scholarly journals First Report of Brenneria nigrifluens as the Causal Agent of Shallow-Bark Canker on Walnut Trees (Juglans regia) in Serbia

Plant Disease ◽  
2013 ◽  
Vol 97 (11) ◽  
pp. 1504-1504 ◽  
Author(s):  
T. Popović ◽  
Ž. Ivanović ◽  
S. Živković ◽  
N. Trkulja ◽  
M. Ignjatov
Keyword(s):  
16S Rdna ◽  
Juglans Regia ◽  
Causal Agent ◽  
Nutrient Agar ◽  
Gene Sequences ◽  
Biochemical Tests ◽  
First Report ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Plant Pathol

In late summer 2011, shallow, irregular cankers were observed on trunks and branches of non-chemically-treated walnut trees (Juglans regia L.) on a 30-year-old orchard in the region of Fruška Gora (Vojvodina, Serbia). Disease incidence was ~80% and yield loss was ~50%. For pathogen isolation, small pieces (~5 mm diameter) of wood tissue collected at the edge of the cankers were macerated in sterile distilled water and streaked onto nutrient agar with 5% sucrose. Plates were then incubated at 28°C for 2 days. The prevalent bacterial colonies and those similar in appearance to Brenneria nigrifluens (Wilson et al.) Hauben et al. were purified on nutrient agar (NA). Eight gram-negative, oxidasenegative, catalase-positive strains, showing oxidative and fermentative metabolism, were selected for further characterization. To identify the bacteria on a molecular basis, we analyzed the 16S rDNA and gyr B gene sequences. The 16S rDNA partial sequences of analyzed strains were amplified using the primers P0 (5′-GAGAGTTTGATCCTGGCTCAG-3′) and P6 (5′-CTACGGCTACCTTGTTACGA-3′) (3). Additionally, the gyr B gene sequences were generated with primers GyrB-F (5′-MGGCGGYAAGTTCGATGACAAYTC-3′) and GyrB-R (5′-TRATBKCAGTCARACCTTCRCGSGC-3′) (2). All amplicons were purified using the QIAquick PCR purification kit (QIAGEN) according to the manufacturer's instructions and sequenced by Macrogen Inc. (Seoul, South Korea) using the same primers used for amplification. The sequences were edited using FinchTV v.1.4.0, assembled using the Clustal W program integrated into MEGA5 software (4), and deposited in NCBI GenBank under accessions JX484738 to 40 for the 16S rDNA gene and KC571240 to 47 for the gyr B gene. The 1,359-bp 16S rDNA sequences obtained for the eight strains were compared to the reference 16S rDNA sequences retrieved from GenBank. BLAST analysis revealed 100% homology of Serbian strains with sequences of B. nigrifluens (Z96095 and FJ611884). The gyr B gene sequences of our strains were 100% homologous to the sequences of B. nigrifluens deposited in GenBank (JF311612 to 15). Pathogenicity of all strains was confirmed on young fruits by infiltration of bacterial suspensions (108 CFU ml–1 from a 48 h NA culture) with syringe into the mesocarp of walnut fruits and by stem infiltration with syringes without needles into branch wounds (1). Inoculated fruits were incubated in plastic boxes for 8 days at 20°C, 80 to 100% RH, with a 12-h photoperiod. Inoculated plants were maintained for 3 months at 22 to 28°C with continuous light and at 70 to 80% RH in plastic tunnels. Inoculated fruits developed bark canker symptoms at the inoculation sites, which became necrotic and released a reddish brown exudate. Necrotic lesions were observed on inoculated branches. B. nigrifluens was reisolated from the margins of necrotic fruit and stem tissue. Physiological and biochemical tests showed that strains grew at 36°C and did not produce arginine dihydrolase, H2S, indole, nitrate, nor a fluorescent pigment on King's B medium. They did not induce a hypersensitive reaction on tobacco leaves and did not hydrolyse gelatin and starch. They produced acid without gas from glucose, inositol, sorbitol, arabinose, and sucrose, but not from maltose and lactose (1). Results of pathogenicity and biochemical tests were also the same for reisolated strains. This is the first report of B. nigrifluens as the causal agent of shallow-bark canker on walnut trees in Serbia. References: (1) E. G. Biosca and M. M. López. J. Plant Pathol. 94:105, 2012. (2) P. Ferrente and M. Scotrichini. Plant Pathol. 59:954, 2010. (3) A. Grifoni et al. FEMS Microbiol. Lett. 127:85, 1995. (4) K. Tamura et al. Mol. Biol. Evol. 28:2731, 2011.

