Bradyrhizobium rifense sp. nov. isolated from effective nodules of Cytisus villosus grown in the Moroccan Rif

The native distribution of a common legume shrub is limited by the range of its nitrogen-fixing mutualist

Plant-microbe mutualisms, such as the legume-rhizobium symbiosis, are influenced by the geographical distributions of both partners. However, limitations on the native range of legumes, resulting from the absence of a compatible mutualist, have rarely been explored. We used a combination of a large-scale field survey and controlled experiments to determine the realized niche of Calicotome villosa, an abundant and widespread legume shrub. Soil type was a major factor affecting the distribution and abundance of C. villosa. In addition, we found a large region within its range in which neither C. villosa nor Bradyrhizobium, the bacterial genus that associates with it, were present. Seedlings grown in soil from this region failed to nodulate and were deficient in nitrogen. Inoculation of this soil with Bradyrhizobium isolated from root nodules of C. villosa resulted in the formation of nodules and higher growth rate, leaf N and shoot biomass compared with un-inoculated plants. We present evidence for the exclusion of a legume from parts of its native range by the absence of a compatible mutualist. This result highlights the importance of the co-distribution of both the host plant and its mutualist when attempting to understand present and future geographical distributions of legumes.

Bradyrhizobium xenonodulans sp. nov. isolated from nodules of Australian Acacia species invasive to South Africa

A genealogical concordance approach was used to delineate strains isolated from Acacia dealbata and Acacia mearnsii root nodules in South Africa. These isolates form part of Bradyrhizobium based on 16S rRNA sequence similarity. Phylogenetic analysis of six housekeeping genes (atpD, dnaK, glnII, gyrB, recA and rpoB) confirmed that these isolates represent a novel species, while pairwise average nucleotide identity (ANIb) calculations with the closest type strains (B. cosmicum 58S1T, B. betae PL7HG1T, B. ganzhouense CCBAU 51670 T, B. cytisi CTAW11T and B. rifense CTAW71T) resulted in values well below 95-96%. We further performed phenotypic tests which revealed that there are high levels of intraspecies variation, while an additional analysis of the nodA and nifD loci indicated that the symbiotic loci of the strains are closely related to those of Bradyrhizobium isolates with an Australian origin. Strain 14ABT (=LMG 31415 T = SARCC-753 T) is designated as the type strain of the novel species for which we propose the name Bradyrhizobium xenonodulans sp. nov.

High Diversity of Bradyrhizobial Species Fix Nitrogen with Woody Legume Spartocytisus supranubius in a High Mountain Ecosystem

The symbiosis between rhizobia and legumes is of pivotal importance in nitrogen-poor ecosystems. Furthermore, as it is a specific process (most legumes only establish a symbiosis with certain rhizobia), it is of great interest to know which rhizobia are able to nodulate key legumes in a specific habitat. This study describes the diversity of the rhizobia that are able to nodulate the shrub legume Spartocytisus supranubius in the harsh environmental conditions of the high mountain ecosystem of Teide National Park (Tenerife). The diversity of microsymbionts nodulating S. supranubius was estimated from a phylogenetic analysis of root nodule bacteria isolated from soils at three selected locations in the park. The results showed that a high diversity of species of Bradyrhizobium and two symbiovars can nodulate this legume. Phylogenies of ribosomal and housekeeping genes showed these strains distributed into three main clusters and a few isolates on separate branches. These clusters consist of strains representing three new phylogenetic lineages of the genus Bradyrhizobium. Two of these lineages belong to the B. japonicum superclade, which we refer to as B. canariense-like and B. hipponense-like, as the type strains of these species are the closest species to our isolates. The third main group was clustered within the B. elkanii superclade and is referred to as B. algeriense-like as B. algeriense is its closest species. This is the first time that bradyrhizobia of the B. elkanii superclade have been reported for the canarian genista. Furthermore, our results suggest that these three main groups might belong to potential new species of the genus Bradyrhizobium. Analysis of the soil physicochemical properties of the three study sites showed some significant differences in several parameters, which, however, did not have a major influence on the distribution of bradyrhizobial genotypes at the different locations. The B. algeriense-like group had a more restrictive distribution pattern, while the other two lineages were detected in all of the soils. This suggests that the microsymbionts are well adapted to the harsh environmental conditions of Teide National Park.

