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Oryza genus

Sung-Jin Cho, Sang-Seob Lee
A novel Gram-stain positive, aerobic, short rod-shaped, non-motile bacterium, designated strain CHO1(T), was isolated from rhizosphere soil from a ginseng agriculture field. Strain CHO1(T) was observed to form yellow colonies on R2A agar medium. The cell wall peptidoglycan was found to contain alanine, glycine, glutamic acid, D-ornithine and serine. The cell wall sugars were identified as galactose, mannose, rhamnose and ribose. Strain CHO1(T) was found to contain MK-11, MK-12, MK-13 as the predominant menaquinones and anteiso-C15:0, iso-C16:0, and anteiso-C17:0 as the major fatty acids...
September 29, 2016: Antonie Van Leeuwenhoek
Elham Salehi, Mohammad T Hedayati, Jan Zoll, Haleh Rafati, Maryam Ghasemi, Atosa Doroudinia, Mahdi Abastabar, Ali Tolooe, Eveline Snelders, Henrich A van der Lee, Antonius J M M Rijs, Paul E Verweij, Seyedmojtaba Seyedmousavi, Willem J G Melchers
In a retrospective multicenter study, 102 formalin-fixed paraffin-embedded (FFPE) tissue specimens with histopathology results were tested. Two 4-5 μm FFPE tissue sections from each specimen was digested with proteinase K followed by automated nucleic acid extraction.A specific quantitative real-time quantitative PCR (qPCR) assay targeting the internal transcribed spacer (ITS2) region of ribosomal DNA, using fluorescently labeled primers, was performed to identify clinically important genus and species of Aspergillus, Fusarium, Scedosporium and the Mucormycetes...
September 7, 2016: Journal of Clinical Microbiology
Jun Zhang, Xiao-Tong Ma, Jun-Sheng Gao, Juan-Juan Zhao, Hua-Qun Yin, Cai-Wen Zhang, Rui-Jie Zhang, Xiao-Xia Zhang
A novel endophytic bacterium, strain 1DrF-4T, isolated from rice root, was characterized on the basis of its phenotypic characteristics and genotypic information. The novel strain was Gram-positive staining, endospore-forming, facultatively anaerobic, motile and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 1DrF-4T formed a monophyletic clade within the genus Paenibacillus. The most phylogenetically related species was Paenibacillus pinisoli KACC 17472T, with which strain 1DrF-4T showed 16S rRNA gene sequence similarity of 95...
August 26, 2016: International Journal of Systematic and Evolutionary Microbiology
Yanan Du, Xiang He, Xuan Zhou, Shouguo Fang, Qingchao Deng
A novel double-stranded RNA (dsRNA) mycovirus, designated Magnaporthe oryzae partitivirus 1 (MoPV1), was isolated from a strain of the plant pathogenic fungus Magnaporthe oryzae. The MoPV1 genome has two dsRNA genome segments. The larger segment (1763 bp) has a single open reading frame (ORF) with a conserved RNA-dependent RNA polymerase (RdRp) domain. The smaller segment (1491 bp) contains a single ORF encoding a putative coat protein (CP). Homology searches and phylogenetic analysis indicated that MoPV1 is a new member of the genus Gammapartitivirus...
November 2016: Archives of Virology
Matthew Shenton, Chie Iwamoto, Nori Kurata, Kazuho Ikeo
BACKGROUND: Deposition and secretion from roots influences the composition of the microbial communities surrounding them in the rhizosphere, and microbial activities influence the growth and health of the plant. Different host plant genotypes result in differences in those microbial communities. Crop genomes may have a narrow genetic base because of bottlenecks that occurred when domesticated crops were derived from small populations within the progenitor species. Desirable traits influencing root-associated microbial communities might therefore have been lost in the transition from wild species to modern cultivars...