scholarly journals First Report of ‘Candidatus Phytoplasma asteris’-Related Strains Infecting Lily in Mexico

Plant Disease ◽  
2008 ◽  
Vol 92 (6) ◽  
pp. 979-979 ◽  
Author(s):  
N. E. Cortés-Martínez ◽  
E. Valadez-Moctezuma ◽  
L. X. Zelaya-Molina ◽  
N. Marbán-Mendoza
Keyword(s):  
16S Rdna ◽  
The Czech Republic ◽  
First Report ◽  
Rdna Sequences ◽  
Flower Abortion ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Total Dna ◽  
Nested Pcr Assays ◽  
Symptomatic Plant

In recent years, lily (Lilium spp.) has become an important ornamental crop in diverse regions of Mexico. Since 2005, unusual symptoms have been observed on lily plants grown from imported bulbs in both greenhouse and production plots at San Pablo Ixayo, Boyeros, and Tequexquinauac, Mexico State. Symptoms included a zigzag line pattern on leaves, dwarfism, enlargement of stems, shortened internodes, leaves without petioles growing directly from bulbs, air bulbils, death of young roots, atrophy of flower buttons, and flower abortion. Symptoms were experimentally reproduced on healthy lily plants by graft inoculation. Total DNA was extracted from 50 diseased, 10 symptomless, and 10 graft-inoculated plants by the method of Dellaporta et al. (2). DNA samples were analyzed for phytoplasma presence by two different nested PCR assays. One assay employed ribosomal RNA gene primer pair P1/P7 followed by R16F2n/R16R2 (1), whereas ribosomal protein (rp) gene primer pairs rpF1/rpR1 and rp(I)F1A/rp(I)R1A (4) were used in a second assay. A DNA fragment approximately 1.2 kb long was consistently amplified from all symptomatic plant samples only by both assays. A comparative analysis of 16S rDNA sequences (Genbank Accession Nos. EF421158–EF421160 and EU124518–EU124520) and rp gene sequences (EU277012–EU277014), derived from PCR products, revealed that phytoplasma infecting lily were most similar (99.9% to 16S rDNA and 99.7% to rp) to carrot phytoplasma sp. ca2006/5 and also were similar (99.8% to 16SrDNA and 99.2% to rp) to broccoli phytoplasma sp. br273. Both carrot and broccoli phytoplasmas were classified as members of aster yellow 16S rDNA restriction fragment length polymorphism subgroup 16SrI-B (3). Although infection of lilies by aster yellows (‘Ca. phytoplasma asteris’) subgroup 16SrI-B and 16SrI-C was reported from the Czech Republic and Poland, to our knowledge, this is the first report of ‘Ca. phytoplasma asteris’-related strains associated with lily plants in Mexico. References: (1) R. F. Davis et al. Microbiol. Res. 158:229, 2003. (2) S. L. Dellaporta et al. Plant Mol. Biol. Rep. 1:19, 1983. (3) B. Duduk et al. Bull. Insectol. 60 2:341, 2007. (4) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004.

scholarly journals First Report of Bacterial Bark Canker of Walnut Caused by Brenneria nigrifluens in Hungary

Plant Disease ◽  
2014 ◽  
Vol 98 (7) ◽  
pp. 988-988 ◽  
Author(s):  
A. Végh ◽  
A. Tóth ◽  
Á. Zámbó ◽  
G. Borsos ◽  
L. Palkovics
Keyword(s):  
16S Rdna ◽  
Juglans Regia ◽  
Negative Control ◽  
Bacterial Suspension ◽  
Lake Balaton ◽  
Biochemical Tests ◽  
First Report ◽  
Potted Plants ◽  
Sequence Identity ◽  
Plastic Bags

