Diversity among Field Populations of Bradyrhizobium japonicum in Poland

Soybean Nodulation Response to Cropping Interval and Inoculation in European Cropping Systems

To support the adaption of soybean [Glycine max (L) Merrill] cultivation across Central Europe, the availability of compatible soybean nodulating Bradyrhizobia (SNB) is essential. Little is known about the symbiotic potential of indigenous SNB in Central Europe and the interaction with an SNB inoculum from commercial products. The objective of this study was to quantify the capacity of indigenous and inoculated SNB strains on the symbiotic performance of soybean in a pot experiment, using soils with and without soybean history. Under controlled conditions in a growth chamber, the study focused on two main factors: a soybean cropping interval (time since the last soybean cultivation; SCI) and inoculation with commercial Bradyrhizobia strains. Comparing the two types of soil, without soybean history and with 1-4 years SCI, we found out that plants grown in soil with soybean history and without inoculation had significantly more root nodules and higher nitrogen content in the plant tissue. These parameters, along with the leghemoglobin content, were found to be a variable among soils with 1-4 years SCI and did not show a trend over the years. Inoculation in soil without soybean history showed a significant increase in a nodulation rate, leghemoglobin content, and soybean tissue nitrogen concentration. The study found that response to inoculation varied significantly as per locations in soil with previous soybean cultivation history. An inoculated soybean grown on loamy sandy soils from the location Müncheberg had significantly more nodules as well as higher green tissue nitrogen concentration compared with non-inoculated plants. No significant improvement in a nodulation rate and tissue nitrogen concentration was observed for an inoculated soybean grown on loamy sandy soils from the location Fehrow. These results suggest that introduced SNB strains remained viable in the soil and were still symbiotically competent for up to 4 years after soybean cultivation. However, the symbiotic performance of the SNB remaining in the soils was not sufficient in all cases and makes inoculation with commercial products necessary. The SNB strains found in the soil of Central Europe could also be promising candidates for the development of inoculants and already represent a contribution to the successful cultivation of soybeans in Central Europe.

Characterization of Rhizobia for the Improvement of Soybean Cultivation at Cold Conditions in Central Europe

In central Europe, soybean cultivation is gaining increasing importance to reduce protein imports from overseas and make cropping systems more sustainable. In the field, despite the inoculation of soybean with commercial rhizobia, its nodulation is low. In many parts of Europe, limited information is currently available on the genetic diversity of rhizobia and, thus, biological resources for selecting high nitrogen-fixing rhizobia are inadequate. These resources are urgently needed to improve soybean production in central Europe. The objective of the present study was to identify strains that have the potential to increase nitrogen fixation by and the yield of soybean in German soils. We isolated and characterized 77 soybean rhizobia from 18 different sampling sites. Based on a multilocus sequence analysis (MLSA), 71% of isolates were identified as Bradyrhizobium and 29% as Rhizobium. A comparative analysis of the nodD and nifH genes showed no significant differences, which indicated that the soybean rhizobia symbiotic genes in the present study belong to only one type. One isolate, GMF14 which was tolerant of a low temperature (4°C), exhibited higher nitrogen fixation in root nodules and a greater plant biomass than USDA 110 under cold conditions. These results strongly suggest that some indigenous rhizobia enhance biological nitrogen fixation and soybean yield due to their adaption to local conditions.

Phenetic, genetic diversity and symbiotic compatibility of rhizobial strains nodulating pigeon pea in Northern India

