Whole-genome sequence of the non-rhizobial root nodule endophyte Bosea sp. strain 685 isolated from the root nodule of Astragalus umbellatus Bunge., growing on the Kamchatka Peninsula.

This study reports the whole-genome sequence of an endosymbiotic bacteria Bosea sp. strain 685, which was isolated from the root nodule of Astragalus umbellatus Bunge. in the Kamchatka Peninsula, Russia. The genome consists of one chromosome and one plasmid with a total length of 6,795,213 bp and 65.37% of GC content.

Draft genome sequence of Janibacter limosus strain RCAM05316 isolated from Shulgan-Tash cave lime mud.

The Shulgan-Tash (Kapova) cave is a unique object for scientific research. In this article, we report the draft genome sequence of Janibacter limosus strain P1(28)-3 (RCAM05316) isolated from cave lime mud, Russia (53° 2' 0″ N, 57° 3' 0″ E). The sequence was obtained using Oxford Nanopore Technologies MinION.

Synergy between Rhizobial Co-Microsymbionts Leads to an Increase in the Efficiency of Plant-Microbe Interactions.

Combined inoculation of legumes with rhizobia and plant growth-promoting rhizobacteria or endophytes is a known technique for increasing the efficiency of nitrogen-fixing symbiosis and plant productivity. The aim of this work was to expand knowledge about the synergistic effects between commercial rhizobia of pasture legumes and root nodule bacteria of relict legume species. Pot experiments were performed on common vetch (Vicia sativa L.) and red clover (Trifolium pratense L.) co-inoculated with the participation of the corresponding commercial rhizobial strains (R. leguminosarum bv. viciae RCAM0626 and R. leguminosarum bv. trifolii RCAM1365) and seven strains isolated from nodules of relict legumes inhabiting the Baikal Lake region and the Altai Republic: Oxytropis popoviana, Astragalus chorinensis, O. tragacanthoides and Vicia costata. The inoculation of plants with combinations of strains (commercial strain plus the isolate from relict legume) had a different effect on symbiosis depending on the plant species: the increase in the number of nodules was mainly observed on vetch, whereas increased acetylene reduction activity was evident on clover. It was shown that the relict isolates differ significantly in the set of genes related to different genetic systems that affect plant-microbe interactions. At the same time, they had additional genes that are involved in the formation of symbiosis and determine its effectiveness, but are absent in the used commercial strains: symbiotic genes fix, nif, nod, noe and nol, as well as genes associated with the hormonal status of the plant and the processes of symbiogenesis (acdRS, genes for gibberellins and auxins biosynthesis, genes of T3SS, T4SS and T6SS secretion systems). It can be expected that the accumulation of knowledge about microbial synergy on the example of the joint use of commercial and relict rhizobia will allow in the future the development of methods for the targeted selection of co-microsymbionts to increase the efficiency of agricultural legume-rhizobia systems.

Influence of Plant Growth-Promoting Rhizobacteria on the Formation of Apoplastic Barriers and Uptake of Water and Potassium by Wheat Plants.

The formation of apoplastic barriers is important for controlling the uptake of water and ions by plants, thereby influencing plant growth. However, the effects of plant growth-promoting bacteria on the formation of apoplastic barriers, and the relationship between these effects and the ability of bacteria to influence the content of hormones in plants, have not been sufficiently studied. The content of cytokinins, auxins and potassium, characteristics of water relations, deposition of lignin and suberin and the formation of Casparian bands in the root endodermis of durum wheat (Triticum durum Desf.) plants were evaluated after the introduction of the cytokinin-producing bacterium Bacillus subtilis IB-22 or the auxin-producing bacterium Pseudomonas mandelii IB-Ki14 into their rhizosphere. The experiments were carried out in laboratory conditions in pots with agrochernozem at an optimal level of illumination and watering. Both strains increased shoot biomass, leaf area and chlorophyll content in leaves. Bacteria enhanced the formation of apoplastic barriers, which were most pronounced when plants were treated with P. mandelii IB-Ki14. At the same time, P. mandelii IB-Ki14 caused no decrease in the hydraulic conductivity, while inoculation with B. subtilis IB-22, increased hydraulic conductivity. Cell wall lignification reduced the potassium content in the roots, but did not affect its content in the shoots of plants inoculated with P. mandelii IB-Ki14. Inoculation with B. subtilis IB-22 did not change the potassium content in the roots, but increased it in the shoots.