During August 2012, vertical oozing cankers were sporadically observed on trunks and branches of walnut trees (Juglans regia) in the city of Zánka, near Lake Balaton and other parts of Hungary including Budapest, Győr, and Tatabánya cities. Cankers were observed on trunks and branches where brownish-black exudates staining the bark appeared mainly in the summer. Isolations were performed primarily from exudates but also from infected tissues using King's medium B (KB) (3) and EMB medium (2). Colonies similar in appearance to Brenneria nigrifluens (syn.: Erwinia nigrifluens) (1,5) were isolated. The bacterium, first reported in California, was also recorded in Iran, Spain, France, and several Italian locations, on walnut trees. The bacterial strain was gram negative and did not induce a hypersensitive response on tobacco (Nicotiana tabacum L. ‘White Burley’) leaves. The bacterium grew at 26°C. Colonies on KB were white and non-fluorescent, but on EMB medium were a typical dark purple with metallic green sheen. The results of substrate utilization profiling using the API 20E kit (Biomérieux, Marcy l'Etoile, France) showed that the bacterium belonged to the Enterobacteriaceae. The strain was positive for citrate utilization, H2S, and acetoin production and urease, glucose, inositol, saccharose, and arabinose reactions. Pathogenicity was tested by injecting five young healthy walnut branches on two separate 2-year-old grafted potted plants with a bacterial suspension containing 107 CFU/ml. Negative controls were walnut branches injected with sterile distilled water. Branches were enclosed in plastic bags and incubated in a greenhouse under 80% shade at 26°C day and 17°C night temperatures. Three months after inoculation, necrotic lesions were observed in the inner bark and dark lines were observed in internal wood, but no external cankers were observed on inoculated branches. The negative control appeared normal. B. nigrifluens was re-isolated from lesions on inoculated branches and identified as described above; thus, Koch's postulates were fulfilled. For molecular identification of the pathogen, 16S rDNA amplification was performed using genomic DNA from strain Bn-WalnutZa-Hun1 with a universal bacterial primer set (63f and 1389r) (4). The PCR products were cloned into a pGEM T-Easy vector (Promega, Madison, WI) and transformed into Escherichia coli DH5α cells. A recombinant plasmid (2A2.5) was sequenced using M13 forward and reverse primers. The sequence was deposited in NCBI GenBank (Accession No. HF936707) and showed 99% sequence identity with a number of B. nigrifluens strains, including type strains Z96095.1, AJ233415.1, JX484740.1, JX484739.1, JX484738.1, and FJ611884.1. On the basis of the symptoms, colony morphology, biochemical tests, and 16S rDNA sequence identity, the pathogen was identified as Brenneria nigrifluens. To our knowledge, this is the first report of a natural outbreak of bacterial bark canker on walnut in Hungary and the presence of the pathogen may seriously influence in local orchards and garden production in the future. References: (1) L. Hauben et al. Appl Microbiol 21:384, 1998. (2) J. E. Holt-Harris and O. Teague. J. Infect. Dis. 18:596, 1916. (3) E. O. King et al. J. Lab. Clin. Med. 44:301, 1954. (4) A. M. Osborn et al. Environ. Microbiol. 2:39, 2000. (5) E. E. Wilson et al. Phytopathology 47:669, 1957.

scholarly journals First Report of Two Distinct Phytoplasma Species, ‘Candidatus Phytoplasma cynodontis’ and ‘Candidatus Phytoplasma asteris,’ Simultaneously Associated with Yellow Decline of Wodyetia bifurcata (Foxtail Palm) in Malaysia

Plant Disease ◽  
2013 ◽  
Vol 97 (11) ◽  
pp. 1504-1504 ◽  
Author(s):  
N. Naderali ◽  
N. Nejat ◽  
Y. H. Tan ◽  
G. Vadamalai
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Rflp Analysis ◽  
Rrna Gene ◽  
Gene Sequences ◽  
First Report ◽  
White Leaf ◽  
General Decline ◽  
Pcr Products ◽  
Plant Pathol

