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Oryza genus

Paloma Koprovski Menguer, Raul Antonio Sperotto, Felipe Klein Ricachenevsky
Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated...
March 20, 2017: Genetics and Molecular Biology
Momota Potshangbam, S Indira Devi, Dinabandhu Sahoo, Gary A Strobel
In a natural ecosystem, the plant is in a symbiotic relationship with beneficial endophytes contributing huge impact on its host plant. Therefore, exploring beneficial endophytes and understanding its interaction is a prospective area of research. The present work aims to characterize the fungal endophytic communities associated with healthy maize and rice plants and to study the deterministic factors influencing plant growth and biocontrol properties against phytopathogens, viz, Pythium ultimum, Sclerotium oryzae, Rhizoctonia solani, and Pyricularia oryzae...
2017: Frontiers in Microbiology
Juan-Juan Zhao, Jun Zhang, Rui-Jie Zhang, Cai-Wen Zhang, Hua-Qun Yin, Xiao-Xia Zhang
Two novel, Gram-negative, motile, rod-shaped, aerobic bacterial strains, MH17(T) and RD15, were isolated from the sterilized root and rhizosphere soil of rice, respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that the similarity between strains MH17(T) and RD15 was 100%. The isolates exhibit high sequence similarities to Rhizobium oryzae CGMCC 1.7048(T) (98.7%) and Rhizobium petrolearium SL-1(T) (97.0% and 97.1%), which supports that they belong to a novel species in the genus Rhizobium...
May 2017: Antonie Van Leeuwenhoek
Yanfei Huang, Jinglin Wang, Mingxin Zhang, Min Zhu, Mei Wang, Yufeng Sun, Haitong Gu, Jingjing Cao, Xue Li, Shaoya Zhang, Xinxin Lu
PURPOSE: Filamentous fungi are among the most important pathogens, causing fungal rhinosinusitis (FRS). Current laboratory diagnosis of FRS pathogens mainly relies on phenotypic identification by culture and microscopic examination, which is time consuming and expertise dependent. Although matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS has been employed to identify various fungi, its efficacy in the identification of FRS fungi is less clear. METHODOLOGY: A total of 153 FRS isolates obtained from patients were analysed at the Clinical Laboratory at the Beijing Tongren Hospital affiliated to the Capital Medical University, between January 2014 and December 2015...
March 2017: Journal of Medical Microbiology
Juan-Juan Zhao, Jun Zhang, Lei Sun, Rui-Jie Zhang, Cai-Wen Zhang, Hua-Qun Yin, Xiao-Xia Zhang
Two Gram-negative, aerobic, rod-shaped endophytic bacterial strains, N19T and N11-2, were isolated from fresh rice (Oryza sativa) root during investigating the rice endophytic bacterial diversity. The 16S rRNA gene sequence results indicated that the similarity between strains N19T and N11-2 was 100 %. Both of them phylogenetically belong to the genus Rhizobium, with close similarity to Rhizobium taibaishanense CCNWSX 0483T (97.7 %), followed by Rhizobium vitis NCPPB 3554T (97.5 %). The sequence similarities of housekeeping genes recA, gyrB, glnA between the novel isolates and the established species of the genus Rhizobium were less than 87 %...
December 12, 2016: International Journal of Systematic and Evolutionary Microbiology
Jong Woo Hyeon, Hye Rim Kim, Hyo Jung Lee, Sang Eun Jeong, Sang Ho Choi, Che Ok Jeon
A Gram-staining-positive, strictly aerobic bacterium, designated R1T, was isolated from a rice paddy in South Korea. Cells were non-motile cocci showing oxidase-negative and catalase-positive activities. Growth of strain R1T was observed at 10-37 °C (optimum, 30 C) and pH 5.0-9.0 (optimum, pH 7.0). Strain R1T contained iso-C16 : 0, summed feature 9 (comprising iso-C17 : 1 ω9c/C16 : 0 10-methyl) , anteiso-C17 : 0, iso-C17 : 0 and anteiso-C17 : 1 ω9c as the major fatty acids and MK-8 (H4) and MK-8 (H6) as the isoprenoid quinones...