Pigeon pea (Cajanus cajan) is one of the most important legumes grown in the northern province of Uttar Pradesh, India. However, its productively in Uttar Pradesh is lower than the average yield of adjoining states. During the course of the present study, a survey of pigeon pea growing agricultural fields was carried out and it was found that 80% of plants were inadequately nodulated. The study was aimed to evaluate the pigeon pea symbiotic compatibility and nodulation efficiency of root nodulating bacteria isolated from various legumes, and to explore the phenetic and genetic diversity of rhizobial population nodulating pigeon pea growing in fields of Uttar Pradesh. Amongst all the 96 isolates, 40 isolates showed nodulation in pigeon pea. These 40 isolates were further characterized by phenotypic, biochemical and physiological tests. Intrinsic antibiotic resistance pattern was taken to generate similarity matrix revealing 10 phenons. The study shows that most of the isolates nodulating pigeon pea in this region were rapid growers. The dendrogram generated using the NTSYSpc software grouped RAPD patterns into 19 clusters. The high degree of phenetic and genetic diversity encountered is probably because of a history of mixed cropping of legumes. The assessment of diversity is a very important tool and can be used to improve the nodulation and quality of pigeon pea crop. It is also concluded that difference between phenetic and RAPD clustering pattern is an indication that rhizobial diversity of pigeon pea is not as yet completely understood and settled.

Phenotypic and molecular assessment of chickpea rhizobia from different chickpea cultivars of India

In the present study, heterogeneity in natural chickpea rhizobia populations associated with 18 different chickpea (Cicer arientinum) cultivars of India was investigated. Physiological diversity of 20 chickpea rhizobia was characterized based on phenotypic parameters such as Bromothymol blue (BTB) test, pH, temperature and salinity tolerance. Based on response to BTB test and pH tolerance, all chickpea rhizobia were further divided into slow growers/alkali producers (14 isolates) and fast growers/acid producers (6 isolates). The temperature (upto 40 °C) and salinity (NaCl) tolerance (upto 6%) tests provided a wide description of physiological diversity among the rhizobial isolates. The intrinsic antibiotic resistance of each isolate against 14 different antibiotics distinguished all chickpea rhizobia into five clades at the level of 80% similarity coefficient. Further, based on UPGMA phylogeny of carbon utilization profile, all isolates were dispersed into six clusters at the level of 85% similarity coefficient, which indicated a remarkable variability among the rhizobia. The evaluation of nodule-forming efficiency of all isolates revealed that the isolate ACR15 was more competent for nodule formation than all other isolates. The representative strain from each carbon metabolic cluster was further subjected for molecular identification through 16S rRNA gene characterization. Neighbour-joining method-based phylogeny of 16S rRNA gene sequence revealed a high degree of species diversity among the isolates. Further, the prominent nodule-forming isolate such as ACR15 was identified as Mesorhizobium ciceri, while other isolates showed similarity with other species of Mesorhizobium genus. The present study contributed to the knowledge that besides M. ciceri and M. mediterraneum, chickpea can also be nodulated by many other native chickpea rhizobia which indicates the impact of exploration of promising native populations. These findings may support the further investigation of symbiotic as well as stress responsive genes of chickpea rhizobia leading to develop more effective inoculant strains for wide agricultural applications.

Survival and Competitiveness of Bradyrhizobium japonicum Strains 20 Years after Introduction into Field Locations in Poland

It was previously demonstrated that there are no indigenous strains of Bradyrhizobium japonicum forming nitrogen-fixing root nodule symbioses with soybean plants in arable field soils in Poland. However, bacteria currently classified within this species are present (together with Bradyrhizobium canariense) as indigenous populations of strains specific for nodulation of legumes in the Genisteae tribe. These rhizobia, infecting legumes such as lupins, are well established in Polish soils. The studies described here were based on soybean nodulation field experiments, established at the Poznań University of Life Sciences Experiment Station in Gorzyń, Poland, and initiated in the spring of 1994. Long-term research was then conducted in order to study the relation between B. japonicum USDA 110 and USDA 123, introduced together into the same location, where no soybean rhizobia were earlier detected, and nodulation and competitive success were followed over time. Here we report the extra-long-term saprophytic survival of B. japonicum strains nodulating soybeans that were introduced as inoculants 20 years earlier and where soybeans were not grown for the next 17 years. The strains remained viable and symbiotically competent, and molecular and immunochemical methods showed that the strains were undistinguishable from the original inoculum strains USDA 110 and USDA 123. We also show that the strains had balanced numbers and their mobility in soil was low. To our knowledge, this is the first report showing the extra-long-term persistence of soybean-nodulating strains introduced into Polish soils and the first analyzing the long-term competitive relations of USDA 110 and USDA 123 after the two strains, neither of which was native, were introduced into the environment almost 2 decades ago.

