Luis A. Maldonado

Statistical Approaches for Estimating Actinobacterial Diversity in Marine Sediments

ABSTRACT Bacterial diversity in a deep-sea sediment was investigated by constructing actinobacterium-specific 16S ribosomal DNA (rDNA) clone libraries from sediment sections taken 5 to 12, 15 to 18, and 43 to 46 cm below the sea floor at a depth of 3,814 m. Clones were placed into operational taxonomic unit (OTU) groups with ≥99% 16S rDNA sequence similarity; the cutoff value for an OTU was derived by comparing 16S rRNA homology with DNA-DNA reassociation values for members of the class Actinobacteria. Diversity statistics were used to determine how the level of dominance, species richness, and genetic diversity varied with sediment depth. The reciprocal of Simpsons index (1/D) indicated that the pattern of diversity shifted toward dominance from uniformity with increasing sediment depth. Nonparametric estimation of the species richness in the 5- to 12-, 15- to 18-, and 43- to 46-cm sediment sections revealed a trend of decreasing species number with depth, 1,406, 308, and 212 OTUs, respectively. Application of the LIBSHUFF program indicated that the 5- to 12-cm clone library was composed of OTUs significantly (P = 0.001) different from those of the 15- to 18- and 43- to 46-cm libraries. FST and phylogenetic grouping of taxa (P tests) were both significant (P < 0.00001 and P < 0.001, respectively), indicating that genetic diversity decreased with sediment depth and that each sediment community harbored unique phylogenetic lineages. It was also shown that even nonconservative OTU definitions result in severe underestimation of species richness; unique phylogenetic clades detected in one OTU group suggest that OTUs do not correspond to real ecological groups sensu Palys (T. Palys, L. K. Nakamura, and F. M. Cohan, Int. J. Syst. Bacteriol. 47:1145-1156, 1997). Mechanisms responsible for diversity and their implications are discussed.

Diversity of cultivable actinobacteria in geographically widespread marine sediments

Reports describing actinobacteria isolated from marine environments have been dominated by Micromonospora, Rhodococcus and Streptomyces species. Recent culture-independent studies have shown that marine environments contain a high diversity of actinobacterial species that are rarely, if at all, recovered by cultivation-based methods. In this study, it is shown that cultivation-independent methods can be used to guide the application of selective isolation methods. The detection of marine-derived actinobacterial species that have previously only been reported from terrestrial habitats is highlighted. This study provides good evidence that the previously described low diversity of actinobacterial species isolated from marine environments does not reflect an actual low species diversity, and that the use of informed selective isolation procedures can aid in the isolation of members of novel taxa.

Proximicin A,B and C, Novel Aminofuran Antibiotic and Anticancer Compounds Isolated from Marine Strains of the Actinomycete Verrucosispora

A family of three novel aminofuran antibiotics named as proximicins was isolated from the marine Verrucosispora strain MG-37. Proximicin A was detected in parallel in the marine abyssomicin producer “Verrucosispora maris” AB-18-032. The characteristic structural element of proximicins is 4-amino-furan-2-carboxylic acid, a hitherto unknown γ-amino acid. Proximicins show a weak antibacterial activity but a strong cytostatic effect to various human tumor cell lines.

Actinobacterial diversity from marine sediments collected in Mexico

Seventeen different media known to support the growth and isolation of members of the class Actinobacteria were evaluated as selective isolation media for the recovery of this microbial group from marine sediments samples collected in the Gulf of California and the Gulf of Mexico. A general selective isolation procedure was employed for six sediments and nearly 300 actinomycetes were recovered from the selective isolation plates. Full 16S rRNA gene sequencing revealed that the isolates belonged to several actinobacterial taxa, notably to the genera Actinomadura, Dietzia, Gordonia, Micromonospora, Nonomuraea, Rhodococcus, Saccharomonospora, Saccharopolyspora, Salinispora, Streptomyces, “Solwaraspora” and Verrucosispora. Previous works on marine sediments have been restricted to the isolation of members of the genera Micromonospora, Rhodococcus and Streptomyces. This study provides further evidence that Actinobacteria present in marine habitats are not restricted to the Micromonospora-Rhodococcus-Streptomyces grouping. Indeed, this first systematic study shows the extent of actinobacterial diversity that can be found in marine sediments collected in Mexico and probably, worldwide.

