Williamsia limnetica sp. nov., isolated from a limnetic lake sediment

Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-Antarctic Rhodococcus and Williamsia Species

Bacteria containing mycolic acids in their cell envelope are often recalcitrant to cell lysis, so extracting DNA of sufficient quality for third-generation sequencing and high-fidelity genome assembly requires optimization, even when using commercial kits with protocols for hard-to-lyse bacteria. We benchmarked three spin-column-based kits against a classical DNA extraction method employing lysozyme, proteinase K and SDS for six lysozyme-resistant, sub-Antarctic strains of Corynebaceriales. Prior cultivation in broths containing glycine at highly growth-inhibitory concentrations (4.0–4.5%) improved cell lysis using both classical and kit methods. The classical method produced DNA with average fragment sizes of 27–59 Kbp and tight fragment size ranges, meeting quality standards for genome sequencing, assembly and phylogenomic analyses. By 16S rRNA gene sequencing, we classified two strains as Williamsia and four strains as Rhodococcus species. Pairwise comparison of average nucleotide identity (ANI) and alignment fraction (AF), plus genome clustering analysis, confirmed Rhodococcus sp. 1163 and 1168 and Williamsia sp. 1135 and 1138 as novel species. Phylogenetic, lipidomic and biochemical analyses classified psychrotrophic strains 1139 and 1159 as R. qingshengii and R. erythropolis, respectively, using ANI similarity of >98% and AF >60% for species delineation. On this basis, some members of the R. erythropolis genome cluster groups, including strains currently named as R. enclensis, R. baikonurensis, R. opacus and R. rhodochrous, would be reclassified either as R. erythropolis or R. qingshengii.

Role of Williamsia and Segniliparus in human infections with the approach taxonomy, cultivation, and identification methods

The genera Williamsia and Segniliparus are of aerobic actinomycetes and at the time of writing, they have 12 and 2 species, respectively. These genera cause various infections in humans. In this review, we surveyed their taxonomy, isolation, identification, as well as their role to cause human infections.

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

An antibiotic-producing actinobacterium, designated isolate B375^T, 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 B375^T was most closely related to Williamsia serinedens DSM 45037^T and Williamsia spongiae DSM 46676^T 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 C_16:0 (23.3%), C_18:0 10-methyl (23.2%) and C_18:1 ω9c (21.6%) as the major cellular fatty acids. The strain B375^T inhibited growing of Staphylococcus aureus and Colletotrichum gloeosporioides strains and was considered a producer of antimicrobial compounds. Based on the data obtained, the isolate B375^T (= CBMAI 1090^T = DSM 46677^T) 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.

Williamsia spongiae sp. nov., an actinomycete isolated from the marine sponge Amphimedon viridis

A novel actinobacterium, designated isolate B138T, was isolated from the marine sponge, Amphimedon viridis, which was collected from Praia Guaecá (São Paulo, Brazil), and its taxonomic position was established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological characteristics consistent with its classification in the genus Williamsia and it formed a distinct phyletic line in the Williamsia 16S rRNA gene tree. It was most closely related to Williamsia serinedens DSM 45037T and Williamsia deligens DSM 44902T (99.0 % 16S rRNA gene sequence similarity) and Williamsia maris DSM 44693T (97.5 % 16S rRNA gene sequence similarity), but was distinguished readily from these strains by the low DNA-DNA relatedness values (62.3-64.4 %) and by the discriminatory phenotypic properties. Based on the data obtained, the isolate B138T (=CBMAI 1094T=DSM 46676T) should be classified as the type strain of a novel species of the genus Williamsia, for which the name Williamsia spongiae sp. nov. is proposed.

Williamsia herbipolensis sp. nov., isolated from the phyllosphere of Arabidopsis thaliana

A Gram-stain-positive, non-endospore-forming actinobacterium (ARP1T) was isolated from the phyllosphere of Arabidopsis thaliana. On the basis of 16S rRNA gene sequence phylogeny strain ARP1T was placed into the genus Williamsia and the closest related species were Williamsia phyllosphaerae (98.5 % 16S rRNA gene sequence similarity), Williamsia deligens (98.5 %), Williamsia maris (98.3 %) and Williamsia serinedens (98.2 %). Genome-based comparison indicated a clear distinction to the type strains of those species with pairwise average nucleotide identities (ANI) between 76.4-78.4 %. The quinone system of strain ARP1T consisted predominantly of menaquinones MK-9(H2), MK-7(H2) and MK-8(H2), and the polar lipid profile contained the major compound diphosphatidylglycerol, and moderate amounts of phosphatidylethanolamine, phosphatidylglycerol and numerous unidentified lipids. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1ω7c, C16 : 0, C18 : 0, C18 : 1ω9c and tuberculostearic acid supported the affiliation of strain ARP1T to the genus Williamsia. Genotypic, physiological and biochemical testing revealed clear differences of strain ARP1T to the most closely related species of the genus Williamsia. Therefore strain ARP1T represents a novel species of this genus, for which the name Williamsia herbipolensis sp. nov. is proposed. The type strain is ARP1T (=DSM 46872T=LMG 28679T).

Draft genome of the Arabidopsis thaliana phyllosphere bacterium, Williamsia sp. ARP1

The Gram-positive actinomycete Williamsia sp. ARP1 was originally isolated from the Arabidopsis thaliana phyllosphere. Here we describe the general physiological features of this microorganism together with the draft genome sequence and annotation. The 4,745,080 bp long genome contains 4434 protein-coding genes and 70 RNA genes. To our knowledge, this is only the second reported genome from the genus Williamsia and the first sequenced strain from the phyllosphere. The presented genomic information is interpreted in the context of an adaptation to the phyllosphere habitat.

Draft Genome Sequence of Williamsia sp. Strain D3, Isolated From the Darwin Mountains, Antarctica

Actinobacteria are the dominant taxa in Antarctic desert soils. Here, we describe the first draft genome of a member of the genus Williamsia (strain D3) isolated from Antarctic soil. The genome of this psychrotolerant bacterium may help to elucidate crucial survival mechanisms for organisms inhabiting cold desert soil systems.

Williamsia sterculiae sp. nov., isolated from a Chinese medicinal plant

Two actinobacterial strains, CPCC 203464(T) and CPCC 203448, isolated from surface-sterilized stems of medicinal plants were subjected to a polyphasic taxonomic study. These two aerobic organisms formed pale yellow colonies on tryptic soy agar (TSA). Cells were Gram-stain-positive, non-acid-fast, non-motile, rod- or coccoid-like elements. Comparative 16S rRNA gene sequence analysis indicated that strains CPCC 203464(T) and CPCC 203448 were most closely related to the type strains of the species of the genus Williamsia. Chemotaxonomic properties such as containing meso-diaminopimelic acid in the cell wall, arabinose, galactose and ribose being the whole-cell hydrolysate sugars, phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the phospholipids, and C16 : 0, 10-methyl C18 : 0, C18 : 1ω9c, C16 : 1ω7c and/or iso-C15 : 0 2-OH as major fatty acids supported the affiliation of strains CPCC 203464(T) and CPCC 203448 to the genus Williamsia. The DNA-DNA hybridization values in combination with differentiating chemotaxonomic and physiological characteristics strongly suggested that these two isolates should be classified as representatives of a novel species of the genus Williamsia. The name Williamsia sterculiae sp. nov. is proposed, with strain CPCC 203464(T) ( = DSM 45741(T) = KCTC 29118(T)) as the type strain.