Diversity of rhizobia, symbiotic effectiveness, and potential of inoculation in Acacia mearnsii seedling production

Black wattle (Acacia mearnsii) is a forest species of significant economic importance in southern Brazil; as a legume, it forms symbiotic associations with rhizobia, fixing atmospheric nitrogen. Nonetheless, little is known about native rhizobia in soils where the species is cultivated. Therefore, this study aimed to evaluate the diversity and symbiotic efficiency of rhizobia nodulating A. mearnsii in commercial planting areas and validate the efficiency of a potential strain in promoting seedling development. To this end, nodules were collected from four A. mearnsii commercial plantations located in Rio Grande do Sul State, southern Brazil. A total of 80 rhizobia isolates were obtained from black wattle nodules, and thirteen clusters were obtained by rep-PCR. Higher genetic diversity was found within the rhizobial populations from the Duas Figueiras (H' = 2.224) and Seival (H' = 2.112) plantations. Twelve isolates were evaluated belonging to the genus Bradyrhizobium, especially to the species Bradyrhizobium guangdongense. The principal component analysis indicated an association between rhizobia diversity and the content of clay, Ca, Mg, and K. Isolates and reference strains (SEMIA 6163 and 6164) induced nodulation and fixed N via symbiosis with black wattle plants after 60 days of germination. The isolates DF2.4, DF2.3, DF3.3, SEMIA 6164, SEMIA 6163, CA4.3, OV3.4, and OV1.4 showed shoot nitrogen accumulation values similar to the N + control treatment. In the second experiment (under nursery conditions), inoculation with the reference strain SEMIA 6164 generally improved the growth of A. mearnsii seedlings, reinforcing its efficiency even under production conditions.

The Fodder Legume Chamaecytisus albidus Establishes Functional Symbiosis with Different Bradyrhizobial Symbiovars in Morocco

In this work, we analyzed the symbiotic performance and diversity of rhizobial strains isolated from the endemic shrubby legume Chamaecytisus albidus grown in soils of three different agroforestry ecosystems representing arid and semi-arid forest areas in Morocco. The analysis of the rrs gene sequences from twenty-four representative strains selected after REP-PCR fingerprinting showed that all the strains belong to the genus Bradyrhizobium. Following multi-locus sequence analysis (MLSA) using the rrs, gyrB, recA, glnII, and rpoB housekeeping genes, five representative strains, CA20, CA61, CJ2, CB10, and CB61 were selected for further molecular studies. Phylogenetic analysis of the concatenated glnII, gyrB, recA, and rpoB genes showed that the strain CJ2 isolated from Sahel Doukkala soil is close to Bradyrhizobium canariense BTA-1 ^T (96.95%); that strains CA20 and CA61 isolated from the Amhach site are more related to Bradyrhizobium valentinum LmjM3^T, with 96.40 and 94.57% similarity values; and that the strains CB10 and CB60 isolated from soil in the Bounaga site are more related to Bradyrhizobium murdochi CNPSo 4020 ^T and Bradyrhizobium. retamae Ro19^T, with which they showed 95.45 and 97.34% similarity values, respectively. The phylogenetic analysis of the symbiotic genes showed that the strains belong to symbiovars lupini, genistearum, and retamae. All the five strains are able to nodulate Lupinus luteus, Retama monosperma, and Cytisus monspessilanus, but they do not nodulate Glycine max and Phaseolus vulgaris. The inoculation tests showed that the strains isolated from the 3 regions improve significantly the plant yield as compared to uninoculated plants. However, the strains of Bradyrhizobium sp. sv. retamae isolated from the site of Amhach were the most performing. The phenotypic analysis showed that the strains are able to use a wide range of carbohydrates and amino acids as sole carbon and nitrogen source. The strains isolated from the arid areas of Bounaga and Amhach were more tolerant to salinity and drought stress than strains isolated in the semi-arid area of Sahel Doukkala.