Predominant populations of indigenous soybean-nodulating Bradyrhizobium japonicum strains obtained from organic farming systems in Minnesota

AIMS

Bradyrhizobium from organic fields in Minnesota were isolated and genotyped to assess diversity of soybean-bradyrhizobia in organic farming systems that can be used to improve soybean productivity.

METHODS AND RESULTS

Soil samples were collected from 25 organic fields in Minnesota during May to July 2012. Soybean (cv. Lambert) was used as a host to trap indigenous bradyrhizobia in each sample. Genetic diversity of Bradyrhizobium strains (n=733) was determined using the horizontal, fluorophore-enhanced, repetitive extragenic palindromic-PCR (HFERP) DNA fingerprinting technique and the soybean-bradyrhizobia were classified into 79 different genotypes. Of these, 15 dominant genotypes were found and were highly similar (>92% fingerprint similarity) to serotypes USDA 127 (40.4%), USDA 4 (31.8%) and USDA 123 (15.5%), which were the three main populations of soybean-bradyrhizobia in organic fields.

CONCLUSIONS

Bradyrhizobium japonicum serogroup USDA 4 strains were found to make up a previously unrecognized, predominant rhizobial population in the organic farming soils examined. The relative abundance of strain USDA 4 was negatively correlated with that of USDA 127 and this relationship may be influenced by the levels of NO3 -N and other soil edaphic factors.

SIGNIFICANCE AND IMPACT OF THE STUDY

The local community of bradyrhizobia can be affected by applying inoculant bacteria to organic fields. Based on these results, soybean production in organic farms may be improved by displacing strains similar to USDA 4 with those better at nitrogen fixation and competitive ability than indigenous strains.

Mesorhizobium sangaii sp. nov., isolated from the root nodules of Astragalus luteolus and Astragalus ernestii

Our previous published data indicated that the two rhizobial strains SCAU7T and SCAU27, which were isolated from the root nodules of Astragalus luteolus and Astragalus ernestii respectively, in Sichuan Province, China, might be novel species of the genus Mesorhizobium . Their exact taxonomic position was determined in the present study by using polyphasic approaches. Comparative analysis of nearly full-length 16S rRNA gene sequences showed that these strains belonged to the genus Mesorhizobium , with Mesorhizobium ciceri USDA 3383T, Mesorhizobium loti NZP 2213T, Mesorhizobium shangrilense CCBAU 65327T and Mesorhizobium australicum WSM2073T as the closest neighbours (>99 % 16S rRNA gene sequence similarity). Phylogenies of the housekeeping genes atpD and recA confirmed their distinct position, showing low similarity with respect to those of M. loti LMG 6125T (96.5 % and 92.3 % similarity respectively), M. ciceri USDA 3383T (96.8 % and 93.3 % similarity, respectively), M. shangrilense CCBAU 65327T (96.5 % and 92.7 % similarity, respectively) and M. australicum WSM2073T (95.4 % and 90.6 % similarity, respectively). The DNA–DNA relatedness values between strain SCAU7T and strain SCAU27 were 83.0 %, showing that they belong to the same species. The DNA–DNA relatedness values of SCAU7T with M. loti NZP 2213T, M. ciceri USDA 3383T and M. shangrilense CCBAU 65327T were 41.1 %, 48.8 % and 23.4 %, respectively, clearly indicating that strain SCAU7T represents a novel species. A series of phenotypic and genotypic tests and comparison of cellular fatty acids indicated that the novel group of isolates was distinct from previously described species. Therefore, we propose that strains SCAU7T and SCAU27 represent a novel species of the genus Mesorhizobium , Mesorhizobium sangaii sp. nov., with strain SCAU7T ( = HAMBI 3318T = ACCC 13218T) as the type strain.

