Biochemical and symbiotic properties of the rhizobia

The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies

Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics-technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.

Soil fertility interactions with Sinorhizobium-legume symbiosis in a simulated Martian regolith; effects on nitrogen content and plant health

Due to increasing population growth and declining arable land on Earth, astroagriculture will be vital to terraform Martian regolith for settlement. Nodulating plants and their N-fixing symbionts may play a role in increasing Martian soil fertility. On Earth, clover (Melilotus officinalis) forms a symbiotic relationship with the N-fixing bacteria Sinorhizobium meliloti; clover has been previously grown in simulated regolith yet without bacterial inoculation. In this study, we inoculated clover with S. meliloti grown in potting soil and regolith to test the hypothesis that plants grown in regolith can form the same symbiotic associations as in soils and to determine if greater plant biomass occurs in the presence of S. meliloti regardless of growth media. We also examined soil NH₄ concentrations to evaluate soil augmentation properties of nodulating plants and symbionts. Greater biomass occurred in inoculated compared to uninoculated groups; the inoculated average biomass in potting mix and regolith (2.23 and 0.29 g, respectively) was greater than the uninoculated group (0.11 and 0.01 g, respectively). However, no significant differences existed in NH₄ composition between potting mix and regolith simulant. Linear regression analysis results showed that: i) symbiotic plant-bacteria relationships differed between regolith and potting mix, with plant biomass positively correlated to regolith-bacteria interactions; and, ii) NH₄ production was limited to plant uptake yet the relationships in regolith and potting mix were similar. It is promising that plant-legume symbiosis is a possibility for Martian soil colonization.

Function of pea amino acid permease AAP6 in nodule nitrogen metabolism and export, and plant nutrition

Legumes fix atmospheric nitrogen through a symbiotic relationship with bacteroids in root nodules. Following fixation in pea (Pisum sativum L.) nodules, nitrogen is reduced to amino acids that are exported via the nodule xylem to the shoot, and in the phloem to roots in support of growth. However, the mechanisms involved in amino acid movement towards the nodule vasculature, and their importance for nodule function and plant nutrition, were unknown. We found that in pea nodules the apoplasmic pathway is an essential route for amino acid partitioning from infected cells to the vascular bundles, and that amino acid permease PsAAP6 is a key player in nitrogen retrieval from the apoplasm into inner cortex cells for nodule export. Using an miRNA interference (miR) approach, it was demonstrated that PsAAP6 function in nodules, and probably in roots, and affects both shoot and root nitrogen supply, which were strongly decreased in PsAAP6-miR plants. Further, reduced transporter function resulted in increased nodule levels of ammonium, asparagine, and other amino acids. Surprisingly, nitrogen fixation and nodule metabolism were up-regulated in PsAAP6-miR plants, indicating that under shoot nitrogen deficiency, or when plant nitrogen demand is high, systemic signaling leads to an increase in nodule activity, independent of the nodule nitrogen status.

Identification and characterization of phages parasitic on bradyrhizobia nodulating groundnut (Arachis hypogaea L.) in South Africa

In this study, three lytic phages (namely, PRSA-1, PRSA-2 and PRSA-26) were isolated and characterized for their morphology, host range, profile and restriction endonuclease banding pattern of genome size. The susceptible rhizobial isolates were identified by nifH and glnII sequence analysis. The results showed that all phages had polyhedral head with non-contractile tail which confirmed their relationship with the Siphoviridae family. All the three phages produced highly distinct plaques on their host bradyrhizobial lawn, and were highly sensitive to chloroform. The phage genome sizes ranged from 34.7 to 53.1 kbp. The phages were tested against groundnut-nodulating bradyrhizobial strains TUTAHSA75, TUTAHSA155 and TUTAHSA126 isolated from South African soils. The results revealed different bacterial susceptibilities to phages. Bradyrhizobial isolate TUTAHSA126 was susceptible to all three phages (i.e. PRSA-1, PRSA-2 and PRSA-26), TUTAHSA155 to two phages (i.e. PRSA-1, PRSA-2), and TUTAHSA75 to only one phage (i.e. PRSA-1). Phylogenetic analysis of nifH and glnII gene sequences of the phage-susceptible bradyrhizobial isolates revealed their close relatedness to a diverse group of Bradyrhizobium species. Phage PRSA-1 could parasitize on all three bradyrhizobial strains, which indicates its potential role in horizontal gene transfer through lysogenic conversion, and/or genetic transduction in soil microbial environments.

Effect of antibiotics on callus regeneration during transformation of IR 64 rice

We report here the effect of antibiotics on the regeneration potential of recalcitrant indica rice cultivar, IR64. Different protocols reporting high-efficiency agro-bacterium-mediated transformation of mature seed-derived regenerative calli were used and compared. The putative transgenic (T0) plants were analyzed for integration of the transgene through polymerase chain reaction and Southern blotting analyses. It was observed that the high-efficiency transformation of scutellar-derived regenerative calli could be obtained by using maltose as a carbon source and increased quantity of 2,4-D on a medium containing a higher concentration of gelling agent. The percentage of regeneration is greatly affected by the presence of antibiotics.

