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Oryza genus

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https://www.readbyqxmd.com/read/28736890/insect-frass-in-stored-cereal-products-as-a-potential-source-of-lactobacillus-sanfranciscensis-for-sourdough-ecosystem
#1
Federica Boiocchi, Davide Porcellato, Lidia Limonta, Claudia Picozzi, Ileana Vigentini, Daria Patrizia Locatelli, Roberto Foschino
AIM: Insect frass samples were collected from Drosophila melanogaster, Plodia interpunctella, Rhyzopertha dominica, Sitophilus granarius, S. oryzae, S. zeamais, Tribolium confusum and T. castaneum to elucidate if they can be the origin of Type I sourdough microorganisms (Lactobacillus sanfranciscensis and Candida milleri). METHODS AND RESULTS: Selective enrichments were carried out to isolate Lactic Acid Bacteria and yeast. A metagenetic analysis, targeted on bacterial 16S rRNA gene and fungal ITS region, was performed by using Illumina MiSeq protocol...
July 23, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28732553/diversity-application-and-synthetic-biology-of-industrially-important-aspergillus-fungi
#2
Hee-Soo Park, Sang-Cheol Jun, Kap-Hoon Han, Seung-Beom Hong, Jae-Hyuk Yu
The filamentous fungal genus Aspergillus consists of over 340 officially recognized species. A handful of these Aspergillus fungi are predominantly used for food fermentation and large-scale production of enzymes, organic acids, and bioactive compounds. These industrially important Aspergilli primarily belong to the two major Aspergillus sections, Nigri and Flavi. Aspergillus oryzae (section Flavi) is the most commonly used mold for the fermentation of soybeans, rice, grains, and potatoes. Aspergillus niger (section Nigri) is used in the industrial production of various enzymes and organic acids, including 99% (1...
2017: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/28714843/roseomonas-suffusca-sp-nov-isolated-from-lagoon-sediments
#3
Y Subhash, Sang-Seob Lee
Three light-brown-coloured, Gram-stain-negative, small rod- to oval-shaped, motile bacteria were isolated from lagoon sediments collected from North Carolina, USA. The strains (S1T, AS3 and AS6) grew aerobically at 13-42 °C (optimum, 30-35 °C) and pH 6.5-9.1 (optimum, pH 7.0-7.5). All three strains were positive for catalase and oxidase activity, and no added NaCl was required for growth. C18 : 1ω6c/C18 : 1ω7c, C16 : 1ω6c/C16 : 1ω7c, C18 : 1ω7c 11-methyl and C16 : 0 were the predominant fatty acids (>5 %)...
July 17, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28643580/cyclophilins-less-studied-proteins-with-critical-roles-in-pathogenesis
#4
Khushwant Singh, Mark Winter, Miloslav Zouhar, Pavel Rysanek
Cyclophilins (EC 5.2.1.8) (CYPs) belong to a subgroup of proteins known as immunophilins, which also include FK-506 binding proteins (FKBPs) and parvulins. Members of the immunophilins have two main characteristic properties: I) peptidyl-prolyl cis-trans isomerase activity (PPIases) and II) the ability to bind immunosuppressant molecules of fungal origin. Cyclophilins are some of the most conserved proteins present in eukaryotes and prokaryotes, and they have been implicated in diverse cellular processes and responses to multiple biotic and abiotic stresses...
June 23, 2017: Phytopathology
https://www.readbyqxmd.com/read/28621110/characterization-of-microbial-communities-in-chinese-rice-wine-collected-at-yichang-city-and-suzhou-city-in-china
#5
Yucai Lyu, Yanli Gong, Yajie Li, Zejiang Pan, Yi Yao, Ning Li, Jinling Guo, Dachun Gong, Yihong Ti, Caiyun Peng
Two typical microbial communities from Chinese rice wine fermentation collected in Yichang city and Suzhou city in China were investigated. Both communities could ferment glutinous rice to rice wine in 2 d. The sugar and ethanol contents were 198.67 and 14.47 mg/g, respectively, for rice wine from Yichang city, and 292.50 and 12.31 mg/g, respectively, for rice wine from Suzhou city. Acetic acid and lactic acid were the most abundant organic acids. Abundant fungi and bacteria were detected in both communities by high-throughput sequencing...