December 2016: Rice
Zheng-Fei Yan, Huan Trinh, Gabriela Moya, Pei Lin, Chang-Tian Li, Moo-Chang Kook, Tae-Hoo Yi
A Gram-negative, aerobic, motile, rod with one polar flagellum, catalase and oxidase-negative strain, designated THG-YS3.6T, was isolated from rhizosphere soil of flower Mugunghwa collected from Kyung Hee University, Yongin, South Korea. Growth occurred at 10-37 oC (optimum 25-30 oC), at pH 6-8 (optimum 7.0) and at 0-2.0% NaCl (optimum 1%). The isoprenoid quinone was ubiquinone-8 (Q-8). The major cellular fatty acids were iso-C11:0, iso-C11:0 3OH, iso-C15:0, iso-C16:0, C16:1 7c alcohol, C16:0, iso-C17:0, summed feature 9 (iso-C17:1 9c and/or C16:0 10-methyl)...
August 12, 2016: International Journal of Systematic and Evolutionary Microbiology
Ramaprasad E V V, Rizvi A, Benerjee S, Sasikala Ch, Ramana Ch V
Gram-stain-positive, acid-fast positive, rapidly growing, rod shaped bacteria (designated as strains JC290T, JC430 and JC431) were isolated from paddy cultivated soils on the Western Ghats of India. The phylogenetic analysis placed the three strains among the rapidly growing mycobacteria, being most closely related to Mycobacterium tokaiense 47503T (98.8%), Mycobacterium murale MA112/96T (98.8%) and a few other Mycobacterium spp. The level of DNA-DNA reassociation of the three strains with M. tokaiense DSM44635T was 23...
August 5, 2016: International Journal of Systematic and Evolutionary Microbiology
Irene Zornetta, Domenico Azarnia Tehran, Giorgio Arrigoni, Fabrizio Anniballi, Luca Bano, Oneda Leka, Giuseppe Zanotti, Thomas Binz, Cesare Montecucco
The genome of Weissella oryzae SG25T was recently sequenced and a botulinum neurotoxin (BoNT) like gene was identified by bioinformatics methods. The typical three-domains organization of BoNTs with a N-terminal metalloprotease domain, a translocation and a cell binding domains could be identified. The BoNT family of neurotoxins is rapidly growing, but this was the first indication of the possible expression of a BoNT toxin outside the Clostridium genus. We performed molecular modeling and dynamics simulations showing that the 50 kDa N-terminal domain folds very similarly to the metalloprotease domain of BoNT/B, whilst the binding part is different...
2016: Scientific Reports
Shan Zhou, Xiang Guo, Huimin Wang, Delong Kong, Yanwei Wang, Jie Zhu, Weiwei Dong, Mingxiong He, Guoquan Hu, Bingqiang Zhao, Bin Zhao, Zhiyong Ruan
A novel facultatively anaerobic, rod-shaped bacterium, designated LAM1188T, was isolated from the roots of rice (Oryza sativa) in Hubei Province. Cells of strain LAM1188T were Gram-stain negative and motile. The temperature and pH ranges for growth were 15-40 °C (optimum: 30 °C) and pH 5-10 (optimum: pH 7), respectively. The strain did not require NaCl for growth but tolerated up to 3.5 % NaCl (w/v). Analysis on the 16S rRNA gene sequence indicated that the isolate was a member of the genus Chromobacterium, and most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98...
July 8, 2016: International Journal of Systematic and Evolutionary Microbiology
Shahina Akter, Md Amdadul Huq, Tae-Hoo Yi
A novel bacterial strain THG-PC4(T) was isolated from soil sample of rice field and was characterized by using a polyphasic approach. Cells were Gram-negative, bright yellow colored, nonmotile and rod shaped. The strain was aerobic and catalase positive, optimum growth temperature, and pH were 28 °C and 7, respectively. On the basis of 16S rRNA gene sequence analysis, strain THG-PC4(T) belongs to the genus Lysobacter and is most closely related to Lysobacter fragariae KCTC 42236(T), followed by Lysobacter oryzae KCTC 22249(T), Lysobacter tyrosinelyticus KCTC 42235(T), Lysobacter terrae KACC 17646(T), Lysobacter yangpyeongensis KACC 11407(T), Lysobacter rhizosphaerae KCTC 42237(T) and Lysobacter niabensis KACC 11587(T)...
