scholarly journals CHARACTERIZATION OF BACTERIAL ISOLATES FOR SUSTAINABLE RICE BLAST CONTROL

2020 ◽  
Vol 33 (3) ◽  
pp. 702-712
Author(s):  
BÁRBARA ESTEVAM DE MELO MARTINS ◽  
AMANDA ABDALLAH CHAIBUB ◽  
MARCIO VINICIUS DE CARVALHO BARROS CORTÊS ◽  
VALÁCIA LEMES DA SILVA LOBO ◽  
MARTA CRISTINA CORSI DE FILIPPI
Keyword(s):  
Rice Blast ◽  
Pcr Amplification ◽  
Morphological Characterization ◽  
Bacterial Isolates ◽  
Specific Primers ◽  
Leaf Blast ◽  
Fluorescent Pigment ◽  
Gram Staining ◽  
Bacillus Spp

ABSTRACT Rice blast (Magnaporthe oryzae) limits rice (Oryza sativa) grain yields worldwide. The objective of this investigation was to morphologically, biochemically, and molecularly characterize six bacterial isolates, BRM 32109, BRM 32110, BRM 32111, BRM 32112, BRM 32113, and BRM 32114, and to determine their potential as antagonists to M. oryzae. Morphological characterization was based on colony formation and color, Gram staining, and fluorescent pigment production. Biochemical studies were based on cellulase, chitinase, phosphatase, indoleacetic acid, and siderophore production, as well as biofilm formation. The molecular identification used specific primers for PCR amplification of the 16S rRNA region, followed by sequencing. The antagonism studies involved three experiments, which had randomized designs. Two of them were conducted in laboratory conditions, pairing bacterial colonies and M. oryzae, using bacterial filtrates, and the third was conducted in greenhouse conditions. BRM 32111 and BRM 32112 were identified as Pseudomonas sp., BRM 32113 as Burkholderia sp., BRM 32114 as Serratia sp., and BRM 32110 and BRM 32109 as Bacillus spp. BRM 32112, BRM 32111, and BRM 32113 inhibited the colony of M. oryzae by 68%, 65%, and 48%, respectively. The bacterial suspensions of the BRM 32111, BRM 32112, and BRM 3212 filtrates suppressed leaf blast by 81.0, 79.2, and 66.3%, respectively. BRM 32111 and BRM 32112 were determined to be antagonists of M. oryzae and were found to solubilize phosphate, produce siderophores and cellulose, form biofilms, and suppress leaf blast. These isolates should be further investigated as potential biological control agents for leaf blast control.

scholarly journals HEAVY METAL-RESISTANT RHIZOBACTERIA FROM GOLD MINE IN PONGKOR INDONESIA AND COPPER MINE IN MARINDUQUE PHILIPPINES

Agric ◽  
2019 ◽  
Vol 31 (1) ◽  
pp. 75-88 ◽  
Author(s):  
Erny Yuniarti ◽  
Ida F Dalmacio ◽  
Erlinda S Paterno
Keyword(s):  
Resistance Mechanism ◽  
Morphological Characterization ◽  
Gold Mine ◽  
Isolation Medium ◽  
Mine Site ◽  
Copper Mine ◽  
Gram Staining ◽  
16S Rna ◽  
Agar Media

The purposes of the study was to isolate, to characterize, and to identify rhizobacteria from plant rhizosphere growing in gold and copper mine. The isolation of rhizobacteria used N-free semisolid agar media, TSA, and SLP plus heavy metals (HMs), namely Pb, Cd, and or Cu. Isolated rhizobacteria were subsequently characterized for resistance to higher level of Pb, Cd, Cu in SLP media. Cultural and morphological characterization of rhizobacteria were conducted for cell morphology, motility, Gram staining, and biofilm formation. The rhizobacteria identification used sequence analysis of the 16S RNA gene fragments. The results showed that the majority of rhizobacterial from Cu mine site (66.7% of 21 isolates) were resistant to Cu (72150 ppm) while the majority of rhizobacteria from gold mine site (77.8% of 18 isolates) were sensitive to 72 ppm Cu. Majority of Cu in the soil was insoluble as granules attaching to gravel so that rhizobacteria of Cu mine site have been exposed and adapted to available Cu. This fact, explaining that the rhizobacteria’s MIC value was lower than the total Cu level in the soil. Three HMs-resistant rhizobacter (PbSM 2.1, MGR 334, and CuNFbM 4.1) formed biofilms, which was as one of the resistance mechanism to HMs. This research informed that HM contaminated-soil is better source for obtaining HM resistant rhizobacteria than HM uncontaminated-soil. The use four isolation media produce rhizobacteria which was more diverse than rhizobacteria from each isolation medium. Further characterization needs to be done to obtain HM resistant-rhizobacteria which can be used as biofertilizers and phytoremediation agent.