June 16, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28619808/first-insights-into-the-genome-sequence-of-clostridium-oryzae-dsm-28571-isolated-from-the-soil-of-a-japanese-rice-field
#6
Anja Poehlein, Anna Lena Gippert, Maaike J Bierenbroodspot, Rolf Daniel
Clostridium oryzae was originally isolated from the soil of a Japanese rice field. C. oryzae represents a novel species within the genus Clostridium and is associated with anaerobic rice straw degradation. Here, we present the draft genome sequence of C. oryzae DSM 28571 (5.076 Mbp), containing 4,590 predicted protein-coding genes.
June 15, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28475028/chthonobacter-albigriseus-gen-nov-sp-nov-isolated-from-grass-field-soil
#7
Dohak Kim, Keunsoo Kang, Tae-Young Ahn
A novel aerobic, Gram-stain-negative and non-motile bacterial strain, designated ED7T, was isolated from grass-field soil in Cheonan, Korea. Strain ED7T utilized methanol and methylamine, but not formate, as carbon and energy sources. The strain was able to grow at 20-42 °C (optimum 30-35 °C), at pH 7.0-8.5 (optimum pH 7.5-8.0), and in the absence of NaCl. According to the similarities of the 16S rRNA gene sequences, strain ED7T was most closely related to the genera Labrenzia (≤93.3 % 16S rRNA gene sequence similarity), Pleomorphomonas (≤93...
April 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28323300/a-walk-on-the-wild-side-oryza-species-as-source-for-rice-abiotic-stress-tolerance
#8
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...
2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28303127/functional-characterization-of-endophytic-fungal-community-associated-with-oryza-sativa-l-and-zea-mays-l
#9
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
https://www.readbyqxmd.com/read/28154946/rhizobium-rhizosphaerae-sp-nov-a-novel-species-isolated-from-rice-rhizosphere
#10
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
https://www.readbyqxmd.com/read/28100314/matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-for-rapid-identification-of-fungal-rhinosinusitis-pathogens
#11
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
https://www.readbyqxmd.com/read/27959784/rhizobium-oryziradicis-sp-nov-isolated-from-rice-roots
#12
Juan-Juan Zhao, Jun Zhang, Lei Sun, Rui-Jie Zhang, Cai-Wen Zhang, Hua-Qun Yin, Xiao-Xia Zhang
Two Gram-stain-negative, aerobic, rod-shaped endophytic bacterial strains, N19T and N11-2, were isolated from fresh rice (Oryza sativa) roots during investigation of 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 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 the housekeeping genes recA, gyrB and glnA between the novel isolates and members of the established species of the genus Rhizobium were less than 87 %...
April 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/27902309/flexivirga-oryzae-sp-nov-isolated-from-soil-of-a-rice-paddy-and-emended-description-of-the-genus-flexivirga-anzai-et-al-2012
#13
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
https://www.readbyqxmd.com/read/27902265/oharaeibacter-diazotrophicus-gen-nov-sp-nov-a-diazotrophic-and-facultatively-methylotrophic-bacterium-isolated-from-rice-rhizosphere
#14
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
https://www.readbyqxmd.com/read/27889940/sequencing-of-australian-wild-rice-genomes-reveals-ancestral-relationships-with-domesticated-rice
#15
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...
June 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27858291/molecular-characterization-of-a-novel-ssrna-ourmia-like-virus-from-the-rice-blast-fungus-magnaporthe-oryzae
#16
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
https://www.readbyqxmd.com/read/27811915/interfering-tal-effectors-of-xanthomonas-oryzae-neutralize-r-gene-mediated-plant-disease-resistance
#17
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
https://www.readbyqxmd.com/read/27688210/microbacterium-rhizosphaerae-sp-nov-isolated-from-a-ginseng-field-south-korea
#18
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
https://www.readbyqxmd.com/read/27605714/discrimination-of-aspergillosis-mucormycosis-fusariosis-and-scedosporiosis-in-formalin-fixed-paraffin-embedded-tissue-specimens-by-use-of-multiple-real-time-quantitative-pcr-assays
#19
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
https://www.readbyqxmd.com/read/27565704/paenibacillusoryzae-sp-nov-isolated-from-rice-roots
#20
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
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