Putative novel Bradyrhizobium and Phyllobacterium species isolated from root nodules of Chamaecytisus ruthenicus

In this study, the diversity and the phylogenetic relationships of bacteria isolated from root nodules of Chamaecytisus ruthenicus growing in Poland were investigated using ERIC-PCR fingerprinting and by multilocus sequence analysis (MLSA). Two major clusters comprising 13 and 3 isolates were detected which 16S rRNA gene sequencing identified as Bradyrhizobium and Phyllobacterium. The results of phylogenetic analysis of individual and concatenated atpD, gyrB and recA gene sequences showed that the studied strains may represent novel species in the genera Bradyrhizobium and Phyllobacterium. In the phylogenetic tree based on the atpD-gyrB-recA concatemers, Bradyrhizobium isolates were split into two groups closely related to Bradyrhizobium algeriense STM89^T and Bradyrhizobium valentinum LmjM3^T. The genus Phyllobacterium isolates formed a separate cluster close to Phyllobacterium ifriqiyense LMG27887^T in the atpD-gyrB-recA phylogram. Analysis of symbiotic gene sequences (nodC, nodZ, nifD, and nifH) showed that the Bradyrhizobium isolates were most closely related to Bradyrhizobium algeriense STM89^T, Bradyrhizobium valentinum LmjM3^T and Bradyrhizobium retamae Ro19^T belonging to symbiovar retamae. This is the first report on the occurrence of members of symbiovar retamae from outside the Mediterranean region. No symbiosis related genes were amplified from Phyllobacterium strains, which were also unable to induce nodules on C. ruthenicus roots. Based on these findings Phyllobacterium isolates can be regarded as endophytic bacteria inhabitating root nodules of C. ruthenicus.

Widespread Distribution of Highly Adapted Bradyrhizobium Species Nodulating Diverse Legumes in Africa

Bradyrhizobium is one of the most cosmopolitan and diverse bacterial group nodulating a variety of host legumes in Africa, however, the diversity and distribution of bradyrhizobial symbionts nodulating indigenous African legumes are not well understood, though needed for increased food legume production. In this review, we have shown that many African food legumes are nodulated by bradyrhizobia, with greater diversity in Southern Africa compared to other parts of Africa. From a few studies done in Africa, the known bradyrhizobia (i.e., Bradyrhizobium elkanii, B. yuanmingense) along with many novel Bradyrhizobium species are the most dominant in African soils. This could be attributed to the unique edapho-climatic conditions of the contrasting environments in the continent. More studies are needed to identify the many novel bradyrhizobia resident in African soils in order to better understand the biogeography of bradyrhizobia and their potential for inoculant production.

Phylogeny and Phylogeography of Rhizobial Symbionts Nodulating Legumes of the Tribe Genisteae

The legume tribe Genisteae comprises 618, predominantly temperate species, showing an amphi-Atlantic distribution that was caused by several long-distance dispersal events. Seven out of the 16 authenticated rhizobial genera can nodulate particular Genisteae species. Bradyrhizobium predominates among rhizobia nodulating Genisteae legumes. Bradyrhizobium strains that infect Genisteae species belong to both the Bradyrhizobium japonicum and Bradyrhizobium elkanii superclades. In symbiotic gene phylogenies, Genisteae bradyrhizobia are scattered among several distinct clades, comprising strains that originate from phylogenetically distant legumes. This indicates that the capacity for nodulation of Genisteae spp. has evolved independently in various symbiotic gene clades, and that it has not been a long-multi-step process. The exception is Bradyrhizobium Clade II, which unlike other clades comprises strains that are specialized in nodulation of Genisteae, but also Loteae spp. Presumably, Clade II represents an example of long-lasting co-evolution of bradyrhizobial symbionts with their legume hosts.

A database for the taxonomic and phylogenetic identification of the genus Bradyrhizobium using multilocus sequence analysis

Background

Biological nitrogen fixation, with an emphasis on the legume-rhizobia symbiosis, is a key process for agriculture and the environment, allowing the replacement of nitrogen fertilizers, reducing water pollution by nitrate as well as emission of greenhouse gases. Soils contain numerous strains belonging to the bacterial genus Bradyrhizobium, which establish symbioses with a variety of legumes. However, due to the high conservation of Bradyrhizobium 16S rRNA genes - considered as the backbone of the taxonomy of prokaryotes - few species have been delineated. The multilocus sequence analysis (MLSA) methodology, which includes analysis of housekeeping genes, has been shown to be promising and powerful for defining bacterial species, and, in this study, it was applied to Bradyrhizobium, species, increasing our understanding of the diversity of nitrogen-fixing bacteria.

Description

Classification of bacteria of agronomic importance is relevant to biodiversity, as well as to biotechnological manipulation to improve agricultural productivity. We propose the construction of an online database that will provide information and tools using MLSA to improve phylogenetic and taxonomic characterization of Bradyrhizobium, allowing the comparison of genomic sequences with those of type and representative strains of each species.

