Strains Of Root Nodule Bacteria Research Articles

A Temperate Sinorhizobium Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis.

Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960s-1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place.

Responsiveness to inoculation and application of micronutrient fertilizers in common vetch (Vicia sativa L.) new varieties at seed production

The responsiveness of common vetch varieties to inoculation with Rhizobium leguminosarum biovar-viciae of different genotypes and applications of molybdenum and boron micronutrients has been revealed. It is shown that the effect of interactions between molybdenum and boron on the plants at the joint application is nonadditive. The artificial colonization of seeds by the complementary strains of root nodule bacteria and the molybdenum treatment are expedient to increase the efficiency of the symbiotic interactions between rhizobia and common vetch varieties. Inoculation with strain no. 145 and supplementation with molybdenum improved the seed yields of the common vetch Valentina and Lugovskaya-98 varieties by 20% and 17%, respectively.

GENOTYPIC ANALYSIS OF NODULE BACTERIA NODULATING SOYBEAN IN UKRAINE SOILS

Background. Distribution of root nodule bacteria of soybean in soils of Ukraine is the result of intensive cultivation of soybeans over the last 20 years. During the observation the structure of soybean rhizobia populations for the first time we have determined the strains which significantly differ in phenotypic properties from typical slow-growing bacteria of B. japonicum species previously described. These strains are characterized by high speed growth and we tentatively called them “stains with intensive growth”. The aim of our work was to investigate the genotypic properties of microsymbionts of soybeans with different rates of growth spreading in soils of Ukraine. Materials and methods. The 16S rRNA gene and intergenic 16S-23S rRNA region of six strains - typical representatives of soybean nodule bacteria with slow- and intensive growth-rates was carried out. The strains were picked up from different Ukrainian soils. Results. Analysis of the 16S rRNA nucleotide sequences showed the 100% similarity of slow-growing strains to B. japonicum USDA 6T and USDA 4 ones. This analysis proved propinquity of strains with intensive growth to the strain B. japonicum USDA 127 (USDA 123 group). Representatives of this group possessed increased saprophytic competence so as the examined strains. With use of restriction analysis of ITS intergenic region soybean rhizobia were divided among two ITS types: 1st ITS type - strains with intensive growth, 2nd ITS type - slow- growing strains. According to results of ITS-region sequencing soybean rhizobia form 3 reliably different clusters: two of which include slow-growing strains (group USDA 6 and USDA 4), and a third include soybean microsymbionts with intensive growth (USDA 123 group). Conclusion. On the basis of phenotypic and genotypic (16S rRNA and 16S-23S rRNA) analysis all of the investigated soybean strains of root nodule bacteria were related to the Bradyrhizobium japonicum species. The division of strains by the structure of the ITS-region into two genotypes corresponds to the division of strains into two physiological groups: the strains of an intense and slow growth.

Genetic description of root nodule bacteria of Lathyrus species growing on the territory of the Republic of Bashkortostan

The genetic diversity and phylogeny of rhizobia isolated from nodules of nine wild-growing Lathyrus L. species (Fabaceae) growing in the Republic of Bashkortostan were studied. It is shown that, for the given plants, a large variety of heterogeneous strains of root nodule bacteria is characteristic. Nevertheless, it is revealed that the majority of them, in terms of phylogenetics, are closely related to Rhizobium leguminosarum. However, some plant species are found also: nodule bacteria, which were earlier considered unusual for Lathyrus. Thus, L. vernus L. Bernh. and L. sylvestris L. are found to have a root nodule bacteria close to R. tropici, L. palustris L. Agrobacterium sp., and L. gmelinii Fritsch, all bacteria isolated by us from root nodules by the sequence of genes of 16S rRNA, are closely related to Phyllobacterium myrsinacearum.

