Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov., isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Central Andes in Chile

Two novel Micromonospora strains, STR1-7T and STR1S-6T, were isolated from the rhizosphere of a Parastrephia quadrangularis plant growing in the Salar de Tara region of the Atacama Desert, Chile. Chemotaxonomic, cultural and phenotypic features confirmed that the isolates belonged to the genus Micromonospora. They grew from 20 to 37 °C, from pH7 to 8 and in the presence of up to 3 %, w/v NaCl. The isolates formed distinct branches in Micromonospora gene trees based on 16S rRNA gene sequences and on a multi-locus sequence analysis of conserved house-keeping genes. A phylogenomic tree generated from the draft genomes of the isolates and their closest phylogenetic neighbours showed that isolate STR1-7T is most closely related to Micromonospora orduensis S2509T, and isolate STR1S-6 T forms a distinct branch that is most closely related to 12 validly named Micromonospora species, including Micromonospora saelicesensis the earliest proposed member of the group. The isolates were separated from one another and from their closest phylogenomic neighbours using a combination of chemotaxonomic, genomic and phenotypic features, and by low average nucleotide index and digital DNA-DNA hybridization values. Consequently, it is proposed that isolates STR1-7T and STR1S-6T be recognized as representing new species in the genus Micromonospora, namely as Micromonospora parastrephiae sp. nov. and Micromonospora tarensis sp. nov.; the type strains are STR1-7T (=CECT 9665T=LMG 30768T) and STR1S-6T (=CECT 9666T=LMG 30770T), respectively. Genome mining showed that the isolates have the capacity to produce novel specialized metabolites, notably antibiotics and compounds that promote plant growth, as well as a broad-range of stress-related genes that provide an insight into how they cope with harsh abiotic conditions that prevail in high-altitude Atacama Desert soils.

Microbacterium plantarum sp. nov. and Microbacterium thalli sp. nov., two endophytic metal-resistant bacteria isolated from Sphaeralcea angustifolia (Cav.) G. Don and Prosopis laevigata (Humb. et Bonpl. ex Willd) M.C. Johnston

Four Gram-positive, aerobic, catalase- and oxidase-negative, rod-shaped, motile endophytic bacterial strains, designated NM3R9T, NE1TT3, NE2TL11 and NE2HP2T, were isolated from the inner tissues (leaf and stem) of Sphaeralcea angustifolia and roots of Prosopis laevigata. They were characterized using a polyphasic approach, which revealed that they represent two novel Microbacterium species. Phylogenetic analysis based on 16S rRNA gene sequencing showed that the species closest to NE2HP2T was Microbacterium arborescens DSM 20754T (99.6 %) and that closest to NM3R9T, NE2TL11 and NE2TT3 was Microbacterium oleivorans NBRC 103075T (97.4 %). The whole-genome average nucleotide identity value between strain NM3R9T and Microbacterium imperiale DSM 20530T was 90.91 %, and that between strain NE2HP2T and M. arborecens DSM 20754T was 91.03 %. Digital DNA-DNA hybridization showed values of less than 70 % with the type strains of related species. The polar lipids present in both strains included diphosphatidylglycerol, phosphatidylglycerol, glycolipids and unidentified lipids, whereas the major fatty acids included anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Whole-cell sugars included mannose, rhamnose and galactose. Strains NM3R9T and NE2HP2T showed physiological characteristics different from those present in closely related Microbacterium species. According to the taxonomic analysis, both strains belong to two novel species. The name Microbacterium plantarum sp. nov. is proposed for strain NE2HP2T (=LMG 30875T=CCBAU 101117T) and Microbacterium thalli sp. nov. for strains NM3R9T (=LMG 30873T=CCBAU 101116T), NE1TT3 (=CCBAU 101114) and NE2TL11 (=CCBAU 101115).

Frankia alni Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles

A phyloprofile of Frankia genomes was carried out to identify those genes present in symbiotic strains of clusters 1, 1c, 2 and 3 and absent in non-infective strains of cluster 4. At a threshold of 50% AA identity, 108 genes were retrieved. Among these were known symbiosis-associated genes such as nif (nitrogenase), and genes which are not know as symbiosis-associated genes such as can (carbonic anhydrase, CAN). The role of CAN, which supplies carbonate ions necessary for carboxylases and acidifies the cytoplasm, was thus analyzed by staining cells with pH-responsive dyes; assaying for CO₂ levels in N-fixing propionate-fed cells (that require a propionate-CoA carboxylase to yield succinate-CoA), fumarate-fed cells and N-replete propionate-fed cells; conducting proteomics on N-fixing fumarate and propionate-fed cells and direct measurement of organic acids in nodules and in roots. The interiors of both in vitro and nodular vesicles were found to be at a lower pH than that of hyphae. CO₂ levels in N₂-fixing propionate-fed cultures were lower than in N-replete ones. Proteomics of propionate-fed cells showed carbamoyl-phosphate synthase (CPS) as the most overabundant enzyme relative to fumarate-fed cells. CPS combines carbonate and ammonium in the first step of the citrulline pathway, something which would help manage acidity and NH₄⁺. Nodules were found to have sizeable amounts of pyruvate and acetate in addition to TCA intermediates. This points to CAN reducing the vesicles' pH to prevent the escape of NH₃ and to control ammonium assimilation by GS and GOGAT, two enzymes that work in different ways in vesicles and hyphae. Genes with related functions (carboxylases, biotin operon and citrulline-aspartate ligase) appear to have undergone decay in non-symbiotic lineages.

Descriptions of Micromonospora grosourdyae nom. nov., Micromonospora sonchi comb. nov. and Micromonospora thawaii sp. nov. to resolve problems with the taxonomy and nomenclature of strains named Micromonospora endophytica

The name Micromonospora endophytica has been used for three different organisms. The first organism with this name is the species represented by strain DCWR9-8-2^T, a species published in 2015 but whose name was never validated. In 2019 the type species of the genus Jishengella was reclassified into the genus Micromonospora, while maintaining its original epithet, thus establishing the second group of organisms known as M. endophytica, but the first for which the name was validated. Additionally, in 2018 the reclassification of the genus Verrucosispora into the genus Micromonospora was proposed, but a new epithet has not been specified for the species named Verrucosispora endophytica, which remains an orphaned species. Therefore, it is necessary to propose new names that can unequivocally identify these taxa. We have analysed the taxonomic position of the strains, comparing them with the species with valid published names of the genus Micromonospora. We here propose Micromonospora thawaii sp. nov. for the species represented by strain DCWR9-8-2^T, and Micromonospora grosourdyae nom. nov. and Micromonospora sonchi comb. nov. for the two orphaned species of Verrucosispora, V. endophytica and Verrucosispora sonchi, respectively. Genomic analysis also showed that M. trujilloniae is a later heterotypic synonym of M. andamanensis.

