Nocardia rhizosphaerae sp. nov., a novel actinomycete isolated from the coastal rhizosphere of Artemisia Linn., China

Updated Review on Nocardia Species: 2006-2021

This review serves as an update to the previous Nocardia review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.

Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov

BACKGROUND

Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants.

RESULTS

The taxonomic status of an actinobacterium strain, designated ncl2T, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2T was most closely related to N. vaccinii DSM 43285T. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2T (= DSM 110931T = CECT 30122T) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription.

CONCLUSIONS

Our genome-based taxonomic study showed that isolate ncl2T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.

Community Composition and Metabolic Potential of Endophytic Actinobacteria From Coastal Salt Marsh Plants in Jiangsu, China

The diversity and functional roles of the plant associated endophytic actinobacteria in unique habitats remain poorly understood. In this paper, we examined the phylogenetic diversity and community composition of endophytic actinobacteria associated with native coastal salt marsh plants in Jiangsu, China using a combination of cultivation and 16S rRNA gene-based high-throughput sequencing (HTS) methods. Further, we evaluated the antifungal, fibrinolytic activities and the secondary metabolite biosynthesis potential of isolates via gene screening. A total of 278 actinobacterial isolates were isolated from 19 plant samples. 16S rRNA gene sequencing revealed that the isolates were highly diverse and belonged to 23 genera within the Actinomycetales order, with Streptomyces, Saccharopolyspora, and Pseudonocardia comprising the most abundant genera. In addition, more than 10 of the isolates were novel actinobacterial taxa distributed across eight genera. HTS analyses of seven representative plant root samples revealed that Actinobacteria phylum constituted 0.04–28.66% of root endophytic bacterial communities. A total of four actinobacterial classes, 14 orders, 35 families, and 63 known genera were detected via HTS, and these communities were found to be dominated by the members of the order Actinomycetales including the genera Streptomyces, Mycobacterium, Arthrobacter, Nocardioides, and Micromonospora. In addition, 30.4% of the representative isolates exhibited antifungal activities, 40.5% of them showed fibrinolytic activities, while 43.0% of the strains harbored secondary metabolite biosynthesis genes. These results demonstrated that coastal salt marsh plants in the Jiangsu Province represented an underexplored new reservoir of diverse and novel endophytic actinobacteria that may be of potential interest in the discovery of bioactive compounds with potential as biocontrol agents and for fibrinolytic enzyme production.

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China

Actinobacteria from special habitats are of interest due to their producing of bioactive compounds and diverse ecological functions. However, little is known of the diversity and functional traits of actinobacteria inhabiting coastal salt marsh soils. We assessed actinobacterial diversity from eight coastal salt marsh rhizosphere soils from Jiangsu Province, China, using culture-based and 16S rRNA gene high throughput sequencing (HTS) methods, in addition to evaluating their plant growth-promoting (PGP) traits of isolates. Actinobacterial sequences represented 2.8%-43.0% of rhizosphere bacterial communities, as determined by HTS technique. The actinobacteria community comprised 34 families and 79 genera. In addition, 196 actinobacterial isolates were obtained, of which 92 representative isolates were selected for further 16S rRNA gene sequencing and phylogenetic analysis. The 92 strains comprised seven suborders, 12 families, and 20 genera that included several potential novel species. All representative strains were tested for their ability of producing indole acetic acid (IAA), siderophores, 1-aminocyclopropane-1-carboxylate deaminase (ACCD), hydrolytic enzymes, and phosphate solubilization. Based on the presence of multiple PGP traits, two strains, Streptomyces sp. KLBMP S0051 and Micromonospora sp. KLBMP S0019 were selected for inoculation of wheat seeds grown under salt stress. Both strains promoted seed germination, and KLBMP S0019 significantly enhanced seedling growth under NaCl stress. Our study demonstrates that coastal salt marsh rhizosphere soils harbor a diverse reservoir of actinobacteria that are potential resources for the discovery of novel species and functions. Moreover, several of the isolates identified here are good candidates as PGP bacteria that may contribute to plant adaptions to saline soils.