The foxtail palm (Wodyetia bifurcata), an Australian native species, is an adaptable and fast-growing landscape tree. The foxtail palm is most commonly used in landscaping in Malaysia. Coconut yellow decline (CYD) is the major disease of coconut associated with 16SrXIV phytoplasma group in Malaysia (1). Symptoms consistent with CYD, such as severe chlorosis, stunting, general decline, and death were observed in foxtail palms from the state of Selangor in Malaysia, indicating putative phytoplasma infection. Symptomatic trees loses their green and vivid appearance as a decorative and landscape ornament. To determine the presence of phytoplasma, samples were collected from the fronds of 12 symptomatic and four asymptomatic palms in September 2012, and total DNA was extracted using the CTAB method (3). Phytoplasma DNA was detected in eight symptomatic palms using nested PCR with universal phytoplasma 16S rDNA primer pairs, P1/P7 followed by R16F2n/R16R2 (2). Amplicons (1.2 kb in length) were generated from symptomatic foxtail palms but not from symptomless plants. Phytoplasma 16S rDNAs were cloned using a TOPO TA cloning kit (Invitrogen). Several white colonies from rDNA PCR products amplified from one sample with R16F2n/R16R2 were sequenced. Phytoplasma 16S rDNA gene sequences from single symptomatic foxtail palms showed 99% homology with a phytoplasma that causes Bermuda grass white leaf (AF248961) and coconut yellow decline (EU636906), which are both members of the 16SrXIV ‘Candidatus Phytoplasma cynodontis’ group. The sequences also showed 99% sequence identity with the onion yellows phytoplasma, OY-M strain, (NR074811), from the ‘Candidatus Phytoplasma asteris’ 16SrI-B subgroup. Sequences were deposited in the NCBI GenBank database (Accession Nos. KC751560 and KC751561). Restriction fragment length polymorphism (RFLP) analysis was done on nested PCR products produced with the primer pair R16F2n/R16R2. Amplified products were digested separately with AluI, HhaI, RsaI, and EcoRI restriction enzymes based on manufacturer's specifications. RFLP analysis of 16S rRNA gene sequences from symptomatic plants revealed two distinct profiles belonging to groups 16SrXIV and 16SrI with majority of the 16SrXIV group. RFLP results independently corroborated the findings from DNA sequencing. Additional virtual patterns were obtained by iPhyclassifier software (4). Actual and virtual patterns yielded identical profiles, similar to the reference patterns for the 16SrXIV-A and 16SrI-B subgroups. Both the sequence and RFLP results indicated that symptoms in infected foxtail palms were associated with two distinct phytoplasma species in Malaysia. These phytoplasmas, which are members of two different taxonomic groups, were found in symptomatic palms. Our results revealed that popular evergreen foxtail palms are susceptible to and severely affected by phytoplasma. To our knowledge, this is the first report of a mixed infection of a single host, Wodyetia bifurcata, by two different phytoplasma species, Candidatus Phytoplasma cynodontis and Candidatus Phytoplasma asteris, in Malaysia. References: (1) N. Nejat et al. Plant Pathol. 58:1152, 2009. (2) N. Nejat et al. Plant Pathol. J. 9:101, 2010. (3) Y. P. Zhang et al. J. Virol. Meth. 71:45, 1998. (4) Y. Zhao et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

scholarly journals First Report of a Group 16SrI-B Phytoplasma Associated with Gardenia jasminoides in China

Plant Disease ◽  
2012 ◽  
Vol 96 (10) ◽  
pp. 1576-1576 ◽  
Author(s):  
X. C. Sun ◽  
W. J. Zhao
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Consensus Sequence ◽  
Rrna Gene ◽  
Reference Pattern ◽  
Green Belt ◽  
First Report ◽  
Rdna Sequences ◽  
Gardenia Jasminoides ◽  
16S Rdna Sequences