scholarly journals Morphological characterization of gram-positive and gram-negative bacteria from treated latex processing wastewater

2021 ◽  
Vol 1 (2) ◽  
pp. 32-36
Author(s):  
Farrah Aini Dahalan ◽  
Nor Azizah Parmin
Keyword(s):  
Oxygen Demand ◽  
Morphological Characterization ◽  
The Other ◽  
Morphological Properties ◽  
Morphological Observation ◽  
Gram Positive ◽  
Bacterial Colony ◽  
Gram Negative ◽  
Gram Staining

A preliminary morphological screening and isolation of bacterial colony from latex industrial wastewater was carried out. Bacteria colonies from latex processing wastewater were isolated from a local latex processing industry. It was found that 17 bacterial isolates had been purified grown on nutrient agar under 35˚C. The colonies were then purified and morphologically indicated via Gram staining and motility test. After morphological observation, it was identified that out of 17 isolates, 9 isolates were Gram positive and 8 isolates were Gram negative. There are 11 out of 17 colonies were rod-shaped bacterial colonies, while the other 6 colonies were cocci-shaped bacteria. There were 11 colonies of gliding bacteria, three colonies were non-motile bacteria and the other three colonies were flagellated bacteria. This study is only limited to morphological observation as the main aim of this study was to investigate the potential occurrence of viable growth in treated latex processing wastewater. The bacterial colonies were classified base on their morphological properties shown. This study has classified several genera such as Staphylococcus, Escherichia, Thiobacillus, Arthrobacter and other Genus. The growth curve of 17 isolates studied and the chemical oxygen demand were determined.

scholarly journals Characterization of a Novel Spirochete Associated with the Hydrothermal Vent Polychaete Annelid, Alvinella pompejana

2001 ◽  
Vol 67 (1) ◽  
pp. 110-117 ◽  
Author(s):  
Barbara J. Campbell ◽  
S. Craig Cary
Keyword(s):  
High Temperature ◽  
Hydrothermal Vent ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pcr Amplification ◽  
Dorsal Surface ◽  
Specific Primers ◽  
Gradient Gel Electrophoresis ◽  
Polychaetous Annelid ◽  
Alvinella Pompejana

ABSTRACT A highly integrated, morphologically diverse bacterial community is associated with the dorsal surface of Alvinella pompejana, a polychaetous annelid that inhabits active high-temperature deep-sea hydrothermal vent sites along the East Pacific Rise (EPR). Analysis of a previously prepared bacterial 16S ribosomal DNA (rDNA) library identified a spirochete most closely related to an endosymbiont of the oligochete Olavius loisae. This spirochete phylotype (spirochete A) comprised only 2.2% of the 16S rDNA clone library but appeared to be much more dominant when the same sample was analyzed by denaturing gradient gel electrophoresis (DGGE) and the terminal restriction fragment length polymorphism procedure (12 to 18%). PCR amplification of the community with spirochete-specific primers used in conjunction with DGGE analysis identified two spirochete phylotypes. The first spirochete was identical to spirochete A but was present in only one A. pompejana specimen. The second spirochete (spirochete B) was 84.5% similar to spirochete A and, more interestingly, was present in the epibiont communities of all of theA. pompejana specimens sampled throughout the geographic range of the worm (13°N to 32°S along the EPR). The sequence variation of the spirochete B phylotype was less than 3% for the range of A. pompejana specimens tested, suggesting that a single spirochete species was present in the A. pompejanaepibiotic community. Additional analysis of the environments surrounding the worm revealed that spirochetes are a ubiquitous component of high-temperature vents and may play an important role in this unique ecosystem.

scholarly journals Characterization of Molecular Identity and Pathogenicity of Rice Blast Fungus in Hunan Province of China

