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Pseudonocardia acaciae sp. nov., isolated from roots of Acacia auriculiformis A. Cunn. ex Benth
Abstract and Figures
A novel Gram-positive-staining actinomycete designated strain GMKU095(T) was isolated from surface-sterilized roots of Acacia auriculiformis A. Cunn. ex Benth. (earpod wattle). The organism produced branching mycelium. The spores were non-motile and had a spiny surface. Growth of strain GMKU095(T) occurred at 18-42 degrees C, pH 5.0-8.0 and at NaCl concentrations up to 5 %. Whole-cell hydrolysates contained arabinose and galactose as major characteristic sugars. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The glycan moiety of the murein contained acetyl residues. The menaquinone was MK-8(H(4)); mycolic acids were not detected. The G+C content of the DNA was 71.6 mol%. iso-C(16 : 0) was detected as the major cellular fatty acid. Comparative studies of 16S rRNA gene sequences indicated that the strain was phylogenetically related to members of the genus Pseudonocardia. The most closely related type strain is Pseudonocardia spinosispora IMSNU 50581(T), which is 96.2 % similar in 16S rRNA gene sequence. On the basis of the genotypic and phenotypic properties presented, a novel species of the genus Pseudonocardia is proposed, Pseudonocardia acaciae sp. nov. The type strain is strain GMKU095(T) (=NRRL B-24609(T) =BCC 28481(T) =TISTR 1862(T) =NBRC 104274(T)).
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Nucleotide Sequence
July 2008
... T he observed elongated and br anc hing cell types incr ease the nutrient absor ption surface. Char acteristic mor photypes can be associated with our results obtained by 16S rRNA amplicon sequencing and the pr e vious cultiv ation: pr osthecated Verrucomicrobium (Fig. 3 F (Duangmal et al. 2009 ). In low organic matter containing environments, the bacterial cell size tends to decrease below 0.1 μm 3 . ...
The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.
... [3]. Novel species of the genus Pseudonocardia have been isolated from various habitats such as soils [4,5], sediment samples [6][7][8], termite nests [9], activated sludge [10] and plant roots [11][12][13]. Most of them were isolated from soils [3]. ...
A novel actinomycete, designated strain RS11V-5T, was isolated from rhizosphere soil of Oryza sativa L. collected from Roi Et Province, Thailand, and its taxonomic position was evaluated. Cells of strain RS11V-5T were Gram-stain-positive, aerobic, and non-motile. Whole-cell hydrolysates contained meso-diaminopimelic acid, arabinose, galactose, glucose and ribose. MK-8(H4) was detected as the predominant menaquinone of this strain. The polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylmethylethanolamine, hydroxy-phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminolipid and an unidentified glycolipid. The major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c. Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain RS11V-5T belonged to the genus Pseudonocardia and had high 16S rRNA sequence similarity of 99.3 % to Pseudonocardia kujensis KCTC 29062T and less than 98.4 % to other members of the genus Pseudonocardia. The DNA G+C content of the strain RS11V-5T was 73.3 mol%. Strain RS11V-5T showed 46.5 % digital DNA-DNA hybridization, 92.2 % orthologous average nucleotide identity (OrthoANI), 90.2 % ANI based on blast and 92.7 % ANI based on MUMmer to P. kujensis KCTC 29062T. Based its phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain RS11V-5T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia terrae sp. nov. is proposed. The type strain is RS11V-5T (=TBRC 15286T=NBRC 115296T).