A Nonspecific Lipid Transfer Protein with Potential Functions in Infection and Nodulation

The response of Alnus glutinosa to Frankia alni ACN14a is driven by several sequential physiological events from calcium spiking and root-hair deformation to the development of the nodule. Early stages of actinorhizal symbiosis were monitored at the transcriptional level to observe plant host responses to Frankia alni. Forty-two genes were significantly upregulated in inoculated compared with noninoculated roots. Most of these genes encode proteins involved in biological processes induced during microbial infection, such as oxidative stress or response to stimuli, but a large number of them are not differentially modulated or downregulated later in the process of nodulation. In contrast, several of them remained upregulated in mature nodules, and this included the gene most upregulated, which encodes a nonspecific lipid transfer protein (nsLTP). Classified as an antimicrobial peptide, this nsLTP was immunolocalized on the deformed root-hair surfaces that are points of contact for Frankia spp. during infection. Later in nodules, it binds to the surface of F. alni ACN14a vesicles, which are the specialized cells for nitrogen fixation. This nsLTP, named AgLTP24, was biologically produced in a heterologous host and purified for assay on F. alni ACN14a to identify physiological effects. Thus, the activation of the plant immunity response occurs upon first contact, while the recognition of F. alni ACN14a genes switches off part of the defense system during nodulation. AgLTP24 constitutes a part of the defense system that is maintained all along the symbiosis, with potential functions such as the formation of infection threads or nodule primordia to the control of F. alni proliferation. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Rossellomorea arthrocnemi sp. nov., a novel plant growth-promoting bacterium used in heavy metal polluted soils as a phytoremediation tool

Strain EAR8^T is a root endophyte isolated from Arthrocnemum macrostachyum plants collected from the Odiel marshes, Huelva (Spain). It presented in vitro plant growth-promoting properties and improved the plant growth and heavy metal accumulation in polluted soils playing an important role in phytoremediation strategies. Phenotypically, strain EAR8^T cells were Gram-positive, aerobic and non-motile rods with terminal oval endospores and non-swollen sporangia which form beige, opaque, butyrous, raised and irregular colonies with undulate margins. The strain was able to grow between 15–45 °C, at pH 6.0–9.0 and tolerated 0–25 % NaCl (w/v) showing optimal growth conditions on trypticase soy agar plates supplemented with 2.5 % NaCl (w/v) at pH 7.0 and 37 °C for 24 h. Chemotaxonomic analyses showed that the isolate has meso-diaminopimelic acid as the peptidoglycan in the cell wall and MK-7 as the major respiratory quinone. The predominant fatty acids were anteiso-C_15 : 0 and iso-C_15 : 0 and the polar lipid profile was composed of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic analyses based on the whole proteomes of closest sequenced relatives confirmed that strain EAR8^T is affiliated to the genus Rossellomorea and forms a clade with Rossellomorea vietnamensis 15-1^T with maximum support. Genome analyses showed that EAR8^T has indole-3-acetic acid and siderophore biosynthesis and transporters genes and genes related to resistance against heavy metals. Phenotypic and phylogenomic comparative studies suggested that strain EAR8^T is a new representative of the genus Rossellomorea and the name Rossellomorea arthrocnemi sp. nov. is proposed. Type strain is EAR8^T (=CECT 9072^T=DSM 103900^T).

Micromonospora metallophores: A plant growth promotion trait useful for bacterial-assisted phytoremediation?

Heavy metal pollution in the environment is an increasing problem due to natural and anthropogenic activities. The use of bacteria for bioremediation of soils contaminated with heavy metals has gained a lot of attention as it can be considered effective, economic and environmentally sustainable. In this work, we investigated the capacity of endophytic Micromonospora strains isolated from different legumes, to produce metallophores against a variety of heavy metals in vitro. Genome mining using available endophytic Micromonospora genome sequences revealed the presence of genes related to metal acquisition, iron metabolism and resistance to toxic compounds. In vitro production of metallophores demonstrated that all strains tested produced chelates against arsenic, cobalt, copper, chromium, iron, mercury, molybdenum, nickel, vanadium and zinc in different amounts. In addition, the plant growth promotion effect of strains GAR05 and PSN13 on Arabidopsis thaliana grown in the presence of several heavy metals was tested. Under these conditions, the plants inoculated with the strain GAR05 showed significant growth when compared to the control plants suggesting a plant growth promotion effect in the form of tolerance to the toxic substances. Furthermore, during this plant-bacterium interaction, a new bacterial structure named root-bead was observed on the roots of A. thaliana suggesting a strong interaction between the two organisms and a clear positive effect of the bacterium on the plant. Overall, these results highlight the potential use of endophytic Micromonospora strains for bacterial-assisted phytoremediation of contaminated sites.

Pseudoalteromonas rhizosphaerae sp. nov., a novel plant growth-promoting bacterium with potential use in phytoremediation

Strain RA15^T was isolated from the rhizosphere of the halophyte plant Arthrocnemum macrostachyum growing in the Odiel marshes (Huelva, Spain). RA15^T cells were Gram stain-negative, non-spore-forming, aerobic rods and formed cream-coloured, opaque, mucoid, viscous, convex, irregular colonies with an undulate margin. Optimal growth conditions were observed on tryptic soy agar (TSA) plates supplemented with 2.5 % NaCl (w/v) at pH 7.0 and 28 °C, although it was able to grow at 4–32 °C and at pH values of 5.0–9.0. The NaCl tolerance range was from 0 to 15 %. The major respiratory quinone was Q8 but Q9 was also present. The most abundant fatty acids were summed feature 3 (C_16 : 1 ω7c and/or C_16 : 1 ω6c), C_17 : 1 ω8c and C_16 : 0. The polar lipids profile comprised phosphatidylglycerol and phosphatidylethanolamine as the most abundant representatives. Phylogenetic analyses confirmed the well-supported affiliation of strain RA15^T within the genus Pseudoalteromonas, close to the type strains of Pseudoalteromonas neustonica, Pseudoalteromonas prydzensis and Pseudoalteromonas mariniglutinosa. Results of comparative phylogenetic and phenotypic studies between strain RA15^T and its closest related species suggest that RA15^T could be a new representative of the genus Pseudoalteromonas, for which the name Pseudoalteromonas rhizosphaerae sp. nov. is proposed. The type strain is RA15^T (=CECT 9079^T=LMG 29860^T). The whole genome has 5.3 Mb and the G+C content is 40.4 mol%.

Micromonospora acroterricola sp. nov., a novel actinobacterium isolated from a high altitude Atacama Desert soil

A Micromonospora strain, designated 5R2A7^T, isolated from a high altitude Atacama Desert soil was examined by using a polyphasic approach. Strain 5R2A7^T was found to have morphological, chemotaxonomic and cultural characteristics typical of members of the genus Micromonospora. The cell wall contains meso- and hydroxy-diaminopimelic acid, the major whole-cell sugars are glucose, ribose and xylose, the predominant menaquinones MK-10(H₄), MK-10(H₆), MK-10(H₈) and MK-9(H₆), the major polar lipids diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and an unknown glycolipid, and the predominant cellular fatty acids iso-C_16 : 0, iso-C_15 : 0 and 10-methyl C_17 : 0. The digital genomic DNA G+C content is 72.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain 5R2A7^T was closely related to Micromonospora coriariae DSM 44875^T (99.8 %) and Micromonospora cremea CR30^T (99.7 %), and was separated readily from the latter, its closest phylogenetic neighbour, based on gyrB and multilocus sequence data, by low average nucleotide identity (92.59 %) and in silico DNA-DNA relatedness (51.7 %) values calculated from draft genome assemblies and by a range of chemotaxonomic and phenotypic properties. Consequently, strain 5R2A7^T is considered to represent a novel species of Micromonospora for which the name Micromonospora acroterricola sp. nov. is proposed. The type strain is 5R2A7^T (=LMG 30755^T=CECT 9656^T).

