Characterization ofBacillusandPseudomonasstrains with suppressive traits isolated from tomato hydroponic-slow filtration unit

2007 ◽  
Vol 53 (6) ◽  
pp. 784-797 ◽  
Author(s):  
D. Renault ◽  
F. Déniel ◽  
E. Benizri ◽  
D. Sohier ◽  
G. Barbier ◽  
...  
Keyword(s):  
Pathogenic Fungi ◽  
Polymerase Chain Reaction Primer ◽  
Filtration Process ◽  
Phenotypic Differences ◽  
Pseudomonas Plecoglossicida ◽  
Rdna Sequencing ◽  
Primer Sets ◽  
Filtration Unit ◽  
Slow Filtration ◽  
Bacillus Strains

Bacillus and Pseudomonas spp. are known to be involved in plant pathogenic fungi elimination during the slow filtration process used in tomato soilless cultures. We isolated 6–8 strains of both Bacillus and Pseudomonas from the top, middle, and bottom sections of filters and identified them after 16S rDNA sequencing. Four Pseudomonas strains were identified as Pseudomonas fulva , 5 as Pseudomonas plecoglossicida , and 12 as Pseudomonas putida . The use of specific oligonucleotide polymerase chain reaction primer sets designed from gyrB gene sequences additionally permitted the identification of 17 Bacillus cereus and 3 Bacillus thuringiensis strains. Ribotyping with EcoRI pointed out an important polymorphism within Bacillus and Pseudomonas strains. Molecular characterization did not reveal a correlation between the location of isolates within the filter (top, middle, or bottom) and bacterial identification or riboclusters. Functional aspects assessed by community-level physiological profiling showed marked phenotypic differences between Pseudomonas communities isolated from the top and bottom filter layers; differences were lower between Bacillus communities of different layers and far less noticeable between mixed communities of Bacillus and Pseudomonas. These strains were tested for several suppressive activities. Conversely to most Bacillus, the majority of Pseudomonas strains were auxin producers and promoted the growth of tomato plantlet roots. On the other hand, only Bacillus strains displayed antagonistic activities by inhibiting the growth of pathogenic fungi frequently detected in soilless cultures. Siderophores were produced by nearly all bacteria, but at higher amounts by Pseudomonas than Bacillus strains. The biocontrol agent potentiality of certain strains to optimize the slow filtration process and to promote the suppressive potential of nutrient solution is discussed.

scholarly journals Polymerase chain reaction primer sets for the detection of genetically diverse human sapoviruses

2020 ◽  
Vol 165 (10) ◽  
pp. 2335-2340
Author(s):  
Tomoichiro Oka ◽  
Seiji P. Yamamoto ◽  
Nobuhiro Iritani ◽  
Shigenori Sato ◽  
Chika Tatsumi ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Primer ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Primer Sets

scholarly journals Effects of Particles Diffusion on Membrane Filters Performance

Fluids ◽  
2020 ◽  
Vol 5 (3) ◽  
pp. 121
Author(s):  
Shi Yue Liu ◽  
Zhengyi Chen ◽  
Pejman Sanaei
Keyword(s):  
Pore Structure ◽  
Flow Rate ◽  
Membrane Filtration ◽  
Membrane Filter ◽  
Membrane Properties ◽  
Filtration Process ◽  
Membrane Pore ◽  
Filtration Performance ◽  
Structure Flow ◽  
Slow Filtration

Membrane filtration fouling is a very complex process and is determined by many properties such as the membrane internal morphology, membrane pore structure, flow rate and contaminant properties. In a very slow filtration process or during the late stage of filtration, when the flow rate is naturally low and Péclet number is small, particle diffusion is essential and cannot be neglected, while in typical filtration models, especially in moderate and fast filtration process, the main contribution stems from the particle advection. The objectives of this study is to formulate mathematical models that can (i) investigate how filtration process varies under possible effects of particles diffusion; and (ii) describe how membrane morphology evolves and investigate the filtration performance during the filtration process. We also compare the results with the case that diffusion is less important and make a prediction about what kind of membrane filter pore structure should be employed to achieve a particular optimum filtration performance. According to our results, the filtrate and efficiency of particle separation are found to be under the trade-off relationship, and the selection of the membrane properties depends on the requirement of the filtration.

