Frankia [NiFe] uptake hydrogenases and genome reduction: different lineages of loss.

Uptake hydrogenase (Hup) recycles H2 formed by nitrogenase during nitrogen fixation, thereby preserving energy. Among root nodule bacteria, most rhizobial strains examined are Hup-, while only one Hup-  Frankia inoculum had been identified. Previous analyses had led to the identification of two different [NiFe] hydrogenase syntons.

Effect of gamma irradiation on the proteogenome of cold-acclimated Kocuria rhizophila PT10.

The effects of ionizing radiation (IR) on the protein dynamics of cold-stressed cells of a radioresistant actinobacterium, Kocuria rhizophila PT10, isolated from the rhizosphere of the desert plant Panicum turgidum were investigated using a shotgun methodology based on nanoflow liquid chromatography coupled to tandem mass spectrometry. Overall, 1487 proteins were certified, and their abundances were compared between the irradiated condition and control. IR of cold-acclimated PT10 triggered the over-abundance of proteins involved in (1) a strong transcriptional regulation, (2) amidation of peptidoglycan and preservation of cell envelope integrity, (3) detoxification of reactive electrophiles and regulation of the redox status of proteins, (4) base excision repair and prevention of mutagenesis and (5) the tricarboxylic acid (TCA) cycle and production of fatty acids.

sp. nov., a non-infective non-nitrogen-fixing isolate from root nodules of Wall.

Strains CN4, CN6, CN7 and CNm7 were isolated from root nodules of from Murree in Pakistan. They do not form root nodules on nor on although they deformed root hairs of . The colonies are bright red-pigmented, the strains form hyphae and sporangia but no N-fixing vesicles and do not fix nitrogen .

Identification and evolution of nsLTPs in the root nodule nitrogen fixation clade and molecular response of Frankia to AgLTP24.

Non-specific lipid transfer proteins (nsLTPs) are antimicrobial peptides, involved in several plant biological processes including root nodule nitrogen fixation (RNF). Nodulating plants belonging to the RNF clade establish symbiosis with the nitrogen-fixing bacteria rhizobia (legumes symbiosis model) and Frankia (actinorhizal symbiosis model) leading to root nodule formation. nsLTPs are involved in processes active in early step of symbiosis and functional nodule in both models.

Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis.

Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis.

Carbonic Anhydrase Regulates Cytoplasmic pH of Nitrogen-Fixing Vesicles.

A phyloprofile of 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 (nitrogenase), and genes which are not know as symbiosis-associated genes such as (carbonic anhydrase, CAN).

Draft Genomes of strains AiPa1 and AiPs1 Retrieved from Soil with Monocultures of or using as Capture Plant.

The genomes of two nitrogen-fixing strains, AiPa1 and AiPs1, are described as representatives of two novel candidate species Both strains were isolated from root nodules of , used as capture plants in bioassays on soils from a reforested site at Karttula, Finland, that was devoid of actinorhizal plants but contained 25 year-old monocultures of spruce ( (L.) Karsten) or pine ( L.), respectively.

Correction: Pujic et al. The Proteogenome of Symbiotic in Nodules. 2022, , 651.

The authors wish to make the following corrections to this paper [...

Draft Genome of sp. Strain R82, an Isolate from Root Nodules of Myrica gale.

The sp. strain R82 genome is described as representative of a novel candidate species within cluster 1, as indicated by average nucleotide identity (ANI) analyses, with its closest relatives being Frankia nodulisporulans AgTrs and strains Ag45/Mut15 and AgPM24 (86% identity).

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

The response of to 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 . Forty-two genes were significantly upregulated in inoculated compared with noninoculated roots.

ST1 and Paga Strains Cohabit in Olive Knots.

Two bacteria belonging to the and genera were isolated from olive knots. Both bacterial strains were omnipresent in this study's olive orchard with high susceptibility of the autochthonous olive genotypes indicating coevolution of bacteria with host plants. Genomes of two endemic bacteria show conserved core genomes and genome plasticity.

Draft Genomes of Symbiotic Strains AgB32 and AgKG'84/4 from Root Nodules of growing under Contrasted Environmental Conditions.

The genomes of two nitrogen-fixing strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of , but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.

Draft Genomes of Nitrogen-fixing Strains Ag45/Mut15 and AgPM24 Isolated from Root Nodules of .