Gardenia jasminoides J. Ellis, (also known as common gardenia, cape jasmine, or cape jessamine) is a fragrant flowering evergreen tropical plant, a favorite in gardens worldwide. G. jasminoides were found with small, seriously yellowed leaves, stunted growth, and witches'-broom in a green belt on the Southwest University campus in October 2011. The incidence was lower than 2%. In another green belt, G. jasminoides with only slightly yellowing leaves were found. The incidence was about 5%. Five months later, most seriously yellowed leaves withered. However, no withered leaf was observed among the slightly yellowing leaves. Leaf samples from each symptomatic plant, together with asymptomatic plants from the same belt, were collected for total DNA extraction using a modified cetyltrimethylammoniumbromide method (1). The resulting DNA extracts were analyzed by a nested PCR assay using the phytoplasma 16S rRNA gene primer pairs R16mF2/R16mR1 followed by R16F2n/R16R2 (2). DNA fragments of 1.2 kb that corresponded to 16S rDNA were amplified only from the DNA samples of the five plants with the symptoms mentioned above. The purified nested PCR products were cloned in pGEM-T Easy Vector (Promega) and then sequenced. The resulting 16S rDNA sequences were found to be identical (GenBank Accession No. JQ675713). The consensus sequence was analyzed by the iPhyClassifier online tool ( http://plantpathology.ba.ars.usda.gov/cgi-bin/resource/iphyclassifier.cgi ) and found to share 99.4% similarity with the 16S rDNA sequence of the ‘Candidatus Phytoplasma asteris’ reference strain (GenBank Accession No. M30790) that belongs to the 16SrI-B subgroup (3). The virtual RFLP pattern of the G. jasminoides phytoplasma 16S rDNA gene sequence showed maximum similarity to the reference pattern of NC005303 (similarity coefficient of 1.0). The phylogenetic tree based on the 16S rDNA sequences of phytoplasmas belonging to group 16SrI and other distinct phytoplasma groups also showed that our sequences clustered with members of subgroup 16SrI-B. Subsequently, the presence of the phytoplasmas in symptomatic plants was also confirmed by transmission electron microscopy. Taken together, the phytoplasma was classified as a member of subgroup 16SrI-B. To our knowledge, this is the first report of a subgroup 16SrI-B phytoplasma associated with diseased G. jasminoides in China. G. jasminoides yellowing is often considered to result from nutrient deficiency (especially iron compounds). However, our findings showed that a phytoplasma can cause G. jasminoides yellowing, which should be considered in the control of leaves yellowing. References: (1) E. Angelini et al. Vitis 40:79, 2001. (2) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (3) Y. Zhao, et al. Int. J. Syst. Evol. Microbiol. 59:2582, 2009.

scholarly journals First Report of ‘Candidatus Phytoplasma asteris’-Related Strain Associated with Peach Rosette in Canada

Plant Disease ◽  
2010 ◽  
Vol 94 (7) ◽  
pp. 916-916 ◽  
Author(s):  
S. Zunnoon-Khan ◽  
R. Michelutti ◽  
Y. Arocha-Rosete ◽  
J. Scott ◽  
W. Crosby ◽  
...  
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
The United States ◽  
Polymorphism Analysis ◽  
Plant Host ◽  
First Report ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Short Internodes