Genomic Insights Into Plant-Growth-Promoting Potentialities of the Genus Frankia

This study was designed to determine the plant growth promoting (PGP) potential of members of the genus Frankia. To this end, the genomes of 21 representative strains were examined for genes associated directly or indirectly with plant growth. All of the Frankia genomes contained genes that encoded for products associated with the biosynthesis of auxins [indole-3-glycerol phosphate synthases, anthranilate phosphoribosyltransferases (trpD), anthranilate synthases, and aminases (trpA and B)], cytokinins (11 well-conserved genes within the predicted biosynthetic gene cluster), siderophores, and nitrogenases (nif operon except for atypical Frankia) as well as genes that modulate the effects of biotic and abiotic environmental stress (e.g., alkyl hydroperoxide reductases, aquaporin Z, heat shock proteins). In contrast, other genes were associated with strains assigned to one or more of four host-specific clusters. The genes encoding for phosphate solubilization (e.g., low-affinity inorganic phosphate transporters) and lytic enzymes (e.g., cellulases) were found in Frankia cluster 1 genomes, while other genes were found only in cluster 3 genomes (e.g., alkaline phosphatases, extracellular endoglucanases, pectate lyases) or cluster 4 and subcluster 1c genomes (e.g., NAD(P) transhydrogenase genes). Genes encoding for chitinases were found only in the genomes of the type strains of Frankia casuarinae, F. inefficax, F. irregularis, and F. saprophytica. In short, these in silico genome analyses provide an insight into the PGP abilities of Frankia strains of known taxonomic provenance. This is the first study designed to establish the underlying genetic basis of cytokinin production in Frankia strains. Also, the discovery of additional genes in the biosynthetic gene cluster involved in cytokinin production opens up the prospect that Frankia may have novel molecular mechanisms for cytokinin biosynthesis.

Uncovering the potential of novel micromonosporae isolated from an extreme hyper-arid Atacama Desert soil

The taxonomic status, biotechnological and ecological potential of several Micromonospora strains isolated from an extreme hyper arid Atacama Desert soil were determined. Initially, a polyphasic study was undertaken to clarify the taxonomic status of five micromonosporae, strains LB4, LB19, LB32^T, LB39^T and LB41, isolated from an extreme hyper-arid soil collected from one of the driest regions of the Atacama Desert. All of the isolates were found to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Micromonospora. Isolates LB32^T and LB39^T were distinguished from their nearest phylogenetic neighbours and proposed as new species, namely as Micromonospora arida sp. nov. and Micromonospora inaquosa sp. nov., respectively. Eluted methanol extracts of all of the isolates showed activity against a panel of bacterial and fungal indicator strains, notably against multi-drug resistant Klebsiella pneumoniae ATCC 700603 while isolates LB4 and LB41 showed pronounced anti-tumour activity against HepG2 cells. Draft genomes generated for the isolates revealed a rich source of novel biosynthetic gene clusters, some of which were unique to individual strains thereby opening up the prospect of selecting especially gifted micromonosporae for natural product discovery. Key stress-related genes detected in the genomes of all of the isolates provided an insight into how micromonosporae adapt to the harsh environmental conditions that prevail in extreme hyper-arid Atacama Desert soils.

Genome-Based Taxonomic Classification of the Phylum Actinobacteria

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.

Kushneria phyllosphaerae sp. nov. and Kushneria endophytica sp. nov., plant growth promoting endophytes isolated from the halophyte plant Arthrocnemum macrostachyum

Two endophytic bacteria (EAod3^T and EAod7^T) were isolated from the aerial part of plants of Arthrocnemum macrostachyum growing in the Odiel marshes (Huelva, Spain). Phylogenetic analysis based on 16S rRNA gene sequences indicated their affiliation to the genus Kushneria. 16S rRNA gene sequences of strains EAod3^T and EAod7^T showed the highest similarity to Kushneria marisflavi DSM 15357T (99.0 and 97.6 %, respectively). Digital DNA-DNA hybridization studies between the draft genomes of strain EAod3^T and K. marisflavi DSM 15357^T corresponded to 28.5 % confirming the novel lineage of strain EAod3^T in the genus Kushneria. Cells of both strains were Gram-staining-negative, aerobic and motile rods able to grow at 4-37 °C, at pH 5.0-8.0 and tolerate 0.5-25 % NaCl (w/v). They presented ubiquinone Q9 and C16 : 0, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c as the major fatty acids. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Based on the phenotypic and phylogenetic results, strains EAod3^T (=CEC^T 9073^T=LMG 29856^T) and EAod7^T (=CECT 9075^T=LMG 29858^T) are proposed as new representatives of the genus Kushneria, and the proposed names are Kushneria phyllosphaerae sp. nov. and Kushneria endophytica sp. nov., respectively. The whole genome sequence of strain EAod3^T has a total length of 3.8 Mbp and a G+C content of 59.3 mol%.

Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics

The type isolates of species Micromonospora saelicesensis and Micromonospora noduli are Gram-stain positive actinobacteria that were originally isolated from nitrogen fixing nodules of the legumes Lupinus angustifolius and Pisum sativum, respectively. These two species are very closely related and questions arise as to whether they should be merged into a single species. To better delineate the relationship of M. saelicesensis and M. noduli, 10 strains isolated from plant tissue (nodules and leaves) and identified by their 16S rRNA gene sequences as either M. saelicensesis or M. noduli, based on a cut-off value of ≥99.5% were selected for whole-genome sequencing and compared with the type strains of M. saelicesensis Lupac 09^T and M. noduli GUI43^T using overall genome relatedness indices (OGRI) which included ANI, OrthoANI and digital DNA-DNA hybridization. Whole- and core-genome phylogenomic analyses were also carried out. These results were compared with the topologies of the 16S rRNA and gyrB gene phylogenies. Good correlation was found between all trees except for the 16S rRNA gene. Overall results also supported the current classification of M. saelicesensis and M. noduli as separate species. Especially useful was the core-genome phylogenetic analyses based on 92 genes and the dDDH results which were highly correlated. The importance of using more than one strain for a better definition of a species was also shown. A series of in vitro phenotypic assays performed at different times were compared with in silico predictions based on genomic data. In vitro phenotypic tests showed discrepancies among the independent studies, confirming the lack of reproducibility even when tests were performed in the same laboratory. On the other hand, the use of in silico predictions proved useful for defining a stable phenotype profile among the strains analyzed. These results provide a working framework for defining Micromonospora species at the genomic and phenotypic level.