November 11, 2016: International Journal of Systematic and Evolutionary Microbiology
Haoxin Lv, Sachiko Masuda, Yoshiko Fujitani, Nurettin Sahin, Akio Tani
A novel facultatively methanol-utilizing bacterial strain, SM30T, was isolated from rice rhizosphere. Strain SM30T was Gram-stain-negative, aerobic, motile, short rods, and grew optimally at pH 7 and at 28 °C. It could tolerate 0 to 2 % (w/v) NaCl. Based on 16S rRNA gene sequence comparisons, strain SM30T was most closely related to Pleomorphomonas oryzae DSM 16300T, with a low similarity of 94.17 %. One of the lanthanide metals, lanthanum, could enhance its growth slightly on methanol. Phylogenetic trees, based on the mxaF, xoxF and cpn60 genes of SM30T showed its distinct phylogenetic position with respect to species with validly published names...
April 2017: International Journal of Systematic and Evolutionary Microbiology
Marta Brozynska, Dario Copetti, Agnelo Furtado, Rod A Wing, Darren Crayn, Glen Fox, Ryuji Ishikawa, Robert J Henry
The related A genome species of the Oryza genus are the effective gene pool for rice. Here we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short and long read next generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A, has a sequence that is much closer to that of domesticated rice (O...
November 27, 2016: Plant Biotechnology Journal
Adriana Illana, Marco Marconi, Julio Rodríguez-Romero, Ping Xu, Tamas Dalmay, Mark D Wilkinson, Maria Ángeles Ayllón, Ane Sesma
In this study we characterize a novel positive and single stranded RNA (ssRNA) mycovirus isolated from the rice field isolate of Magnaporthe oryzae Guy11. The ssRNA contains a single open reading frame (ORF) of 2,373 nucleotides in length and encodes an RNA-dependent RNA polymerase (RdRp) closely related to ourmiaviruses (plant viruses) and ourmia-like mycoviruses. Accordingly, we name this virus Magnaporthe oryzae ourmia-like virus 1 (MOLV1). Although phylogenetic analysis suggests that MOLV1 is closely related to ourmia and ourmia-like viruses, it has some features never reported before within the Ourmiavirus genus...
March 2017: Archives of Virology
Zhiyuan Ji, Chonghui Ji, Bo Liu, Lifang Zou, Gongyou Chen, Bing Yang
Plant pathogenic bacteria of the genus Xanthomonas possess transcription activator-like effectors (TALEs) that activate transcription of disease susceptibility genes in the host, inducing a state of disease. Here we report that some isolates of the rice pathogen Xanthomonas oryzae use truncated versions of TALEs (which we term interfering TALEs, or iTALEs) to overcome disease resistance. In comparison with typical TALEs, iTALEs lack a transcription activation domain but retain nuclear localization motifs and are expressed from genes that were previously considered pseudogenes...
November 4, 2016: Nature Communications
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...
January 2017: 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- to 5-μm FFPE tissue sections from each specimen were digested with proteinase K, followed by automated nucleic acid extraction. Multiple real-time quantitative PCR (qPCR) assays targeting the internal transcribed spacer 2 (ITS2) region of ribosomal DNA, using fluorescently labeled primers, was performed to identify clinically important genera and species of Aspergillus, Fusarium, Scedosporium, and the Mucormycetes The molecular identification was correlated with results from histological examination...
November 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 roots, 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 pinesoli KACC 17472T, with which strain 1DrF-4T showed 16S rRNA gene sequence similarity of 95...
December 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-staining-negative, aerobic, motile, rod-shaped, catalase- and oxidase-negative strain with one polar flagellum, designated THG-YS3.6T, was isolated from rhizosphere soil of a mugunghwa flower collected from Kyung Hee University, Yongin, South Korea. Growth occurred at 10-37 °C (optimum 25-30 °C), at pH 6-8 (optimum 7.0) and with 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 3-OH, iso-C15 : 0, iso-C16 : 0, C16 : 1ω7c alcohol, C16 : 0, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl)...
November 2016: International Journal of Systematic and Evolutionary Microbiology
E V V Ramaprasad, A Rizvi, S Banerjee, Ch Sasikala, Ch V Ramana
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. Phylogenetic analysis placed the three strains among the rapidly growing mycobacteria, being most closely related to Mycobacterium tokaiense 47503T (98.8 % 16S rRNA gene sequence similarity), Mycobacterium murale MA112/96T (98.8 %) and a few other Mycobacterium species. The level of DNA-DNA reassociation of the three strains with M...
November 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 (Oryzasativa) in Hubei Province. Cells of 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 of the 16S rRNA gene sequence indicated that the isolate represented a member of the genus Chromobacterium, and was most closely related to Chromobacterium haemolyticum MDA0585T and Chromobacterium aquaticum CC-SEYA-1T with 98...
October 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)...
December 2016: Archives of Microbiology
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