Plant Disease ◽  
2017 ◽  
Vol 101 (4) ◽  
pp. 557-561 ◽  
Author(s):  
Junjie Xing ◽  
Yulin Jia ◽  
Zhirong Peng ◽  
Yinfeng Shi ◽  
Qiang He ◽  
...  
Keyword(s):  
Rice Blast ◽  
Blast Resistance ◽  
Pcr Amplification ◽  
Blast Disease ◽  
Hunan Province ◽  
R Genes ◽  
Rice Blast Resistance ◽  
Molecular Identity ◽  
Polymerase Chain

The blast (Magnaporthe oryzae) resistance (R) gene is the most economical and environmental method to control rice blast disease. Characterization of molecular identity and pathogenicity of M. oryzae benefits the deployment of effective blast R genes. In order to identify blast R genes that would be effective in Hunan Province,182 M. oryzae strains were analyzed with a Chinese differential system (CDS), repetitive element-based polymerase chain reaction (rep-PCR), and the presence and absence of avirulence (AVR) genes by PCR amplification with gene-specific primers. Identified blast R genes were validated with 24 monogenic lines (ML) carrying 24 major R genes. In total, 28 races (isolates) of M. oryzae was identified with CDS, and classified into 20 distinct groups with rep-PCR. Interestingly, AVR-Pia, AVR-Pik, AVR-Pizt, AVR-Pib, and AVR-Pi9 were detected in more than 86.8% of the isolates; AVR-Pita1 was in 51.3% and AVR-Pii was in only 2.5%. In contrast, pathogenicity assays on 24 ML demonstrated that Pi9, Piz5, Pikh, and Pikm were more effective, with resistant frequencies of 91.6, 91, 87.9, and 87.3%, respectively; Pia, Piks, Pit, Pi12, and Pib were less than 15%. These findings revealed the complexity of a genetic basis of rice blast resistance, and shed light on useful blast R genes in Hunan Province.

scholarly journals Histopathology and Molecular Characterization of Microsporidian Parasites in Cultured Shrimp Penaeus Monodon Fabricius 1798 of Bangladesh

2019 ◽  
Vol 45 (2) ◽  
pp. 187-196 ◽  
Author(s):  
Md Munjur Hossain ◽  
Nusrat Jahan Punom ◽  
Md Mostavi Enan Eshik ◽  
Mst Khadiza Begum ◽  
Md Aminul Islam Bhuiyan ◽  
...  
Keyword(s):  
Penaeus Monodon ◽  
Pcr Amplification ◽  
Histological Section ◽  
Rrna Gene ◽  
Microsporidian Parasite ◽  
Specific Primers ◽  
West Region ◽  
Field Samples ◽  
Enterocytozoon Hepatopenaei

Black tiger shrimp (Penaeus monodon Fabricius 1798) cultured in Bangladesh was investigated for the presence of microsporidian parasite. Histological section of hepatopancreas showed a large number of microsporidian spores under light microscopy. Spores under scanning electron microscope appeared oval shapes. Histology of infected shrimps showed severe degeneration of hepatopancreatic tubules. Early and late stage of microsporidian parasites in hepatopancreatic tubules were also observed. DNA extracted from the hepatopancreas of shrimps were subjected to PCR amplification using primers targeting microsporidian SSU rRNA gene. The PCR amplified an expected product of ~328 bp and the sequences showed 81 - 82% identity with the Paranucleospora theridion reported from western Norway in 2008. Further screening of field samples was carried out using EHP-specific primers. DNA extracted from ten hepatopancreas samples of P. monodon were tested and none found to be positive for EHP (Enterocytozoon hepatopenaei). This is the first report for the identification of microsporidian parasites in cultured shrimp along the south-west region of Bangladesh. Asiat. Soc. Bangladesh, Sci. 45(2): 187-196, December 2019

scholarly journals Quantitative assay of Indole Acetic Acid-producing bacteria isolated from several lakes in East Java, Indonesia

