  
S. K. Bhandari ◽  
J. D. House ◽  
C. M. Nyachoti
Keyword(s):  
Escherichia Coli ◽  
Potato Starch ◽  
Control Diet ◽  
Community Analysis ◽  
Positive Control ◽  
Microbial Community Analysis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
E Coli

ABSTRACT Postweaning diarrhea in pigs is frequently caused by enterotoxigenic Escherichia coli K88 (ETEC). The aim of this study was to test the efficacy of E. coli probiotics (PRO) in young pigs challenged with E. coli K88. We also tested the synbiotic interaction with raw potato starch (RPS), which can be used as a prebiotic. Forty 17-day-old weaned piglets were randomly assigned to four treatments: treatment 1, positive-control diet (C), no probiotics or RPS but containing in-feed antibiotics; treatment 2, probiotic (PRO), no feed antibiotics plus a 50:50 mixture of probiotic E. coli strains UM-2 and UM-7; treatment 3, 14% RPS, no antibiotics (RPS); treatment 4, 14% RPS plus a 50:50 mixture of probiotic E. coli strains UM-2 and UM-7, no antibiotics (PRO-RPS). The pigs were challenged with pathogenic E. coli K88 strains on day 7 of the experiment (24-day-old pigs) and euthanized on day 10 of the experiment (35-day-old pigs). Probiotic and pathogenic E. coli strains were enumerated by selective enrichment on antibiotics, and microbial community analysis was conducted using terminal restriction length polymorphism analysis (T-RFLP) of 16S rRNA genes. The combination of raw potato starch and the probiotic had a beneficial effect on piglet growth performance and resulted in a reduction of diarrhea and increased microbial diversity in the gut. We conclude that the use of E. coli probiotic strains against E. coli K88 in the presence of raw potato starch is effective in reducing the negative effects of ETEC in a piglet challenge model.

scholarly journals Ficus microcarpa Bonsai “Tiger bark” Parasitized by the Root-Knot Nematode Meloidogyne javanica and the Spiral Nematode Helicotylenchus dihystera, a New Plant Host Record for Both Species

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1085
Author(s):  
Duarte Santos ◽  
Isabel Abrantes ◽  
Carla Maleita
Keyword(s):  
Host Record ◽  
The Body ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Parasitic Nematodes ◽  
Soil Nematode ◽  
Root Knot Nematode ◽  
Plant Host ◽  
Meloidogyne Spp ◽  
Ficus Microcarpa

In December 2017, a Ficus microcarpa “Tiger bark” bonsai tree was acquired in a shopping center in Coimbra, Portugal, without symptoms in the leaves, but showing small atypical galls of infection caused by root-knot nematodes (RKN), Meloidogyne spp. The soil nematode community was assessed and four Tylenchida genera were detected: Helicotylenchus (94.02%), Tylenchus s.l. (4.35%), Tylenchorynchus s.l. (1.09%) and Meloidogyne (0.54%). The RKN M. javanica was identified through analysis of esterase isoenzyme phenotype (J3), PCR-RFLP of mitochondrial DNA region between COII and 16S rRNA genes and SCAR-PCR. The Helicotylenchus species was identified on the basis of female morphology that showed the body being spirally curved, with up to two turns after relation with gentle heat, a key feature of H. dihystera, and molecular characterization, using the D2D3 expansion region of the 28S rDNA, which revealed a similarity of 99.99% with available sequences of the common spiral nematode H. dihystera. To our knowledge, M. javanica and H. dihystera are reported for the first time as parasitizing F. microcarpa. Our findings reveal that more inspections are required to detect these and other plant-parasitic nematodes, mainly with quarantine status, to prevent their spread if found.

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