Nocardiopsis mwathae sp. nov., isolated from the haloalkaline Lake Elmenteita in the African Rift Valley

Comprehensive updates on the biological features and metabolic potential of the versatile extremophilic actinomycete Nocardiopsis dassonvillei

Nocardiopsis dassonvillei prevails under harsh environmental conditions and the purpose of this review is to highlight its biological features and recent biotechnological applications. The organism prevails in salt-rich soils/marine systems and some strains endure extreme temperatures and pH. A few isolates are associated with marine organisms and others cause human diseases. Comparative genomic analysis indicates its versatility in producing biotechnologically relevant metabolites. Antimicrobial, cytotoxic, anticancer and growth promoting biomolecules are obtained from this organism. It also synthesizes biotechnologically important enzymes. Bioactive compounds and enzymes obtained from this actinomycete provide evidence regarding its metabolic competence and its potential economic value.

Nocardiopsis changdeensis sp. nov., an endophytic actinomycete isolated from the roots of Eucommia ulmoides Oliv

Strain Mg02T was isolated from roots of Eucommia ulmoides Oliv. collected from Changde City, Hunan Province, China. Strain Mg02T, which exhibited distinct chemotaxonomic characteristics of the genus Nocardiopsis: cell-wall chemotype III/C, i.e., meso-diaminopimelic acid as diagnostic amino acid in whole-cell hydrolysates and menaquinone MK-10 with variable degrees of saturation in the side chain as the predominant isoprenoid quinone, was investigated by a polyphasic approach to determine their taxonomic position. Sequence analysis of the 16S rRNA gene indicated that strain Mg02T is affiliated to the genus Nocardiopsis, having highest sequence similarity to Nocardiopsis flavescens CGMCC 4.5723T (99.1%) and <98.7% to other species of the genus Nocardiopsis with validly published names. Phylogenetic analysis of 16S rRNA gene indicated strain Mg02T formed a separate evolutionary clade, suggesting that it could be a novel Nocardiopsis species. Phylogenomic analysis showed that strain Mg02T was closely related to N. flavescens CGMCC 4.5723T and distinct from the latter according to the clustering patterns. The Average Nucleotide Identity and digital DNA-DNA hybridization values between strain Mg02T and N. flavescens CGMCC 4.5723T were far below the species-level thresholds. Based on phenotypic, phylogenetic and chemotaxonomic characteristics, we think that strain Mg02T should represent a novel Nocardiopsis species, for which the name Nocardiopsis changdeensis sp. nov. is proposed. The type strain is Mg02T (=MCCC 1K06174T = JCM 34709T).

Nocardiopsis eucommiae sp. nov., a novel endophytic actinomycete isolated from leaves of Eucommia ulmoides Oliv

A novel Gram-stain-positive, endophytic actinobacterium, designated strain HDS5^T, was isolated from leaves of Eucommia ulmoides Oliv. collected from Changde City, Hunan Province, PR China. Strain HDS5^T produced yellowish oil green substrate mycelia on Gause's synthetic medium, which also carried yellowish oil green aerial hyphae, fragmenting into rod-shaped elements with smooth surfaces. Strain HDS5^T grew at pH 5.0-11.0 (optimum, pH 7), at 20-40 °C (optimum, 28 °C) and in the presence of 0-8.0% NaCl (w/v; optimum, 0-1.0 %). Whole-cell hydrolysates contained meso-diaminopimelic acid as the diagnostic amino acid and no diagnostic sugars. The predominant fatty acids were iso-C_16:0 and C_18 : 1 ω9c. The menaquinones were MK-10(H₂), MK-10(H₄) and MK-10(H₆). Strain HDS5^T showed high 16S rRNA gene sequence similarity to Nocardiopsis prasina DSM 43845^T (99.72 %), Nocardiopsis ganjiahuensis DSM 45031^T (99.31 %), Nocardiopsis exhalans JCM 11759^T (99.17 %), Nocardiopsis alba DSM 43377^T (99.11 %), Nocardiopsis metallicus KBS6^T (99.11 %), Nocardiopsis valliformis DSM 45023^T (99.04 %), Nocardiopsis listeri NBRC 13360^T (98.97 %), Nocardiopsis lucentensis DSM 44048^T (98.83 %), Nocardiopsis terrae YIM 90022^T (98.83 %) and <98.7 % similarities to other type strains. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences showed that strain HDS5^T was closely related to N. prasina DSM 43845^T. However, the average nucleotide identity based on blast and digital DNA-DNA hybridization values between them were determined to be 90.1 and 40.9 %, respectively, below the threshold of 95-96 and 70 % for the delineation of prokaryotic genomic species, suggesting that strain HDS5^T represents a novel Nocardiopsis species. Furthermore, the morphological and physio-biochemical characteristics were sufficient to distinguish strain HDS5^T from N. prasina DSM 43845^T. Consequently, based on phenotypic and genotypic characteristics, strain HDS5^T represents a new Nocardiopsis species, for which the name Nocardiopsis eucommiae sp. nov. is proposed. The type strain is HDS5^T (=MCCC 1K06172^T=JCM 34707^T).

