Micromonospora rifamycinica sp. nov., a novel actinomycete from mangrove sediment

Abstract

An actinomycete strain, AM105T , that produces rifamycin, was isolated from mangrove sediment samples collected from the South China Sea. The strain showed closest 16S rRNA gene sequence similarity to Micromonospora matsumotoense (98.0 %). Chemotaxonomic characteristics of the isolate coincided with members of the genus Micromonospora. The value of DNA-DNA relatedness to M. matsumotoense (53.6 %) and phenotypic differences from phylogenetically related Micromonospora species indicated that this isolate belongs to a novel species, for which the name Micromonospora rifamycinica sp. nov. is proposed. The type strain is AM105 T (5CGMCC 4.2495 T 5DSM 44983 T ).Mangroves are a unique woody plant community of intertidal coasts in the tropical and subtropical zones, which are regarded as highly productive ecosystems and abode to large unexplored microbial diversity (Bashan & Holguin, 1997). Strain AM105 T was isolated from mangrove sediment samples from the South China Sea. Isolation was carried out by the standard dilution-plating technique on modified Gause inorganic agar (Gause et al., 1983), which contained 20 g soluble starch, 1 g KNO 3 , 0.5 g K 2 HPO 4 , 0.5 g MgSO 4 . 7H 2 O, 0.01 g FeSO 4 . 7H 2 O, 15 g agar, 1 l old sea water (pH 7.2-7.4). Plates were incubated for 30 days at 28 u C. A pure culture was maintained in a glycerol suspension (20 %, w/v) at 270 u C.Cultural features were observed on oatmeal agar (DSMZ medium 609), glycerol-asparagine agar (Shirling & Gottlieb, 1966), GYM agar (DSMZ medium 65), potato dextrose agar (DSMZ medium 129), Sauton's agar (Mordarska et al., 1972) and Gause inorganic agar after 7, 14 and 21 days incubation at 28 u C. Cell morphology and spore production were observed by light and scanning electron microscopy using 6-and 20-day-old cultures grown on various agar media. The ability to grow on sole carbon sources (1 %, w/v) was tested as described by Williams et al. (1983). NaCl tolerance (0-4.5 %, w/v) and temperatures (4-45 u C) for growth were tested on GYM agar. Methods and media for other physiological tests and the assays for enzymic activities were performed according to Wang (1986).For chemotaxonomic studies, the strain was grown in GYM broth in a shaking incubator at 200 r.p.m. and 28 u C for 5 days. Biomass was harvested by centrifugation and washed with distilled water. Isomers of diaminopimelic acid (DAP) and sugars were determined in whole-cell hydrolysates by TLC on microcrystalline cellulose (Wang, 1986).Genomic DNA was isolated as described by Pitcher et al. (1989). The DNA G+C content was determined using the thermal melting method (Mandel & Marmur, 1968). PCR amplification of the 16S rRNA gene and sequencing of the purified PCR product were done as described previously (Rivas et al., 2003). The sequence of isolate AM105T was aligned and compared with representative sequences of members of the genus Micromonospora obtained from GenBank using the CLUSTAL_X 1.8 program (Thompson et al., 1997). Phylogenetic analysis was performed with the MEGA version 2.1 progra...

Isolation and characterization of potential antibiotic producing actinomycetes from water and sediments of Lake Tana, Ethiopia

“…The inoculated plates were left at room temperature for [3][4][5] minutes to allow for any surface moisture to be absorbed before applying the extract. Ten mg/mL of each crude extracts was impregnated with filter paper (6 mm diameter disc) and placed on the surface of MHA medium. Standard antibiotic (tetracycline) disc was used as a positive control and filter paper disc soaked with methanol as a negative control.…”

“…The well was prepared in the plate by using sterile cork borer (6 mm in diameter). A volumn of 100 µL of 10 mg/mL of crude extracts was carefully dispensed into each well and allowed to diffuse for 2 h and incubated at 37 °C for 24 h. The sterilized methanol was filtered and used as negative control.…”

“…In perpendicular streak method, nutrient agar media was used and each plate was streaked with individual isolates at the center/diameter of the plate and incubated at 30 °C for 7 d. Later, 24 h fresh sub-cultured test bacteria were prepared and streaked perpendicular to the isolates and incubated at 37 °C for 24 h [30] . In agar overlay method, [5][6][7] d old colony of actinomycetes was spot inoculated on nutrient agar plates and incubated for 7 d at 30 °C . Then overlaid with 5 mL of semisolid nutrient agar with standardized suspension of test bacteria was inoculated and incubated at 37 °C for 24 h. The zone of inhibition (in mm) around the colonies was measured.…”

“…The dominant actinomycetes Micromonospora can be isolated from aquatic habitats such as streams, rivers, lake mud, river sediments, beach sands, sponge and marine sediments [4,5] . Several novel bioactive compounds were discovered from aquatic actinomycetes, for example rifamycin from Micromonospora [6] ; salinosporamide-A, an anticancer metabolite from a Salinispora strain [7] ; marinomycins from Marinophilus sp. [8] ; abyssomicin-C from Verrucosispora sp.…”

Antimycins A19 and A20, two new antimycins produced by marine actinomycete Streptomyces antibioticus H74-18

“…[6][7][8][9][10] Sediments of mangrove sites along the coast of the South China Sea have been a rich source of marine microorganism, especially actinomycetes. [11][12][13][14][15][16][17] Our research group has isolated 42000 strains of actinomycetes from the sediment soils collected at several mangrove sites in the South China Sea, of which about 40 strains were found to show antifungal activity against Candida albicans by primary in vitro screening. Further characterization of antifungal compounds, which was produced by a cultured broth of Streptomyces antibioticus H74-18, led to the isolation of two new antibiotic compounds-antimycins A 19 and A 20 (Figure 1).…”