Growth of fast- and slow-growing rhizobia on ethanol

Free-living soybean rhizobia and Bradyrhizobium spp. (lupine) have the ability to catabolize ethanol. Of the 30 strains of rhizobia examined, only the fast- and slow-growing soybean rhizobia and the slow-growing Bradyrhizobium sp. (lupine) were capable of using ethanol as a sole source of carbon and energy for growth. Two strains from each of the other Rhizobium species examined (R. meliloti, R. loti, and R. leguminosarum biovars phaseoli, trifolii, and viceae) failed to grow on ethanol. One Rhizobium fredii (fast-growing) strain, USDA 191, and one (slow-growing) Bradyrhizobium japonicum strain, USDA 110, grew in ethanol up to concentrations of 3.0 and 1.0%, respectively. While three of the R. fredii strains examined (USDA 192, USDA 194, and USDA 205) utilized 0.2% acetate, only USDA 192 utilized 0.1% n-propanol. None of the three strains utilized 0.1% methanol, formate, or n-butanol as the sole carbon source.

TheRhizobium etli bioMNYoperon is involved in biotin transport

Because Rhizobium etli CE3 is normally dependent on an external source of biotin and lacks orthodox biotin biosynthesis genes, we undertook an analysis of biotin uptake in this organism. By complementation of a Sinorhizobium meliloti bioM mutant we isolated an R. etli chromosomal region encoding homologs of the S. meliloti bioMNB genes, whose products have been implicated in intracellular biotin retention in that organism. Disruption of the R. etli bioM resulted in a mutant which took up biotin at a lower rate and accumulated significantly less biotin than the wild type. As in S. meliloti, the R. etli bioMN gene-products resemble the ATPase and permease components, respectively, of an ABC-type transporter. The bioB gene product is in fact similar to members of the BioY family, which has been postulated to function in biotin transport, and we refer to this gene as bioY. An R. etli bioY mutant exhibited lower biotin uptake than the wild-type, providing the first experimental evidence for a role of BioY in biotin transport. We show that the bioMNY operon is transcriptionally repressed by biotin. An analysis of the competitiveness of the wild-type strain versus the bioM mutant showed that the mutant had a diminished capacity to form nodules on bean plants.

Sinorhizobium meliloti cells require biotin and either cobalt or methionine for growth

Sinorhizobium meliloti is usually cultured in rich media containing yeast extract. It has been suggested that some components of yeast extract are also required for growth in minimal medium. We tested 27 strains of this bacterium and found that none were able to grow in minimal medium when methods to limit carryover of yeast extract were used during inoculation. By fractionation of yeast extract, two required growth factors were identified. Biotin was found to be absolutely required for growth, whereas previously the need for this vitamin was considered to be strain specific. All strains also required supplementation with cobalt or methionine, consistent with the requirement for a vitamin B(12)-dependent homocysteine methyltransferase for methionine biosynthesis.

The genetic and biochemical basis for nodulation of legumes by rhizobia

Soil bacteria of the genera Azorhizobium, Bradyrhizobium, and Rhizobium are collectively termed rhizobia. They share the ability to penetrate legume roots and elicit morphological responses that lead to the appearance of nodules. Bacteria within these symbiotic structures fix atmosphere nitrogen and thus are of immense ecological and agricultural significance. Although modern genetic analysis of rhizobia began less than 20 years ago, dozens of nodulation genes have now been identified, some in multiple species of rhizobia. These genetic advances have led to the discovery of a host surveillance system encoded by nodD and to the identification of Nod factor signals. These derivatives of oligochitin are synthesized by the protein products of nodABC, nodFE, NodPQ, and other nodulation genes; they provoke symbiotic responses on the part of the host and have generated immense interest in recent years. The symbiotic functions of other nodulation genes are nonetheless uncertain, and there remain significant gaps in our knowledge of several large groups of rhizobia with interesting biological properties. This review focuses on the nodulation genes of rhizobia, with particular emphasis on the concept of biological specificity of symbiosis with legume host plants.

Studies on phosphate-solubilizing bacteria in soil and rhizosphere of different plants. II. Selection of the most efficient phosphate-dissolvers and their morphological grouping

Two hundred colonies which showed positive reaction on the plates prepared for the phosphate-dissolving bacteria from control soil rhizosphere soils and rhizoplane samples of maize, peas, or cotton were isolated at random. Fifty isolates were selected as the most efficient isolates according to their capability for increasing the amounts of available phosphorus in the media with corresponding decreases in pH values. The percentage of the most efficient isolates differed according to type of plant and location of isolation. Not only the morphological types of the phosphate-dissolving bacteria differed in soil and in rhizosphere, but they also differed in the rhizosphere soil of each special plant. Morphological differences in the isolates from rhizosphere soil and from rhizoplane samples of the same plant were also occurring. The abundance of mycelial-forming bacteria and of aerobic sporeformers in Egyptian soil is important as they are well known to resist adverse conditions, such as high temperature and dryness to which our soils are subjected most time of the year.