2020 ◽  
Vol 21 (11) ◽  
Author(s):  
Sulistya Ika Ramadhani Sulistya ◽  
Sitoresmi Prabaningtyas Sitoresmi ◽  
Agung Witjoro Agung ◽  
Rina Triturani Saptawati Rina ◽  
Achmad Rodiansyah Achmad
Keyword(s):  
Acetic Acid ◽  
Indole Acetic Acid ◽  
Fossil Fuels ◽  
Morphological Characterization ◽  
Biofuel Production ◽  
Quantitative Assay ◽  
Phenotypic Characterization ◽  
Bacterial Isolates ◽  
Acid Producing Bacteria

Abstract. Ramadhani SI, Prabaningtyas S, Witjoro A, Saptawati TR, Rodiansyah A. 2020. Quantitative assay of Indole Acetic Acid-producing bacteria isolated from several lakes in East Java, Indonesia. Biodiversitas 21: 5448-5454. Biofuel is an alternative to fossil fuels that are environmentally friendly with low emissions. Biofuel from biomass microalgae, especially Chlorella vulgaris, has an essential role in biofuel production. Increasing biomass microalgae was done by co-culture between microalgae and bacteria. This research aims to determine the potential of bacterial isolates to produce the IAA hormone and identify the highest isolate with the ability to synthesis IAA from four lakes in East Java. This research was conducted by culturing bacterial isolates in the Tryptic Soy Broth (TSB) to add tryptophan media in various periods of incubation. The absorbance was measured with UV-Vis spectrophotometry at a wavelength of 530 nm for determining IAA-production from bacterial isolates. The results showed that the "12" code bacterial isolate from Ranu Grati produced the highest IAA hormone concentration, with an average of 30.23 ppm. The morphological characterization of the highest IAA-producing bacteria showed that isolate included the Enterobacteriaceae group and phenotypic characterization include Enterobacter cloacae complex (ECC).

Single spore isolation and morphological characterization of local Malaysian isolates of rice blast fungus Magnoporthe grisea

2015 ◽  
Author(s):  
Ankitta Mishra ◽  
Wickneswari Ratnam ◽  
Md Atiqur Rahman Bhuiyan ◽  
Ariane Ponaya ◽  
Khisord K. Jena
Keyword(s):  
Rice Blast ◽  
Rice Blast Fungus ◽  
Morphological Characterization ◽  
Single Spore ◽  
Blast Fungus

scholarly journals Typing of Intimin Genes in Human and Animal Enterohemorrhagic and Enteropathogenic Escherichia coli: Characterization of a New Intimin Variant

2000 ◽  
Vol 68 (1) ◽  
pp. 64-71 ◽  
Author(s):  
E. Oswald ◽  
H. Schmidt ◽  
S. Morabito ◽  
H. Karch ◽  
O. Marchès ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Animal Species ◽  
Pcr Amplification ◽  
Binding Activity ◽  
Cell Binding ◽  
Specific Primers ◽  
E Coli ◽  
Specific Manner ◽  
Tight Association

ABSTRACT Enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) produce the characteristic “attaching and effacing” (A/E) lesion of the brush border. Intimin, an outer membrane protein encoded by eae, is responsible for the tight association of both pathogens with the host cell. Severaleae have been cloned from different EPEC and EHEC strains isolated from humans and animals. These sequences are conserved in the N-terminal region but highly variable in the last C-terminal 280 amino acids (aa), where the cell binding activity is localized. Based on these considerations, we developed a panel of specific primers to investigate the eae heterogeneity of the variable 3′ region by using PCR amplification. We then investigated the distribution of the known intimin types in a large collection of EPEC and EHEC strains isolated from humans and different animal species. The existence of a yet-unknown family of intimin was suspected because several EHEC strains, isolated from human and cattle, did not react with any of the specific primer pairs, although these strains were eaepositive when primers amplifying the conserved 5′ end were used. We then cloned and sequenced the eae present in one of these strains (EHEC of serotype O103:H2) and subsequently designed a PCR primer that recognizes in a specific manner the variable 3′ region of this new intimin type. This intimin, referred to as “ɛ,” was present in human and bovine EHEC strains of serogroups O8, O11, O45, O103, O121, and O165. Intimin ɛ is the largest intimin cloned to date (948 aa) and shares the greatest overall sequence identity with intimin β, although analysis of the last C-terminal 280 aa suggests a greater similarity with intimins α and γ.

scholarly journals Molecular Characterization of Lactic Acid Organisms Isolated from Spontaneous Fermentation of Cassava- fufu and gari

