Pseudomonas flavocrustae sp. nov., an endophyte with plant growth promoting traits isolated from Passiflora incarnata.

A polyphasic approach was applied to characterize taxonomically a novel endophytic bacterial strain, designated as EP178T, which was previously isolated from Passiflora incarnata leaves and characterized as plant-growth promoter. The strain EP178T forms Gram stain-negative and rod-shaped cells, and circular and yellow-pigmented colonies. Its growth occurs at 10-37 °C, at pH 6.0-8.0, and tolerates up to 7% (w/v) NaCl. The major cellular fatty acids found were summed feature 8 (C18:1 ω7c), summed feature 3 (C16:1 ω6c /C16:1 ω7c), and C16:0, and the predominant ubiquinone was Q-9. The phylogenetic and nucleotide-similarity analysis with 16S rRNA gene sequences showed that strain EP178T belongs to Pseudomonas genus. The genomic-based G + C content was 65.5%. The average nucleotide identity and digital DNA-DNA hybridization values between strains EP178T and the closest type strain, P. oryzihabitans DSM 6835T, were 92.6% and 52.2%, respectively. Various genes associated with plant-growth promoting mechanisms were annotated from genome sequences. Based on the phenotypic, genomic, phylogeny and chemotaxonomic data, strain EP178T represents a new species of the genus Pseudomonas, for which the name Pseudomonas flavocrustae sp. nov. was proposed. The type strain is EP178T (= CBMAI 2609T = ICMP 24844T = MUM 23.01T).

Williamsia aurantiacus sp. nov. a novel actinobacterium producer of antimicrobial compounds isolated from the marine sponge.

An antibiotic-producing actinobacterium, designated isolate B375T, was isolated from marine sponge Glodia corticostylifera collected from Praia Guaecá, São Paulo, Brazil (23°49S; 45°25W), and its taxonomic position established using data from a polyphasic study. The organism showed a combination of morphological, physiological, biochemical and chemotaxonomic characteristics consistent with its classification in the genus Williamsia. Comparative 16S rRNA gene sequence analysis indicated that the strain B375T was most closely related to Williamsia serinedens DSM 45037T and Williamsia spongiae DSM 46676T and having 99.43% and 98.65% similarities, respectively, but was distinguished from these strains by a low level of DNA-DNA relatedness (53.2-63.2%) and discriminatory phenotypic properties. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV and N-glycolated muramic acid residues present in the wall cells. The cells contained C16:0 (23.3%), C18:0 10-methyl (23.2%) and C18:1 ω9c (21.6%) as the major cellular fatty acids. The strain B375T inhibited growing of Staphylococcus aureus and Colletotrichum gloeosporioides strains and was considered a producer of antimicrobial compounds. Based on the data obtained, the isolate B375T (= CBMAI 1090T = DSM 46677T) should, therefore, be classified as the type strain of a novel species of the genus Williamsia, for which the name Williamsia aurantiacus sp. nov. is proposed.

Functional metagenomics of oil-impacted mangrove sediments reveals high abundance of hydrolases of biotechnological interest.

Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms. For this, an in-depth survey of the taxonomic and functional microbial diversity recovered in a fosmid library (Library_Oil Mgv) constructed from oil-impacted Brazilian mangrove sediment was carried out. Fosmid DNA of the whole library was extracted and submitted to Illumina HiSeq sequencing. The resulting Library Oil_Mgv dataset was further compared with those obtained by direct sequencing of environmental DNA from Brazilian mangroves (from distinct regions and affected by distinct sources of contamination), focusing on hydrolases with potential use in biotechnological processes. The most abundant hydrolases found were proteases, esterases and amylases, with similar occurrence profile in all datasets. The main microbial groups harboring such hydrolase-encoding genes were distinct in each mangrove, and in the fosmid library these enzymes were mainly assigned to Chloroflexaceae (for amylases), Planctomycetaceae (for esterases) and Bradyrhizobiaceae (for proteases). Assembly and analysis of Library_Oil Mgv reads revealed three potentially novel enzymes, one epoxide hydrolase, one xylanase and one amylase, to be further investigated via heterologous expression assays.