... website. Strains of this genus have been isolated from various environmental samples, such as industrial sludge (Mahendra and Alvarez-Cohen 2005;Kämpfer et al. 2006;Cuesta et al. 2013), coastal sediment , deep-sea sediment (Tian et al. 2013;Zhang et al. 2014Zhang et al. , 2017, mangrove sediment (Liu et al. 2015), soil (Henssen et al. 1983;Lee et al. 2002;Park et al. 2008;Qin et al. 2008;Li et al. 2010;Ara et al. 2011;Nie et al.2012;Sahin et al. 2014), surface sterilised roots (Gu et al. 2006;Duangmal et al. 2009;Kaewkla and Franco 2011;Zhao et al. 2011aZhao et al. , b, c, 2012Qin et al. 2011) and stems or leaves of higher plants (Chen et al. 2009;Kaewkla and Franco 2010;Qin et al. 2010;Xing et al. 2012). They have also been found in a gold mine cave (Lee et al. 2001), rock , termite nest (Sujarit et al. 2017), indoor environment (Schäfer et al. 2009) and plant litter (Sakiyama et al. 2010). ...
An aerobic, non-motile, Gram-stain positive actinomycete, designated strain NEAU-YY211T, was isolated from the rhizosphere soil of wheat (Triticum aestivum L.) collected from Zhumadian, Henan Province, mid-eastern China, and characterised taxonomically using a polyphasic approach. Comparative analysis of the 16S rRNA gene sequence indicated that strain NEAU-YY211T belongs to the genus Pseudonocardia, showing high similarities with respect to Pseudonocardia ammonioxydans H9T (99.1%) and Pseudonocardia antitumoralis SCSIO 01299T (99.0%), respectively. The cell wall was found to contain meso-diaminopimelic acid and the whole cell sugars were identified as arabinose and galactose. The predominant menaquinone of strain NEAU-YY211T was identified as MK-8(H4) and the major fatty acids were identified as iso-C16:0, C17:1ω8c and iso-C16:1. The phospholipid profile was found to consist of diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unidentified phospholipid. The G+C content of the genomic DNA was determined to be 72.6 mol%. Levels of DNA–DNA relatedness with P. ammonioxydans JCM 12462T and P. antitumoralis DSM 45322T were 54.5 ± 3.5% and 49.8 ± 2.5% (mean ± SD), respectively. Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate can be distinguished from closely related type strains and thus represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia tritici sp. nov. is proposed. The type strain is NEAU-YY211T (= DSM 106068T = CGMCC 4.7474T).
... One of the reasons was that the GC content of these monooxygenase genes was differential with that of the genome. Genus Pseudonocardia was recognized as high G+C bacteria with GC content always high than 70% (Kampfer et al., 2006;Park et al., 2008;Chen et al., 2009;Duangmal et al., 2009). Base composition analysis clarified that GC content of the monooxygenase gene cluster was about 60% both in Pseudonocardia sp.K1 and Rhodococcus sp.YYL, which was mostly close to that of the genome of genus Rhodococcus usually between 60 to 70% (Goodfellow and Alderson, 1977). ...
Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the Rhizobiaceae familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that Bacillus and Pseudomonas are the most prevalent genera of nodule endophytic bacteria, succeeded by Paenibacillus, Enterobacter, Pantoea, Agrobacterium, and Microbacterium. To date, the bibliographic data available show that Glycine max followed by Vigna radiata, Phaseolus vulgaris and Lens culinaris are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of Bacillus and Pseudomonas as the most abundant nodule endophytic bacteria, alongside Paenibacillus, Agrobacterium, and Enterobacter. Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.
The genus Pseudonocardia belongs to a group of actinomycetes, and is a member of the family Pseudonocardiacea. The members of this genus are aerobic, Gram‐positive, non‐motile bacteria that are commonly found in soil, plant, and environment. Although this genus has a low clinical significance, however it has an important role in biotechnology due to the production of secondary metabolites, some of which have anti‐bacterial, anti‐fungal, and anti‐tumor effects. The use of phenotypic tests such as gelatinase activity, starch hydrolysis, catalase, and oxidase tests, as well as molecular methods, such as polymerase chain reaction (PCR), are necessary for Pseudonocardia identification at the genus and species levels.