Aluminum-Immobilizing Rhizobacteria Modulate Root Exudation and Nutrient Uptake and Increase Aluminum Tolerance of Pea Mutant E107 (brz).

It is well known that plant-growth-promoting rhizobacteria (PGPRs) increase the tolerance of plants to abiotic stresses; however, the counteraction of Al toxicity has received little attention. The effects of specially selected Al-tolerant and Al-immobilizing microorganisms were investigated using pea cultivar Sparkle and its Al-sensitive mutant E107 (brz). The strain Cupriavidus sp. D39 was the most-efficient in the growth promotion of hydroponically grown peas treated with 80 µM AlCl3, increasing the plant biomass of Sparkle by 20% and of E107 (brz) by two-times. This strain immobilized Al in the nutrient solution and decreased its concentration in E107 (brz) roots. The mutant showed upregulated exudation of organic acids, amino acids, and sugars in the absence or presence of Al as compared with Sparkle, and in most cases, the Al treatment stimulated exudation. Bacteria utilized root exudates and more actively colonized the root surface of E107 (brz). The exudation of tryptophan and the production of IAA by Cupriavidus sp. D39 in the root zone of the Al-treated mutant were observed. Aluminum disturbed the concentrations of nutrients in plants, but inoculation with Cupriavidus sp. D39 partially restored such negative effects. Thus, the E107 (brz) mutant is a useful tool for studying the mechanisms of plant-microbe interactions, and PGPR plays an important role in protecting plants against Al toxicity.

Draft Genome Sequence of Rhizobium sp. Strain 32-5/1, Isolated from Vicia cracca L. Root Nodules in the Russian Arctic.

This study reports the whole-genome sequence of an endosymbiotic bacterium, Rhizobium sp. strain 32-5/1, isolated from root nodules of the legume Vicia cracca L. in the Arctic region of Russia. The genome consists of two plasmids and one chromosome, with a total length of 5,621,108 bp and 59.5% GC content.

Draft Genome Sequence of Guar (Cyamopsis tetragonoloba L.) Microsymbiont Rhizobium sp. Strain RCAM05973.

Here, we present the draft genome sequence of Rhizobium sp. strain RCAM05973 which was isolated from a Cyamopsis tetragonoloba (guar) root nodule. The genome contains 6,937,221 bp in 2 contigs and has a GC content of 60%.

Whole-Genome Sequence of Rhizobacterium Sphingomonas sp. Strain 7/4-4, Isolated from the Root Nodule of Astragalus tugarinovii Basil Growing in the Russian Arctic.

The complete genome sequence of Sphingomonas sp. strain 7/4-4, which was isolated from the root nodule of the circumpolar legume Astragalus tugarinovii Basil, is reported. The assembly contains 4,423,370 bp in 1 circular chromosome, with a GC content of 65.94%. The genome sequence of strain 7/4-4 could provide insights into the metabolic potential of Arctic rhizobacteria.

Strain Streptomyces sp. P-56 Produces Nonactin and Possesses Insecticidal, Acaricidal, Antimicrobial and Plant Growth-Promoting Traits.

Streptomycetes produce a huge variety of bioactive metabolites, including antibiotics, enzyme inhibitors, pesticides and herbicides, which offer promise for applications in agriculture as plant protection and plant growth-promoting products. The aim of this report was to characterize the biological activities of strain Streptomyces sp. P-56, previously isolated from soil as an insecticidal bacterium. The metabolic complex was obtained from liquid culture of Streptomyces sp. P-56 as dried ethanol extract (DEE) and possessed insecticidal activity against vetch aphid (Medoura viciae Buckt.), cotton aphid (Aphis gossypii Glov.), green peach aphid (Myzus persicae Sulz.), pea aphid (Acyrthosiphon pisum Harr.) and crescent-marked lily aphid (Neomyzus circumflexus Buckt.), as well as two-spotted spider mite (Tetranychus urticae). Insecticidal activity was associated with production of nonactin, which was purified and identified using HPLC-MS and crystallographic techniques. Strain Streptomyces sp. P-56 also showed antibacterial and antifungal activity against various phytopathogenic bacteria and fungi (mostly for Clavibacfer michiganense, Alternaria solani and Sclerotinia libertiana), and possessed a set of plant growth-promoting traits, such as auxin production, ACC deaminase and phosphate solubilization. The possibilities for using this strain as a biopesticide producer and/or biocontrol and a plant growth-promoting microorganism are discussed.

Draft Genome Sequence of the Bacterium Cupriavidus sp. Strain D39, Inhabiting the Rhizosphere of Pea Plants (Pisum sativum L.).

