Micromonospora oryzae sp. nov., isolated from roots of upland rice

Abstract

An actinomycete strain, designated CP2R9-1 T , was isolated from root internal tissues of upland rice (Oryza sativa). Based on a polyphasic approach, strain CP2R9-1 T was characterized as a member of the genus Micromonospora. meso-Diaminopimelic acid and 3-OH-diaminopimelic acid were present in the cell-wall peptidoglycan. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unidentified phospholipids and four unidentified polar lipids. Predominant menaquinones were MK-9(H 4 ), MK-9(H 6 ) and MK-10(H 4 ). Whole-cell sugars consisted of ribose, xylose, arabinose and glucose. Phylogenetic analysis of the nearly complete 16S rRNA gene sequence suggested that strain CP2R9-1 T was closely related to Micromonospora haikouensis 232617 T (99.32 % similarity), Micromonospora carbonacea DSM 43168 T (99.18 %) and Micromonospora krabiensis MA-2 T (99.16 %). Strain CP2R9-1 T was distinct from its closest relatives based on low levels of DNA-DNA relatedness (21.3¡0.1-41.7¡0.7 %) and phenotypic differences. The results presented in this study showed that strain CP2R9-1 T represents a novel species of the genus Micromonospora, for which the name Micromonospora oryzae sp. nov. is proposed. The type strain is CP2R9-1 T (5BCC 67266 T 5NBRC 110007 T ).The genus Micromonospora was first proposed by Ørskov (1923). It is classified as a member of the family Micromonosporaceae that belongs to the order Actinomycetales (Stackebrandt et al., 1997). Effort has been made to identify novel species in the genus Micromonospora. This is largely due to their ability to produce secondary metabolites that have antibiotic properties (Supong et al., 2013). Additionally, several strains have been proposed as potential candidates for plant growth-promoting bacteria through nitrogen fixation and antagonistic activities against phytopathogens (Martínez-Hidalgo et al., 2014;Raaijmakers & Mazzola, 2012). The typical characteristic of members in this genus is the formation of single, nonmotile spores on sporophores of the substrate mycelium and the absence of aerial mycelium (Nimaichand et al., 2013;Ren et al., 2013). Recently, two new species of the genus Micromonospora, Micromonospora palomenae and Micromonospora harpali, were reported (Fang et al., 2015). In the present study, we report on the isolation and characterization of actinomycete strain CP2R9-1 T . The results obtained from the polyphasic study indicate that strain CP2R9-1 T represents a novel species of the genus Micromonospora.Upland rice plants were collected from Chumporn province, Thailand. Dirt was removed from root samples by rinsing with water several times. Surface sterilization was carried out by submerging roots in 70 % ethanol for 5 min and absolute ethanol for 1 min. Samples were air-dried and placed in 6 % (v/v) sodium hypochlorite solution for 2 min. Subsequently, excessive sodium hypochlorite solution was removed by rinsing the samples five times in sterilized distilled water. ...

Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics

“…The type species of the genus is Micromonospora chalcea and currently includes 81 species with validly published names http://www.bacterio.net/micromonospora.html (Parte, 2014 ). Most of these species have been described in the past 10 years with representative strains isolated from diverse habitats such as soil (Li and Hong, 2016 ; Lee and Whang, 2017 ), aquatic habitats (Trujillo et al, 2005 ; de Menezes et al, 2012 ), plant tissues (Carro et al, 2012 , 2013 ; Kittiwongwattana et al, 2015 ; Trujillo et al, 2015 ; Kaewkla et al, 2017 ) and other environments (Hirsch et al, 2004 ; Nimaichand et al, 2013 ; Lin et al, 2015 ). Recently, a revised classification of the genus Micromonospora based on genome sequence data has been proposed (Carro et al, 2018 ).…”

Recent progress on the development of antibiotics from the genus Micromonospora

“…This remained the only known strain among the actinomycetes bearing the generic name Micromonospora until Jensen in 1930 described a large number of soil micro-organisms which corresponded with Ørskov's description [19]. At the time of writing, the genus consisted of 61 validly named species (http://www.bacterio.net) [20], in addition to the recently described species, like: M. spongicola [21], M. jinlongensis [22], M. zeae [23], M. maoerensis [24], M. endophytica [25], M. palomenae [26], M. harpali [26], M. oryzae [27], M. vulcania [28], M. fluostatini [29], M. nickelidurans [30], M.…”

Bryophytes Harbor Cultivable Actinobacteria With Plant Growth Promoting Potential

“…Members of this genus have been isolated from various habitats including plants ( Trujillo et al, 2010 , 2015 ; Carro et al, 2012 , 2013 ; Genilloud, 2015 ). Several new species of Micromonospora are endophytes of various plants as exemplified by the description of M. costi ( Thawai, 2015 ), M. globbae ( Kuncharoen et al, 2018 ), M. phytophila ( Carro et al, 2018b ), M. luteiviridis ( Carro et al, 2018b ), M. oryzae ( Kittiwongwattana et al, 2015 ), and M. terminaliae ( Kaewkla et al, 2017 ). Streptomyces isolates also dominant represent around 38.5%.…”