Conclusion

A database for the taxonomic and phylogenetic identification of the Bradyrhizobium, genus, using MLSA, will facilitate the use of biological data available through an intuitive web interface. Sequences stored in the on-line database can be compared with multiple sequences of other strains with simplicity and agility through multiple alignment algorithms and computational routines integrated into the database. The proposed database and software tools are available at http://mlsa.cnpso.embrapa.br, and can be used, free of charge, by researchers worldwide to classify Bradyrhizobium, strains; the database and software can be applied to replicate the experiments presented in this study as well as to generate new experiments. The next step will be expansion of the database to include other rhizobial species.

Revision of the taxonomic status of the species Rhizobium lupini and reclassification as Bradyrhizobium lupini comb. nov

The species Rhizobium lupini was isolated from Lupinus nodules and included in the Approved Lists of Bacterial Names in 1980. Nevertheless, on the basis of the analysis of the type strain of this species available in DSMZ, DSM 30140T, whose 16S rRNA gene was identical to that of the type strain of Bradyrhizobium japonicum , R. lupini was considered a later synonym of this species. In this study we confirmed that the strain DSM 30140T belongs to the species B. japonicum , but also that it cannot be the original strain of R. lupini because this species effectively nodulated Lupinus whereas strain DSM 30140T was able to nodulate soybean but not Lupinus. Since the original type strain of R. lupini was deposited into the USDA collection by L. W. Erdman under the accession number USDA 3051T we analysed the taxonomic status of this strain showing that although it belongs to the genus Bradyrhizobium instead of genus Rhizobium , it is phylogenetically distant from B. japonicum and closely related to Bradyrhizobium canariense . The type strains R. lupini USDA 3051T and B. canariense BTA-1T share 16S rRNA, recA and glnII gene sequences with similarities of 99.8 %, 96.5 % and 97.1 %, respectively. They presented a DNA–DNA hybridization value of 36 % and also differed in phenotypic characteristics and slightly in the proportions of some fatty acids. Therefore we propose the reclassification of the species Rhizobium lupini as Bradyrhizobium lupini comb. nov. The type strain is USDA 3051T ( = CECT 8630T = LMG 28514T).

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

Bradyrhizobium ganzhouense sp. nov., an effective symbiotic bacterium isolated from Acacia melanoxylon R. Br. nodules

Three slow-growing rhizobial strains, designated RITF806^T, RITF807 and RITF211, isolated from root nodules of Acacia melanoxylon grown in Ganzhou city, Jiangxi Province, China, had been previously defined, based on amplified 16S rRNA gene restriction analysis, as a novel group within the genus Bradyrhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. According to 16S rRNA gene sequence analysis, the isolates formed a group that was closely related to ‘Bradyrhizobium rifense’ CTAW71, with a similarity value of 99.9 %. In phylogenetic analyses of the housekeeping and symbiotic gene sequences, the three strains formed a distinct lineage within the genus Bradyrhizobium, which was consistent with the results of DNA–DNA hybridization. In analyses of cellular fatty acids and phenotypic features, some differences were found between the novel group and related species of the genus Bradyrhizobium, indicating that these three strains constituted a novel group distinct from any recognized species of the genus Bradyrhizobium. Based on the data obtained in this study, we conclude that our strains represent a novel species of the genus Bradyrhizobium, for which the name Bradyrhizobium ganzhouense sp. nov. is proposed, with RITF806^T ( = CCBAU 101088^T = JCM 19881^T) as the type strain. The DNA G+C content of strain RITF806^T is 64.6 mol% (T_m).

MALDI-TOF mass spectrometry as a tool for differentiation of Bradyrhizobium species: application to the identification of Lupinus nodulating strains

Genus Bradyrhizobium includes slow growing bacteria able to nodulate different legumes as well as species isolated from plant tumours. The slow growth presented by the members of this genus and the phylogenetic closeness of most of its species difficults their identification. In the present work we applied for the first time Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to the analysis of Bradyrhizobium species after the extension of MALDI Biotyper 2.0 database with the currently valid species of this genus. With this methodology it was possible to identify strains belonging to phylogenetically closely related species of genus Bradyrhizobium allowing the discrimination among species with rrs gene identities higher than 99%. The application of MALDI-TOF MS to strains isolated from nodules of different Lupinus species in diverse geographical locations allowed their correct identification when comparing with the results of rrs gene and ITS analyses. The nodulation of Lupinus gredensis, an endemic species of the west of Spain, by B. canariense supports the European origin of this species.