emergence of multi drug resistant bacteria has become more frequent, the search is on for novel antibiotics. Under explored and unique habitats are being prospected for novel strains of Actinomycetes which has the potential to produce new antibiotics. Accordingly, the present study has been taken up with an objective to explore the diversity of actinomycetes from Vembandu estuary, the biggest and one of the 3 Ramsar sites in Kerala. Sediment samples were collected seasonally, using van veen grab from selected stations for a period of one year. Actinomycetes were isolated using Kusters agar and characterized by polyphasic taxonomy. Physiological capabilities of isolates were evaluated and the antibacterial activities against a range of pathogens were studied using standard methods. Various genera of Actinomycetes such as Actinobispora, Actinokineospora, Actinosynnema, Catellospora, Kibdelosporangium, Micromonospora, Nocardiopsis, Rhodococcus, Saccharopolyspora, Streptoalloteichus, Streptomyces, Streptosporangium, Thermoactinomyces and atypical Nocardia asteroids were encountered in the lake sediments. More than 90% of the actinomycete isolates revealed good antibacterial activity against pathogenic bacteria. While 81% of them were able to produce protease, 56% of them decomposed hypoxanthine and tyrosine. Ability to decompose xanthine was relatively low (11%). Molecular identification of potential Actinomycete strains were carried out based on 16s rRNA gene, which revealed their identity as Streptomyces olivaceus, Streptomyces costaricanus, Nocardiopsis flavescens and Nocardiopsis alkaliphila. This study revealed that lake sediments could be good source of potential actinomycetes and reconfirms the need for exploring under explored and unexplored habitats for diverse actinomycetes which could probably yield novel antibiotics to fight the emerging threat of multidrug resistant pathogens.
The Japanese effluent standard for 1,4-dioxane was set in 2012; however, the provisional standards have been applied for specific industries until 2021. Due to high physicochemical stability of 1,4-dioxane, most conventional wastewater treatment techniques are ineffective for the removal of 1,4-dioxane from industrial wastewater. Moreover, the advanced oxidation process, which has been proven to be effective for 1,4-dioxane degradation, has serious problems with regard to economic efficiency and practical utility. On the other hand, in recent years, several effective 1,4-dioxane-degrading bacteria were isolated, and biological wastewater treatments using those 1,4-dioxane-degrading bacteria have attracted much attention as a promising 1,4-dioxane treatment technique. In this paper, performances and problems of conventional wastewater treatment technology for 1,4-dioxane treatment are reviewed, and recent advances in the development of wastewater treatment techniques using 1,4-dioxane degrading bacteria are summarized.
Medicinal plants are important bio-resources for human existence and development. Endophytic actinobacteria with rich biodiversity, widely existing inside the tissues of medicinal plants, are important components of plant micro-ecosystems, and some can produce same or similar bioactive substances generated by their host plants. Therefore, utilizing endophytic actinobacteria to produce bioactive substances with antimicrobial and antitumor effects can not only provide a new way for the development of new drugs, but also effectively protect the endangered medicinal plant resources. Furthermore, this process has important ecological significance and economic value. In this review, research advances on the diversity of endophytic actinobacteria, genes related to natural product biosynthesis, and diversity of their natural bioactive substances are summarized, and a reference for the research of endophytic actinobacteria from the medicinal plants is provided.
In the quantitative phyletic approach to evolutionary taxonomy, quantitative methods are used for inferring evolutionary relationships. The methods are chosen both for their operationism and for their connection to evolutionary theory and the goals of evolutionary taxonomy. As an example of this approach, a detailed analysis of a set of anuran characters is presented and taxonomic conclusions based on those characters are drawn. The methods and conclusions of the quantitative phyletic analysis are compared and contrasted with the methods of previous workers in the field of anuran classification.
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
DNA base composition was determined by reversed-phase high-performance liquid chromatography (HPLC). DNA was hydrolysed into nucleosides with nuclease P1 and bacterial alkaline phosphatase. The mixture of nucleosides was applied to HPLC without any further purification. One determination by chromatography needed 2 μg of hydrolysed nucleosides and took only 8 min. The relative standard error of nucleoside analysis was less than 1%. The system described here gives a direct and precise method for determining DNA base composition.