Hunting for cultivable Micromonospora strains in soils of the Atacama Desert

Innovative procedures were used to selectively isolate small numbers of Micromonospora strains from extreme hyper-arid and high altitude Atacama Desert soils. Micromonosporae were recognised on isolation plates by their ability to produce filamentous microcolonies that were strongly attached to the agar. Most of the isolates formed characteristic orange colonies that lacked aerial hyphae and turned black on spore formation, whereas those from the high altitude soil were dry, blue-green and covered by white aerial hyphae. The isolates were assigned to seven multi- and eleven single-membered groups based on BOX-PCR profiles. Representatives of the groups were assigned to either multi-membered clades that also contained marker strains or formed distinct phyletic lines in the Micromonospora 16S rRNA gene tree; many of the isolates were considered to be putatively novel species of Micromonospora. Most of the isolates from the high altitude soils showed activity against wild type strains of Bacillus subtilis and Pseudomonas fluorescens while those from the rhizosphere of Parastrephia quadrangulares and from the Lomas Bayas hyper-arid soil showed resistance to UV radiation.

Formal description of Mycobacterium neglectum sp. nov. and Mycobacterium palauense sp. nov., rapidly growing actinobacteria

The taxonomic positions of two fast growing mycobacteria (CECT 8778^T and CECT 8779^T) were established using a polyphasic approach. The strains were shown to have chemotaxonomic, cultural and morphological properties consistent with their classification in the genus Mycobacterium. Multi-locus sequence analyses (MLSA) show that strain CECT 8778^T forms a well-supported clade together with the type strains of Mycobacterium aurum, Mycobacterium austroafricanum and Mycobacterium vanbaalenii while strain CECT 8779^T presents as a distinct branch that is well separated from its near phylogenetic neighbours; it is also apparent from the MLSA genetic distances that these strains are most closely related to the type strains of Mycobacterium mageritense and M. vanbaalenii, respectively. Digital DNA:DNA hybridization and average nucleotide identity values between each of the strains and its close phylogenetic neighbour are below the 70 and 96% threshold values for definition of prokaryotic species; these results are underpinned by corresponding phenotypic data. Based upon the consensus of the phenotypic and phylogenetic analyses, it can be concluded that the two strains represent novel species within the genus Mycobacterium for which the following names are proposed: Mycobacterium neglectum sp. nov., with the type strain CECT 8778^T (BN 3150^T = DSM 44756^T) and Mycobacterium palauense sp. nov., with the type strain CECT 8779^T (= DSM 44914^T).

Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential

There is a need to clarify relationships within the actinobacterial genus Micromonospora, the type genus of the family Micromonosporaceae, given its biotechnological and ecological importance. Here, draft genomes of 40 Micromonospora type strains and two non-type strains are made available through the Genomic Encyclopedia of Bacteria and Archaea project and used to generate a phylogenomic tree which showed they could be assigned to well supported phyletic lines that were not evident in corresponding trees based on single and concatenated sequences of conserved genes. DNA G+C ratios derived from genome sequences showed that corresponding data from species descriptions were imprecise. Emended descriptions include precise base composition data and approximate genome sizes of the type strains. antiSMASH analyses of the draft genomes show that micromonosporae have a previously unrealised potential to synthesize novel specialized metabolites. Close to one thousand biosynthetic gene clusters were detected, including NRPS, PKS, terpenes and siderophores clusters that were discontinuously distributed thereby opening up the prospect of prioritising gifted strains for natural product discovery. The distribution of key stress related genes provide an insight into how micromonosporae adapt to key environmental variables. Genes associated with plant interactions highlight the potential use of micromonosporae in agriculture and biotechnology.

Micromonospora phytophila sp. nov. and Micromonospora luteiviridis sp. nov., isolated as natural inhabitants of plant nodules

Two actinobacterial isolates, strains SG15T and SGB14T, were recovered through a microbial diversity study of nitrogen fixing nodules from Pisum sativum plants collected in Salamanca (Spain). The taxonomic status of these isolates was determined using a polyphasic approach and both presented chemotaxonomic and morphological properties consistent with their classification in the genus Micromonospora. For strains SG15T and SGB14T, the highest 16S rRNA gene sequence similarities were observed with Micromonospora coxensis JCM 13248T (99.2 %) and Micromonospora purpureochromogenes DSM 43821T (99.4 %), respectively. However, strains SG15T and SGB14T were readily distinguished from their phylogenetic neighbours both genetically and phenotypically indicating that they represent two new Micromonospora species. The following names are proposed for these species: Micromonosporaphytophila sp. nov. type strain SG15T (=CECT 9369T; =DSM 105363T), and Micromonosporaluteiviridis sp. nov. type strain SGB14T (=CECT 9370T; =DSM 105362T).

Two novel species of rapidly growing mycobacteria: Mycobacterium lehmannii sp. nov. and Mycobacterium neumannii sp. nov

Two rapidly growing mycobacteria with identical 16S rRNA gene sequences were the subject of a polyphasic taxonomic study. The strains formed a well-supported subclade in the mycobacterial 16S rRNA gene tree and were most closely associated with the type strain of Mycobacterium novocastrense. Single and multilocus sequence analyses based on hsp65, rpoB and 16S rRNA gene sequences showed that strains SN 1900^T and SN 1904^T are phylogenetically distinct but share several chemotaxonomic and phenotypic features that are are consistent with their classification in the genus Mycobacterium. The two strains were distinguished by their different fatty acid and mycolic acid profiles, and by a combination of phenotypic features. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values for strains SN 1900^T and SN 1904^T were 61.0 % and 94.7 %, respectively; in turn, the corresponding dDDH and ANI values with M. novocastrense DSM 44203^T were 41.4 % and 42.8 % and 89.3 % and 89.5 %, respectively. These results show that strains SN1900^T and SN 1904^T form new centres of taxonomic variation within the genus Mycobacterium. Consequently, strains SN 1900^T (40^T=CECT 8763^T=DSM 43219^T) and SN 1904^T (2409^T=CECT 8766^T=DSM 43532^T) are considered to represent novel species, for which the names Mycobacteriumlehmannii sp. nov. and Mycobacteriumneumannii sp. nov. are proposed. A strain designated as 'Mycobacteriumacapulsensis' was shown to be a bona fide member of the putative novel species, M. lehmannii.

Mycobacterium eburneum sp. nov., a non-chromogenic, fast-growing strain isolated from sputum

A polyphasic study was undertaken to establish the taxonomic position of a non-chromogenic, rapidly growing Mycobacterium strain that had been isolated from sputum. The strain, CECT 8775T, has chemotaxonomic and cultural properties consistent with its classification in the genus Mycobacterium and was distinguished from the type strains of closely related mycobacterial species, notably from Mycobacterium paraense DSM 46749T, its nearest phylogenetic neighbour, based on 16S rRNA, hsp65 and rpoB gene sequence data. These organisms were also distinguished by a broad range of chemotaxonomic and phenotypic features and by a digital DNA-DNA relatedness value of 22.8 %. Consequently, the strain is considered to represent a novel species of Mycobacterium for which the name Mycobacterium eburneum sp. nov is proposed; the type strain is X82T (CECT 8775T=DSM 44358T).

