Root Nodule Bacteria Research Articles

Oddziaływanie zaprawy chemicznej na efektywność szczepienia nasion grochu bakteriami brodawkowymi

Oddziaływanie zaprawy chemicznej na efektywność szczepienia nasion grochu bakteriami brodawkowymi

Contribution of Arbuscular Mycorrhizal Fungi (AM Fungi) and Rhizobium Inoculation on Crop Growth and Chemical Properties of Rhizospheric Soils in High Plants

Soil microorganisms commonly named biofertilizers can be used to decrease input of fertilizers, pesticides and other chemicals in Agriculture. Among soil microorganisms, arbuscular mycorrhizal (AM) fungi and Rhizobium spp. can promote plant growth and control plant fungal diseases. However these microorganisms are not yet used in commercial biocontrol products. Integration of Arbuscular Mycorrhizal Fungi with Rhizobium sp. thus appears to be a promising approach for sustainable agriculture especially in legume crops where the net influence of this combination is supposed to be very high compare to other types of crop families. Arbuscular Mycorrhizal fungi and root-nodule bacterium Rhizobium are two root symbionts. Arbuscular mycorrhizal fungi increases soil nutrients and water absorption, while root-nodule bacteria fix atmospheric nitrogen and produce antibiotics and phytoalexins. These microbes modify the quality and abundance of rhizosphere microflora and alter overall microbial activity of the rhizosphere. They induce changes in the host root exudation pattern. A procedure for successful development of these microorganisms is required by selection and screening of efficient isolates. Knowledge of culture systems that are adapted to their establishment and multiplication is needed. Arbuscular mycorrhizal fungi provide specific niches for bacteria. Arbuscular mycorrhizal bacteria improve nutrient acquisition in plants and subsequently, growth of the particular crops is advantaged indeed. Arbuscular mycorrhizal bacteria may contribute to ability of arbuscular mycorrhizal fungi to inhibit pathogens acquire mineral nutrients and modify plant root growth. Combined use of these microorganisms is more beneficial than their use alone. Together, they Influence plant root morphology changes and chemical properties of Rhizospheric soils of high plants with the significant extent. These symbionts also interact with other beneficial microorganisms synergistically and can be exploited for sustainable agriculture. The sound influence of these symbionts on root morphology and growth of the whole

Alternative substrates for the amylase and cellulase production with rhizobial isolates

In the present study sixty root nodule bacteria were isolated from Vigna radiate and Cicer arietinum. As we know that nutrients and growth conditions promote the yield of microbial enzymes. However, carbon sources such as dextrin, fructose, glucose, lactose, maltose and starch are very expensive for commercial production of enzymes. These expensive products could be replaced in the medium with economically available agricultural by-products like corn flour, wheat flour, rice flour, sorghum and baggase as carbon substrate. The aim of this study was the production of amylases and cellulases from rhizobia using cheap carbon sources to reduce the production cost of enzymes .All isolates were screened for the amylase and cellulase production using starch and carboxy methyl cellulase (CMC) hydrolysis respectively .Isolates showing better screening results were further subjected for different starchy carbon substrates for CFU/ml at different time intervals and enzyme (amylase and cellulase) production. The results obtained in the study revealed that wheat flour yields the highest levels of amylase, and baggase promotes the highest amount of cellulase. Statistical analyses between cellulase and amylase data showed that there is a significant difference between their productions. Amount of cellulase (0.1513 u/ml) is significantly greater than that of amylase (0.0091u/ml).

Distribution and Diversity of Rhizobial Populations Associated with <i>Acacia senegal</i> (L.) Willd. Provenances in Senegalese Arid and Semiarid Regions

Abstract: Distribution and diversity of rhizobial strains associated with Acacia senegal (L.) Willd. in relation to seed provenances in soils from arid (Dahra) and semiarid (Goudiry) zones of Senegal were investigated. PCR-RFLP performed on 16S-23S rDNA intergenic spacer (IGS) of nodule crude extracts revealed a high genetic diversity of rhizobial strains, which was higher in the semiarid region than in the arid region. The distribution of rhizobial populations was influenced by soil physical and chemical characteristics, and by A. senegal provenances as shown by the analysis of correspondence. In contrast, the phenotypic diversity of rhizobial strains was not correlated with the soil origin. The phylogenetic tree (performed by the maximum likelihood algorithm) of IGS 16S-23S sequences showed that most of the rhizobial strains nodulating A. senegal were closely related to Mesorhizobium plurifarium. Our results showed that rhizobial taxa associated with A. senegal were mainly distributed according to soil physical and chemical characteristics, and A. senegal provenances. A large subset of A. senegal root-nodulating bacteria had high diversity that correlated with the most favourable environmental conditions. Understanding the diversity and distribution of rhizobial strains may be exploited in the formulation of A. senegal inoculants for different seed provenances for resilience to soil stresses in various environmental conditions.

Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557(T.).

Microvirga lotononidis is a recently described species of root-nodule bacteria that is an effective nitrogen- (N2) fixing microsymbiont of the symbiotically specific African legume Listia angolensis (Welw. ex Bak.) B.-E. van Wyk & Boatwr. M. lotononidis possesses several properties that are unusual in root-nodule bacteria, including pigmentation and the ability to grow at temperatures of up to 45°C. Strain WSM3557T is an aerobic, motile, Gram-negative, non-spore-forming rod isolated from a L. angolensis root nodule collected in Chipata, Zambia in 1963. This is the first report of a complete genome sequence for the genus Microvirga. Here we describe the features of Microvirga lotononidis strain WSM3557T, together with genome sequence information and annotation. The 7,082,538 high-quality-draft genome is arranged in 18 scaffolds of 104 contigs, contains 6,956 protein-coding genes and 84 RNA-only encoding genes, and is one of 20 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Community Sequencing Program.

Genome sequence of Ensifer sp. TW10; a Tephrosia wallichii (Biyani) microsymbiont native to the Indian Thar Desert

Ensifer sp. TW10 is a novel N2-fixing bacterium isolated from a root nodule of the perennial legume Tephrosia wallichii Graham (known locally as Biyani) found in the Great Indian (or Thar) desert, a large arid region in the northwestern part of the Indian subcontinent. Strain TW10 is a Gram-negative, rod shaped, aerobic, motile, non-spore forming, species of root nodule bacteria (RNB) that promiscuously nodulates legumes in Thar Desert alkaline soil. It is fast growing, acid-producing, and tolerates up to 2% NaCl and capable of growth at 40oC. In this report we describe for the first time the primary features of this Thar Desert soil saprophyte together with genome sequence information and annotation. The 6,802,256 bp genome has a GC content of 62% and is arranged into 57 scaffolds containing 6,470 protein-coding genes, 73 RNA genes and a single rRNA operon. This genome is one of 100 RNB genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

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 diversity of rhizobia isolated from nodules of the relic species Vavilovia formosa (Stev.) Fed.

Sixteen bacterial strains were isolated from root nodules of Vavilovia formosa plants originated from the North Ossetian State Natural Reserve (Caucasus, Russia). Phylogenetic analysis of these strains was performed using partial 16S rRNA gene and internally transcribed spacer (ITS) sequences. The results showed that the isolates belong to three families of root nodule bacteria. Twelve of them were related to the genus Rhizobium (family Rhizobiaceae) but four strains can be most probably identified as Phyllobacterium-related (family Phyllobacteriaceae), Bosea- and Rhodopseudomonas-related (family Bradyrhizobiaceae). Amplified fragment length polymorphism clustering was congruent with ITS phylogeny but displayed more variability for Rhizobium isolates, which formed a single group at the level of 30 % similarity. We expect that the isolates obtained can belong to new taxa at genus, species or subspecies levels. The results of PCR amplification of the nodulation genes nodC and nodX showed their presence in all Rhizobium isolates and one Rhodopseudomonas-related isolate. The nodC gene sequences of V. formosa isolates were closely related to those of the species Rhizobium leguminosarum bv. viciae but formed separate clusters and did not intermingle with any reference strains. The presence of the nodX gene, which is necessary for nodulation of Afghan peas (Pisum sativum L.) originated from the Middle East, allows the speculation that these wild-type pea cultivars may be the closest existing relatives of V. formosa. Thus, the studies of genetic diversity and symbiotic genes of V. formosa microsymbionts provide the primary information about their phylogeny and contribute to the conservation of this relict leguminous species.

