Microterricola viridarii gen. nov., sp. nov., a new member of the family Microbacteriaceae

Abstract

The Kitasato Institute, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8642, Japan 2 Kitasato Institute for Life Sciences, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, JapanStrain KV-677 T , a Gram-positive, aerobic, motile, rod-shaped bacterium, was isolated from park soil in Tokyo, Japan, and characterized. It grew well at 15-30 6C on nutrient agar and colonies were pale yellow. The cell-wall peptidoglycan contained diaminobutyric acid, glycine, alanine and glutamic acid and the muramic acid acyl type was acetyl. The predominant menaquinone was MK-12. Mycolic acids were not detected. The DNA G+C content was 70 mol%. 16S rRNA gene sequence analysis revealed that strain KV-677 T fell within the cluster of the family Microbacteriaceae and formed a separate lineage joining the genera Salinibacterium, Rhodoglobus, Subtercola and Agreia, showing 95.5-96.9 % sequence similarities with the type strains of the type species of the above genera. However, strain KV-677 T clearly differed from these and other genera with relatively high sequence similarity in its chemotaxonomic characteristics. Therefore, it is proposed that strain KV-677 T represents a novel species in a new genus, Microterricola viridarii gen. nov., sp. nov., in the family Microbacteriaceae. The type strain of Microterricola viridarii is KV-677 T (5NRRL B-24538 T 5NBRC 102123 T ).A novel strain, KV-677 T , was isolated from park soil in Tokyo. The strain contained diaminobutyric acid (DAB) as the diamino acid in the cell wall and other chemotaxonomic characteristics and phylogenetic analysis showed that the strain belonged to the family Microbacteriaceae (Park et al., 1993;Stackebrandt et al., 1997). Currently, the family Microbacteriaceae consists of 21 genera, including Agreia ( Strain KV-677 T was isolated using GPM agar (1 % Dglucose, 0.5 % peptone, 0.5 % meat extract, 0.3 % NaCl, 1.2 % agar, pH 7) containing 0.002 % Benlate (Dupont) and 0.0025 % nalidixic acid (Sigma) from soil collected at Arisugawa Park in the Tokyo metropolitan area, Japan, after incubation for 1 week at 27 u C. Morphological characteristics of the strain were observed by scanning electron microscopy (SEM) (JSM-5600; JEOL) and transmission electron microscopy (TEM) (JEM-1200EXII; JEOL). For SEM, cells grown in TSB (Difco) for 3 days at 27 u C were rinsed with 0.05 M Tris/HCl buffer (pH 7.6) and filtered onto a membrane. The sample was fixed using 4 % osmium tetroxide vapour following lyophilization with liquid nitrogen. For TEM, cells grown on nutrient agar for 2 days at 27 u C were stained with 1.5 % (w/v) uranyl acetate after cell motility was observed with a light microscope. Gram-staining was performed using a Gram's stain reagent kit (Nacalai Tesque). Cultural and physiological characteristics were observed after incubation for 2 days at 27 u C. The NaCl tolerance and pH range for growth were determined on YD agar (1.0 % yeast extract, Abbreviations: DAB, diaminobutyric acid; SEM, scanning electron microscopy; TEM, transmission electron microscopy.The GenBank/EMBL...

Lysinimonas soli gen. nov., sp. nov., isolated from soil, and reclassification of Leifsonia kribbensis Dastager et al. 2009 as Lysinimonas kribbensis sp. nov., comb. nov.

“…Table 1. Differential characteristics of closely related genera of the family Microbacteriaceae Genera: 1, Lysinimonas gen. nov.; 2, Agreia (Evtushenko et al, 2001;Behrendt et al, 2002, Schumann et al, 2003; 3, Agrococcus (Groth et al, 1996;Wieser et al, 1999;Zlamala et al, 2002;Mayilraj et al, 2006;Bora et al, 2007;Lee, 2008;Behrendt et al, 2008;Zhang et al, 2010;Dhanjal et al, 2011); 4, Chryseoglobus (Baik et al, 2010); 5, Glaciibacter (Katayama et al, 2009); 6, Herbiconiux (Qiu et al, 2007;Behrendt et al, 2011;Kim et al, 2012); 7, Labedella (Lee, 2007); 8, Leifsonia (Leifson, 1962;Davis et al, 1984;Suzuki et al, 1999;Evtushenko et al, 2000;Reddy et al, 2003;An & Yokota, 2007;Qiu et al, 2007;Dastager et al, 2008Dastager et al, , 2009Pindi et al, 2009;An et al, 2009An et al, , 2010Madhaiyan et al, 2010;Ganzert et al, 2011); 9, Microcella (Tiago et al, 2005(Tiago et al, , 2006; 10, Microterricola (Matsumoto et al, 2008); 11, Phycicola (Lee et al, 2008); 12, Rhodoglobus (Reddy et al, 2003;Sheridan et al, 2003;An et al, 2010); 13, Salinibacterium (Han et al, 2003;Zhan...…”

Micromonospora pelagivivens sp. nov., a new species of the genus Micromonospora isolated from deep-sea sediment in Japan

“…Total genomic DNA for the 16S rRNA gene of strain KJ-029 T was extracted using a sonication method [35], and the 16S rRNA gene was amplified using the primers described by Takahashi et al [36]. PCR amplification and sequencing of the 16S rRNA gene were carried out as previously described [37] with an automated DNA sequencer (Applied Biosystems 3130 Genetic Analyser) using a BigDye Terminator v3.1 cycle Sequencing kit (Applied Biosystems), according to the manufacturer's instructions. Levels of sequence similarity among the most closely related strains were computed using the EzBioCloud server (http:// eztaxon-e. ezbiocloud.…”

Actinokineospora bangkokensis sp. nov., isolated from rhizospheric soil

“…DNA G+C content was examined according to the method of Tamaoka & Komagata (1984) using HPLC and DNA–DNA hybridization analysis was performed by the method of Ezaki et al (1989). PCR amplification and sequencing of the 16S rRNA gene were carried out as previously described (Matsumoto et al , 2008) with an ABI PRISM 3130 Genetic Analyzer (Applied Biosystems) according to the manufacturer’s instructions. An almost full-length 16S rRNA gene sequence (1398 bp) of strain 44EHW T was aligned with the twelve type strains of the genus Actinokineospora using clustal _ x version 1.83 (Thompson et al , 1997).…”