Genetic diversity of nodulating and non-nodulating rhizobia associated with wild soybean (Glycine soja Sieb. & Zucc.) in different ecoregions of China

A total of 99 bacterial isolates that originated from root nodules of Glycine soja were characterized with restriction analyses of amplified 16S ribosomal DNA and 16S-23S rDNA intergenic spacers (ITS), and sequence analyses of 16S rRNA, rpoB, atpD, recA and nodC genes. When tested for nodulation of G. soja, 72 of the isolates were effective symbionts, and these belonged to five species: Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense and Sinorhizobium fredii. All of these, except some B. yuanmingense strains, also formed effective nodules on the domesticated soybean Glycine max. The remaining 27 isolates did not nodulate either host, but were identified as Rhizobium. Phylogeny nodC in the G. soja symbionts suggested that this symbiosis gene was mainly maintained by vertical gene transfer. Different nodC sublineages and rrs-ITS clusters reflected the geographic origins of isolates in this study.

Diversity and biogeography of rhizobia isolated from root nodules of Glycine max grown in Hebei Province, China

A total of 215 rhizobial strains were isolated and analyzed with 16S rRNA gene, 16S-23S intergenic spacer, housekeeping genes atpD, recA, and glnII, and symbiotic genes nifH and nodC to understand the genetic diversity of soybean rhizobia in Hebei province, China. All the strains except one were symbiotic bacteria classified into nine genospecies in the genera of Bradyrhizobium and Sinorhizobium. Surveys on the distribution of these rhizobia in different regions showed that Bradyrhizobium japonicum and Bradyrhizobium elkanii strains were found only in neutral to slightly alkaline soils whereas Bradyrhizobium yuanmingense, Bradyrhizobium liaoningense-related strains and strains of five Sinorhizobium genospecies were found in alkaline-saline soils. Correspondence and canonical correspondence analyses on the relationship of rhizobial distribution and their soil characteristics reveal that high soil pH, electrical conductivity, and potassium content favor distribution of the B. yuanmingense and the five Sinorhizobium species but inhibit B. japonicum and B. elkanii. High contents of available phosphorus and organic matters benefit Sinorhizobium fredii and B. liaoningense-related strains and inhibit the others groups mentioned above. The symbiotic gene (nifH and nodC) lineages among B. elkanii, B. japonicum, B. yuanmingense, and Sinorhizobium spp. were observed in the strains, signifying that vertical gene transfer was the main mechanism to maintain these genes in the soybean rhizobia. However, lateral transfer of symbiotic genes commonly in Sinorhizobium spp. and rarely in Bradyrhizobium spp. was also detected. These results showed the genetic diversity, the biogeography, and the soil determinant factors of soybean rhizobia in Hebei province of China.

Bradyrhizobium canariense and Bradyrhizobium japonicum are the two dominant rhizobium species in root nodules of lupin and serradella plants growing in Europe

Forty three Bradyrhizobium strains isolated in Poland from root nodules of lupin species (Lupinus albus, L. angustifolius and L. luteus), and pink serradella (Ornithopus sativus) were examined based on phylogenetic analyses of three housekeeping (atpD, glnII and recA) and nodulation (nodA) gene sequences. Additionally, seven strains originating from root-nodules of yellow serradella (O. compressus) from Asinara Island (Italy) were included in this study. Phylogenetic trees revealed that 15 serradella strains, including all yellow serradella isolates, and six lupin strains grouped in Bradyrhizobium canariense (BC) clade, whereas eight strains from pink serradella and 15 lupin strains were assigned to Bradyrhizobium japonicum (BJ1). Apparently, these species are the two dominant groups in soils of central Europe, in the nodules of lupin and serradella plants. Only three strains belonged to other chromosomal lineages: one formed a cluster that was sister to B. canariense, one strain grouped outside the branch formed by B. japonicum super-group, and one strain occupied a distant position in the genus Bradyrhizobium, clustering with strains of the Rhodopseudomonas genus. All strains in nodulation nodA gene tree grouped in a cluster referred to as Clade II, which is in line with earlier data on this clade dominance among Bradyrhizobium strains in Europe. The nodA tree revealed four well-supported subgroups within Clade II (II.1-II.4). Interestingly, all B. canariense strains clustered in subgroup II.1 whereas B. japonicum strains dominated subgroups II.2-II.4.