Gordonia didemni sp. nov. an actinomycete isolated from the marine ascidium Didemnum sp.

A novel actinobacterium, designated isolate B204(T), was isolated from a marine ascidian Didemnum sp., collected from São Paulo, Brazil, and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Gordonia and formed a distinct phyletic line in the Gordonia 16S rRNA gene tree. It was closely related to Gordonia terrae DSM 43249(T) (99.9 % 16S rRNA gene sequence similarity) and Gordonia lacunae DSM 45085(T) (99.3 % 16S rRNA gene sequence similarity) but was distinguished from these strains by a moderate level of DNA-DNA relatedness (63.0 and 54.7 %) and discriminatory phenotypic properties. Based on the data obtained, the isolate B204(T) (=CBMAI 1069(T) = DSM 46679(T)) should therefore be classified as the type strain of a novel species of the genus Gordonia, for which the name Gordonia didemni sp. nov. is proposed.

Marmoricola aquaticus sp. nov., an actinomycete isolated from a marine sponge.

A novel marine actinomycete, designated B374(T), was isolated from a marine sponge, Glodia corticostylifera, which was collected from São Paulo, Brasil. The taxonomic position of B374(T) was established by using data derived from a polyphasic approach. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Marmoricola and it formed a distinct phyletic line in the clade of the genus Marmoricola, based on 16S rRNA gene sequences. Strain B374(T) was most closely related to Marmoricola aequoreus SST-45(T) (98.5% 16S rRNA gene sequence similarity), but was distinguished from this strain and from the other type strains of species of the genus Marmoricola on the basis of a combination of phenotypic properties. The data obtained, therefore, indicates that isolate B374(T) ( = CBMAI 1089(T) = DSM 28169(T)) should be classified as a novel species of the genus Marmoricola, for which the name Marmoricola aquaticus sp. nov. is proposed.

Chromobacterium amazonense sp. nov. isolated from water samples from the Rio Negro, Amazon, Brazil.

The taxonomic position of a bacterium isolated from water samples from the Rio Negro, in Amazon, Brazil, was determined by using a polyphasic approach. The organism formed a distinct phyletic line in the Chromobacterium 16S rRNA gene tree and had chemotaxonomic and morphological properties consistent with its classification in this genus. It was found to be closely related to Chromobacterium vaccinii DSM 25150(T) (98.6 % 16S rRNA gene similarity) and shared 98.5 % 16S rRNA gene similarity with Chromobacterium piscinae LGM 3947(T). DNA-DNA relatedness studies showed that isolate CBMAI 310(T) belongs to distinct genomic species. The isolate was readily distinguished from the type strain of these species using a combination of phenotypic and chemotaxonomic properties. Thus, based on genotypic and phenotypic data, it is proposed that isolate CBMAI 310(T) (=DSM 26508(T)) be classified in the genus Chromobacterium as the type strain of a novel species, namely, Chromobacterium amazonense sp. nov.

Streptomyces araujoniae sp. nov.: an actinomycete isolated from a potato tubercle.

The taxonomic position of a streptomycete isolated from a potato tubercle was determined by using a polyphasic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Streptomyces and formed a distinct phyletic line in the Streptomyces 16S rRNA gene tree. It was found to be closely related to Streptomyces celluloflavus NRRL B-2493(T) (99.4 % 16S rRNA gene similarity) and shared a 99.0 % 16S rRNA gene similarity value with Streptomyces albolongus NRRL B-3604(T) and Streptomyces cavourensis subsp. cavourensis NBRC 13026(T); low levels of DNA-DNA relatedness with these organisms showed that the isolate belonged to a distinct genomic species. The isolate was distinguished readily from the type strains of these species using a combination of morphological and other phenotypic properties. On the basis of these results, it is proposed that isolate ASBV-1(T) (= CBMAI 1465(T) = CCMA 894(T) = NRRL B-24922(T)) be classified as the type strain of Streptomyces araujoniae sp. nov.