Assessing Genotypic Diversity and Symbiotic Efficiency of Five Rhizobial Legume Interactions Under Cadium Stress for Soil Phytoremediation

In the framework of soil phytoremediation using local legume plants coupled with their native root-nodulating bacteria to increase forage yields and preserve contaminated soils in arid regions of Tunisia, we investigated the diversity of bacteria from root nodules of Lathyrus sativus, Lens culinaris, Medicago marina, M. truncatula, and M. minima and the symbiotic efficiency of these five legume symbiosis under Cadmium stress. Fifty bacterial strains were characterized using physiological and biochemical features such heavy metals resistant, and PCR-RFLP of 16S rDNA. Taxonomically, the isolates nodulating L. sativus, and L. culinaris are species within the genera Rhizobium and the ones associated to Medicago sp, within the genera Sinorhizobium. The results revealed also that the cadmium tolerance of the different legumes-rhizobia interaction was as follows: M. minima<M. truncatula<M. marina<L. sativus<L. culinaris indicating that the effect of Cadmium on root nodulation and biomass production is more deleterious on M. minima-S. meliloti and M. truncatula-S. meliloti than in other symbiosis. Knowledge on genetic and functional diversity of M. marina, L. sativus and L. culinaris microsymbiotes is very useful for inoculant strain selection and can be selected to develop inoculants for soil phytoremediation.

Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau

BackgroundAs the largest low-latitude permafrost region, the Tibetan Plateau (TP) is an important part of the earth’s terrestrial ecosystem and one of the most vulnerable areas to climate change and human activities. However, to the best of our knowledge, the bacterial communities in TP soils and their roles in biogeochemical cycles remain limited.ResultsIn this study, we report the bacterial community structure and function as well as their correlation with environmental factors in TP major ecosystems (farmland, alpine meadow and oligosaline lake) by using metagenomic approaches. Compared with other soil samples in various environments, TP soils share a core set of microorganisms with a distinct abundance and composition. Among TP soil samples, the taxonomic and functional composition of bacterial communities among the upper (3-5 cm) and lower (18-20 cm) soils of farmland sites were highly similar, whereas the dissimilarities within alpine meadow samples were significantly greater than among farmland samples. A similar pattern was observed in elements cycles and pathways associated with adaption to environment and land use types. Canonical correlation analysis revealed that the bacterial communities in most of farmland and alpine meadow soil samples were also significantly correlated with geogenic variables. Specifically, the root-nodule bacteria are negatively correlated with the soil moisture and pH, while Thiobacillus associated with sulfur cycles show potential responses to low temperature and intense UV radiation.ConclusionsThese findings indicate that the bacterial community structure and functions in TP soils were influenced by both human activities and soil environmental properties, and that the bacterial communities appeared to be more homogenized in the farmland soils compared with pristine alpine meadows.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-820) contains supplementary material, which is available to authorized users.

Legume Genomics: From Genomic Resources to Molecular Breeding

With an explosive growth rate, especially in developing countries, the world population of 7.2 billion is expected to reach 9.6 billion by 2050. There is a need to produce about 70% more food to feed this predicted population. Legumes form important constituents of a vegetarian diet and are rich sources of dietary protein (Duranti and Gius, 1997). Legumes comprise the third largest family of flowering plants and provide important sources of food, fodder, oil, and fiber products. Legume seeds typically contain 20 to 25% protein and are also a rich source of dietary fiber. In addition, legumes have the capability to fix atmospheric N2 with the help of symbiotic nitrogen fixing bacteria in root nodules, thereby reducing fertilizer use in agriculture, and the cost of nitrogen inputs by smallholder farmers in developing countries. Due to their higher protein content and other nutrients, legumes are considered important to confront malnutrition among resource-poor people in developing countries. In brief, legumes including beans (Phaseolus vulgaris), chickpea (Cicer arietinum), cowpea (Vigna unguiculata), lentils (Lens culinaris), pea (Pisum sativum), peanut (Arachis hypogaea), and soybean (Glycine max), etc. play an important role in ensuring food security, reducing poverty, improving human health and nutrition, and enhancing ecosystem resilience, especially in developing countries....

Invasion of rhizobial infection thread by non-rhizobia for colonization ofVigna radiataroot nodules

Legumes develop symbiotic relationships with Rhizobium by a complex exchange of signals. Despite the high specificity between symbiotic partners, the presence of non-rhizobial bacteria in root nodules has been reported. To investigate how these rhizobacteria enter root nodules, fluorescently tagged Pseudomonas fluorescens and Klebsiella pneumoniae were co-inoculated with host-nodulating Ensifer adhaerens to Vigna radiata seedlings and root hair infection was monitored using confocal microscopy at 5days post inoculation. Pseudomonas fluorescens and K.pneumoniae invaded the root hair only when co-inoculated with E.adhaerens. Recovery of inoculated tagged strains and confirmation through CLSM and 16S rRNA gene sequencing confirmed that the test rhizobacteria occupied nodules. We hereby report with the help of confocal microscopy that rhizobacteria migrate along the length of host-nodulating rhizobial strain and become localized in root nodules. We further report isolation of eight non-rhizobial bacterial genera, predominantly Bacillus spp. and Paenibacillus spp., from nodules of field-grown V.radiata.