2019 ◽  
pp. 1-10
Author(s):  
Femi, Ayoade ◽  
Scott Fayemi ◽  
Olumide Olukanni ◽  
Tosin Ogunbiyi ◽  
Paul Oluniyi
Keyword(s):  
Quality Assurance ◽  
Lactic Acid ◽  
Safety Assessment ◽  
Molecular Methods ◽  
Bacterial Isolates ◽  
Biochemical Methods ◽  
Fungal Isolates ◽  
Bacillus Spp ◽  
Fungal Organisms

Aim: The present work was aimed at ensuring the accurate taxonomic identification of the fermentation organisms previously isolated from spontaneously fermented cassava for the purpose of safety assessment and quality assurance. Study Design: Purposive sampling method was used as all the five isolated organisms (from the previous study); 2 bacterial and 3 fungal organisms were characterized using molecular methods. Place and Duration of Study:  The genotypically characterized organisms are from a previous study carried out in May 2016 where lactic acid bacterial and fungal organisms were isolated from spontaneously fermented cassava.  Methodology: Genomic DNA was extracted from the lactic acid microorganisms and this was used as a template in a polymerase chain reaction (PCR) reaction. The 16s rRNA genes were amplified for the bacterial isolates while nuclear ribosomal internal transcribed spacer (ITS) genes were targeted for the fungal isolates. The amplicons were electrophoresed on 2% agarose gel prepared with Tris Borate Ethylenediamintetraacetate (TBE) buffers stained with ethidium bromide. The sizes of the corresponding amplicon captured on gel images were compared with that of the ladder to determine their sizes. Furthermore, sequences of the PCR products were analyzed and the chromatograms subjected to BLAST (Basic Local Alignment Search Tool) analyses to identify the lactic acid organisms. Results: The 3 fungal isolates were identified as Schizophyllum commune (MK 431022), Aspergillus oryzae (MK434151), Aspergillus sydowii (MK434152), while the bacterial isolates were identified as Bacillus spp (MK450345) and Bacillus spp (MK 449018). A high level of discrepancies was observed when the results of identification of the same isolates by biochemical methods in an earlier report were compared with the results from the present study using molecular methods.  Conclusion: The identification and characterization of the isolates and the discrepancies between the outcomes of the biochemical and molecular methods underscore the limitations of phenotypic (biochemical) methods in characterizing organisms that may eventually be used as starter organisms in food fermentation. The present result makes quality assurance and safety assessment of foods prepared using these organisms as starter organisms possible.

scholarly journals Phylogenetic Characterization of a Novel Insect-Specific Flavivirus Detected in a Culex Pool, Collected from Assam, India

Intervirology ◽  
2015 ◽  
Vol 58 (3) ◽  
pp. 149-154 ◽  
Author(s):  
Sibnarayan Datta ◽  
Reji Gopalakrishnan ◽  
Soumya Chatterjee ◽  
Vijay Veer
Keyword(s):  
Direct Detection ◽  
Nonstructural Protein ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Specific Primers ◽  
Phylogenetic Characterization ◽  
Dna And Rna ◽  
Indian State ◽  
Mosquito Pool

Objective: We report the phylogenetic characterization of a unique flavivirus sequence detected in a wild Culex tritaeniorhynchus mosquito pool, collected from the northeast Indian state of Assam. Methods: DNA and RNA were extracted from field-collected mosquito pools. Extracts were subjected to PCR and reverse transcriptase PCR amplification using universal and type-specific primers for direct detection of flavivirus-specific viral nucleic acids. An amplified flavivirus nonstructural protein 5 (NS5) genetic region was sequenced and BLAST searched, and phylogenetic analyses performed with reference sequences retrieved from GenBank. Results: Phylogenetic analyses revealed the sequence to be related to insect-specific flaviviruses (ISFs) of the genus Flavivirus, family Flaviviridae. Despite being related to the Palm Creek virus (PCV; an ISF very recently reported from Northern Australia), the present sequence (provisionally named Assam virus) was found to be highly divergent from PCV and other ISF sequences available in GenBank. The partial NS5 sequence analysis demonstrated low nucleotide sequence identity (66-77%) with known ISFs reported from other parts of the globe. Conclusion: Findings of this study suggest the presence of a candidate novel ISF - the first to be reported from India.

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