Julio Martínez

Reclassification of Rhizobium tropici type A strains as Rhizobium leucaenae sp. nov.

Rhizobium tropici is a well-studied legume symbiont characterized by high genetic stability of the symbiotic plasmid and tolerance to tropical environmental stresses such as high temperature and low soil pH. However, high phenetic and genetic variabilities among R. tropici strains have been largely reported, with two subgroups, designated type A and B, already defined within the species. A polyphasic study comprising multilocus sequence analysis, phenotypic and genotypic characterizations, including DNA-DNA hybridization, strongly supported the reclassification of R. tropici type A strains as a novel species. Type A strains formed a well-differentiated clade that grouped with R. tropici, Rhizobium multihospitium, Rhizobium miluonense, Rhizobium lusitanum and Rhizobium rhizogenes in the phylogenies of the 16S rRNA, recA, gltA, rpoA, glnII and rpoB genes. Several phenotypic traits differentiated type A strains from all related taxa. The novel species, for which the name Rhizobium leucaenae sp. nov. is proposed, is a broad host range rhizobium being able to establish effective root-nodule symbioses with Leucaena leucocephala, Leucaena esculenta, common beans (Phaseolus vulgaris) and Gliricidia sepium. Strain CFN 299(T) (u200a=u200aUSDA 9039(T)u200a=u200aLMG 9517(T)u200a=u200aCECT 4844(T)u200a=u200aJCM 21088(T)u200a=u200aIAM 14230(T)u200a=u200aSEMIA 4083(T)u200a=u200aCENA 183(T)u200a=u200aUMR1026(T)u200a=u200aCNPSo 141(T)) is designated the type strain of Rhizobium leucaenae sp. nov.

Rhizobium etli taxonomy revised with novel genomic data and analyses

The taxonomic position of Phaseolus vulgaris rhizobial strains with available sequenced genomes was examined. Phylogenetic analyses with concatenated conserved genomic fragments accounting for over half of each genome showed that Rhizobium strains CIAT 652, Ch24-10 (newly reported genome) and CNPAF 512 constituted a well-supported group independent from Rhizobium etli CFN 42(T). DNA-DNA hybridization results indicated that CIAT 652, Ch24-10 and CNPAF 512 could correspond to R. etli, although the hybridization values were at the borderline that distinguishes different species. In contrast, experimental hybridization results were higher (over 80%) with Rhizobium phaseoli type strain ATCC 14482(T) in congruence to phylogenetic and ANIm analyses. The latter criterion allowed the reclassification of R. etli strains 8C-3 and Brasil5 as R. phaseoli. It was therefore concluded, based on all the evidence, that the CIAT 652, Ch24-10, and CNPAF 512 strains should be reclassified as R. phaseoli in spite of several common features linking them to R. etli. The R. phaseoli and R. etli speciation process seems to be a more recent event than the speciation that has occurred among other sister species, such as R. leguminosarum-R. etli or R. rhizogenes-R. tropici.

Rhizobium grahamii sp. nov., from nodules of Dalea leporina, Leucaena leucocephala and Clitoria ternatea, and Rhizobium mesoamericanum sp. nov., from nodules of Phaseolus vulgaris, siratro, cowpea and Mimosa pudica

Two novel related Rhizobium species, Rhizobium grahamii sp. nov. and Rhizobium mesoamericanum sp. nov., were identified by a polyphasic approach using DNA-DNA hybridization, whole-genome sequencing and phylogenetic and phenotypic characterization including nodulation of Leucaena leucocephala and Phaseolus vulgaris (bean). As similar bacteria were found in the Los Tuxtlas rainforest in Mexico and in Central America, we suggest the existence of a Mesoamerican microbiological corridor. The type strain of Rhizobium grahamii sp. nov. is CCGE 502(T) (= ATCC BAA-2124(T) = CFN 242(T) = Dal4(T) = HAMBI 3152(T)) and that of Rhizobium mesoamericanum sp. nov. is CCGE 501(T) (= ATCC BAA-2123(T) = HAMBI 3151(T) = CIP 110148(T) = 1847(T)).

Gut and root microbiota commonalities.

ABSTRACT Animal guts and plant roots have absorption roles for nutrient uptake and converge in harboring large, complex, and dynamic groups of microbes that participate in degradation or modification of nutrients and other substances. Gut and root bacteria regulate host gene expression, provide metabolic capabilities, essential nutrients, and protection against pathogens, and seem to share evolutionary trends.

Rhizobium calliandrae sp. nov., Rhizobium mayense sp. nov. and Rhizobium jaguaris sp. nov., rhizobial species nodulating the medicinal legume Calliandra grandiflora.

Calliandra grandiflora has been used as a medicinal plant for thousands of years in Mexico. Rhizobial strains were obtained from root nodules of C. grandiflora collected from different geographical regions in Chiapas and characterized by BOX-PCR, amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis. Most isolates corresponded to members of the genus Rhizobium and those not related to species with validly published names were further characterized by recA, atpD, rpoB and nifH gene phylogenies, phenotypic and DNA-DNA hybridization analyses. Three novel related species of the genus Rhizobium within the Rhizobium tropici group share the same symbiovar that may be named sv. calliandrae. The names proposed for the three novel species are Rhizobium calliandrae sp. nov. (type strain, CCGE524(T)u200a=ATCC BAA-2435(T)u200a=CIP 110456(T)u200a=LBP2-1(T)), Rhizobium mayense sp. nov. (type strain, CCGE526(T)u200a=ATCC BAA-2446(T)u200a=u200aCIP 110454(T)u200a=NSJP1-1(T)) and Rhizobium jaguaris sp. nov. (type strain, CCGE525(T)u200a=ATCC BAA-2445(T)u200a=CIP 110453(T)u200a=SJP1-2(T)).