South African Papilionoid Legumes Are Nodulated by Diverse Burkholderia with Unique Nodulation and Nitrogen-Fixation Loci

The root-nodule bacteria of legumes endemic to the Cape Floristic Region are largely understudied, even though recent reports suggest the occurrence of nodulating Burkholderia species unique to the region. In this study, we considered the diversity and evolution of nodulating Burkholderia associated with the endemic papilionoid tribes Hypocalypteae and Podalyrieae. We identified distinct groups from verified rhizobial isolates by phylogenetic analyses of the 16S rRNA and recA housekeeping gene regions. In order to gain insight into the evolution of the nodulation and diazotrophy of these rhizobia we analysed the genes encoding NifH and NodA. The majority of these 69 isolates appeared to be unique, potentially representing novel species. Evidence of horizontal gene transfer determining the symbiotic ability of these Cape Floristic Region isolates indicate evolutionary origins distinct from those of nodulating Burkholderia from elsewhere in the world. Overall, our findings suggest that Burkholderia species associated with fynbos legumes are highly diverse and their symbiotic abilities have unique ancestries. It is therefore possible that the evolution of these bacteria is closely linked to the diversification and establishment of legumes characteristic of the Cape Floristic Region.

Novel Rhizobium lineages isolated from root nodules of the common bean (Phaseolus vulgaris L.) in Andean and Mesoamerican areas

The taxonomic affiliations of nineteen root-nodule bacteria isolated from the common bean (Phaseolus vulgaris L.) in Mexico, Ecuador and Brazil were investigated by analyses of 16S rRNA and of four protein-coding housekeeping genes. One strain from Mexico could be assigned to Rhizobium etli and two from Brazil to Rhizobium leucaenae, whereas another from Mexico corresponded to a recently described bean-nodulating species-level lineage related to R. etli and Rhizobium phaseoli. Ten strains isolated in Ecuador and Mexico corresponded to three novel Rhizobium lineages that fall into the R. phaseoli/R. etli/Rhizobium leguminosarum clade. One of those lineages, with representatives isolated mostly from Ecuador, seems to be dominant in beans from that Andean region. Only one of the Mexican strains clustered within the Rhizobium tropici clade, but as an independent lineage. Interestingly, four strains were affiliated with species within the Rhizobium radiobacter clade. The existence of yet non-described native Rhizobium lineages in both the Andean and Mesoamerican areas is discussed in relation to common-bean diversity and environmental conditions.

Evaluation of effective Myanmar Bradyrhizobium strains isolated from Myanmar soybean and effects of coinoculation with Streptomyces griseoflavus P4 for nitrogen fixation

In order to substitute the use of chemical fertilizers in legume production, there is a need for the production of rhizobial inoculants which are capable of being used as biofertilizers. To achieve this, an effective symbiotic nitrogen (N) fixation between legumes and root nodule bacteria will be essential. Evaluation of effective Myanmar Bradyrhizobium (Jordan 1982) strains isolated from Myanmar soybean (Glycine max L. Merr.) and effects of coinoculation with Streptomyces griseoflavus Krainsky 1914 P4 for N fixation were studied in pot experiments using sterilized vermiculite and Hoagland solution in the Phytotron (25°C and 70% relative humidity) with completely randomized design and three replicates. N fixation ability of soybean was evaluated by acetylene reduction activity (ARA) by gas chromatography. It was found that MAS23 showed a relatively high degree of stability and a high level of ARA per plant on both Yezin-3 and Yezin-6 soybean varieties. In the symbiotic relationship between Bradyrhizobium strains and P4 experiments, the treatments consisted of six Bradyrhizobium strains (MAS23, MAS33, MAS34, MAS43, MAS48 and USDA110) and Streptomyces griseoflavus P4 were evaluated with four Myanmar soybean varieties (Yezin-3, Yezin-6, Hinthada and Shan Sein). In the Yezin-3 soybean variety, the best treatment for ARA per plant was found in the dual inoculation of P4 and MAS34. In the Yezin-6 soybean variety, the highest nodule dry weight was found in dual inoculation of P4 with MAS34 but the highest ARA per plant was observed in the dual inoculation of P4 and MAS23. On the other hand, single inoculation of MAS43 and coinoculation of P4 with MAS48 were significantly higher in N fixation of Hinthada, and coinoculation of P4 with MAS33 was significant improvement of ARA per plant (P < 0.05) in Shan Sein soybean.