Polyphasic evidence supporting the reclassification of Bradyrhizobium japonicum group Ia strains as Bradyrhizobium diazoefficiens sp. nov

Bradyrhizobium japonicum was described from soybean root-nodule bacterial isolates. Since its description, several studies have revealed heterogeneities among rhizobia assigned to this species. Strains assigned to B. japonicum group Ia have been isolated in several countries, and many of them are outstanding soybean symbionts used in inoculants worldwide, but they have also been isolated from other legume hosts. Here, we summarize published studies that indicate that group Ia strains are different from the B. japonicum type strain USDA 6T and closely related strains, and present new morphophysiological, genotypic and genomic evidence to support their reclassification into a novel species, for which the name Bradyrhizobium diazoefficiens sp. nov. is proposed. The type strain of the novel species is the well-studied strain USDA 110T ( = IAM 13628T  = CCRC 13528T  = NRRL B-4361T  = NRRL B-4450T  = TAL 102T  = BCRC 13528T  = JCM 10833T  = TISTR 339T  = SEMIA 5032T  = 3I1B110T  = ACCC 15034T  = CCT 4249T  = NBRC 14792T  = R-12974T  = CNPSo 46T).

Centrosema is a promiscuous legume nodulated by several new putative species and symbiovars of Bradyrhizobium in various American countries

Centrosema is an American indigenous legume that can be used in agroecosystems for recovery of acidic and degraded soils. In this study, a Centrosema-nodulating rhizobial collection of strains isolated in a poor acid savanna soil from Venezuela was characterized, and the members of the collection were compared to other Centrosema strains from America. The analysis of the rrs gene showed that the strains nodulating Centrosema in American countries were closely related to different species of the genus Bradyrhizobium. However, the analysis of the atpD and recA genes, as well as the 16S-23S ITS region, showed that they formed several new phylogenetic lineages within this genus. The Venezuela strains formed three lineages that were divergent among themselves and with respect to those formed by Centrosema strains isolated in other countries, as well as to the currently described species and genospecies of Bradyrhizobium. In addition, the symbiotic genes nodC and nifH carried by Centrosema-nodulating strains were analyzed for the first time, and it was shown that they belonged to three new phylogenetic lineages within Bradyrhizobium. The nodC genes of the Centrosema strains were divergent among themselves and with respect to the genistearum and glycinearum symbiovars, indicating that Centrosema is a promiscuous legume. According to these results, the currently known Centrosema-nodulating strains represent several new putative species and symbiovars of the genus Bradyrhizobium.

Nodulation in Dimorphandra wilsonii Rizz. (Caesalpinioideae), a threatened species native to the Brazilian Cerrado

The threatened caesalpinioid legume Dimorphandra wilsonii, which is native to the Cerrado biome in Brazil, was examined for its nodulation and N(2)-fixing ability, and was compared with another, less-threatened species, D. jorgei. Nodulation and potential N(2) fixation was shown on seedlings that had been inoculated singly with five bradyrhizobial isolates from mature D. wilsonii nodules. The infection of D. wilsonii by two of these strains (Dw10.1, Dw12.5) was followed in detail using light and transmission electron microscopy, and was compared with that of D. jorgei by Bradyrhizobium strain SEMIA6099. The roots of D. wilsonii were infected via small transient root hairs at 42 d after inoculation (dai), and nodules were sufficiently mature at 63 dai to express nitrogenase protein. Similar infection and nodule developmental processes were observed in D. jorgei. The bacteroids in mature Dimorphandra nodules were enclosed in plant cell wall material containing a homogalacturonan (pectic) epitope that was recognized by the monoclonal antibody JIM5. Analysis of sequences of their rrs (16S rRNA) genes and their ITS regions showed that the five D. wilsonii strains, although related to SEMIA6099, may constitute five undescribed species of genus Bradyrhizobium, whilst their nodD and nifH gene sequences showed that they formed clearly separated branches from other rhizobial strains. This is the first study to describe in full the N(2)-fixing symbiotic interaction between defined rhizobial strains and legumes in the sub-family Caesalpinioideae. This information will hopefully assist in the conservation of the threatened species D. wilsonii.