We report the draft genome sequence of Cupriavidus sp. strain D39, associated with the roots of pea plants. The genome is characterized by a GC content of 63.62% and a total length of 7.7 Mbp and contains several putative genes associated with resistance to metals and plant growth promotion.

Complete Genome Sequences of Massilia sp. Strains B-10 and H-1, Isolated from the Water in the Shulgan-Tash Cave.

In this article, we report the complete genome sequences of Massilia sp. strains B-10 (RCAM05335) and H-1 (RCAM05339), which were isolated from the water of the Dal'nee Verkhnee Lake in the Shulgan-Tash cave in Russia (53°2'0″N, 57°3'0″E). The sequences were obtained using an Oxford Nanopore Technologies MinION system.

Water Stress, Cadmium, and Plant Genotype Modulate the Rhizosphere Microbiome of Pisum sativum L.

Drought and heavy metals seriously affect plant growth and the biodiversity of the associated rhizosphere microbiomes, which, in turn, could be involved in the adaptation of plants to these environmental stresses. Rhizosphere soil was collected from a three-factor pot experiment, where pea line SGE and its Cd-tolerant mutant SGECdt were cultivated under both optimal and limited water conditions and treated with a toxic Cd concentration. The taxonomic structure of the prokaryotic rhizosphere microbiome was analyzed with the high-throughput sequencing of 16S rRNA amplicon libraries. A permutation test demonstrated statistically significant effects of Cd and water stress but not of pea genotype on the rhizosphere microbiome structure. Phylogenetic isometric log-ratio data transformation identified the taxonomic balances that were affected by abiotic factors and pea genotypes. A small number of significant (log ratio [-3.0:+3.0]) and phylogenetically deep balances characterized water stress, while a larger number of weak (log ratio [-0.8:+0.8]) phylogenetically lower balances described the influence of the plant genotype. Stress caused by cadmium took on an intermediate position. The main conclusion of the study is that the most powerful factor affecting the rhizosphere microbiome was water stress, and the weakest factor was plant genotype since it demonstrated a very weak transformation of the taxonomic structure of rhizosphere microbiomes in terms of alpha diversity indices, beta diversity, and the log ratio values of taxonomic balances.

Isolation and Characterization of 1-Hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic Acid, a Metabolite in Bacterial Transformation of Abscisic Acid.

We report the discovery of a new abscisic acid (ABA) metabolite, found in the course of a mass spectrometric study of ABA metabolism by the rhizosphere bacterium Rhodococcus sp. P1Y. Analogue of (+)-ABA, enriched in tritium in the cyclohexene moiety, was fed in bacterial cells, and extracts containing radioactive metabolites were purified and analyzed to determine their structure. We obtained mass spectral fragmentation patterns and nuclear magnetic resonance spectra of a new metabolite of ABA identified as 1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexene-1-acetic acid, which we named rhodococcal acid (RA) and characterized using several other techniques. This metabolite is the second bacterial ABA degradation product in addition to dehydrovomifoliol that we described earlier. Taken together, these data reveal an unknown ABA catabolic pathway that begins with side chain disassembly, as opposed to the conversion of the cyclohexene moiety in plants. The role of ABA-utilizing bacteria in interactions with other microorganisms and plants is also discussed.

Complete Genome Sequence of Rhizobium sp. Strain RCAM05350 from Shulgan-Tash Karst Cave.

The Shulgan-Tash cave is an extremely interesting object for scientific research, located in the Republic of Bashkortostan (Russia). In this article, we report the complete genome sequence of Rhizobium sp. strain RCAM05350 isolated from the "cave silver" biofilms. The sequence was obtained using Oxford Nanopore Technologies MinION.

Rhizobacteria Mitigate the Negative Effect of Aluminum on Pea Growth by Immobilizing the Toxicant and Modulating Root Exudation.