Delftia rhizosphaerae sp. nov. isolated from the rhizosphere of Cistus ladanifer

A bacterial strain, designated RA6T, was isolated from the rhizosphere of Cistus ladanifer. Phylogenetic analyses based on 16S rRNA gene sequence placed the isolate into the genus Delftia within a cluster encompassing the type strains of Delftia lacustris, Delftia tsuruhatensis, Delftia acidovorans and Delftia litopenaei, which presented greater than 97 % sequence similarity with respect to strain RA6T. DNA-DNA hybridization studies showed average relatedness ranging from of 11 to 18 % between these species of the genus Delftia and strain RA6T. Catalase and oxidase were positive. Casein was hydrolysed but gelatin and starch were not. Ubiquinone 8 was the major respiratory quinone detected in strain RA6T together with low amounts of ubiquinones 7 and 9. The major fatty acids were those from summed feature 3 (C16 : 1ω7c/C16 : 1 ω6c) and C16 : 0. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RA6T should be considered as a representative of a novel species of genus Delftia, for which the name Delftia rhizosphaerae sp. nov. is proposed. The type strain is RA6T (=LMG 29737T= CECT 9171T).

Taxonomy and systematics of plant probiotic bacteria in the genomic era

Recent decades have predicted significant changes within our concept of plant endophytes, from only a small number specific microorganisms being able to colonize plant tissues, to whole communities that live and interact with their hosts and each other. Many of these microorganisms are responsible for health status of the plant, and have become known in recent years as plant probiotics. Contrary to human probiotics, they belong to many different phyla and have usually had each genus analysed independently, which has resulted in lack of a complete taxonomic analysis as a group. This review scrutinizes the plant probiotic concept, and the taxonomic status of plant probiotic bacteria, based on both traditional and more recent approaches. Phylogenomic studies and genes with implications in plant-beneficial effects are discussed. This report covers some representative probiotic bacteria of the phylum Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, but also includes minor representatives and less studied groups within these phyla which have been identified as plant probiotics.

Complete genome sequence of Jiangella gansuensis strain YIM 002T (DSM 44835T), the type species of the genus Jiangella and source of new antibiotic compounds

Jiangella gansuensis strain YIM 002^T is the type strain of the type species of the genus Jiangella, which is at the present time composed of five species, and was isolated from desert soil sample in Gansu Province (China). The five strains of this genus are clustered in a monophyletic group when closer actinobacterial genera are used to infer a 16S rRNA gene sequence phylogeny. The study of this genome is part of the GenomicEncyclopedia ofBacteria andArchaea project, and here we describe the complete genome sequence and annotation of this taxon. The genome of J. gansuensis strain YIM 002^T contains a single scaffold of size 5,585,780 bp, which involves 149 pseudogenes, 4905 protein-coding genes and 50 RNA genes, including 2520 hypothetical proteins and 4 rRNA genes. From the investigation of genome sizes of Jiangella species, J. gansuensis shows a smaller size, which indicates this strain might have discarded too much genetic information to adapt to desert environment. Seven new compounds from this bacterium have recently been described; however, its potential should be higher, as secondary metabolite gene cluster analysis predicted 60 gene clusters, including the potential to produce the pristinamycin.

High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea

Nakamurella lactea DLS-10^T, isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10^T and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10^T presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.

Micromonospora ureilytica sp. nov., Micromonospora noduli sp. nov. and Micromonospora vinacea sp. nov., isolated from Pisum sativum nodules

A diversity study on the presence of strains representing the genus Micromonospora in Pisum sativum nodules collected from Cañizal (Spain) has provided evidence of the high number of isolates that might represent novel species. In the present work, we have characterized three of these isolates: GUI23T, GUI43T and GUI63T. Phenotypic and genotypic analyses confirmed that all strains represent novel species of the genus Micromonospora with the following proposed names: Micromonospora ureilytica sp. nov., type strain GUI23T (=CECT 9022T=DSM 101692T), Micromonospora noduli sp. nov., type strain GUI43T (=CECT 9020T=DSM 101694T), and Micromonospora vinacea sp. nov., type strain GUI63T (=CECT 9019T=DSM 101695T).

Micromonospora profundi sp. nov., isolated from deep marine sediment

A novel actinobacterial strain, designated DS3010T, was isolated from a Black Sea marine sediment and characterized using a polyphasic approach. The strain was shown to have chemotaxonomic, morphological and phylogenetic properties consistent with classification as representing a member of the genus Micromonospora. Comparative 16S rRNA gene sequence studies showed that the strain was most closely related to the type strains of Micromonospora saelicesensis (99.5 %), Micromonospora chokoriensis (99.4 %) and Micromonospora violae (99.3 %). Similarly, a corresponding analysis based on partial gyrB gene sequences showed that it formed a distinct phyletic branch in a subclade that included the type strains of Micromonosporazamorensis, 'Micromonospora zeae', 'Micromonospora jinlongensis', M. saelicesensis and Micromonospora lupini. DS3010T was distinguished from its closest phylogenetic neighbours by low levels of DNA-DNA relatedness and by a combination of chemotaxonomic and phenotypic properties. On the basis of these data, it is proposed that the isolate should be assigned to the genus Micromonospora as Micromonospora profundi sp. nov. with isolate DS3010T (=DSM 45981T=KCTC 29243T) as the type strain.

Micromonospora luteifusca sp. nov. isolated from cultivated Pisum sativum

Three novel actinobacterial strains, GUI2(T), GUI42 and CR21 isolated from nodular tissues and the rhizosphere of a sweet pea plant collected in Cañizal, Spain were identified according to their 16S rRNA gene sequences as new members of the genus Micromonospora. The closest phylogenetic members were found to be Micromonospora saelicesensis (99.2%) "Micromonospora zeae" (99.1%), "Micromonospora jinlongensis" (99%), Micromonospora lupini (98.9%) and Micromonospora zamorensis (98.8%). To resolve their full taxonomic position, four additional genes (atpD, gyrB, recA, rpoB) were partially sequenced and compared to available Micromonospora type strain sequences. DNA-DNA hybridization, BOX-PCR and ARDRA profiles confirmed that these strains represent a novel genomic species. All strains contained meso-diaminopimelic and hydroxy-diaminopimelic acids in their cell wall. Their fatty acid profiles comprised iso-C15:0, iso-C16:0 and anteiso-C15:0 as major components. The polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were found in the type strain GUI2(T) which also contained MK-10(H4) as the major menaquinone. Physiological and biochemical characteristics also differentiated the new isolates. Based on the integration of the above studies, strains GUI2(T), GUI42 and CR21 represent a novel Micromonospora species and we propose the name Micromonospora luteifusca sp. nov. The type strain is GUI2(T) (=CECT 8846(T); =DSM 100204(T)).

