A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense

Joko, Tri; Soffan, Alan; Rohman, Muhammad Saifur

doi:10.13057/biodiv/d201037

Cited by 10 publications

(5 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The symbionts were located in clade I in the amount of 9 isolates, in clade III -1 isolate, and most of the isolates clustered in clade II (19 isolates), suggesting that, they may belong to different taxons. The gyrB gene is an example of a housekeeping gene that is frequently used in classification and identification of different groups of bacteria (Joko et al, 2019). The PCR-amplification of the gyrB gene, which encodes DNA gyrase subunit B, yielded a 584-bp band.…”

Section: Resultsmentioning

confidence: 99%

Genetic and physiological diversity of white Spanish broom (Chamaecytisus albus) endophytes

et al. 2021

View full text Add to dashboard Cite

Chamaecytisus albus (Spanish broom) is a legume shrub that can be found in only one natural locality in Poland. This specimen is critically endangered; therefore, different actions focusing on protection of this plant in the natural habitat are undertaken, and one of them involves studies of the population of Chamaecytisus albus bacterial endophytes, which in the future could be used as bioprotectants and/or biofertilizers. A collection of 94 isolates was obtained from Spanish broom nodules, and the physiological and genetic diversity of these strains was studied. A few potentially beneficial traits were detected, i.e. secretion of cellulases (66 isolates), production of siderophores (60 isolates), phosphate solubilization (25 isolates), and production of IAA (58 isolates), indole (16 isolates), or HCN (3 isolates). Twenty-nine of the 94 tested isolates were able to induce the development of root nodules in plants grown in vitro and can therefore be assumed as Chamaecytisus albus symbionts. Genome fingerprinting by BOX-PCR, as well as gyrB and nodZ gene sequencing revealed a great genetic diversity of specimens in the collection. The symbiotic isolates were classified in different clades, suggesting they could belong to different species, however, most of them revealed sequence similarity to Bradyrhizobium genus.

show abstract

Section: Resultsmentioning

confidence: 99%

Genetic and physiological diversity of white Spanish broom (Chamaecytisus albus) endophytes

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Bakteri busuk lunak yang digunakan pada uji ini adalah Pectobacterium brasiliense, koleksi Laboratorium Ilmu Penyakit Tumbuhan, Departemen Hama dan Penyakit Tumbuhan, Fakultas Pertanian UGM (Joko et al 2019). Antagonisme bakteri endofit anggrek terhadap P. brasiliense diujikan terhadap 10 isolat bakteri endofit terseleksi.…”

Section: Pengujian Antagonisme Bakteri Endofit Terhadap Bakteri Busuk...unclassified

Potensi dan Keragaman Bakteri Endofit sebagai Agens Pemacu Pertumbuhan dan Biokontrol Anggrek

Amba Linggi,

Joko,

Widada

2023

J. Ilmu. Pertan. Indones.

View full text Add to dashboard Cite

Soft rot disease in orchid plants is a factor in decreasing orchid production. One way of biological control that has the potential to spur growth is to utilize endophytic bacteria. This study aims to describe the diversity of orchid endophytic bacteria that have the potential as growth promoters and biocontrol agents. Observation parameters include indole acetic acid (IAA) production, inorganic phosphate dissolution, ammonia production of orchid endophytic bacteria, and antagonism of endophytic bacteria to pathogenic bacteria that cause soft rot in vitro. The diversity of orchid endophytic bacteria was analyzed using rep-PCR with BOX-A1R primer. The results showed that 10 isolates of orchid endophytic bacteria were able to produce IAA with a concentration of 79–321 μg/mL, able to dissolve phosphate, and produce ammonia. In antagonism testing against soft rot-causing bacteria, all isolates were able to form an inhibitory zone with a diameter of 3–7.2 cm. Furthermore, diversity analysis using rep-PCR showed that isolates of endophytic bacteria DnPh5, BgCt2, BgVt10, DnLp7, DnBl1, and DnAr4 had a uniform DNA band pattern so that they were grouped together. Meanwhile, isolates of TbPh7, IbtPhm1, DnDr2, and AkOc1 showed different DNA band patterns, indicating that the four isolates were different species or subspecies of bacteria. In dendrogram analysis, DnPh5, BgCt2, BgVt10, DnLp7, DnBl1, and DnAr4 isolates have a similarity of 100%. The similarity of isolates IbtPhm1, DnDr2, and AkOc1 was 90%, 79%, and 68%, respectively, against the other six isolates. TbPh7 isolate is an isolate with a low level of similarity to other isolates, which is about 51%. Keywords: orchid, endophytic bacteria, growth promoter, biocontrol agent, rep-PCR

show abstract

“…DNA was amplified using gyrB specific primer, i.e. forward primer 5'-CCCAAGCTTAACTGCACTGGGAAA TYGTHGAYAAYAG-3' and reverse primer 5'-CGGAATTCGGATCCACRTCGGCRT CBGTCATRAT-3' (Joko et al 2019). PCR was run with the composition: 1 µL forward primer, 1 µL reverse primer, 5 µL master mix green, and 3 µL DNA Bacillus sp.…”

Section: Identification Of Bacillus Sp Rj09mentioning

confidence: 99%

The Potential of Bacillus subtilis subsp. subtilis RJ09 as a Biological Control Agent Against Leaf Spot Diseases on Clove

Wisanggeni,

Suryanti,

Joko

2023

J Fitopatol Indones

View full text Add to dashboard Cite

Cloves is one of the main plantation commodities and is native to Indonesia. Leaf spot disease with necrosis symptom is often found in clove plants. Interferences to photosynthesis caused by leaf spot disease can cause plant death. Bacillus is known to inhibit the development of pathogens through nutrient competition and antibiosis mechanism. This study aims to identify Bacillus sp. RJ09 through molecular approach and determine its potential in suppressing the development of Pestalotiopsis sp., the cause of clove leaf spot by in vitro examination. Identification of the fungus was carried out by observing the morphology which included the color of the colony, the shape and size of the conidium of the isolated fungus. Identification of Bacillus sp. RJ09 was performed by polymerase chain reaction (PCR) using a pair of primers that amplified gyrB gene region of ±1400 bp, followed by sequence analysis. The ability of Bacillus sp. RJ09 as a biological agent against fungi associated with leaf spot was determined using an in vitro double culture method. Pestalotiopsis sp. was found as the fungus associated with leaf spot disease and can cause black necrotic spots on the leaves. Molecular identification of Bacillus sp. RJ09 showed the highest similarity value of 99.40% with B. subtilis subsp. subtitles. In vitro dual culture showed B. subtilis subsp. subtilis RJ09 can inhibit the growth of Pestalotiopsis sp. colonies by 75%.

show abstract

A novel subspecies-specific primer targeting the gyrase B gene for the detection of Pectobacterium carotovorum subsp. brasiliense

Cited by 10 publications

References 45 publications

Genetic and physiological diversity of white Spanish broom (Chamaecytisus albus) endophytes

Genetic and physiological diversity of white Spanish broom (Chamaecytisus albus) endophytes

Potensi dan Keragaman Bakteri Endofit sebagai Agens Pemacu Pertumbuhan dan Biokontrol Anggrek

The Potential of Bacillus subtilis subsp. subtilis RJ09 as a Biological Control Agent Against Leaf Spot Diseases on Clove

Contact Info

Product

Resources

About