The Potential of Phylogenetically Diverse Culturable Actinobacteria from Litopenaeus vannamei Pond Sediment as Extracellular Proteolytic and Lipolytic Enzyme Producers

Enzymes are catalysts that can increase the reaction time of a biochemical process. Hydrolytic enzymes have a pivotal role in degrading organic waste in both terrestrial and aquatic environments. The aims of this study were (1) to investigate the ability of actinobacteria isolated from Litopenaeus vannamei pond sediment to produce proteolytic and lipolytic enzymes, (2) to identify promising candidates using 16S rRNA gene amplification, and (3) to construct a phylogenetic tree based on the 16S rRNA genes. A skim milk agar medium was used in the preliminary experiment of the proteolytic assay, and a Tween 20/80 medium was used in the lipolytic assay. Fifteen and 20 (out of 40) actinobacterial isolates showed great potential for proteolytic and lipolytic activities, respectively. Furthermore, four actinobacteria isolates produced both enzyme types with proteolytic and lipolytic index scores of 1-6.5. The most promising candidates were SA 2.2 (IM8), SC 2.1 (IM6), SD 1.5 (IM6) and SE 1.1 (IM8). BLAST homology results showed a high similarity between the actinobacteria isolates and Streptomyces verucosisporus, S. mangrovicola, S. barkulensis and Nocardiopsis lucentensis, respectively. Therefore, actinobacteria from Litopenaeus vannamei pond sediment are high-potential proteolytic and lipolytic enzyme producers.

Marinactinospora rubrisoli sp. nov., isolated from red soil

A novel Marinactinospora strain JX35-4^T was isolated from red soil which was collected from Wushan, northern Jiangxi Province, China. Analysis of the 16S rRNA gene sequences showed that strain JX35-4^T belongs to the genus Marinactinospora and formed a distinct phylogenetic clade with Marinactinospora thermotolerans SCSIO 00652^T and Marinactinospora endophytica YIM 690053^T with sequence similarity of 96.97% and 96.42%, respectively. The strain was Gram-positive and formed branched substrate hyphae with no fragmentation, and abundant aerial hyphae that differentiated into long spore chains, and short rod-shaped spores. Growth occurred at 20-45 °C, pH 7.0-12.0 and in the presence of 0-7.5% (w/v) NaCl. The genomic DNA G + C content was determined to be 68.3 mol%. The cell wall of strain JX35-4^T contained meso-diaminopimelic acid and xylose. Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol mannosides and one unidentified phospholipid. The major fatty acids of strain JX35-4^T consisted of anteiso-C_17:0 and iso-C_16:0. Major menaquinones were MK-9(H₁₀), MK-12 and MK-10(H₂). Based on the polyphasic data, strain JX35-4^T (= CGMCC 4.7382^T = DSM 104977^T) is concluded to represent a novel species of the genus Marinactinospora, for which the name Marinactinospora rubrisoli sp. nov. is proposed.

Nocardiopsis rhizosphaerae sp. nov., isolated from rhizosphere soil of Halocnermum strobilaceum (Pall.) Bieb

An alkalitolerant actinomycete strain, designated EGI 80674T, was isolated from a rhizosphere soil of Halocnermumstrobilaceum (Pall.) Bieb in Xinjiang, north-west China and subjected to a taxonomic characterization using a polyphasic approach. Strain EGI 80674T formed white aerial hyphae with long spore chains. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the diagnostic diamino acid with no diagnostic sugars. The major fatty acids identified were iso-C16 : 0, anteiso-C17 : 0 and 10-methyl-C18 : 0TBSA. The predominant menaquinones detected were MK-10(H8) and MK-10(H6). The G+C content of the genomic DNA of strain EGI 80674T was 70.9 mol%. Strain EGI 80674T showed the highest 16S rRNA gene sequence similarity (97.24 %) to Nocardiopsis nikkonensis NBRC 102170T. The DNA-DNA relatedness value of strain EGI 80674T and N. nikkonensis NBRC 102170T was 18.4±1.3 %. Phenotypical, chemotaxonomic and phylogenetic characteristics and DNA-DNA hybridization data suggest that strain EGI 80674T represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis rhizosphaerae sp. nov. is proposed. The type strain is EGI 80674T (=CGMCC 4.7228T=KCTC 39673T).