Paenibacillus periandrae sp. nov., isolated from nodules of Periandra mediterranea

A bacterial strain designated PM10T was isolated from root nodules of Periandra mediterranea in Brazil. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus with its closest relatives being Paenibacillus vulneris CCUG 53270T and Paenibacillus yunnanensis YN2T with 95.6 and 95.9% 16S rRNA gene sequence similarity, respectively. The isolate was a Gram-stain-variable, motile, sporulating rod that was catalase-negative and oxidase-positive. Caseinase was positive, amylase was weakly positive and gelatinase was negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 was the major fatty acid. Major polar lipids were diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PM10T should be considered representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus periandrae sp. nov. is proposed. The type strain is PM10T (=LMG 28691T=CECT 8827T).

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants

For a long time, it was believed that a healthy plant did not harbor any microorganisms within its tissues, as these were often considered detrimental for the plant. In the last three decades, the numbers of studies on plant microbe-interactions has led to a change in our view and we now know that many of these invisible partners are essential for the overall welfare of the plant. The application of Next Generation Sequencing techniques is a powerful tool that has permitted the detection and identification of microbial communities in healthy plants. Among the new plant microbe interactions recently reported several actinobacteria such as Micromonospora are included. Micromonospora is a Gram-positive bacterium with a wide geographical distribution; it can be found in the soil, mangrove sediments, and freshwater and marine ecosistems. In the last years our group has focused on the isolation of Micromonospora strains from nitrogen fixing nodules of both leguminous and actinorhizal plants and reported for the first time its wide distribution in nitrogen fixing nodules of both types of plants. These studies have shown how this microoganism had been largely overlooked in this niche due to its slow growth. Surprisingly, the genetic diversity of Micromonospora strains isolated from nodules is very high and several new species have been described. The current data indicate that Micromonospora saelicesensis is the most frequently isolated species from the nodular tissues of both leguminous and actinorhizal plants. Further studies have also been carried out to confirm the presence of Micromonospora inside the nodule tissues, mainly by specific in situ hybridization. The information derived from the genome of the model strain, Micromonospora lupini, Lupac 08, has provided useful information as to how this bacterium may relate with its host plant. Several strategies potentially necessary for Micromonospora to thrive in the soil, a highly competitive, and rough environment, and as an endophytic bacterium with the capacity to colonize the internal plant tissues which are protected from the invasion of other soil microbes were identified. The genome data also revealed the potential of M. lupini Lupac 08 as a plant growth promoting bacterium. Several loci involved in plant growth promotion features such as the production of siderophores, phytohormones, and the degradation of chitin (biocontrol) were also located on the genome and the functionality of these genes was confirmed in the laboratory. In addition, when several host plants species were inoculated with Micromonospora strains, the plant growth enhancing effect was evident under greenhouse conditions. Unexpectedly, a high number of plant-cell wall degrading enzymes were also detected, a trait usually found only in pathogenic bacteria. Thus, Micromonospora can be added to the list of new plant-microbe interactions. The current data indicate that this microorganism may have an important application in agriculture and other biotechnological processes. The available information is promising but limited, much research is still needed to determine which is the ecological function of Micromonospora in interaction with nitrogen fixing plants.

Arthroamide, a Cyclic Depsipeptide with Quorum Sensing Inhibitory Activity from Arthrobacter sp

Nonfilamentous actinobacteria have been less studied as secondary metabolite producers than their filamentous counterparts such as Streptomyces. From our collection of nonfilamentous actinobacteria isolated from sandstone, an Arthrobacter strain was found to produce a new cyclic peptide arthroamide (1) together with the known compound turnagainolide A (2). These compounds inhibited the quorum sensing signaling of Staphylococcus aureus in the submicromolar to micromolar range.

Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia

Actinorhizal plant growth in pioneer ecosystems depends on the symbiosis with the nitrogen-fixing actinobacterium Frankia cells that are housed in special root organs called nodules. Nitrogen fixation occurs in differentiated Frankia cells known as vesicles. Vesicles lack a pathway for assimilating ammonia beyond the glutamine stage and are supposed to transfer reduced nitrogen to the plant host cells. However, a mechanism for the transfer of nitrogen-fixation products to the plant cells remains elusive. Here, new elements for this metabolic exchange are described. We show that Alnus glutinosa nodules express defensin-like peptides, and one of these, Ag5, was found to target Frankia vesicles. In vitro and in vivo analyses showed that Ag5 induces drastic physiological changes in Frankia, including an increased permeability of vesicle membranes. A significant release of nitrogen-containing metabolites, mainly glutamine and glutamate, was found in N2-fixing cultures treated with Ag5. This work demonstrates that the Ag5 peptide is central for Frankia physiology in nodules and uncovers a novel cellular function for this large and widespread defensin peptide family.

Identification of potential transcriptional regulators of actinorhizal symbioses in Casuarina glauca and Alnus glutinosa

BACKGROUND

Trees belonging to the Casuarinaceae and Betulaceae families play an important ecological role and are useful tools in forestry for degraded land rehabilitation and reforestation. These functions are linked to their capacity to establish symbiotic relationships with a nitrogen-fixing soil bacterium of the genus Frankia. However, the molecular mechanisms controlling the establishment of these symbioses are poorly understood. The aim of this work was to identify potential transcription factors involved in the establishment and functioning of actinorhizal symbioses.

RESULTS

We identified 202 putative transcription factors by in silico analysis in 40 families in Casuarina glauca (Casuarinaceae) and 195 in 35 families in Alnus glutinosa (Betulaceae) EST databases. Based on published transcriptome datasets and quantitative PCR analysis, we found that 39% and 26% of these transcription factors were regulated during C. glauca and A. glutinosa-Frankia interactions, respectively. Phylogenetic studies confirmed the presence of common key transcription factors such as NSP, NF-YA and ERN-related proteins involved in nodule formation in legumes, which confirm the existence of a common symbiosis signaling pathway in nitrogen-fixing root nodule symbioses. We also identified an actinorhizal-specific transcription factor belonging to the zinc finger C1-2i subfamily we named CgZF1 in C. glauca and AgZF1 in A. glutinosa.

CONCLUSIONS

We identified putative nodulation-associated transcription factors with particular emphasis on members of the GRAS, NF-YA, ERF and C2H2 families. Interestingly, comparison of the non-legume and legume TF with signaling elements from actinorhizal species revealed a new subgroup of nodule-specific C2H2 TF that could be specifically involved in actinorhizal symbioses. In silico identification, transcript analysis, and phylogeny reconstruction of transcription factor families paves the way for the study of specific molecular regulation of symbiosis in response to Frankia infection.

Micromonospora is a normal occupant of actinorhizal nodules

Actinorhizal plants have been found in eight genera belonging to three orders (Fagales, Rosales and Cucurbitales). These all bear root nodules inhabited by bacteria identified as the nitrogen-fixing actinobacterium Frankia. These nodules all have a peripheral cortex with enlarged cells filled with Frankia hyphae and vesicles. Isolation in pure culture has been notoriously difficult, due in a large part to the growth of fast-growing contaminants where, it was later found, Frankia was slow-growing. Many of these contaminants, which were later found to be Micromonospora, were obtained from Casuarina and Coriaria. Our study was aimed at determining if Micromonospora were also present in other actinorhizal plants. Nodules from Alnus glutinosa, Alnus viridis, Coriaria myrtifolia, Elaeagnus x ebbingei, Hippophae rhamnoides, Myrica gale and Morella pensylvanica were tested and were all found to contain Micromonospora isolates. These were found to belong to mainly three species: Micromonospora lupini, Micromonospora coriariae and Micromonospora saelicesensis. Micromonospora isolates were found to inhibit some Frankia strains and to be innocuous to other strains.

Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus

A bacterial strain designated RLAHU15(T) was isolated from root nodules of Lupinus albus in Spain. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus, with its closest relatives being Paenibacillus catalpae D75(T), Paenibacillus glycanilyticus DS-1(T), Paenibacillus endophyticus PECAE04(T) and Paenibacillus xinjiangensis B538(T) with 98.8 %, 98.9 %, 97.4 % and 97.4 % similarity, respectively. DNA-DNA hybridization studies showed values lower than 45 % between the strain RLAHU15(T) and any of these species. The isolate was a Gram-stain positive, motile and sporulating rod. Catalase activity was weak and oxidase activity was positive. Casein and starch were hydrolysed but gelatin was not. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and an unidentified lipid. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 54.4 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RLAHU15(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lupini sp. nov. is proposed. The type strain is RLAHU15(T) ( = LMG 27296(T) = CECT 8235(T)).

Inoculation of the nonlegume Capsicum annuum L. with Rhizobium strains. 2. Changes in sterols, triterpenes, fatty acids, and volatile compounds

Peppers (Capsicum spp.) are consumed worldwide, imparting flavor, aroma, and color to foods, additionally containing high concentrations of biofunctional compounds. This is the first report about the effect of the inoculation of two Rhizobium strains on sterols, triterpenes, fatty acids, and volatile compounds of leaves and fruits of pepper (Capsicum annuum L.) plants. Generally, inoculation with strain TVP08 led to the major changes, being observed a decrease of sterols and triterpenes and an increase of fatty acids, which are related to higher biomass, growth, and ripening of pepper fruits. The increase of volatile compounds may reflect the elicitation of plant defense after inoculation, since the content on methyl salicylate was significantly increased in inoculated material. The findings suggest that inoculation with Rhizobium strains may be employed to manipulate the content of interesting metabolites in pepper leaves and fruits, increasing potential health benefits and defense abilities of inoculated plants.

Inoculation of the nonlegume Capsicum annuum (L.) with Rhizobium strains. 1. Effect on bioactive compounds, antioxidant activity, and fruit ripeness

Pepper (Capsicum annuum L.) is an economically important agricultural crop and an excellent dietary source of natural colors and antioxidant compounds. The levels of these compounds can vary according to agricultural practices, like inoculation with plant growth-promoting rhizobacteria. In this work we evaluated for the first time the effect of the inoculation of two Rhizobium strains on C. annuum metabolites and bioactivity. The results revealed a decrease of organic acids and no effect on phenolics and capsaicinoids of leaves from inoculated plants. In the fruits from inoculated plants organic acids and phenolic compounds decreased, showing that fruits from inoculated plants present a higher ripeness stage than those from uninoculated ones. In general, the inoculation with Rhizobium did not improve the antioxidant activity of pepper fruits and leaves. Considering the positive effect on fruit ripening, the inoculation of C. annuum with Rhizobium is a beneficious agricultural practice for this nonlegume.

Cohnella lupini sp. nov., an endophytic bacterium isolated from root nodules of Lupinus albus

A bacterial strain designated RLAHU4BT was isolated from root nodules of Lupinus albus in León (Spain). The 16S rRNA gene sequence of this strain showed similarities lower than 97 % with respect to species of the genus Cohnella . The strain was a Gram-variable, sporulating rod, motile by means of peritrichous flagella, and facultatively anaerobic. It was positive for oxidase, catalase and β-galactosidase production but negative for urease, amylase and gelatinase. Strain RLAHU4BT grew in the presence of 5 % NaCl. MK-7 was the predominant menaquinone and meso-diaminopimelic acid was present in the peptidoglycan. anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0 and C16 : 0 were the major fatty acids. Major polar lipids of strain RLAHU4BT were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, two unknown aminophospholipids and one unknown lipid. The DNA G+C content was 57.8 mol%. Strain RLAHU4BT presented phenotypic differences from all recognized species of the genus Cohnella . The phylogenetic, chemotaxonomic and phenotypic data indicated that strain RLAHU4BT belongs to a novel species of the genus Cohnella , for which the name Cohnella lupini sp. nov. is proposed, with strain RLAHU4BT ( = LMG 27416T = CECT 8236T) as the type strain.

Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum

A bacterial strain, designated PECAE04(T), was isolated from root nodules of Cicer arietinum in Spain. Phylogenetic analysis based on 16S rRNA gene sequence placed the isolate into the genus Paenibacillus with its closest relative being Paenibacillus castaneae Ch-32(T) with 98.4 % 16S rRNA gene sequence similarity followed by Paenibacillus glycanilyticus DS-1(T), Paenibacillus prosopidis PW21(T), Paenibacillus xinjiangensis B538(T) and Paenibacillus catalpae D75(T) with similarities ranging from 97.9 to 96.8 %. DNA-DNA hybridization measurements showed values lower than 20 % between the strain PECAE04(T) and any of these species. The isolate was a Gram-stain-positive, motile, sporulating rod. Catalase and oxidase activities were positive. Aesculin was hydrolysed but casein and gelatin were not. Acetoin production, H2S production, nitrate reduction and urease and caseinase production were negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the predominant menaquinone and anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, three phospholipids and an unidentified lipid. Meso-diaminopimelic acid was not detected in the peptidoglycan. The DNA G+C content was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PECAE04(T) should be considered to be a representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus endophyticus sp. nov. is proposed. The type strain is PECAE04(T) ( = LMG 27297(T) = CECT 8234(T)).

Micromonospora halotolerans sp. nov., isolated from the rhizosphere of a Pisum sativum plant

A filamentous actinomycete strain designated CR18(T) was isolated on humic acid agar from the rhizosphere of a Pisum sativum plant collected in Spain. This isolate was observed to grow optimally at 28 °C, pH 7.0 and in the presence of 5 % NaCl. Phylogenetic analyses based on the 16S rRNA gene sequence indicated a close relationship with the type strains of Micromonospora chersina and Micromonospora endolithica. A further analysis based on a concatenated DNA sequence stretch of 4,523 bp that included partial sequences of the atpD, gyrB, recA, rpoB and 16S rRNA genes clearly differentiated the new strain from recognized Micromonospora species compared. DNA-DNA hybridization studies further supported the taxonomic position of strain CR18(T) as a novel genomic species. Chemotaxonomic analyses which included whole cell sugars, polar lipids, fatty acid profiles and menaquinone composition confirmed the affiliation of the new strain to the genus Micromonospora and also highlighted differences at the species level. These studies were finally complemented with an array of physiological tests to help differentiate between the new strain and its phylogenetic neighbours. Consequently, strain CR18(T) (= CECT 7890(T) = DSM 45598(T)) is proposed as the type strain of a novel species, Micromonospora halotolerans sp. nov.

