Nocardiopsis potens sp. nov., isolated from household waste

Abstract

The taxonomic position of an actinomycete, designated strain IMMIB L-21 T , was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA-DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21 T (5DSM 45234 T 5CCUG 56587 T ).The genus Nocardiopsis was proposed by Meyer (1976) on the basis of chemotaxonomic and morphological characteristics. At the time of writing, the taxon encompasses 28 recognized species and 4 subspecies, which form a distinct clade within the evolutionary radiation occupied by members of the family Nocardiopsaceae (Rainey et al., 1996). Nocardiopsis strains are frequently isolated from saline soils (Yassin et al., 1993a;Li et al., , 2006, but they have also been recovered from an alkaline slag dump (Schippers et al., 2002), indoor environments (Peltola et al., 2001), the atmosphere of a composting facility (Kämpfer et al., 2002) and clinical material (Bernatchez & Lebreux, 1991;Yassin et al., 1997). In the present polyphasic study, an actinomycete isolated from household waste was shown to represent a novel species of the genus Nocardiopsis.Strain IMMIB L-21 T was isolated from a household dustbin on Brain Heart Infusion (BHI; BD) agar, glucose-yeast extract-malt extract agar (GYM; medium 65; DSMZ) and Columbia agar (BD) supplemented with 5 % sheep blood. The organism was grown on yeast extract-malt extract agar (ISP 2), oatmeal agar (ISP 3) and inorganic salts-starch agar (ISP 4) as described by Shirling & Gottlieb (1966) and examined for pigmentation and colour of aerial and substrate mycelia. Gram and ZiehlNeelsen stains were applied to hyphae grown on Columbia agar. Growth at different temperatures was determined at 10, 20, 27, 37 and 42 u C and a range of phenotypic characteristics was examined using standard procedures (Gordon, 1966(Gordon, , 1967Gordon & Mihm, 1957;Yassin et al., 1995). Tolerance to NaCl (0-16 %) was tested in GYM broth. Biomass for chemotaxonomic studies was derived from a 7-day-old BHI broth shake culture incubated at 37 u C, harvested by centrifugation and washed with distilled water. Standard procedures were used to determine the isomeric form of diaminopimelic acid (Becker et al., 1964), whole-cell sugars (Lechevalier, 1968), nonhydroxylated fatty acids (Minnikin et al., 1980;Yassin et al., 2007), polar lipids (Yassin et al., 1993b) and isoprenoid quinones (Collins et al., 1977;Yassin & Hupfer, 2006). Genomic DNA extraction and PCR-mediated amplification of the 16S rRNA gene sequence were carried out using established procedures (Rainey et al., 1996). The purified PCR products were sequenced using a Taq DyeDeoxy...

Marininema mesophilum gen. nov., sp. nov., a thermoactinomycete isolated from deep sea sediment, and emended description of the family Thermoactinomycetaceae

“…Yassin et al 2009emend. von Jan et al 2011 The description of the family Thermoactinomycetaceae is as given by Matsuo et al (2006), Yassin et al (2009) andvon Jan et al (2011), with the following amendment: aerial mycelium may be produced.…”

“…At the time of writing, the family Thermoactinomycetaceae (Matsuo et al, 2006) accommodated the genera Thermoactinomyces, Laceyella, Seinonella, Thermoflavimicrobium (Yoon et al, 2005), Planifilum (Hatayama et al, 2005), Mechercharimyces (Matsuo et al, 2006), Shimazuella (Park et al, 2007), Desmospora (Yassin et al, 2009) and Kroppenstedtia (von Jan et al, 2011). The members of this family are aerobic, Gram-positive and show filamentous growth.…”

“…Most species of the family are thermophilic (Hatayama et al, 2005;von Jan et al, 2011). However, several species, including Seinonella peptonophila, Mechercharimyces mesophilus, Mechercharimyces asporophorigenens and Shimazuella kribbensis, are mesophilic and only grow below 45 u C (Matsuo et al, 2006;Park et al, 2007;Yassin et al, 2009). Strains of this family have been isolated from various environmental samples, such as soil, marine sediments, sugar cane, mushroom compost and sputa from a patient with suspected pulmonary tuberculosis, and other clinical and environmental sources.…”

Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae

“…Subsequently, the family Thermoactinomycetaceae was described by Matsuo et al (2006) to accommodate these four genera together with Planifilum (Hatayama et al, 2005) and Mechercharimyces (Matsuo et al, 2006). Other genera have since been described and included in the family, such as Shimazuella (Park et al, 2007), Desmospora (Yassin et al, 2009), Kroppenstedtia (von Jan et al, 2011), Melghirimyces (Addou et al, 2012), Lihuaxuella (Yu et al, 2012), Marininema , Polycladomyces (Tsubouchi et al, 2013) and Hazenella (Buss et al, 2013). The description of the family has been emended by Yassin et al (2009), von Jan et al (2011 and Li et al (2012).…”

“…Other genera have since been described and included in the family, such as Shimazuella (Park et al, 2007), Desmospora (Yassin et al, 2009), Kroppenstedtia (von Jan et al, 2011), Melghirimyces (Addou et al, 2012), Lihuaxuella (Yu et al, 2012), Marininema , Polycladomyces (Tsubouchi et al, 2013) and Hazenella (Buss et al, 2013). The description of the family has been emended by Yassin et al (2009), von Jan et al (2011 and Li et al (2012). The members of the family are characterized by the formation of a single, non-stalked spore on the aerial or substrate hyphae or consecutive spores on straight or branched sporophores.…”