High soil acidity is one of the main unfavorable soil factors that inhibit the growth and mineral nutrition of plants. This is largely due to the toxicity of aluminum (Al), the mobility of which increases significantly in acidic soils. Symbiotic microorganisms have a wide range of beneficial properties for plants, protecting them against abiotic stress factors. This report describes the mechanisms of positive effects of plant growth-promoting rhizobacteria Pseudomonas fluorescens SPB2137 on four pea (Pisum sativum L.) genotypes grown in hydroponics and treated with 80 µM AlCl3. In batch culture, the bacteria produced auxins, possessed 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, alkalized the medium and immobilized Al, forming biofilm-like structures and insoluble phosphates. Inoculation with Ps. fluorescens SPB2137 increased root and/or shoot biomass of Al-treated plants. The bacteria alkalized the nutrient solution and transferred Al from the solution to the residue, which contained phosphorus that was exuded by roots. As a result, the Al concentration in roots decreased, while the amount of precipitated Al correlated negatively with its concentration in the solution, positively with the solution pH and negatively with Al concentration in roots and shoots. Treatment with Al induced root exudation of organic acids, amino acids and sugars. The bacteria modulated root exudation via utilization and/or stimulation processes. The effects of Al and bacteria on plants varied depending on pea genotype, but all the effects had a positive direction and the variability was mostly quantitative. Thus, Ps. fluorescens SPB2137 improved the Al tolerance of pea due to immobilization and exclusion of toxicants from the root zone.

Phosphate Mobilization by Culturable Fungi and Their Capacity to Increase Soil P Availability and Promote Barley Growth.

Large-scale screening of 848 culturable soil and endophytic filamentous fungi and yeasts for the ability to mobilize inorganic and organic P compounds was performed. Five strains of filamentous fungi having the highest level of phosphate-mobilizing ability were selected: Penicillium bilaiae Pb14, P. bilaiae C11, P. rubens EF5, Talaromyces pinophilus T14, and Aspergillus sp. D1. These strains in vitro actively solubilized Ca, Al, and Fe phosphates and Ca phytate. The amount of mobilized P negatively correlated with pH of the medium and positively correlated with fungal biomass. The proposed mechanisms for P mobilization were acidification of the medium, organic acid release, and phosphatase activity. The fungi decreased pH of the medium from 7.0 to 2.3-5.0. Ten different organic acids were produced by fungi with pyruvic acid being a major component. Acid phosphatase activity varied from 0.12 EU to 0.84 EU, and alkaline phosphatase activity varied from 0.08 EU to 0.61 EU depending on the strain. Available P concentration in soil was increased by 13-28% after introduction of the fungi. The fungi also produced phytohormones auxins, salicylic acid, and abscisic acid. All the strains, except Aspergillus sp. D1, promoted elongation and increased biomass of barley seedlings grown in soil. Shoot P concentration increased by 17-26% after inoculation with P. bilaiae Pb14, T. pinophilus T14, and Aspergillus sp. D1. It was concluded that the selected fungal strains promoted plant growth due to P mobilization and phytohormone production.

Rhizosphere Bacterium Rhodococcus sp. P1Y Metabolizes Abscisic Acid to Form Dehydrovomifoliol.

The phytohormone abscisic acid (ABA) plays an important role in plant growth and in response to abiotic stress factors. At the same time, its accumulation in soil can negatively affect seed germination, inhibit root growth and increase plant sensitivity to pathogens. ABA is an inert compound resistant to spontaneous hydrolysis and its biological transformation is scarcely understood. Recently, the strain Rhodococcus sp. P1Y was described as a rhizosphere bacterium assimilating ABA as a sole carbon source in batch culture and affecting ABA concentrations in plant roots. In this work, the intermediate product of ABA decomposition by this bacterium was isolated and purified by preparative HPLC techniques. Proof that this compound belongs to ABA derivatives was carried out by measuring the molar radioactivity of the conversion products of this phytohormone labeled with tritium. The chemical structure of this compound was determined by instrumental techniques including high-resolution mass spectrometry, NMR spectrometry, FTIR and UV spectroscopies. As a result, the metabolite was identified as (4RS)-4-hydroxy-3,5,5-trimethyl-4-[(E)-3-oxobut-1-enyl]cyclohex-2-en-1-one (dehydrovomifoliol). Based on the data obtained, it was concluded that the pathway of bacterial degradation and assimilation of ABA begins with a gradual shortening of the acyl part of the molecule.

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil.

Aluminium being one of the most abundant elements is very toxic for plants causing inhibition of nutrient uptake and productivity. The aim of this study was to evaluate the potential of microbial consortium consisting of arbuscular mycorrhizal fungus (AMF), rhizobia and PGPR for counteracting negative effects of Al toxicity on four pea genotypes differing in Al tolerance. Pea plants were grown in acid soil supplemented with AlCl3 (pHKCl = 4.5) or neutralized with CaCO3 (pHKCl = 6.2). Inoculation increased shoot and/or seed biomass of plants grown in Al-supplemented soil. Nodule number and biomass were about twice on roots of Al-treated genotypes after inoculation. Inoculation decreased concentrations of water-soluble Al in the rhizosphere of all genotypes grown in Al-supplemented soil by about 30%, improved N2 fixation and uptake of fertilizer 15N and nutrients from soil, and increased concentrations of water-soluble nutrients in the rhizosphere. The structure of rhizospheric microbial communities varied to a greater extent depending on the plant genotype, as compared to soil conditions and inoculation. Thus, this study highlights the important role of symbiotic microorganisms and the plant genotype in complex interactions between the components of the soil-microorganism-plant continuum subjected to Al toxicity.