Nocardia africana sp. nov., a New Pathogen Isolated from Patients with Pulmonary Infections

ABSTRACT Eight actinomycete strains, isolated from 8 out of 400 sputum samples examined, taken from patients with pulmonary diseases at the Chest Unit of Khartoum Teaching Hospital in the Sudan, were provisionally assigned to the genus Nocardia according to morphological criteria. These isolates were studied further in order to establish their taxonomic status. They were found to have morphological and chemical properties typical of nocardiae and formed a monophyletic clade in the 16S ribosomal DNA tree together withNocardia vaccinii. The strains showed a unique pattern of phenotypic properties that distinguished them from representatives of recognized Nocardia species, includingNocardia vaccinii. The strains were considered to merit species status and were designated Nocardia africana sp. nov. The findings of the present study are consistent with the view that pulmonary nocardiosis may occur in a substantial proportion of patients who exhibit chronic lung diseases in African countries. It is important, therefore, that clinicians in such countries consider this condition, especially when patients with respiratory infections fail to respond to antitubercular therapy.

The Nocardia salmonicida clade, including descriptions of Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov.

Large numbers of strains selectively isolated from soil, water and deteriorating vulcanised natural rubber pipe rings were provisionally assigned to the genus Nocardia. Twenty-eight representative isolates were found to have chemical and morphological properties typical of nocardiae. These organisms formed a monophyletic clade in the 16S rDNA tree together with Nocardia salmonicida. Three of the strains, isolates S1, W30 and R89, were distinguished from one another and from representatives of the validly described species of Nocardia using genotypic and phenotypic data. These organisms were considered to merit species status and were named Nocardia cummidelens sp. nov., Nocardia fluminea sp. nov. and Nocardia soli sp. nov. respectively. Additional comparative studies are needed to resolve the finer taxonomic relationships of the remaining isolates assigned to the Nocardia salmonicida clade and to further unravel the extent of nocardial diversity in artificial and natural ecosystems.

Nocardia beijingensis sp. nov., a novel isolate from soil.

The taxonomic status of a soil isolate, provisionally assigned to the genus Nocardia, was established following a polyphasic study. An almost complete sequence of the 16S rDNA of the strain was determined and aligned with available sequences for nocardiae and phylogenetic trees were inferred using four tree-making algorithms. The organism was associated consistently with the type strains of Nocardia brasiliensis and Nocardia farcinica in the neighbour-joining analysis, albeit with low bootstrap values. It was also found to have chemotaxonomic and morphological properties consistent with its assignment to the genus Nocardia. The organism was readily separated from representatives of other Nocardia species by a broad range of phenotypic properties. The name proposed for the novel species is Nocardia beijingensis sp. nov. The type strain is AS4.1521T (= IFO 16342T = JCM 10666T).

Rhodococcus aetherivorans sp. nov., a new species that contains methyl t-butyl ether-degrading actinomycetes.

The taxonomic positions of two actinomycetes, strains Bc663 and 10bc312T, provisionally assigned to the genus Rhodococcus were determined using a combination of genotypic and phenotypic properties. The organisms have phenotypic properties typical of members of the genus Rhodococcus and were assigned to the 16S rRNA subgroup which contains Rhodococcus rhodochrous and closely related species. The two strains, which have many phenotypic features in common, belong to the same genomic species albeit one readily separated from Rhodococcus ruber with which they form a distinct phyletic line. The organisms were also distinguished from all of the species classified in the R. rhodochrous subgroup, including R. ruber, using a combination of phenotypic properties. The genotypic and phenotypic data show that strains Bc663 and 10bc312T merit recognition as a new species of Rhodococcus. The name proposed for the new species is Rhodococcus aetherivorans (10bc312T = DSM 44752T = NCIMB 13964T).

Nonomuraea terrinata sp. nov., a novel soil actinomycete.

The taxonomic position of a soil isolate, strain E626, was evaluated using the polyphasic approach. The organism was found to have chemical and morphological features consistent with its assignment to the genus Nonomuraea, a member of the family Streptosporangiaceae. Strain E626 consistently formed a distinct phyletic line within the Streptosporangiaceae 16S rDNA tree using four different algorithms. Furthermore, the taxonomic distinctness of the organism is underpinned by a range of phenotypic properties, notably morphological features. It is, therefore, proposed that the organism be classified in the genus Nonomuraea as Nonomuraea terrinata sp. nov.

Synthesis of Terpenoids. II. A New Total Synthesis of β-Cuparenone

Abstract The vicinal dicuaternary arrangement, typical of cuparenetype sesquiterpenoids2, has been constructed in a variety of ways3. In this paper we describe an alternate solution to this problem exemplified in a new total synthesis of β-cuparenone 1, which involves an application of the recently introduced Stork “protected” cyanohydrin reagents4,5.