Comigration of root nodule bacteria and bean plants to new habitats: Coevolution mechanisms and practical importance

Comigration of root nodule bacteria and bean plants to new habitats: Coevolution mechanisms and practical importance

Establishment and survival of the South African legume Lessertia spp. and rhizobia in Western Australian agricultural systems

Background and aims The South African herbaceous legume species Lessertia capitata, L. diffusa, L. excisa L. incana and L. herbacea were introduced to Australia to assess plant establishment and survival, as well as the saprophytic ability of their root nodule bacteria (RNB). Methods Five Lessertia spp., were inoculated with selected RNB strains and were sown in five different agroclimatic areas of the Western Australian wheatbelt during 2007 and 2008. Plant population and summer survival were evaluated in situ. Soil samples and nodules from host plants were also taken from each site. The re-isolated rhizobia were RPO1-PCR fingerprinted and their partial dnaK and nodA genes were sequenced to confirm their identity. Results Plants achieved only poor establishment followed by weak summer survival. More than 83 % of the rhizobia re-isolated from Lessertia did not correlate with the original inoculants’ fingerprints, and were identified as Rhizobium leguminosarum. The nodA sequences of the naturalised strains were also

Characterization of root-nodule bacteria isolated from Vicia faba and selection of plant growth promoting isolates

A collection of 104 isolates from root-nodules of Vicia faba was submitted to 16S rRNA PCR-RFLP typing. A representative sample was further submitted to sequence analysis of 16S rRNA. Isolates were assigned to 12 genera. All the nodulating isolates (45%) were closely related to Rhizobium leguminosarum USDA2370(T) (99.34%). The remaining isolates, including potential human pathogens, failed to nodulate their original host. They were checked for presence of symbiotic genes, P-solubilization, phytohormone and siderophore production, and then tested for their growth promoting abilities. Results indicated that 9 strains could induce significant increase (41-71%) in shoot dry yield of faba bean. A Pseudomonas strain was further assessed in on-farm trial in combination with a selected rhizobial strain. This work indicated that nodule-associated bacteria could be a valuable pool for selection of effective plant growth promoting isolates. Nevertheless, the possible involvement of nodules in increasing risks related to pathogenic bacteria should not be neglected and needs to be investigated further.

Novel Burkholderia bacteria isolated from Lebeckia ambigua – A perennial suffrutescent legume of the fynbos

We investigated symbiotic and physiological properties, and taxonomic position, of 23 bacterial strains isolated from Lebeckia ambigua root nodules collected from the South African fynbos region. The capacity for nodulation and nitrogen fixation on three provenances of L. ambigua was investigated for these strains together with several physiological characters, including growth rate on peat and in betonite clay, survival on polyethylene beads and pH tolerance. Additionally, the 16S rRNA gene phylogeny was determined. The root nodule bacteria isolated clustered in five different groups belonging to the genus Burkholderia, most closely related to B. caledonica, B. graminis and B. tuberum. Moreover there was a very strong influence of collection site on the taxonomy of the Burkholderia strains. The physiological characterisation revealed two promising strains, WSM4174 and WSM4184, achieved rapid growth in normal media and reached high, stable numbers in sterile peat. However, there was a worrying susceptibility to desiccation amongst these Burkholderia. Additionally, evidence was found for isolation of non-symbiotic strains from the nodule material collected in South Africa.

Studi Penggunaan Pupuk Hayati Pada Tanaman Kedelai

Study of the use of biological fertilizers on soybean. One of the efforts to improve the growth and yield of soybean is to utilize biological fertilizer in the form of inoculants, both root nodule bacteria and endophytic bacteria. Assessment carried out on land formerly used for rice cultivation in Palangki, District Ampek Nagari, Sijunjung regency, West Sumatra, in the dry season (June to September 2010). The design used was a randomized block design (RBD) with 4 treatments and 4 replications, plot size of 5 x 4 m, using Anjasmoro soybean varieties, spacing of 40 x 10 cm, each planted 2 seeds / hole. Treatment in this study, namely: Land given lime without bacterial inoculation (A1); Land without lime, and soy beans inoculated bacteria (A2); Land given lime and soy beans inoculated bacteria (A3); and Land sown with soybean planting land former, given lime and seeds not inoculated bacteria (A4). Data were collected for plant height, number of primary branches, total number of pods, number of pods, amount number of seeds, seed fresh weight and dry weight of seeds. The study showed that treatment of ex-land sprinkled with soybean planting, and seeds were not inoculated lime and (A4) gives the highest response for each parameter of observation compared with other treatments. Keywords: soybean, bio-fertilizers, bacteria.