The genomes of two nitrogen-fixing strains, Ag45/Mut15 and AgPM24, isolated from root nodules of are described as representatives of a novel candidate species Phylogenomic and ANI analyses confirmed that both strains are related to cluster 1 frankiae, and that both strains belong to a novel species. At 6.4 - 6.

The Proteogenome of Symbiotic in Nodules.

Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic A proteogenomic analysis of symbiotic was done by comparing those proteins more and less abundant in nodules relative to N-fixing pure cultures with propionate as the carbon source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-fixing pure culture. Nitrogenase, SuF (Fe-Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis.

Roots of the xerophyte host a cohort of ionizing-radiation-resistant biotechnologically-valuable bacteria.

Bacterial communities associated with roots of , exposed to arid conditions, were investigated with a combination of cultural and metataxonomic approaches. Traditional culture-based techniques were used and 32 isolates from the irradiated roots were identified as belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria phyla. Four actinobacterial strains were shown to be ionizing-radiation (IR)-resistant: sp.

Seed Paternity Analysis Using SSR Markers to Assess Successful Pollen Donors in Mixed Olive Orchards.

The olive tree ( L.) is a wind-pollinated crop that exhibits an extreme alternate bearing habit. To improve fruit set, several methods have been used to determine the most successful compatible combinations of cultivars.

Microbial risk assessment of in polluted environments, case of urban rainfall water.

Unlabelled: Urban Infiltration Basins (UIBs) are used to manage urban runoff transfers and feed aquifers. These UIBs can accumulate urban pollutants and favor the growth of potentially pathogenic biological agents as .

Objectives: To assess the spatio-temporal dynamics of pathogenic in UIBs and to stablish phylogenetic relationships between clinical and UIB strains.

Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal.

A new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant actinobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide.

Draft genome sequence of Promicromonospora panici sp. nov., a novel ionizing-radiation-resistant actinobacterium isolated from roots of the desert plant Panicum turgidum.

A novel strain of the genus Promicromonospora, designated PT9, was recovered from irradiated roots of the xerophyte Panicum turgidum collected from the Ksar Ghilane oasis in southern Tunisia. Strain PT9 is aerobic, non-spore-forming, Gram- positive actinomycete that produces branched hyphae and forms white to yellowish-white colonies. Chemotaxonomic features, including fatty acids, whole cell sugars and polar lipid profiles, support the assignment of PT9 to the genus Promicromonospora.

Genome Sequence of sp. Strain ST1, Isolated from Olive (Olea europaea L.) Knot Galls in Croatia.

We report the genome sequence of a sp. strain isolated from olive knot galls. The genome size is 6.

Whole-Genome Sequence of a sp. Strain Isolated from an Olive (Olea europaea L.) Knot.

Here, we present the total genome sequence of sp. strain paga, a plant-associated bacterium isolated from knots present on olive trees grown on the Adriatic Coast. The genome size of sp.

Omics of the early molecular dialogue between Frankia alni and Alnus glutinosa and the cellulase synton.

The early Frankia-Alnus symbiotic molecular exchanges were analyzed in detail by protein and RNA omics. For this, Frankia cells were placed in the presence of Alnus roots but separated by a dialysis membrane for 64 h. The bacterial cells were then harvested and analyzed by high-throughput proteomics and transcriptomics (RNA-seq).

Actinorhizal Signaling Molecules: Root Hair Deforming Factor Shares Properties With NIN Inducing Factor.

Actinorhizal plants are able to establish a symbiotic relationship with bacteria leading to the formation of root nodules. The symbiotic interaction starts with the exchange of symbiotic signals in the soil between the plant and the bacteria. This molecular dialog involves signaling molecules that are responsible for the specific recognition of the plant host and its endosymbiont.

Generation of a cluster-free Streptomyces albus chassis strains for improved heterologous expression of secondary metabolite clusters.

Natural products are a rich source of potential drugs for many applications. Discovery of natural products through the activation of cryptic gene clusters encoding their biosynthetic pathways, engineering of those biosynthetic pathways and optimization of production yields often rely on the expression of these gene clusters in suitable heterologous host strains. Streptomyces albus J1074 provides high success rates of heterologous cluster expression with high levels of metabolite production, rapid growth and amenability to genetic manipulations.