Nocardia zhihengii sp. nov., an actinobacterium isolated from rhizosphere soil of Psammosilene tunicoides

A Nocardia-like actinobacterial strain, designated YIM TG2190^T, was isolated from rhizosphere soil of Psammosilene tunicoides collected from Gejiu, Yunnan province, China. The cells of strain YIM TG2190^T were observed to be Gram-stain positive and non-motile. The strain forms extensively branched substrate mycelia that fragments into rod-shaped elements. The 16S rRNA gene sequence analysis showed that strain YIM TG2190^T is closely related to Nocardia nova (97.5%), Nocardia jiangxiensis (97.1%) and Nocardia miyunensis (96.8%). Growth occurs at 4-30 °C (optimum 28 °C), pH 6.0-8.0 (optimum pH 7.0) and the strain can tolerate NaCl (w/v) up to 3% (optimum 0-1%). The cell walls were found to contain meso-diaminopimelic acid. The whole-cell sugars were identified as glucose, mannose, ribose, galactose, arabinose and fucose. The polar lipids were identified as diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylglycerol and an unidentified phospholipid. The menaquinones detected were MK-9 (H₂) and MK-8 (H₄). The major fatty acids (> 5%) were found to be C_16:0 (33.9%), summed feature 3 (21.7%), C_18:0 10-methyl TBSA (13.7%) and C_18:1ω9c (7.0%). The DNA G+C content was determined to be 61.1 mol%. DNA-DNA relatedness between the strain YIM TG2190^T and N. nova CGMCC 4.1705^T, N. jiangxiensis CGMCC 4.1905^T and N. miyunensis CGMCC 4.1904^T were 46.9 ± 2.6, 36.8 ± 1.3, and 35.7 ± 2.6%, respectively, values which are less than the threshold value (70%) for the delineation of prokaryotic genomic species. The phenotypic, chemotaxonomic and phylogenetic data indicates that strain YIM TG2190^T represents a novel species of the genus Nocardia, for which the name Nocardia zhihengii sp. nov. is proposed. The type strain is YIM TG2190^T (=KCTC 39596^T = DSM 100515^T).

Nocardiosis from 1888 to 2017

The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.

Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil

An actinomycete strain, designated KLBMP S0039^T, was isolated from the rhizosphere soil of Lycium Linn., collected from the coastal region in Lianyungang, Jiangsu Province, eastern PR China, and was studied to determine its taxonomic position. The isolate showed a combination of morphological and chemotaxonomic properties typical of the members of the genus Nocardia. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were galactose, arabinose, glucose and ribose. The predominant menaquinone was identified as MK-8(H4ω-cycl). The diagnostic phospholipids were found to be diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and unknown lipids. The predominant cellular fatty acids were identified as C16 : 0, C18 : 0, C18 : 1ω9c, and 10-methyl C18 : 0 [tuberculostearic acid (TBSA)]. The G+C content of the genomic DNA was determined to be 68.2 mol%. The 16S rRNA gene sequence similarity indicated that KLBMP S0039^T was most closely related to Nocardia neocaledoniensis NBRC 108232^T (99.4 % 16S rRNA gene sequence similarity) and Nocardia asteroides NBRC 15531^T (99.2 %), similarities to other type strains of species of the genus Nocardia were found to be less than 98.6 %. However, DNA-DNA relatedness values and phenotypic data indicated that KLBMP S0039^T could be clearly distinguished from the closely related species of the genus Nocardia. On the basis of polyphasic taxonomic data, it is concluded that KLBMP S0039^T represents a novel species of the genus Nocardia, for which the name Nocardiarhizosphaerihabitans sp. nov. is proposed. The type strain is KLBMP S0039^T (=KCTC 39693^T=CGMCC 4.7329^T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. Note that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.