Nocardiopsis akebiae sp. nov., a novel endophytic actinomycete isolated from fruits of Akebia trifoliata.

A novel actinobacterium, designated strain HDS12T, was isolated from fruits collected from Changde city located in the northwest of Hunan Province, China and characterized using a polyphasic approach. The 16S rRNA gene sequence analysis indicated that strain HDS12T belonged to the genus Nocardiopsis, and had highest similarities to N. dassonvillei subsp. dassonvillei CGMCC 4.1231T (99.79%), N. deserti H13T (99.73%), N. alborubida NBRC 13392T (99.66%), N. dassonvillei subsp. crassaminis D1T (99.64%), N. synnemataformans DSM 44143T (99.45%), N. lucentensis DSM 44048T (99.04%), N. aegyptia DSM 44442T (98.90%), N. flavescens CGMCC 4.5723T (98.76%), N. alba DSM 43377T (98.69%) and N. halotolerans DSM 44410T (98.63%), respectively. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain HDS12T formed an independent subclade, suggesting that strain HDS12T could belong to a potential novel species. Phylogenomic analysis demonstrated that strain HDS12T was closely related to N. dassonvillei subsp. dassonvillei CGMCC 4.1231T and N. dassonvillei subsp. crassaminis D1T. However, the average nucleotide identity value and the digital DNA-DNA hybridization value between them were well below 95-96% and 70% cut-off point recommended for delineating species. Based on its phenotypic and chemotaxonomic characteristics, strain HDS12T (= MCCC 1K06173T = JCM 34708T) represents the type strain of a novel species, for which the name Nocardiopsis akebiae sp. nov. is proposed.

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

A novel Gram-stain-positive, endophytic actinobacterium, designated strain HDS5T, was isolated from leaves of Eucommia ulmoides Oliv. collected from Changde City, Hunan Province, PR China. Strain HDS5T 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 HDS5T 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-C16:0 and C18 : 1 ω9c. The menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). Strain HDS5T showed high 16S rRNA gene sequence similarity to Nocardiopsis prasina DSM 43845T (99.72 %), Nocardiopsis ganjiahuensis DSM 45031T (99.31 %), Nocardiopsis exhalans JCM 11759T (99.17 %), Nocardiopsis alba DSM 43377T (99.11 %), Nocardiopsis metallicus KBS6T (99.11 %), Nocardiopsis valliformis DSM 45023T (99.04 %), Nocardiopsis listeri NBRC 13360T (98.97 %), Nocardiopsis lucentensis DSM 44048T (98.83 %), Nocardiopsis terrae YIM 90022T (98.83 %) and <98.7 % similarities to other type strains. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences showed that strain HDS5T was closely related to N. prasina DSM 43845T. 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 HDS5T represents a novel Nocardiopsis species. Furthermore, the morphological and physio-biochemical characteristics were sufficient to distinguish strain HDS5T from N. prasina DSM 43845T. Consequently, based on phenotypic and genotypic characteristics, strain HDS5T represents a new Nocardiopsis species, for which the name Nocardiopsis eucommiae sp. nov. is proposed. The type strain is HDS5T (=MCCC 1K06172T=JCM 34707T).

Streptomyces akebiae sp. nov., a novel actinomycete isolated from rhizosphere soil of Akebia trifoliate.

A novel actinomycete strain, designated as MG28T, was isolated from rhizosphere soil of Akebia trifoliate. The taxonomic position of the strain was investigated by using a polyphasic approach. BLAST search of the full-length 16S rRNA gene sequence of strain MG28T indicated it represented a member of the genus Streptomyces, and displayed 99.03%, 98.90%, 98.90%, 98.89%, 98.83% and less than 98.70% sequence similarities with S. phaeolivaceus GY16T, S. deccanensis KCTC 19241T, S. europaeiscabiei KACC 20186T, S. fructofermentans CGMCC 4.1593T, S. scabiei NRRL B-16523T and other species of the genus Streptomyces with validly published names, respectively. Phylogenomic analysis indicated that strain MG28T was closely related to Streptomyces deccanensis KCTC 19241T. However, the average nucleotide identity values and the digital DNA-DNA hybridization values between them indicated that strain MG28T represented a distinct species. Furthermore, strain MG28T was also distinctly differentiated from strain KCTC 19241T by morphological, physiological and biochemical characteristics. Therefore, strain MG28T (= MCCC 1K06895T = JCM 34922T) represents a novel species of the genus Streptomyces, for which the name Streptomyces akebiae sp. nov. is proposed.

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).

Recruitment-promoting of dormant Microcystis aeruginosa by three benthic bacterial species.

The frequent occurrence of Microcystis aeruginosa blooms benefit from the dormant Microcystis cells, which will be recruited from sediment into overlying water to form a dominant population and algal blooms when external environmental conditions are suitable. Previous studies have unveiled factors involved in M. aeruginosa recruitment and bloom initiation, including nutrition, illumination, temperature, and hydrodynamic force. In this study, three dominant benthic bacterial species isolated from Lake Chongtian with frequent blooms-forming were identified through next generation sequencing (NGS) techniques, and laboratory experiments were conducted on the recruitment of dormant M. aeruginosa cells via co-culture with these bacteria at 10 °C, 15 °C, 20 °C and 25 °C. The results showed that the bacterial strains in sediment proliferated quickly before recruitment of dormant M. aeruginosa cells, subsequently significantly promoted the recruitment of dormant M. aeruginosa via allelochemical (metabolite) production, lower N:P values and lower dissolved oxygen concentrations in the sediment-water interface, and enhanced photosynthesis of M. aeruginosa cells. Furthermore, dormant M. aeruginosa was recruited from sediment at 10 °C when bacterial activity was present, but not recruited when bacterial activity was absent. At 15 °C,20 °Cand 25 °C, there were no remarkable differences in the recruitment rate of dormant M. aeruginosa cells among all bacterial groups, although their recruitment rate were significantly higher than that at 10 °C.These findings suggested that, under laboratory conditions, three benthic bacteria not only had a great influence on promoting the recruitment of dormant M. aeruginosa cells under desirable temperatures, but also can spur recruitment of dormant M. aeruginosacells from sediment at lower temperature (10 °C).