Development of pre-coagulation and bio-filtration process for advanced treatment of sewage

2004 ◽  
Vol 4 (1) ◽  
pp. 13-22 ◽  
Author(s):  
H. Tsuno ◽  
T. Hidaka ◽  
M. Nakamoto
Keyword(s):  
Control Systems ◽  
Retention Time ◽  
Hydraulic Retention Time ◽  
Advanced Treatment ◽  
Filtration Process ◽  
Automatic Control Systems ◽  
Side Stream ◽  
Addition Rate ◽  
Filtration Unit ◽  
Filter Backwashing

A pre-coagulation and bio-filtration process for advanced treatment of sewage is developed and experimentally discussed with a pilot plant. The bio-filtration unit consists of a denitrification filter, a nitrification filter with side stream to the denitrification filter, and a polishing filter with anoxic and aerobic parts. Concentrations of SS, T-CODCr, T-C-BOD, T-N and T-P in the effluent were stably kept at less than mg/L, 20 mg/L, 5 mg/L, 2 mg N/L and 0.2 mg P/L, respectively, and transparency at higher than 100 cm, under total hydraulic retention time (HRT) of 3.2 h in the bio-filtration parts. S-CODCr/NOx−-N ratio of higher than 12 mg COD/mg N is required to keep the remaining NOx−-N concentrations less than 1 mg N/L in the effluent from the denitrification filter. Methanol addition rate of higher than 4.5 mg COD/mg N is necessary to accomplish denitrification with the remaining NOx−-N of less than 0.5 mg N/L in the effluent from the polishing filter. Backwashing in each filter as well as methanol addition and aeration in the polishing filter were able to be operated successfully by the automatic control systems. Therefore this process is proved to be applicable to advanced treatment of sewage with easy maintenance.

scholarly journals New Histoplasma Diagnostic Assays Designed via Whole Genome Comparisons

2021 ◽  
Vol 7 (7) ◽  
pp. 544
Author(s):  
Juan E. Gallo ◽  
Isaura Torres ◽  
Oscar M. Gómez ◽  
Lavanya Rishishwar ◽  
Fredrik Vannberg ◽  
...  
Keyword(s):  
Pathogenic Fungi ◽  
Positive Control ◽  
Detection Sensitivity ◽  
Analytical Sensitivity ◽  
Protein Coding ◽  
Control Plasmid ◽  
Formalin Fixed Paraffin Embedded ◽  
Pcr Assays ◽  
Primer Sets

Histoplasmosis is a systemic fungal disease caused by the pathogen Histoplasma spp. that results in significant morbidity and mortality in persons with HIV/AIDS and can also affect immunocompetent individuals. Although some PCR and antigen-detection assays have been developed, conventional diagnosis has largely relied on culture, which can take weeks. Our aim was to provide a proof of principle for rationally designing and standardizing PCR assays based on Histoplasma-specific genomic sequences. Via automated comparisons of aligned genome contigs/scaffolds and gene (sub)sequences, we identified protein-coding genes that are present in existing sequences of Histoplasma strains but not in other genera. Two of the genes, PPK and CFP4, were used for designing primer sets for conventional and real-time PCR assays. Both resulted in a 100% analytical specificity in vitro and detected 62/62 H. capsulatum isolates using purified DNA. We also obtained positive detections of 2/2 confirmed H. capsulatum clinical FFPE (formalin-fixed paraffin-embedded) samples using both primer sets. Positive control plasmid 10-fold serial dilutions confirmed the analytical sensitivity of the assays. The findings suggest that these novel primer sets should allow for detection sensitivity and reduce false positive results/cross-reactions. New assays for detecting pathogenic fungi, constructed along these lines, could be simple and affordable to implement.

scholarly journals Comparison of Molecular Procedures for Detection and Identification of Guignardia citricarpa and G. mangiferae

Plant Disease ◽  
2007 ◽  
Vol 91 (5) ◽  
pp. 525-531 ◽  
Author(s):  
N. A. Peres ◽  
R. Harakava ◽  
G. C. Carroll ◽  
J. E. Adaskaveg ◽  
L. W. Timmer
Keyword(s):  
Extraction Procedure ◽  
Citrus Fruit ◽  
Black Spot ◽  
Polymerase Chain Reaction Primer ◽  
Internal Transcribed Spacer Region ◽  
Guignardia Citricarpa ◽  
Detection And Identification ◽  
Specificity And Sensitivity ◽  
Fruit Spot ◽  
Primer Sets