Mesorhizobium robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia

Previously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36T and Mesorhizobium temperatum SDW018T were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA–DNA relatedness values between the representative strain, CCNWYC 115T, and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115T (=ACCC 14543T =HAMBI 3082T). Strain CCNWYC 115T can form effective nodules only on its original host.

Influence of Bovine Slurry Deposition on the Structure of Nodulating Rhizobium leguminosarum bv. viciae Soil Populations in a Natural Habitat

The population of nodulating R. leguminosarum bv. viciae in soil from a grass-covered valley area which had been used for bovine slurry deposition over a period of 5 years was analyzed. For these studies, a rapid and reproducible method based on enterobacterial repetitive intergenic consensus (ERIC)-PCR was applied to identify Rhizobium strains which had infected pea nodules. Soil samples were taken from different areas and further analyzed in plant tests to determine the impact of the application of slurry (polluted or nonpolluted), the slope position (summit or toe), and exposure (north or south). After comparison of all PCR fingerprint patterns, 24 strain groups were defined. Some strain groups from the nonpolluted soil were suppressed in the polluted samples, and new strain groups were detected in the slurry-polluted soil. After analyzing relationships between the strain groups, we determined the influences of local factors on the nodulating R. leguminosarum bv. viciae population. We show that one of those local parameters, slope position, had significantly greater impact on the composition of the Rhizobium population than the presence of slurry.

Phylogenetic and symbiotic characterization of rhizobial bacteria nodulating Argyrolobium uniflorum in Tunisian arid soils

Forty-two bacterial isolates from root nodules of Argyrolobium uniflorum growing in the arid areas of Tunisia were characterized by phenotypic features, RFLP, and sequencing of PCR-amplified 16S rRNA genes. The isolates were found to be phenotypically diverse. The majority of the isolates tolerated 3% NaCl and grew at temperatures up to 40 °C. Phylogenetically, the new isolates were grouped in the genera Sinorhizobium (27), Rhizobium (13), and Agrobacterium (2). Except for the 2 Agrobacterium isolates, all strains induced nodulation on Argyrolobium uniflorum, but the number of nodules and nitrogen fixation efficiency varied among them. Sinorhizobium sp. strains STM 4034, STM 4036, and STM 4039, forming the most effective symbiosis, are potential candidates for inoculants in revegetalisation programs.

Lipopolysaccharide profiles from nodules as markers of bradyrhizobium strains nodulating wild legumes

To develop the use of electrophoretic lipopolysaccharide profiles for Bradyrhizobium strain identification, we studied the feasibility of using electrophoresis of whole legume nodule homogenates to obtain distinctive lipopolysaccharide profiles. The electrophoretic patterns were the same whether we used nodule extracts, bacteroids, or cultured bacteria as samples, and there was no evidence of changes in the ladder-like pattern during the nodulation process. To assess the reliability of using lipopolysaccharide profiling performed with individual nodules for studying the diversity and microdistribution of the rhizobia nodulating wild shrub legumes, we used a population of Adenocarpus foliolosus seedlings. We obtained 75 different profiles from the 147 nodules studied. There was no dominant profile in the sample, and a plant with different nodules generally produced different profiles. Electrophoresis of legume root nodules proved to be a fast and discriminating technique for determining the diversity of a bradyrhizobial population, although it did not allow the genetic relationships among the nodulating strains to be studied.