July 4, 2016: Archives of Microbiology
Xiu Chen, Qin-Yuan Li, Gui-Ding Li, Fang-Ji Xu, Yi Jiang, Li Han, Cheng-Lin Jiang, Xue-Shi Huang
A novel aerobic, non-motile, Gram-positive, rod-shaped actinobacterium, designated YIM 100951(T), was isolated from the faeces of civets (Viverra zibetha) living in the National Nature Protect Region in Selangor, Malaysia. Strain YIM 100951(T) shows high similarities with Microbacterium barkeri DSM 20145(T) (97.6 %), Microbacterium oryzae MB10(T) (97.3 %), Microbacterium lemovicicum ViU22(T) (97.1 %) and Microbacterium indicum BBH6(T) (97.0 %) based on their 16S rRNA genes. However, phylogenetic analysis showed that strain YIM 100951(T) formed a clade with Microbacterium halotolerans YIM 70130(T) (96...
September 2016: Antonie Van Leeuwenhoek
Sophie Mantelin, Stéphane Bellafiore, Tina Kyndt
: Taxonomy: The rice root-knot nematode Meloidogyne graminicola (Golden and Birchfield 1965). Superkingdom Eukaryota; Kingdom Metazoa; Phylum Nematoda; Class Chromadorea; Order Tylenchida; Suborder Tylenchina; Infraorder Tylenchomorpha; Superfamily Tylenchoidea; Family Meloidogynidae; Subfamily Meloidogyninae; Genus Meloidogyne. Biology: Microscopic non-segmented roundworm. Plant pathogen; obligate sedentary endoparasitic root-knot nematode. Reproduction: facultative meiotic parthenogenetic species in which amphimixis can occur at a low frequency (ca...
March 7, 2016: Molecular Plant Pathology
R Kachuei, S Khodavaisy, S Rezaie, S Sharifynia
OBJECTIVE: Among filamentous fungal pathogens, Aspergillus spp. and zygomycetes account for highest rates of morbidity and mortality among immunocompromised patients. Recently developed antifungal drugs offer the potential to improve management and therapeutic outcomes of fungal infections. The aim of this study was to analyse the in vitro activities of voriconazole, itraconazole, amphotericin B and caspofungin against clinical isolates of Aspergillus spp. and Rhizopus oryzae. MATERIAL AND METHODS: The in vitro antifungal susceptibility of 54 isolates belonging to different clinical isolates of Aspergillus spp...
March 2016: Journal de Mycologie Médicale
Yu-Chia Hsu, Chang-Sheng Wang, Yann-Rong Lin, Yong-Pei Wu
Retrotransposons with long terminal repeats (LTRs) are the most abundant transposable elements in plant genomes. A novel LTR retrotransposon named RTPOSON primarily occurs in the genus Oryza and in several species of the Poaceae family. RTPOSON has been identified in the Ty1-copia group of retrotransposons because two of its open reading frames encode an uncharacterized protein and UBN2_2 and zinc knuckle, respectively. More than 700 RTPOSONs were identified in Oryza genomes; 127 RTPOSONs with LTRs and gag-pol elements were classified into three subgroups...
2016: Evolutionary Bioinformatics Online
L Delhalle, N Korsak, B Taminiau, C Nezer, S Burteau, V Delcenserie, J B Poullet, G Daube
Steak tartare is a popular meat dish in Belgium. It is prepared with raw minced beef and is eaten with sauce, vegetables, and spices. Because it contains raw meat, steak tartare is highly prone to bacterial spoilage. The objective of this study was to explore the diversity of bacterial flora in steak tartare in Belgium according to the source and to determine which bacteria are able to grow during shelf life. A total of 58 samples from butchers' shops, restaurants, sandwich shops, and supermarkets were collected...