Genetic description of root nodule bacteria of Lathyrus species growing in the territory of Republic Bashkortostan

The genetic diversity and phylogeny of rhizobia isolated from nodules of 9 wild-growing Lathyrus L. species (Fabaceae) growing in Republic Bashkortostan were studied. It is shown that for the given plants is characteristic that the big variety of heterogeneous strains of root nodule bacteria. Nevertheless, it is revealed that the majority of them in phylogenetics are closely related to Rhizobium leguminosarum. However, some plant species are found out also nodule bacteria which were considered earlier unusual for Lathyrus. So, L. vernus L. Bernh. and L. sylvestris L. are found out a root nodule bacteria close to R. tropici, L. palustris L. — Agrobacterium sp., and L. gmelinii Fritsch all isolated with us bacteria from root nodules by the sequence of genes of 16S рРНК have appeared are closely related to Phyllobacterium myrsinacearum.

Microbiological process in agroforestry systems. A review

Soils around the world are degraded due to inappropriate management practices. There is thus the necessity to find more conservationist agricultural systems. Agroforestry system is an alternative system that helps prevent land degradation while allowing continuing use of land to produce crops and livestock on a sustainable basis. Agroforestry system is a form of sustainable land use that combines trees and shrubs with crops and livestock in ways that increase and diversify farm and forest production while also conserving natural resources. This system enhances organic carbon accumulation in soils by the inclusion of cover crops and permanent vegetation, which is expected to increase the soil microbial biomass. The use of microorganisms aims at improving nutrient availability for plants. Currently, there is an emerging demand to decrease the dependence on chemical fertilizers and achieve sustainable agriculture and agroforestry. Arbuscular mycorrhizal fungi, plant growth-promoting rhizobacteria, and the association of rhizobia with leguminous plants are mutualistic symbioses of high economic importance for increasing agricultural production. The biological nitrogen fixation (BNF) process is an economically attractive and ecologically sound method to reduce external nitrogen input and improve the quality and quantity of internal resources. BNF by associative diazotrophic bacteria is a spontaneous process where soil nitrogen is limited and adequate carbon sources are available. However, the ability of these bacteria to contribute to increased crop yields is only partly a result of BNF. The successful use of legumes is dependent upon appropriate attention to the formation of effective symbioses with root nodule bacteria. An essential component for increasing the use of legumes is the integration of plant breeding and cultivar development, with appropriate research leading to the selection of elite strains of root nodule bacteria. An expansion of the utility of inoculants is also necessary to develop a broad conceptual framework and methodology that is supported by scientific arguments; it is destined to impact assessment of the use of new biological products in agriculture.

Relationships between nitrogen fixation and photosynthesis as the main components of the productivity in alfalfa

Alfalfa (Medicago sativa L.) plants were inoculated with Sinorhizobium meliloti Tn-5 mutants featuring various nitrogen-fixing effectiveness and then grown in sand culture to study relations between CO2 exchange, plant productivity, and nitrogen fixation. At the flowering stage, the relationship between nitrogen fixation and photosynthesis of whole alfalfa plants was described with the logarithmic curve. At the same stage of plant development, a close relationship was observed between nitrogen fixation rate and plant weight; this relationship showed a trend toward saturation at high rates of nitrogen fixation. The increase in nitrogenase activity of root nodules was accompanied by stimulation of root respiration; the relation of respiration to nitrogen-fixing activity was manifested stronger than its relation to the total root weight. It is concluded that highly effective strains of root nodule bacteria can realize their potential only in combination with complementary plant genotypes featuring active photosynthesis that provides a balanced supply of assimilates for both the symbiotic apparatus and growth processes in the macrosymbiont.

A novel symbiotic nitrogen-fixing member of the Ochrobactrum clade isolated from root nodules of Acacia mangium.