Citrus black spot, caused by Guignardia citricarpa, is a serious fruit spot disease and is widely distributed in Asia, southern Africa, and South America, but does not occur in North America or the Mediterranean region. A nonpathogenic species, G. mangiferae, is cosmopolitan with a wide host range and can colonize citrus fruit and leaves saprophytically. Detection and identification of Guignardia spp. on citrus fruit is necessary for epidemiological, management, and regulatory purposes. In this study, we compared published and unpublished polymerase chain reaction primer sets for their specificity and sensitivity in the detection and differentiation of the two Guignardia spp. All primers evaluated successfully identified the two species using purified DNA from fungal cultures or mycelia as source materials. However, some primer sets were not highly effective in detecting G. citricarpa when DNA was extracted directly from single characteristic black spot lesions on fruit. Thus, new primer pairs for both species were designed from the internal transcribed spacer region that were highly sensitive and specific for detection of G. citricarpa using DNA recovered from single lesions on fruit by a rapid DNA extraction procedure.

scholarly journals ISOLASI NON-DESTRUKTIF DAN DESTRUKTIF GEN COI PADA SERANGGA JENIS COLEOPTERA PEMBAWA PATOGEN CERATOCYSTIS

2021 ◽  
Vol 15 (1) ◽  
pp. 1-11
Author(s):  
Anindya Safita Ningtias ◽  
◽  
Istiana Prihatini ◽  
Maryatul Qiptiyah
Keyword(s):  
Species Identification ◽  
Pathogenic Fungi ◽  
Coi Gene ◽  
Chain Reaction ◽  
Crucial Step ◽  
Polymerase Chain ◽  
Primer Sets ◽  
Non Destructive ◽  
Destructive Methods ◽  
Molecular Characters

Identification of insect species using molecular approach is one of the first steps in managing Ceratocystis. Proper species identification of the vectorsof Ceratocystiswill provide an effective way in limiting the distribution of this pathogenic fungi. The isolation of insect DNA is a crucial step in species identification using molecular characters. The aim of this research was to obtain the most effective method for isolating the COI gene and to confirm the insect DNA using amplification of the DNA through polymerase chain reaction (PCR). Twelve unidentified Coleoptera specimen collected from Acacia spp. plantation in Pelalawan Riau were randomly selected for this study. The insect DNA were isolated using the CTAB buffer with four different pre-incubation treatments, involved a non destructive method, i.e. soaking (R), destructive methods, i.e. crushing (H), soaking-crushing (RH) and freezing-crushing (FH). Two sets of primer, LCO1490/HCO2196 and LCO1490/HCO2198 were used to amplify the DNA of COI gene. The results shows, the COI gene was isolated from all pre-incubation treatments, except in the non-destructive treatment. The isolated DNA of COI gene was successfully amplified using both primer sets used in this study

Identification of opportunistic and nonopportunistic Exophiala species using high resolution melting analysis

2020 ◽  
Vol 58 (7) ◽  
pp. 938-945
Author(s):  
Tanaz Bahadori ◽  
Mojtaba Didehdar ◽  
Behzad Khansarinezhad ◽  
Tahereh Shokohi
Keyword(s):  
High Resolution ◽  
High Resolution Melting ◽  
Its Region ◽  
Clinical Samples ◽  
Phenotypic Differences ◽  
Physiological And Biochemical Characteristics ◽  
Environmental Reference ◽  
Melting Analysis ◽  
Primer Sets ◽  
Exophiala Species

Abstract Exophiala is a genus comprising several species of opportunistic black yeasts. Exophiala species identification by morphological, physiological, and biochemical characteristics is challenging because of the low degree of phenotypic differences between species and its polyphyletic nature. We aimed to develop a high-resolution melting (HRM) assay based on the internal transcribed spacer (ITS) region to differentiate between pairs of clinical and environmental Exophiala species. HRM primers were designed based on the conserved ITS region of five Exophiala species (E. dermatitidis, E. phaeomuriformis, E. heteromorpha, E. xenobiotica, and E. crusticola). Environmental and clinical Exophiala isolates representing these five species (n = 109) were analyzed. The HRM assay was optimized using clinical and environmental reference isolates (n = 22), and then the results were compared with those obtained with nonreference isolates of Exophiala (n = 87) using two designed primer sets. The designed HRM assay was based on the normalized melting peak approach and two primer sets, and successfully distinguished between the five Exophiala species. The HRM1 primer set provided sufficient resolution, with a melting temperature (Tm) difference of approximately 2.5°C among the analyzed species and of approximately 1°C between E. dermatitidis and E. phaeomuriformis. HRM typing results were in agreement with those of ITS-sequence typing (100% sensitivity and specificity). The developed HRM assay can be used to ascertain the identity of Exophiala species, which may differ in clinical significance, with high accuracy. Its application to identify species directly in clinical samples and/or environmental niches may be possible in the future.

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