February 2016: Journal of Food Protection
Khomsan Supong, Chitti Thawai, Wilunda Choowong, Chokchai Kittiwongwattana, Dusanee Thanaboripat, Chamroon Laosinwattana, Prommart Koohakan, Nonglak Parinthawong, Pattama Pittayakhajonwut
An endophytic actinomycete strain BCC72023 was isolated from rice (Oryza sativa L.) and identified as the genus Streptomyces, based on phenotypic, chemotaxonomic and 16S rRNA gene sequence analyses. The strain showed 99.80% similarity compared with Streptomyces samsunensis M1463(T). Chemical investigation led to the isolation of three macrolides, efomycins M (1), G (2) and oxohygrolidin (3), along with two polyethers, abierixin (4) and 29-O-methylabierixin (5). To our knowledge, this is the first report of efomycin M being isolated from a natural source...
May 2016: Research in Microbiology
Soo-Jin Kim, Jae-Hyung Ahn, Hang-Yeon Weon, Seung-Beom Hong, Soon-Ja Seok, Jeong-Seon Kim, Soon-Wo Kwon
A strain 5GH22-11T, which was isolated from greenhouse soil in Yangpyeong region, Gyeonggi province, Republic of Korea, was characterized as aerobic, Gram-stain-negative, flagellated, rod-shaped bacterium. It could grow at temperatures from 10-33 °C (optimum of 28-30 °C), in the range of pH 6.0-10.0 (optimum of pH 7.0) and without NaCl. The 16S rRNA gene sequence analysis showed that strain 5GH18-14T showed the highest sequence similarities with Lysobacter niabensis GH34-4T (98.6 %), Lysobacter yangpyeongensis GH19-3T (98...
January 12, 2016: International Journal of Systematic and Evolutionary Microbiology
Jie Zhong, Qian Zhou, Yue Hu, Hong Jian Zhu, Bi Da Gao
Nigrospora oryzae is a worldwide phytopathogenic fungus that can infect many plant host species. In this study, complete sequence of a novel mycovirus from N. oryzae was reported. The viral genome is 5100 base pairs in length and possesses two overlapping open reading frames (ORFs). The two ORFs potentially encode proteins that showed significant similarity to the capsid protein and RNA-dependent RNA polymerase, in the family Totiviridae, respectively. Phylogenetic tree showed that this novel mycovirus is a new member of the genus Victorivirus in the family Totiviridae...
February 2016: Virus Genes
Hao Yin, Masahiro Akimoto, Reunreudee Kaewcheenchai, Masahiro Sotowa, Takashige Ishii, Ryuji Ishikawa
AA genome species in the genus Oryza are valuable resources for improvement of cultivated rice. Oryza rufipogon and O. barthii were progenitors of two domesticated rice species, O. sativa and O. glaberrima, respectively. We used chloroplast single-nucleotide repeats (RCt1-10) to evaluate genetic diversity among AA genome species. Higher diversity was detected in the American species O. glumaepatula and the Asian species O. rufipogon. Other chloroplast sequences indicated that O. glumaepatula shares high similarity with O...
2015: Genes & Genetic Systems
Peter Kämpfer, John A McInroy, Swapnil Doijad, Trinad Chakraborty, Stefanie P Glaeser
A beige pigmented bacterial strain (JM-387(T)), isolated from field-grown corn root tissue, Tallassee, Alabama, was studied for its taxonomic allocation. A comparison of the 16S rRNA gene sequence with those of the type strains of most closely related species of the family Enterobacteriaceae showed highest sequence similarities to the type strain of Kosakonia sacchari (99.5%), "Enterobacter oryzendophyticus" (98.8%), and Kosakonia radicincitans (98.6%). Construction of phylogenetic trees based on the 16S rRNA gene and partial sequences of four protein-coding genes, rpoB, gyrB, infB, and atpD (multilocus sequence analysis, MLSA) showed a distinct clustering of strain JM-387(T) with Kosakonia sacchari...
February 2016: Systematic and Applied Microbiology
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