Effect of soil bradyrhizobia on the success of soybean inoculant strain CB 1809

Four decades of soybean [Glycine max (L.) Merr.] cultivation in South Africa has resulted in the establishment of populations of bradyrhizobia against which the recently introduced inoculant strain CB 1809 must compete. Serological and DNA fingerprinting methods were used to study the diversity of nodule isolates from soils at Bergville, Koedoeskop and Morgenzon. Dominant serogroups included Bradyrhizobium elkanii serotype 76 at Bergville (67%), Bradyrhizobium japonicum serotype 123 at Morgenzon (81%) and B. japonicum serotype 135 at Koedoeskop (100%). Their origin is unknown as they do not correspond in serotype to strains used in previous inoculants. A small percentage of isolates from Bergville (13%) and Morgenzon (16%) were serologically homologous to strain WB 1 (serotype 31/76), applied for two decades before CB 1809 (serotype 122). Nitrogen-fixing effectiveness of CB 1809 was superior to 60% of the isolates tested from Bergville and Morgenzon, but similar to 73% of the Koedoeskop isolates. Seed and liquid-in-furrow application methods increased CB 1809 nodule occupancy at least three-fold above background levels at Bergville (pH 5.16) and Morgenzon (pH 6.33). Inoculation did not, however, increase CB 1809 nodule occupancy at Koedoeskop (pH 7.76), possibly because alkaline soil conditions favoured the serotype 135 population predominant at this site.

Genomic fingerprinting of Bradyrhizobium japonicum isolates by RAPD and rep-PCR

Genetic diversity of indigenous Bradyrhizobium japonicum population in Croatia was studied by using different PCR-based fingerprinting methods. Characteristic DNA profiles for 20 B. japonicum field isolates and two reference strains were obtained using random primers (RAPD) and two sets of repetitive primers (REP- and ERIC-PCR). In comparison with the REP, the ERIC primer set generates fingerprints of lower complexity, but still several strain-specific bands were detected. Different B. japonicum isolates could be more efficiently distinguished by using combined results from REP- and ERIC-PCR. The most polymorphic bands were observed after amplification with four different RAPD primers. Both methods, RAPD and rep-PCR, resulted in identical grouping of the strains. Cluster analysis, irrespective of the fingerprinting method used, revealed that all the isolates could be divided into three major groups. Within the major groups, the degree of relative similarity between B. japonicum isolates was dependent upon the method used. Our results indicate that both RAPD and rep-PCR fingerprinting can effectively distinguish different B. japonicum strains. RAPD fingerprinting proved to be slightly more discriminatory than rep-PCR.

Phenotypic and molecular characterization of chickpea rhizobia isolated from different areas of Morocco

AIMS

To determine the biodiversity of rhizobial strains nodulating Cicer arietinum L. in representative soils from various areas of Morocco.

METHODS AND RESULTS

Symbiotic traits, utilization of 49 carbohydrate sources, resistance to antibiotics and heavy metals, tolerance to salinity, to extreme temperatures and pH were studied as phenotypic markers. In addition, restriction fragment length polymorphism (RFLP) of PCR-amplified 16S rDNAs were compared with those of reference strains. Numerical analysis of the phenotypic characteristics showed that the 48 strains studied fell into three distinct groups. RFLP analysis of 16S rRNA genes revealed an additional heterogeneity and four ribotypes were identified.

CONCLUSIONS

Chickpea rhizobia isolated from Moroccan soils are both phenotypically and genetically diverse. Most of these rhizobia belong to the Mesorhizobium genus. However, some strains originating from a particular soil appeared to have 16S rRNA genes similar to Sinorhizobium as well as very distinct auxanographic characteristics compared with Mesorhizo- bium isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

A well characterized collection of chickpea-nodulating rhizobia in representative soils of Morocco has been generated, which can be used to develop efficient inoculants for this crop. This is the first report evidencing that chickpeas may be nodulated by bacteria from the Sinorhizobium genus.

AFLP fingerprint analysis of Bradyrhizobium strains isolated from Faidherbia albida and Aeschynomene species

The diversity of Bradyrhizobium isolates from Faidherbia albida and Aeschynomenee species was assessed using AFLP analysis, a high-resolution genomic fingerprinting technique. Reference strains from Bradyrhizobium japonicum, Bradyrhizobium elkanii and Bradyrhizobium liaoningense were included for comparison. At a similarity level of 50%, a total of 34 different groups were obtained by cluster analysis of the genomic fingerprints. Four of these clusters correspond to the three reference species, demonstrating the large diversity of the isolates studied. Comparison with other data demonstrates that AFLP has a higher resolution than restriction analysis of 16S rRNA genes, SDS-PAGE analysis of proteins and phenotypic analysis. Results of the latter two methods showed little correspondence with the genotypic data.