Rhizobium japonicum derivatives differing in nitrogen-fixing efficiency and carbohydrate utilization

Four derivatives of Rhizobium japonicum 110 were isolated on the basis of morphologically different colonies formed on yeast extract-mannitol-HM salts medium. All are able to nodulate Lee soybeans. The bacteria-plant associations formed by each clone have measurable acetylene-reducing activity, but those formed by two of these clones (designated L1-110 and L2-110) are 5- to 10-fold less efficient than those formed by the others (designated I-110 and S-110). These derivatives were not detectable with ordinary culture techniques since, because of cell adherence, genetically mixed colonies result. When a detergent (Tween 40 at 0.01%, vol/vol) was added to the dilution medium, separate clones resulted. The metabolic basis for the gross differences in colony morphology on yeast extract-mannitol-HM salts medium was found to be that L1-110 and L2-110 utilized p-mannitol for growth, whereas I-110 and S-110 did not. These clones differ analogously in ability to utilize D-arabitol. Clones I-110 and L1-110 were chosen for studies of growth rates on various carbohydrates. Although clone I-110 and clone L1-110 did not differ in growth rates on a number of sugars, such as gluconate, arabinose, glycerol, and mannose, they differed in growth rates on glucose and fructose. Although clone I-110 grew faster on glucose than did clone L1-110, clone L1-110 grew faster on fructose than did clone I-110. Clones I-110 and L1-110 showed identical responses to several antibiotics and deoxyribonucleic acid (DNA) synthesis inhibitors and identical susceptibility to some highly specific bacteriophages. Identical buoyant densities of their DNAs in isopycnic CsCl density gradients and identical thermal denaturation temperatures of their DNAs suggest that clones I-110 and L1-110 have the same DNA base composition. Preliminary DNA/DNA hybridization experiments show that strain I-110 DNA and strain L1-110 DNA have a high degree of common polynucleotide sequences.

Studies with detached lupin root nodules in culture: I. Maintenance and induction of acetylene reduction activity

A method has been developed for culturing detached nitrogen-fixing root nodules of lupin (Lupinus angustifolius L.) on a simple nutrient medium. Under the best conditions devised, the acetylene reduction activity of mature detached nodules was maintained at 10 to 25 nmoles of ethylene hr(-1) mg(-1) fresh weight for 3 days. Under the same culture conditions, immature nodules increased their acetylene reduction activity from 0.01 nmole or less to about 1 nmole hr(-1) mg(-1) fresh weight.

L-Arabinose metabolism in Rhizobium japonicum

l-Arabinose was metabolized through an oxidative pathway by extracts of a strain of Rhizobium japonicum. The findings showed that l-arabinose is converted into 2-keto-3-deoxy-l-arabonate, which is cleaved into glycoaldehyde and pyruvate.

The bacteroids of the genus Rhizobium

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Studies on Induced Variation in the Rhizobia

The relation between survival and dose of ultraviolet (UV) light or X rays was, with only one exception, nonlinear for late-log-phase cultures of four species of Rhizobium . The ld 90 for different bacterial strains ranged from 400 to 3,000 ergs per mm 2 for UV treatment, and from 3.0 to 7.5 kr for X-ray treatment.

Minor existing differences in response to some antibacterial compounds (disc tests) were usable as secondary markers for genetic experiments. Spontaneous and radiation-induced mutants, resistant to high levels of several antibiotics, notably dihydrostreptomycin and erythromycin, were isolated for primary marker purposes. A significant phenotypic lag for mutation to dihydrostreptomycin resistance was noted for UV-irradiated cells. The UV-induced frequency exceeded the X-ray-induced frequency by a factor of at least three, at a comparable level of lethality. No significant change in the symbiotic capability was observed in rhizobial strains marked with antibiotics resistance.

STUDIES ON THE LEGUME ROOT NODULE BACTERIA: III. GROWTH FACTOR REQUIREMENTS FOR EFFECTIVE, INEFFECTIVE, AND PARASITIC STRAINS

Under the experimental conditions used, amino acids played a very important part in the growth initiation of washed cells of alfalfa – sweet clover rhizobia. There were, however, distinct differences in utilization, both among genetically related mutants, and among other cultures when compared before and after plant passage. None of 15 vitamins, purines, and pyrimidines was able to initiate growth and hence these rhizobia are able to synthesize these compounds when a readily utilizable nitrogen source is present. Because of this fact, the stimulation of these bacteria by yeast extract is probably due, primarily, to the amino acid content. No strain was found able to concentrate free amino acids intracellularly or, when grown in lysine or tyrosine media, to excrete additional amino acids. No differences were found among effective, ineffective, or parasitic rhizobia in biochemical requirements.