Defining the Rhizobium leguminosarum Species Complex

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a 'natural' unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, "R. indicum" and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains.

Agrobacterium cavarae sp. nov., isolated from maize (Zea mays L.) roots

A bacterial strain designated as RZME10^T was isolated from a Zea mays L. root collected in Spain. Results of analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Agrobacterium with Agrobacterium larrymoorei ATCC 51759^T being the most closely related species with 99.9 % sequence similarity. The similarity values of the rpoB, recA, gyrB, atpD and glnII genes between strain RZME10^T and A. larrymoorei ATCC 51759^T were 93.5, 90.0, 88.7, 87.9 and 90.1 %, respectively. The estimated average nucleotide identity using blast and digital DNA-DNA hybridization values between these two strains were 80.4 and 30.2 %, respectively. The major fatty acids of strain RZME10^T are those from summed feature 8 (C_18 : 1 ω6c/C_18 : 1 ω7c) and C_16 : 0. Pathogenicity tests on tomato and carrot roots showed that strain RZME10^T was not able to induce plant tumours. Based on the results of genomic, chemotaxonomic and phenotypic analyses, we propose that strain RZME10^T represents a novel species named Agrobacterium cavarae sp. nov. (type strain RZME10^T=CECT 9795^T=LMG 31257^T).

The Mimosoid tree Leucaena leucocephala can be nodulated by the symbiovar genistearum of Bradyrhizobium canariense

Leucaena leucocephala is a Mimosoid legume tree indigenous to America that has spread to other continents, although it is not still present in some European countries such as Portugal. Nevertheless, we found that this legume can be nodulated in this country by slow-growing rhizobial strains which were identified as Bradyrhizobium canariense trough the analysis of the core genes recA and glnII. The analysis of the symbiotic gene nodC showed that these strains belong to the symbiovar genistearum, which commonly nodulates Genistoid legumes. Although two strains nodulating L. leucocephala in China and Brazil were classified within the genus Bradyrhizobium, they belong to undescribed species and to the symbiovars glycinearum and tropici, respectively. Therefore, we report here for the first time the ability of L. leucocephala to establish symbiosis with strains of B. canariense sv genistearum confirming the high promiscuity of L. leucocephala, that allows it to establish symbiosis with rhizobia native to different continents increasing its invasiveness potential.

The N-fixing legume Periandra mediterranea constrains the invasion of an exotic grass (Melinis minutiflora P. Beauv) by altering soil N cycling

Melinis minutiflora is an invasive species that threatens the biodiversity of the endemic vegetation of the campo rupestre biome in Brazil, displacing the native vegetation and favouring fire spread. As M. minutiflora invasion has been associated with a high nitrogen (N) demand, we assessed changes in N cycle under four treatments: two treatments with contrasting invasion levels (above and below 50%) and two un-invaded control treatments with native vegetation, in the presence or absence of the leguminous species Periandra mediterranea. This latter species was considered to be the main N source in this site due to its ability to fix N2 in association with Bradyrhizobia species. Soil proteolytic activity was high in treatments with P. mediterranea and in those severely invaded, but not in the first steps of invasion. While ammonium was the N-chemical species dominant in plots with native species, including P.mediterranea, soil nitrate prevailed only in fully invaded plots due to the stimulation of the nitrifying bacterial (AOB) and archaeal (AOA) populations carrying the amoA gene. However, in the presence of P. mediterranea, either in the beginning of the invasion or in uninvaded plots, we observed an inhibition of the nitrifying microbial populations and nitrate formation, suggesting that this is a biotic resistance strategy elicited by P. mediterranea to compete with M. minutiflora. Therefore, the inhibition of proteolytic activity and the nitrification process were the strategies elicited by P.mediterranea to constrain M.munitiflora invasion.

