Benjamin Lanoot

Bacterial Populations Associated with Rice Seed in the Tropical Environment

ABSTRACT During the 1995 wet season, harvested rice seed was collected from farmers fields at different locations in Iloilo, Philippines. Bacterial isolations from crushed seed yielded 428 isolates. The isolates were characterized by BOX-polymerase chain reaction fingerprinting of total genomic DNA and represented 151 fingerprint types (FPT). Most FPTs were found on a single occasion, although matching fingerprints for isolates from different samples also were found. Identifications were made by cellular fatty acid methyl ester analysis and additional use of Biolog GN/GP MicroPlates and API 20E/50CHE systems. The predominant bacteria were Enterobacteriaceae (25%), Bacillus spp. (22%), and Pseu-domonas spp. (14%). Other bacteria regularly present were identified as Xanthomonas spp., Cellulomonas flavigena, and Clavibacter michiganense. Of the total number of isolated bacteria, 4% exhibited in vitro antifungal activity against Rhizoctonia solani or Pyricularia grisea. Two percent of isolates were pathogens identified as Burkholderia glumae and Burkholderia gladioli. Five percent of isolates induced sheath necrosis on only 50 to 90% of inoculated plants and were related to Bacillus pumilus, Paenibacillus spp., Pseudomonas spp., and Pantoea spp.

BOX-PCR fingerprinting as a powerful tool to reveal synonymous names in the Genus streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus

The type strains of 451 validly described Streptomyces species were screened using the BOX-PCR fingerprint technique. Of the different primers tested, the BOX primer yielded the most robust and reproducible band patterns. The majority of the species (350) had an unique pattern each. A total number of 30 clusters were delineated comprising species with nearly identical patterns. Four of these clusters grouped synonymous Streptomyces species known from previous studies. A high correlation exists between BOX-PCR fingerprinting and DNA-DNA homology data. In the present study, the latter was confirmed for 7 additional BOX clusters and led to the following emended descriptions: S. cochleatus is a subjective synonym of S. cinereorectus, S. roseoflavus of S. fradiae, S. roseodiastaticus of S. tricolor, S. roseosporus of S. filamentosus, S. distallicus of S. colombiensis, S. arabicus of S. vinaceus and S. phaeoviridis of S. phaeopurpureus. Although not yet confirmed by DNA-DNA pairing studies, rep-PCR data suggested the presence of at least 33 additional junior synonyms.

The search for synonyms among streptomycetes by using SDS-PAGE of whole-cell proteins. Emendation of the species Streptomyces aurantiacus, Streptomyces cacaoi subsp. cacaoi, Streptomyces caeruleus and Streptomyces violaceus.

A collection of 93 Streptomyces reference strains were investigated using SDS-PAGE of whole-cell proteins. Computer-assisted numerical analysis revealed 24 clusters encompassing strains with very similar protein profiles. Five of them grouped several type strains with visually identical patterns. DNA-DNA hybridizations revealed homology values higher than 70% among these type strains. According to the current species concept, it is proposed that Streptomyces albosporeus subsp. albosporeus LMG 19403T is considered as a subjective synonym of Streptomyces aurantiacus LMG 19358T, that Streptomyces aminophilus LMG 19319T is considered as a subjective synonym of Streptomyces cacaoi subsp. cacaoi LMG 19320T, that Streptomyces niveus LMG 19395T and Streptomyces spheroides LMG 19392T are considered as subjective synonyms of Streptomyces caeruleus LMG 19399T, and that Streptomyces violatus LMG 19397T is considered as a subjective synonym of Streptomyces violaceus LMG 19360T.

Streptomyces scopiformis sp. nov., a novel streptomycete with fastigiate spore chains.

A distinct actinomycete strain was isolated from rhizosphere soil of Tsuga chinensis. The isolate, designated A25T, was assigned to the genus Streptomyces on the basis of morphological and chemotaxonomic criteria and was examined by using a polyphasic approach. An almost complete 16S rDNA sequence of the isolate was determined and compared with sequences of representative streptomycetes. The 16S rDNA data not only supported classification of the strain in the genus Streptomyces, but also showed that it formed a separate phyletic line. DNA-DNA hybridization between strain A25T and closely related reference strains confirmed that strain A25T is a novel taxon of Streptomyces. It is proposed, therefore, the strain A25T (= AS 4.1331T = LMG 20251T) is classified in the genus Streptomyces as Streptomyces scopiformis sp. nov.

Streptomyces marokkonensis sp. nov., isolated from rhizosphere soil of Argania spinosa L.

The novel actinomycete strain Ap1(T) was isolated from rhizosphere soil of the argan tree (Argania spinosa L.) in the south of Morocco. Strain Ap1(T) has been reported as a novel producer of the pentaene polyene macrolide isochainin, which strongly inhibits the growth of pathogenic yeasts and phytopathogenic fungi. Strain Ap1(T) shows a greyish-white aerial mycelium with chains of smooth-surfaced spores of the Spiralis type and a cell wall containing ll-diaminopimelic acid. Based on chemotaxonomy and morphological features, strain Ap1(T) was identified as a member of the genus Streptomyces. 16S rRNA gene sequence similarities based on almost-complete 16S rRNA gene sequences showed that strain Ap1(T) is closely associated with members of the Streptomyces violaceoruber species group (S. violaceoruber, S. coelescens, S. violaceorubidus, S. caesius, S. lividans, S. violaceolatus and S. humiferus) and others (Streptomyces aurantiogriseus, S. lienomycini, S. chattanoogensis, S. rubrogriseus and S. tendae). However, protein profiling, DNA-DNA hybridization and BOX-PCR fingerprinting proved a relationship above the species level. In addition, the phenotype also allowed for the differentiation of strain Ap1(T) from its closest neighbours. As a result of this polyphasic approach, we conclude that strain Ap1(T) represents a novel species of the genus Streptomyces, for which the name Streptomyces marokkonensis sp. nov. is proposed. The type strain is Ap1(T) (=R-22003(T) =LMG 23016(T) =DSM 41918(T)).