Ten strains of root nodule bacteria were isolated from the nodules of Acacia mangium grown in the Philippines and Thailand. Partial sequences (approx. 300 bp) of the 16S rRNA gene of each isolate were analyzed. The nucleotide sequences of strain DASA 35030 indicated high homology (>99%) with members of the genus Ochrobactrum in Brucellaceae, although the sequences of other isolates were homologous to those of two distinct genera Bradyrhizobium and Rhizobium. The strain DASA 35030 was strongly suggested to be a strain of Ochrobactrum by full length sequences of the 16S rRNA gene, fatty acids composition, G+C contents of the DNA, and other physiological characteristics. Strain DASA 35030 induced root nodules on A. mangium, A. albida and Paraserianthes falcataria. The nodules formed by strain DASA 35030 fixed nitrogen and the morphology of the nodules is the same as those of nodules formed by the other isolates. This is the first report that the strain of Ochrobactrum possesses complete symbiotic ability with Acacia.

Hydroxamate siderophores of root nodule bacteria

Sixty strains of root nodule bacteria were screened for siderophore production in low-iron broth, among them 40 strains from the Australian Inoculants Research and Control Service (AIRCS) which are the current commercial inoculants used in the pulse and legume pasture industries in Australia. Eleven new siderophore-producing strains were recognised including Sinorhizobium meliloti (WSM826, WSM352, SU47), Rhizobium leguminosarum biovar viciae (WU163, MNF3841, SU391), Rhizobium leguminosarum biovar trifolii (CB782, CC2483g, CC283b) and Rhizobium tropici (WSM1385, CB3060). Siderophores were identified by chemical characterisation for catecholate or hydroxamate, spectral studies, isoelectrofocusing and siderophore-mediated iron-uptake studies. The S. meliloti strains all produced dihydroxamate siderophores. Other siderophore-producing rhizobia, with the exception of R. tropici CB306c, excreted trihydroxamate-type siderophores. No bradyrhizobia were Chromazurol S-positive. 59Fe uptake studies revealed that all strains transported iron complexed to citrate. The sinorhizobia took up 5–10-fold more iron from dihydroxamate than trihydroxamate siderophores. Conversely, other rhizobia and the slow-growing bradyrhizobia transported iron complexed to trihydroxamates at rates 2–5 fold those of dihydroxamate siderophores. Rhizobactin 1021 was excreted by S. meliloti strains 1021, Rm2011 and SU47 and vicibactin by seven strains of R. leguminosarum (bv. viciae and bv. trifolii).

Counting Rhizobium sp. ( Phaseolus) by a plant-infection method using a small-seeded cultivar of Phaseolus silvestre L. grown enclosed in test tubes

We report laboratory experiments that tested the suitability of a wild-type small-seeded cultivar of Phaseolus silvestre L., Morelos 628, for counting Rhizobium sp. ( Phaseolus) by the most probable number method (MPN). There was good agreement between MPN estimates of numbers in pure cultures using Morelos 628 grown in test tubes and a larger commercial variety of P. vulgaris L. grown in Leonard jars, and with colony counts on yeast-mannitol agar (YMA) plates. Morelos 628 did not nodulate in bacteria-free conditions when inoculated with unrelated strains of root nodule bacteria. After 28 days, MPN estimates of R. sp. ( Phaseolus) were not significantly different from counts made after 3 days on YMA, at either low or high cell concentrations in pure culture or in unsterile soil. Nodulation of Morelos 628 was at a maximum after 21 days.

Characteristics of Rhizobium tianshanense sp. nov., a moderately and slowly growing root nodule bacterium isolated from an arid saline environment in Xinjiang, People's Republic of China.

We performed a numerical analysis of 148 phenotypic characteristics of 20 strains of root nodule bacteria isolated from an arid saline desert soil in the Xinjiang region of northwestern People's Republic of China and compared these organisms with 28 Rhizobium and Bradyrhizobium strains obtained from different regions of the People's Republic of China and from other countries, including nine type strains of different species. All of the strains examined clustered into two groups at a similarity level of more than 63%. Group I included all of the previously described Rhizobium species and was divided into eight subgroups, which corresponded to previously described Rhizobium species, at a similarity level of more than 82%. Group II was divided into the following three subgroups at a similarity level of more than 80% Bradyrhizobium japonicum, a cluster containing 17 moderately and slowly growing strains isolated in the Xinjiang region, and a small subgroup containing three fast-growing strains. The generation times of the moderately and slowly growing strains were 5 to 15 h, and these organisms produced acid in medium containing mannitol. The DNA G+C contents of the members of this group ranged from 59 to 63 mol%. DNA-DNA hybridization experiments revealed that the levels of DNA homology among all of the moderately and slowly growing strains obtained from Xinjiang were more than 70% and that the levels of DNA homology between representative strains of this group and the type strains of all previously described species of root- and stem-nodulating bacteria were low.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular Responses of Microbes to Environmental pH stress