Pseudomonas edaphica sp. nov., isolated from rhizospheric soil of Cistus ladanifer L. in Spain

During a study on biodiversity of bacteria inhabiting rhizospheric soil of rockrose (Cistus ladanifer L.), we isolated a strain coded RD25^T in a soil from Northern Spain. The 16S rRNA gene sequence showed 99.5 % identity with respect to the closest related species Pseudomonas brenneri DSM15294^T, and 99.4 % with respect to P. paralactis WS4672^T. The following related Pseudomonas species showed 99.3 % or less identity, and therefore RD25^T was classified within genus Pseudomonas. The phylogenetic analysis of 16S rRNA and the housekeeping genes rpoB, rpoD and gyrB suggested that this strain could be a novel species. The strain RD25^T has several polar-subpolar flagella. It can grow at 36 °C, at 0-6 % NaCl concentration and a range of pH 5-9. Positive for arginine dihydrolase and urease production, and negative for reduction of nitrate. The strain is catalase and oxidase positive. Major fatty acids are C_16 : 1 ω7c / C_16 : 1 ω6c in summed feature 3, C_16 : 0, and C_18 : 1 ω7c / C_18 : 1 ω6c in summed feature 8. The respiratory ubiquinone is Q9. The DNA G+C content was 59.9 mol%. The digital DNA-DNA hybridisation average values (dDDH) ranged between 30-61.2 % relatedness and the ANIb values ranged between 93.9-80.5 % with respect to the type strains of the closely related species. Therefore, the genotypic, genomic, phenotypic and chemotaxonomic data support the classification of strain RD25 as a novel species of genus Pseudomonas, for which the name P. edaphica sp. nov. is proposed. The type strain is RD25^T (=LMG 30152^T=CECT 9373^T).

Legume bioactive compounds: influence of rhizobial inoculation

Legumes consumption has been recognized as beneficial for human health, due to their content in proteins, fiber, minerals and vitamins, and their cultivation as beneficial for sustainable agriculture due to their ability to fix atmospheric nitrogen in symbiosis with soil bacteria known as rhizobia. The inoculation with these baceria induces metabolic changes in the plant, from which the more studied to date are the increases in the nitrogen and protein contents, and has been exploited in agriculture to improve the crop yield of several legumes. Nevertheless, legumes also contain several bioactive compounds such as polysaccharides, bioactive peptides, isoflavones and other phenolic compounds, carotenoids, tocopherols and fatty acids, which makes them functional foods included into the nutraceutical products. Therefore, the study of the effect of the rhizobial inoculation in the legume bioactive compounds content is gaining interest in the last decade. Several works reported that the inoculation of different genera and species of rhizobia in several grain legumes, such as soybean, cowpea, chickpea, faba bean or peanut, produced increases in the antioxidant potential and in the content of some bioactive compounds, such as phenolics, flavonoids, organic acids, proteins and fatty acids. Therefore, the rhizobial inoculation is a good tool to enhance the yield and quality of legumes and further studies on this field will allow us to have plant probiotic bacteria that promote the plant growth of legumes improving their functionality.

Invasion of the Brazilian campo rupestre by the exotic grass Melinis minutiflora is driven by the high soil N availability and changes in the N cycle

The Serra do Rola Moça State Park (PESRM) in Minas Gerais State, Brazil is a preserved site representative of the campo rupestre biome over an ironstone outcrop that has a high level of plant diversity. Almost 60% of this grassy field has been invaded by the exotic molasses grass (Melinis minutiflora), which constitutes a severe threat to the biodiversity and survival of this biome, particularly due to the impacts of annual fires and inappropriate restoration interventions. Many invasive species exhibit a high demand for nitrogen (N). Hence, this work aimed to study the N cycle alterations promoted by M. minutiflora in a site of the campo rupestre, where the leguminous species Mimosa pogocephala was prevalent. The biome's soils exhibited a high natural N fertility and low C:N ratio. The main N source in this biome resulted from the biological N fixation performed by M. pogocephala associated with Burkholderia nodosa, as evidenced by the total leaf N content, leaf δ¹⁵N signature, nodule occupation and bacterial molecular identification analyses. The displacement of native species by molasses grass was associated with changes in the soil N forms, namely the nitrate increased as the ammonium decreased. The latter was the dominant N form in the native species plots, as observed in the soil analysis of total N, ammonium and nitrate contents. The dominant ammonium form was changed to the nitric form by the stimulation of ammonia-oxidising bacteria populations due to the invasive species. Therefore, the key mechanism behind the invasiveness of the exotic grass and the concomitant displacement of the native species may be associated with changes in the soil N chemical species. Based on this finding and on the high N-based soil fertility found in the campo rupestre N fertilisation procedures for restoration of invaded areas should be strictly avoided in this biome.