Micromonospora cremea sp. nov. and Micromonospora zamorensis sp. nov., isolated from the rhizosphere of Pisum sativum

Three actinobacterial strains, CR30(T), CR36 and CR38(T), were isolated from rhizosphere soil of Pisum sativum plants collected in Spain. The strains were filamentous, Gram-stain-positive and produced single spores. Phylogenetic, chemotaxonomic and morphological analyses confirmed that the three strains belonged to the genus Micromonospora. 16S rRNA gene sequence analysis of strains CR30(T) and CR36 showed a close relationship to Micromonospora coriariae NAR01(T) (99.3% similarity) while strain CR38(T) had a similarity of 99.0% with Micromonospora saelicesensis Lupac 09(T). In addition, gyrB gene phylogeny clearly differentiated the novel isolates from recognized Micromonospora species. DNA-DNA hybridization, BOX-PCR and ARDRA profiles confirmed that these strains represent novel genomic species. The cell-wall peptidoglycan of strains CR30(T) and CR38(T) contained meso-diaminopimelic acid. Both strains had MK-10(H(4)) as the main menaquinone and a phospholipid type II pattern. An array of physiological tests also differentiated the isolates from their closest neighbours. Considering all the data obtained, it is proposed that strains CR30(T) and CR36 represent a novel species under the name Micromonospora cremea sp. nov. (type strain CR30(T) = CECT 7891(T) = DSM 45599(T)), whereas CR38(T) represents a second novel species, for which the name Micromonospora zamorensis sp. nov. is proposed, with CR38(T) ( = CECT 7892(T) = DSM 45600(T)) as the type strain.

Herbaspirillum canariense sp. nov., Herbaspirillum aurantiacum sp. nov. and Herbaspirillum soli sp. nov., isolated from volcanic mountain soil, and emended description of the genus Herbaspirillum

Three Gram-negative, motile and slightly curved rod-shaped bacteria, strains SUEMI03T, SUEMI08T and SUEMI10T, were isolated from an old volcanic mountain soil on Tenerife (Canary Islands). The three strains were related phylogenetically to Herbaspirillum seropedicae . 16S rRNA gene sequence similarity was 99.2–99.6 % among strains SUEMI03T, SUEMI08T and SUEMI10T, which presented 97.5, 97.8 and 97.7 % identity, respectively, with respect to H. seropedicae DSM 6445T. The three strains grew optimally in TSB at 28 °C and contained summed features 3 (C16 : 1ω6c and/or C16 : 1ω7c) and 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C16 : 0 as major cellular fatty acids. The DNA G+C contents of strains SUEMI03T, SUEMI08T and SUEMI10T were 61.6, 60.4 and 61.9 mol%, respectively. Strains SUEMI03T, SUEMI08T and SUEMI10T presented less than 60 % interstrain DNA relatedness and less than 30 % relatedness with respect to H. seropedicae DSM 6445T. In spite of their common geographical origin, the three strains isolated in this study presented several phenotypic differences, presenting phenotypic profiles highly divergent from that of H. seropedicae . Therefore, we propose that the strains isolated in this study represent three novel species of the genus Herbaspirillum , named Herbaspirillum canariense sp. nov. (type strain SUEMI03T  = LMG 26151T  = CECT 7838T), Herbaspirillum aurantiacum sp. nov. (type strain SUEMI08T  = LMG 26150T  = CECT 7839T) and Herbaspirillum soli sp. nov. (type strain SUEMI10T  = LMG 26149T  = CECT 7840T).

Rhizobium promotes non-legumes growth and quality in several production steps: towards a biofertilization of edible raw vegetables healthy for humans

The biofertilization of crops with plant-growth-promoting microorganisms is currently considered as a healthy alternative to chemical fertilization. However, only microorganisms safe for humans can be used as biofertilizers, particularly in vegetables that are raw consumed, in order to avoid sanitary problems derived from the presence of pathogenic bacteria in the final products. In the present work we showed that Rhizobium strains colonize the roots of tomato and pepper plants promoting their growth in different production stages increasing yield and quality of seedlings and fruits. Our results confirmed those obtained in cereals and alimentary oil producing plants extending the number of non-legumes susceptible to be biofertilized with rhizobia to those whose fruits are raw consumed. This is a relevant conclusion since safety of rhizobia for human health has been demonstrated after several decades of legume inoculation ensuring that they are optimal bacteria for biofertilization.

Phyllobacterium endophyticum sp. nov., isolated from nodules of Phaseolus vulgaris

A strain, PEPV15(T), was isolated from a nodule on Phaseolus vulgaris grown in soil in northern Spain. Phylogenetic analyses of 16S rRNA and atpD genes showed that this strain belongs to the genus Phyllobacterium. The most closely related species were, in both cases, Phyllobacterium brassicacearum, Phyllobacterium bourgognense and Phyllobacterium trifolii, the type strains of which gave sequence similarities of 98.9, 98.6 and 98.4 %, respectively, in the 16S rRNA gene and 88.1, 87.5 and 88.7 %, respectively, in the atpD gene. PEPV15(T) contained Q-10 as the major quinone (88 %) and low amounts of Q-9 (12 %). It differed from its closest relatives in its growth in diverse culture conditions and in the assimilation of several carbon sources. The strain was not able to produce nodules in Phaseolus vulgaris. The results of DNA-DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain represents a novel species of the genus Phyllobacterium for which the name Phyllobacterium endophyticum sp. nov. is proposed; the type strain is PEPV15(T) ( = LMG 26470(T) = CECT 7949(T)). An emended description of the genus Phyllobacterium is also provided.

Diversity of Micromonospora strains isolated from nitrogen fixing nodules and rhizosphere of Pisum sativum analyzed by multilocus sequence analysis

It was recently reported that Micromonospora inhabits the intracellular tissues of nitrogen fixing nodules of the wild legume Lupinus angustifolius. To determine if Micromonospora populations are also present in nitrogen fixing nodules of cultivated legumes such as Pisum sativum, we carried out the isolation of this actinobacterium from P. sativum plants collected in two man-managed fields in the region of Castilla and León (Spain). In this work, we describe the isolation of 93 Micromonospora strains recovered from nitrogen fixing nodules and the rhizosphere of P. sativum. The genomic diversity of the strains was analyzed by amplified ribosomal DNA restriction analysis (ARDRA). Forty-six isolates and 34 reference strains were further analyzed using a multilocus sequence analysis scheme developed to address the phylogeny of the genus Micromonospora and to evaluate the species distribution in the two studied habitats. The MLSA results were evaluated by DNA-DNA hybridization to determine their usefulness for the delineation of Micromonospora at the species level. In most cases, DDH values below 70% were obtained with strains that shared a sequence similarity of 98.5% or less. Thus, MLSA studies clearly supported the established taxonomy of the genus Micromonospora and indicated that genomic species could be delineated as groups of strains that share > 98.5% sequence similarity based on the 5 genes selected. The species diversity of the strains isolated from both the rhizosphere and nodules was very high and in many cases the new strains could not be related to any of the currently described species.