Publisher Summary This chapter reviews the ways microorganisms respond to pH stress focusing primarily on molecular aspects of adaptation in bacteria. The requirement for co-inducer molecules is frequent among pH-regulated genes. Most pH-stress protection systems include a mechanism for sustaining cytoplasmic pH and many inducible systems offer crossprotection to other stresses. Knowledge of pH-controlled gene expression results in improved biotechnologies necessary for producing recombinant DNA products under special conditions and for the delivery of live recombinant vaccines. Studies of the molecular responses to pH stress provide insight into the pathogenic processes and ultimately lead to better vaccine development or antimicrobial targets. Knowledge of pH-stress survival mechanisms also lead to the construction of hardier strains of root nodule bacteria that will better survive soil acidity and improve crop yields. New insights provided by recent advances in molecular genetics have rekindled interest in this important aspect of communication between microorganisms and their environment.

Siderophore and organic acid production in root nodule bacteria

Nineteen strains of root nodule bacteria were grown under various iron regimes (0.1, 1.0 and 20 microM added iron) and tested for catechol and hydroxamate siderophore production and the excretion of malate and citrate. The growth response of the strains to iron differed markedly. For 12 strains (Bradyrhizobium strains NC92B and 32H1, B. japonicum USDA110 and CB1809, B. lupini WU8, cowpea Rhizobium NGR234, Rhizobium meliloti strains U45 and CC169, Rhizobium leguminosarum bv viciae WU235 and Rhizobium leguminosarum bv trifolii strains TA1, T1 and WU95) the mean generation time showed no variation with the 200-fold increase in iron concentration. In contrast, in Bradyrhizobium strains NC921, CB756 and TAL1000, B. japonicum strain 61A76 and R. leguminosarum bv viciae MNF300 there was a 2-5 fold decrease in growth rate at low iron. R. meliloti strains WSM419 and WSM540 showed decreased growth at high iron. All strains of root nodule bacteria tested gave a positive CAS (chrome azurol S) assay for siderophore production. No catechol-type siderophores were found in any strain, and only R. leguminosarum bv trifolii T1 and bv viciae WU235 produced hydroxamate under low iron (0.1 and 1.0 microM added iron). Malate was excreted by all strains grown under all iron regimes. Citrate was excreted by B. japonicum USDA110 and B. lupini WU8 in all iron concentrations, while Bradyrhizobium TAL1000, R. leguminosarum bv viciae MNF300 and B. japonicum 61A76 only produced citrate under low iron (0.1 and/or 1.0 microM added iron) during the stationary phase of growth.

Cultural and Biochemical Characteristics of Root Nodule Bacteria of Chickpea (Cicer arietinum L.)

Summary The study on cultural and biochemical characteristics of 115 strains of root nodule bacteria of chickpea (henceforth named Cicer-Rhizobium ), suggest that only few characteristics, like the absence of growth on yeast extract mannitol agar (YEMA) in 24 h, no or little growth on glucose peptone agar without change of p H of the medium in 48 h, inability to produce 3-ketolactose, to precipitate calcium glycero-phosphate, to form serum zone coupled with acid production in litmus milk, to tolerate 20 meq Mn ++ /1 lactose medium and p H 10.0 in Hofer's alkaline broth, could be of diagnostic value in the identification of Rhizobium . In other characteristics, the strains were found to vary. The Congo-red colour differentiation was better obtained by pour plate method than by streaking the culture on YEMA plates. The production of acid or alkali on mannitol was found to be independent of the properties of soil from where the strains were isolated; and this did not substantiate Norris's hypothesis that Rhizobium , associated with tropical legumes, produces alkali. The position of Cicer-Rhizobium as a link between the group of fast growing Rhizobium from clover, pea, and beans and the slow growing group of Rhizobium from soybean, lupin, and cowpea miscellany has been indicated.

