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.

sp. nov., isolated from root nodules of L.

strain Ag45/Mut15 was isolated from a root nodule of growing in a swamp at lake Grossensee, Germany. The strain forms root nodules on , in which it produces hyphae and clusters of N-fixing vesicles. N-fixing vesicles are also produced in nitrogen-free growth medium, in addition to hyphae and sporangia.

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.

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.

Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta.

We describe a new Frankia species, for three non-isolated strains obtained from Alnus glutinosa in France and Sweden, respectively. These strains can nodulate several Alnus species (A. glutinosa, A.

Proposal of ' Frankia alpina', the uncultured symbiont of and that forms spore-containing nitrogen-fixing root nodules.

The members of the genus are, with a few exceptions, a group of nitrogen-fixing symbiotic actinobacteria that nodulate mostly woody dicotyledonous plants belonging to three orders, eight families and 23 genera of pioneer dicots. These bacteria have been characterized phylogenetically and grouped into four molecular clusters. One of the clusters, cluster 1 contains strains that induce nodules on spp.

Feedback Regulation of N Fixation in Symbiosis Through Amino Acids Profiling in Field and Greenhouse Nodules.

Symbiosis established between actinorhizal plants and spp., which are nitrogen-fixing actinobacteria, promotes nodule organogenesis, the site of metabolic exchange. The present study aimed to identify amino acid markers involved in - interactions by comparing nodules and associated roots from field and greenhouse samples.

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.

Draft genome sequences for three unisolated -infective Sp+ strains, AgTrS, AiOr and AvVan, the first sequenced strains able to sporulate .

Actinobacteria from genus are able to form symbiotic associations with actinorhizal plants including alders. Among them, Sp+ strains are characterized by their ability to differentiate numerous sporangia inside host plant cells (unlike "Sp-" strains unable of sporulation). Here, we report the first genome sequences of three unisolated Sp+ strains: AgTrS, AiOr and AvVan obtained from , and (previously known as ), respectively (with genome completeness estimated at more than 98%).

Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon.

The taxonomic assignment of uncultured prokaryotes to known taxa is a major challenge in microbial systematics. This relies usually on the phylogenetic analysis of the ribosomal small subunit RNA or a few housekeeping genes. Recent works have disclosed ribosomal proteins as valuable markers for systematics and, due to the boom in complete genome sequencing, their use has become widespread.