Reclassification of strains MAFF 303099T and R7A into Mesorhizobiumjaponicum sp. nov

In this work we revise the taxonomic status of the Lotus-nodulating strains MAFF 303099T and R7A isolated in Japan and New Zealand, respectively. Their 16S rRNA gene sequences are identical and show 98.0, 99.7, 99.8 and 99.9 % similarity values with respect to Mesorhizobium loti NZP 2213T, M. jarvisii ATCC 33669T, M. huakuii USDA 4779T (=CCBAU 2609T) and M. erdmanii USDA 3471T, respectively. The analysis of recA and glnII gene sequeces showed that M. jarvisii ATCC 33669T and M. huakuii USDA 4779T (=CCBAU 2609T) are the most closely related strains to MAFF 303099T and R7A, with similarity values suggesting that these two strains belong to a different species for which MAFF 303099T is selected as the type strain. The DNA-DNA relatedness values between strain MAFF 303099T and its closest phylogenetic relatives ranged from 53 to 60 % in average. Strains MAFF 303099T and R7A presented slight differences in the proportions of C18 : 1ω7c 11-methyl and C19 : 0 cyclo ω8c fatty acids with respect to M. jarvisii ATCC 33669T and M. huakuii USDA 4779T, and also in several phenotypic characteristics. Therefore, we propose the reclassification of these two strains into a novel species named Mesorhizobium japonicum sp. nov., with the type strain being MAFF 303099T (=LMG 29417T=CECT 9101T).

Revision of the taxonomic status of type strains of Mesorhizobium loti and reclassification of strain USDA 3471T as the type strain of Mesorhizobium erdmanii sp. nov. and ATCC 33669T as the type strain of Mesorhizobium jarvisii sp. nov

The species Mesorhizobim loti was isolated from nodules of Lotus corniculatus and its type strain deposited in several collections. Some of these type strains, such as those deposited in the USDA and ATCC collections before 1990, are not coincident with the original strain, NZP 2213T, deposited in the NZP culture collection. The analysis of the 16S rRNA gene showed that strains USDA 3471T and ATCC 33669T formed independent branches from that occupied by Mesorhizobium loti NZP 2213T and related to those occupied by Mesorhizobium opportunistum WSM2075T and Mesorhizobium huakuii IFO 15243T, respectively, with 99.9 % similarity in both cases. However, the analysis of concatenated recA, atpD and glnII genes with similarities lower than 96, 98 and 94 %, respectively, between strains USDA 3471T and M. opportunistum WSM2075T and between strains ATCC 33669T and M. huakuii IFO 15243T, indicated that the strains USDA 3471T and ATCC 33669T represent different species of the genus Mesorhizobium . These results were confirmed by DNA–DNA hybridization experiments and phenotypic characterization. Therefore, the two strains were reclassified as representatives of the two species Mesorhizobium erdmanii sp. nov. (type strain USDA 3471T = CECT 8631T = LMG 17826t2T) and Mesorhizobium jarvisii sp. nov. (type strain ATCC 33669T = CECT 8632T = LMG 28313T).

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).

Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26

Arsenic is widespread in the environment and its presence is a result of natural or anthropogenic activities. Microbes have developed different mechanisms to deal with toxic compounds such as arsenic and this is to resist or metabolize the compound. Here, we present the first reference set of genomic, transcriptomic and proteomic data of an Alphaproteobacterium isolated from an arsenic-containing goldmine: Rhizobium sp. NT-26. Although phylogenetically related to the plant-associated bacteria, this organism has lost the major colonizing capabilities needed for symbiosis with legumes. In contrast, the genome of Rhizobium sp. NT-26 comprises a megaplasmid containing the various genes, which enable it to metabolize arsenite. Remarkably, although the genes required for arsenite oxidation and flagellar motility/biofilm formation are carried by the megaplasmid and the chromosome, respectively, a coordinate regulation of these two mechanisms was observed. Taken together, these processes illustrate the impact environmental pressure can have on the evolution of bacterial genomes, improving the fitness of bacterial strains by the acquisition of novel functions.