CROSS INOCULATION GROUP SPECIFICITY IN CICER‐RHIZOBIUM SYMBIOSIS

SummaryCross‐inoculation group specificity in Cicer arietinum L. (chickpea) was studied. Seventy‐one strains of root nodule bacteria of C. arietinum were examined for nodulation on 87 species of legumes. These species represent all the known cross‐inoculation groups and were selected from various tribes and genera of family Fabaceae and Mimosaceae. In a reciprocal cross‐inoculation study, 287 strains of root nodule bacteria from 52 of the 87 species, were examined on various genotypes of C. arietinum. C. arietinum and its root nodule bacteria did not show cross inoculation affinity with any of the members of the known cross‐inoculation groups: alfalfa, clover, pea, bean, soybean, lupin‐lotus and cowpea miscellany; except for some loose non‐reciprocal kinship with Sesbania, which in its turn has strong affinity with the cowpea miscellany. However, under natural conditions in soil, even the loose non‐reciprocal kinship between Cicer and Sesbania was rare. For practical reasons, it is suggested that C. arietinum and its root nodule bacteria should be considered in a separate cross‐inoculation group.‘Cross‐inoculation host specificity’ appears to be of some help in the revision of the taxonomy of order Leguminosales and supports the placement of Cicer in a monogeneric tribe Cicereae.

Phenetic similarity and DNA base sequence homology of root nodule bacteria from New Zealand native legumes andRhizobiumstrains from agricultural plants

Abstract A comparison was made between 65 strains of root nodule bacteria from indigenous New Zealand legumes and 45 reference strains including: Rhizobium trifolii, R. phaseoli, R. leguminosarum, R. meliloti, and both “acid-producing” and “non-acid-producing” strains from the Lotus-Lupinus-Ornithopus cross-inoculation group. The strains were classified into 10 clusters on the basis of 37 morphological, cultural, and physiological tests. Relationships disclosed among the reference strains were in accordance with current ideas on Rhizobium taxonomy. The indigenous strains were well separated from both the trifolii-leguminosarumphaseoli complex and R. meliloti but acid-producing strains from the Lotus-Lupinus-Ornithopus cross-inoculation group segregated with the indigenous strains. The principal characters differentiating the clusters are discussed. The base composition of DNA from representative indigenous strains was determined and base sequence homology studied. The relative reassociation at 65°c in 0.2...

Genetic control of strain-specific ineffective nodulation in Trifolium subterraneum L.

The nodulation response of the Trifolium subterraneum variety Northam First Early with a range of strains of root nodule bacteria has been investigated. An ineffective response was found with the normally effective bacterial strain NA30. Within F2 populations of crosses between Northam First Early and each of six other varieties of T. subterraneum, the response to inoculation with strain NA30 varied from fully ineffective through intermediate effectiveness to fully effective. The proportion of ineffectively noddated plants in these F, populations was also influenced by the non- Northam First Early parent variety. Differences in response among individual plants within the F, populations were probably due to the segregation of a single major gene and a number of modifying genes. Of 10 other strains examined, one strain showed a similar pattern of response to that obtained with NA30, while a second strain exhibited host x strain specific ineffectiveness of a different type.

ANTIGENIC AFFINITIES OF THE ROOT-NODULE BACTERIA OF LEGUMES.

Antisera prepared against 58 strains of root-nodule bacteria and against 16 strains belonging to the genusAgrobacterium were tested against 113 strains ofRhizobium, 20 strains ofAgrobacterium and 20 strains of other, possibly related, bacteria.