Prunus persica (L.) Bastch (family Rosaceae) is currently represented by 83 accessions at the Canadian Clonal Genebank. Approximately 3,200 ha are devoted to peach cultivation in Canada where Ontario Province accounts for 82% of the national production. The clonal peach accessions, also located in Ontario, are monitored routinely for symptoms of phytoplasma infection, including rosette-like symptoms (3) that are characterized by new shoots with very short internodes, loss of older shoot leaves leaving only bunches of young leaves on the tips of naked shoots, and flowers that rarely set fruit. From June to August 2009, peach accessions PRU0382 and PRU0445 showed typical peach rosette symptoms, while another 14 accessions exhibited either short internodes or no symptoms. Leaf midrib samples were collected from 16 peach accessions, including 17 symptomatic (from which 8 corresponded to accession PRU0382, 6 for PRU0445, 1 for PRU0335, 1 for PRU0179, and 1 for PRU0451) and 16 asymptomatic (from which 5 corresponded to a representative of each accession PRU0382, PRU0445, PRU0335, PRU0179, and PRU0451 and 11 to other peach accessions). Total DNA was extracted (DNeasy Plant Extraction Mini Kit, QIAGEN, Valencia, CA) from 100 mg of each sample and used as a template in a nested PCR with phytoplasma universal primers R16mF2/R1 (1) and fU5/rU3 (2). Nested PCR products of the expected size (~880 bp) were obtained from all symptomatic samples (14 of 14) of accessions PRU0382 (peach-almond cv. Kando from the Czech Republic) and PRU0445 (peach cv. HW271 from Canada) only. All other plants with or without symptoms yielded no PCR products. Amplicons were purified (Wizard PCR Clean-up, Promega, Madison, WI), cloned in pGEM-T Easy Vector (Promega), and sequenced (Robarts Institute, London, Canada). The resulting 16S rDNA sequences were identical; one of each was archived in GenBank as Accession No. GU223904. BLAST analysis determined that the P. persica phytoplasma sequence shared 99% identity with 16S rDNA sequences of ‘Candidatus Phytoplasma asteris’-related strains. This relationship was also supported by restriction fragment length polymorphism analysis (RFLP) of rDNA amplicons using AluI, RsaI, and MseI endonucleases that yielded fragment profiles indicative of phytoplasmas belonging to group 16SrI (Aster Yellows), subgroup B (16SrI-B). Among phytoplasma diseases, those attributed to group 16SrI strains are most numerous and affect the widest plant host range. They include peach rosette in the United States and Europe (3) as well as diseases of various horticultural crops in Canada, including grapevine (4). To our knowledge, this is the first report of a subgroup 16SrI-B phytoplasma affecting peach in Canada. Early detection of phytoplasmas by PCR in accessions with both European and Canadian origins underscores the importance of prompt identification of infected plants for subsequent thermotherapy treatment to maintain the health of the collection and prevent further disease spread. References: (1) D. E Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:1441, 1996. (2) K. H. Lorenz et al. Phytopathology 85:771, 1995. (3) C. Marcone et al. Acta Hortic. 386:471, 1995. (4) C. Y. Olivier et al. Plant Dis. 93:669, 2009.

scholarly journals First Report of a Group 16SrI Phytoplasma Associated with Amaranthus hypochondriacus Cladodes in China

Plant Disease ◽  
2011 ◽  
Vol 95 (7) ◽  
pp. 871-871
Author(s):  
J. Y. Long ◽  
Y. H. Chen ◽  
J. R. Xia
Keyword(s):  
16S Rdna ◽  
Nested Pcr ◽  
Universal Primer ◽  
First Report ◽  
Amaranthus Hypochondriacus ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Ctab Method ◽  
Pcr Products ◽  
Blastn Analysis