Physiological and antioxidant responses of Medicago sativa-rhizobia symbiosis to cyanobacterial toxins (Microcystins) exposure

Toxic cyanobacteria in freshwaters can induce potent harmful effects on growth and development of plants irrigated with contaminated water. In this study, the effect of cyanobacteria extract containing Microcystins (MC) on Medicago sativa-rhizobia symbiosis was investigated in order to explore plants response through biomass production, photosynthetic pigment and antioxidant enzymes analysis: Peroxidase (POD), Polyphenoloxidase (PPO) and Catalase (CAT). Alfalfa plants were inoculated with two endosymbiotic rhizobial strains: RhOL1 (MC less sensitive strain) and RhOL3 (MC more sensitive strain), to evaluate the rhizobial contribution on the plant response cultured under cyanobacterial toxins stress. The two rhizobia strains were identified as Ensifer meliloti by sequence analysis of their rrs and atpD genes. The chronic exposure to MC extract showed shoot, root and nodules dry weight decrease, in both symbiosis cultures. The rate of decline in plants inoculated with RhOL3 was higher than that in symbiosis with RhOL1 mainly at 20 μg L(-1) of MC. Cyanotoxins also reduced photosynthetic pigment content and generated an oxidative stress observed at cellular level. POD, PPO and CAT activities were significantly increased in leaves, roots and nodules of alfalfa plants exposed to MC. These enzyme activities were higher in plants inoculated with RhOL3 especially when alfalfa plants were exposed to 20 μg L(-1) of MC. The present paper reports new scientific finding related to the behavior of rhizobia-M. sativa associations to MC (Microcystins) for later recommendation concerning the possible use of these symbiosis face to crops exposure to MC contaminated water irrigation.

Endobacter medicaginis gen. nov., sp. nov., isolated from alfalfa nodules in an acidic soil

A bacterial strain designated M1MS02(T) was isolated from a surface-sterilized nodule of Medicago sativa in Zamora (Spain). The 16S rRNA gene sequence of this strain showed 96.5 and 96.2 % similarity, respectively, with respect to Gluconacetobacter liquefaciens IFO 12388(T) and Granulibacter bethesdensis CGDNIH1(T) from the family Acetobacteraceae. The novel isolate was a Gram-stain-negative, non-sporulating, aerobic coccoid to rod-shaped bacterium that was motile by a subpolar flagellum. The major fatty acid was C18 : 1ω7c and the major ubiquinone was Q-10. The lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, two aminophospholipids, three aminolipids, four glycolipids, two phospholipids and one lipid. Strain M1MS02(T) was catalase-positive and oxidase- and urease-negative. Acetate and lactate were not oxidized. Acetic acid was produced from ethanol in culture media supplemented with 2 % CaCO3. Ammonium sulphate was assimilated in glucose medium. The strain produced dihydroxyacetone from glycerol. Phylogenetic and phenotypic analyses commonly used to differentiate genera within the family Acetobacteraceae showed that strain M1MS02(T) should be classified as representing a novel species of a new genus within this family, for which the name Endobacter medicaginis gen. nov., sp. nov. is proposed. The type strain of the type species is M1MS02(T) ( = LMG 26838(T) = CECT 8088(T)). To our knowledge, this is the first report of a member of the Acetobacteraceae occurring as a legume nodule endophyte.

Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus

Several strains isolated from the legume Pachyrhizus erosus were characterized on the basis of diverse genetic, phenotypic and symbiotic approaches. These novel strains formed two groups closely related to Bradyrhizobium elkanii according to their 16S rRNA gene sequences. Strains PAC48T and PAC68T, designated as the type strains of these two groups, presented 99.8 and 99.1% similarity, respectively, in their 16S rRNA gene sequences with respect to B. elkanii USDA 76T. In spite of these high similarity values, the analysis of additional phylogenetic markers such as atpD and glnII genes and the 16S-23S intergenic spacer (ITS) showed that strains PAC48T and PAC68T represented two separate novel species of the genus Bradyrhizobium with B. elkanii as their closest relative. Phenotypic differences among the novel strains isolated from Pachyrhizus and B. elkanii were found regarding the assimilation of carbon sources and antibiotic resistance. All these differences were congruent with DNA-DNA hybridization analysis which revealed 21% genetic relatedness between strains PAC48T and PAC68T and 46% and 25%, respectively, between these strains and B. elkanii LMG 6134T. The nodD and nifH genes of strains PAC48T and PAC68T were phylogenetically divergent from those of bradyrhizobia species that nodulate soybean. Soybean was not nodulated by the novel Pachyrhizus isolates. Based on the genotypic and phenotypic data obtained in this study, the new strains represent two novel species for which the names Bradyrhizobium pachyrhizi sp. nov. (type strain PAC48T=LMG 24246T=CECT 7396T) and Bradyrhizobium jicamae sp. nov. (type strain PAC68T=LMG 24556T=CECT 7395T) are proposed.

Revision of the taxonomic status of the species Rhizobium leguminosarum (Frank 1879) Frank 1889AL, Rhizobium phaseoli Dangeard 1926AL and Rhizobium trifolii Dangeard 1926AL. R. trifolii is a later synonym of R. leguminosarum. Reclassification of the strain R. leguminosarum DSM 30132 (=NCIMB 11478) as Rhizobium pisi sp. nov

The taxonomic status of the species Rhizobium leguminosarum, Rhizobium trifolii and Rhizobium phaseoli was analysed in this study on the basis of their molecular and phenotypic characteristics. According to the results, the type strain R. phaseoli ATCC 14482(T) does not belong to any of the already described species of the genus Rhizobium and it should therefore be considered as a different species. In contrast, the strains of R. trifolii examined belonged to R. leguminosarum and thus R. trifolii is a later synonym of R. leguminosarum. The results of the analysis of 16S-23S intergenic spacer region and rrs, recA and atpD gene sequences as well as those of DNA-DNA hybridization experiments and phenotypic characterizations showed that the type strains R. leguminosarum USDA 2370(T) and R. leguminosarum DSM 30132 do not belong to the same species. Taking into account that strain USDA 2370(T) corresponds to the original strain of this species, 3Hoq18(T), this strain should be considered as the true type strain of R. leguminosarum whereas strain DSM 30132 should be reclassified as a different species, for which the name Rhizobium pisi sp. nov. is proposed (type strain, DSM 30132(T)=NCIMB 11478(T)).

Phylogenetic diversity based on rrs, atpD, recA genes and 16S-23S intergenic sequence analyses of rhizobial strains isolated from Vicia faba and Pisum sativum in Peru

In this study 17 isolates from effective nodules of Vicia faba and Pisum sativum var. macrocarpum growing in different soils from Peru were isolated and characterized. The isolates, presenting 11 different RAPD profiles, were distributed in three groups on the basis of their 16S-RFLP patterns. The 16S rRNA gene sequences of strains from 16S-RFLP groups I, II and III were closely related (identities higher than 99.5%) to Rhizobium leguminosarum bv. trifolii DSM 30141 (=ATCC 14480), R. leguminosarum bv. viciae DSM 30132(T) and Rhizobium etli CFN42(T) (=USDA 9032(T)), respectively. The analysis of the 16S-23S intergenic spacer (ITS) and two housekeeping genes, atpD and recA, confirmed the identification of strains from group I, however those from groups II and III were phylogenetically divergent to strains DSM 30132(T) and CFN42(T). These results support the fact that the 16S rRNA gene is not adequate for identification at species level within genus Rhizobium and suggest the existence of putative new species within the phylogenetic group of R. leguminosarum. They also confirm the need of a taxonomic revision of R. leguminosarum since the reference strains of the three biovars included in this study are phylogenetically divergent according to their ITS, atpD and recA gene sequences.