Microbial Consortium of PGPR, Rhizobia and Arbuscular Mycorrhizal Fungus Makes Pea Mutant SGECdt Comparable with Indian Mustard in Cadmium Tolerance and Accumulation.

Cadmium (Cd) is one of the most widespread and toxic soil pollutants that inhibits plant growth and microbial activity. Polluted soils can be remediated using plants that either accumulate metals (phytoextraction) or convert them to biologically inaccessible forms (phytostabilization). The phytoremediation potential of a symbiotic system comprising the Cd-tolerant pea (Pisum sativum L.) mutant SGECdt and selected Cd-tolerant microorganisms, such as plant growth-promoting rhizobacterium Variovorax paradoxus 5C-2, nodule bacterium Rhizobium leguminosarum bv. viciae RCAM1066, and arbuscular mycorrhizal fungus Glomus sp. 1Fo, was evaluated in comparison with wild-type pea SGE and the Cd-accumulating plant Indian mustard (Brassica juncea L. Czern.) VIR263. Plants were grown in pots in sterilized uncontaminated or Cd-supplemented (15 mg Cd kg-1) soil and inoculated or not with the microbial consortium. Cadmium significantly inhibited growth of uninoculated and particularly inoculated SGE plants, but had no effect on SGECdt and decreased shoot biomass of B. juncea. Inoculation with the microbial consortium more than doubled pea biomass (both genotypes) irrespective of Cd contamination, but had little effect on B. juncea biomass. Cadmium decreased nodule number and acetylene reduction activity of SGE by 5.6 and 10.8 times, whereas this decrease in SGECdt was 2.1 and 2.8 times only, and the frequency of mycorrhizal structures decreased only in SGE roots. Inoculation decreased shoot Cd concentration and increased seed Cd concentration of both pea genotypes, but had little effect on Cd concentration of B. juncea. Inoculation also significantly increased concentration and/or accumulation of nutrients (Ca, Fe, K, Mg, Mn, N, P, S, and Zn) by Cd-treated pea plants, particularly by the SGECdt mutant. Shoot Cd concentration of SGECdt was twice that of SGE, and the inoculated SGECdt had approximately similar Cd accumulation capacity as compared with B. juncea. Thus, plant-microbe systems based on Cd-tolerant micro-symbionts and plant genotypes offer considerable opportunities to increase plant HM tolerance and accumulation.

Rhizobial Microsymbionts of Kamchatka Oxytropis Species Possess Genes of the Type III and VI Secretion Systems, Which Can Affect the Development of Symbiosis.

A collection of rhizobial strains isolated from root nodules of the narrowly endemic legume species Oxytropis erecta, O. anadyrensis, O. kamtschatica, and O. pumilio originating from the Kamchatka Peninsula (Russian Federation) was obtained. Analysis of the 16S ribosomal RNA gene sequence showed a significant diversity of isolates belonging to families Rhizobiaceae (genus Rhizobium), Phyllobacteriaceae (genera Mesorhizobium, Phyllobacterium), and Bradyrhizobiaceae (genera Bosea, Tardiphaga). A plant nodulation assay showed that only strains belonging to genus Mesorhizobium could form nitrogen-fixing nodules on Oxytropis plants. The strains M. loti 582 and M. huakuii 583, in addition to symbiotic clusters, possessed genes of the type III and type VI secretion systems (T3SS and T6SS, respectively), which can influence the host specificity of strains. These strains formed nodules of two types (elongated and rounded) on O. kamtschatica roots. We suggest this phenomenon may result from Nod factor-dependent and -independent nodulation strategies. The obtained strains are of interest for further study of the T3SS and T6SS gene function and their role in the development of rhizobium-legume symbiosis. The prospects of using rhizobia having both gene systems related to symbiotic and nonsymbiotic nodulation strategies to enhance the efficiency of plant-microbe interactions by expanding the host specificity and increasing nodulation efficiency are discussed.