Amaranthus spp. are cultivated worldwide as leafy vegetable, cereal, and ornamentals. In China, stems and leaves of Amaranthus hypochondriacus L. are used as a vegetable (2). In July 2010, sporadic amaranth plants exhibiting symptoms of cladodes and spica proliferation were observed in a vegetable garden near Foshan, Guangdong, China. Stem samples were collected from two symptomatic and two asymptomatic plants. Total DNA was extracted with a modified cetyltrimethylammonium bromide (CTAB) method (1). Nested PCR with a combination of phytoplasma-specific universal primer pairs (P1/P7 and R16F2n/R16R2) amplified 16S rDNA sequences with the expected size of 1.2 kb from all samples of symptomatic amaranth plants, but not from the asymptomatic plants (3). Nested PCR products yielded identical AluI, HhaI, HpaII, HaeIII, KpnI, MseI, RsaI, Sau3AI, and TaqI restriction fragment length polymorphism (RFLP) profiles with chinaberry witches'-broom phytoplasma (16SrI-B subgroup), but different from peanut witches'-broom phytoplasma (16SrII group), jujube witches'-broom phytoplasma (16SrV group), and paulownia witches'-broom phytoplasma (16SrI-D subgroup). Nested PCR products were purified, cloned in pMD18-T Simple Vector (TaKaRa, Dalian, China), and sequenced. The 16S rDNA sequences were identical and deposited in GenBank (Accession No. JF323034). GenBank BLASTn analysis indicated that the amaranth extracts showed as high as 99% sequence identity with the members of 16SrI group phytoplasmas, including those associated with arecanut yellow leaf disease (FJ998269) and aster yellow AY-27 (HM467127). A polygenetic tree was constructed using MEGA 4.0 based on the 16S rDNA sequences of amaranth cladode phytoplasma and other phytoplasmas belonging to 16SrI phytoplasma group. In phylogenetic analysis, the sequences clustered on a single branch with members of 16SrI-B subgroup in the tree. Therefore, the phytoplasma was classified in subgroup 16SrI-B. To our knowledge, this is the first report of a subgroup 16SrI-B phytoplasma associated with diseased A. hypochondriacus in China. References: (1) E. Angelini et al. Vitis 40:79, 2001. (2) M. Costea et al. Econ. Bot. 57:646, 2003. (3) I. M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998.

scholarly journals The phylogeny of the genusYersiniabased on 16S rDNA sequences

1993 ◽  
Vol 114 (2) ◽  
pp. 173-177 ◽  
Author(s):  
A. Ibrahim ◽  
B.M. Goebel ◽  
W. Liesack ◽  
M. Griffiths ◽  
E. Stackebrandt
Keyword(s):  
16S Rdna ◽  
Rdna Sequences ◽  
16S Rdna Sequences

scholarly journals Isolation and Identification of Hydrocarbon-Degrading Bacteria that Tolerant to Saponin of Sapindus Rarak Plant

2019 ◽  
Vol 4 (1) ◽  
pp. 79-88
Author(s):  
Evi Octaviany ◽  
Suharjono Suharjono ◽  
Irfan Mustafa
Keyword(s):  
Crude Oil ◽  
16S Rdna ◽  
Bacterial Isolates ◽  
High Concentration ◽  
Isolation And Identification ◽  
Rdna Sequences ◽  
Degrading Bacteria ◽  
16S Rdna Sequences ◽  
Petroleum Contaminated Soil ◽  
Cell Densities

A commercial saponin as biosurfactant can reduce the surface tension of water and increase of hydrocarbon degradation. However, this saponin can be toxic to some hydrocarbonoclastic bac-teria. This study aimed to obtain bacterial isolates that were tolerant and incapable to degrade saponin, and to identify them based on 16S rDNA sequence. Bacteria were isolated from petroleum contaminated soil in Wonocolo Village, Bojonegoro Regency, East Java, Indonesia. The soil samples were acclimated using Bushnell-Haas (BH) broth with 0.5% crude oil at room temperature for 3 weeks. The culture was spread onto BH agar incubated at 30°C for 7 days. The first screened, isolates were grown in nutrient broth with addition of sap-onin 0%, 8%, and 12% (v/v) then incubated at 30°C for three days. The bacterial cell density was measured using a spectrophotometer. Second screened, the isolates were grown on BH broth with addition of 0.5% saponin as a sole carbon source, and their cell densities were measured. The selected isolates were identified based on 16S rDNA sequences. Among 34 bacterial isolates, nine isolates were tol-erant to 12% saponin. Three bacterial isolates IHT1.3, IHT1.5, and IHT3.24 tolerant to high concentration of saponin and did not use this substance as growth nutrition. The IHT1.3, IHT1.5, and IHT3.24 isolates were identified as Ochrobactrum pseudogrignonense (99% similarity), Pseudomonas mendocina (99%), and Ochrobactrum pi-tuitosum; (97%), respectively. Those three selected isolates are good candidates as hydrocarbon-degrading bacteria to bioremediation of soil contaminated crude oil. However, the combined activity of bacteria and saponin to degrade hydrocarbon needs further study. 

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