Change in Land Use Alters the Diversity and Composition of Bradyrhizobium Communities and Led to the Introduction of Rhizobium etli into the Tropical Rain Forest of Los Tuxtlas (Mexico)

Nitrogen-fixing bacteria of the Bradyrhizobium genus are major symbionts of legume plants in American tropical forests, but little is known about the effects of deforestation and change in land use on their diversity and community structure. Forest clearing is followed by cropping of bean (Phaseolus vulgaris) and maize as intercropped plants in Los Tuxtlas tropical forest of Mexico. The identity of bean-nodulating rhizobia in this area is not known. Using promiscuous trap plants, bradyrhizobia were isolated from soil samples collected in Los Tuxtlas undisturbed forest, and in areas where forest was cleared and land was used as crop fields or as pastures, or where secondary forests were established. Rhizobia were also trapped by using bean plants. Bradyrhizobium strains were classified into genospecies by dnaK sequence analysis supported by recA, glnII and 16S-23S rDNA IGS loci analyses. A total of 29 genospecies were identified, 24 of which did not correspond to any described taxa. A reduction in Bradyrhizobium diversity was observed when forest was turned to crop fields or pastures. Diversity seemed to recover to primary forest levels in secondary forests that derived from abandoned crop fields or pastures. The shifts in diversity were not related to soil characteristics but seemingly to the density of nodulating legumes present at each land use system (LUS). Bradyrhizobium community composition in soils was dependent on land use; however, similarities were observed between crop fields and pastures but not among forest and secondary forest. Most Bradyrhizobium genospecies present in forest were not recovered or become rare in the other LUS. Rhizobium etli was found as the dominant bean-nodulating rhizobia present in crop fields and pastures, and evidence was found that this species was introduced in Los Tuxtlas forest.

Native bradyrhizobia from Los Tuxtlas in Mexico are symbionts of Phaseolus lunatus (Lima bean).

Los Tuxtlas is the northernmost rain forest in North America and is rich in Bradyrhizobium with an unprecedented number of novel lineages. ITS sequence analysis of legumes in polycultures from Los Tuxtlas led to the identification of Phaseolus lunatus and Vigna unguiculata in addition to Phaseolus vulgaris as legumes associated with maize in crops. Bacterial diversity of isolates from nitrogen-fixing nodules of P. lunatus and V. unguiculata was revealed using ERIC-PCR and PCR-RFLP of rpoB genes, and sequencing of recA, nodZ and nifH genes. P. lunatus and V. unguiculata nodule bacteria corresponded to bradyrhizobia closely related to certain native bradyrhizobia from the Los Tuxtlas forest and novel groups were found. This is the first report of nodule bacteria from P. lunatus in its Mesoamerican site of origin and domestication.

Species in Wolbachia? Proposal for the designation of 'Candidatus Wolbachia bourtzisii', 'Candidatus Wolbachia onchocercicola', 'Candidatus Wolbachia blaxteri', 'Candidatus Wolbachia brugii', 'Candidatus Wolbachia taylori', 'Candidatus Wolbachia collembolicola' and 'Candidatus Wolbachia multihospitum' for the different species within Wolbachia supergroups.

Wolbachia are highly extended bacterial endosymbionts that infect arthropods and filarial nematodes and produce contrasting phenotypes on their hosts. Wolbachia taxonomy has been understudied. Currently, Wolbachia strains are classified into phylogenetic supergroups. Here we applied phylogenomic analyses to study Wolbachia evolutionary relationships and examined metrics derived from their genome sequences such as average nucleotide identity (ANI), in silico DNA-DNA hybridization (DDH), G+C content, and synteny to shed light on the taxonomy of these bacteria. Draft genome sequences of strains wDacA and wDacB obtained from the carmine cochineal insect Dactylopius coccus were included. Although all analyses indicated that each Wolbachia supergroup represents a distinct evolutionary lineage, we found that some of the analyzed supergroups showed enough internal heterogeneity to be considered as assemblages of more than one species. Thus, supergroups would represent supraspecific groupings. Consequently, Wolbachia pipientis nomen species would apply only to strains of supergroup B and we propose the designation of Candidatus Wolbachia bourtzisii, Candidatus Wolbachia onchocercicola, Candidatus Wolbachia blaxterii, Candidatus Wolbachia brugii, Candidatus Wolbachia taylorii, Candidatus Wolbachia collembolicola and Candidatus Wolbachia multihospitis for other supergroups.

Rhizobial Symbioses in Tropical Legumes and Non-Legumes

Legume diversity is very large in the tropics, and legume evolution appears to have followed a tropical to temperate direction. Many tropical legumes have been domesticated as crops for human or animal food, but there are many other legumes that are underutilized. The high protein content in legume seeds and leaves appears to be related to the nitrogen fixation that occurs in legumes through their symbioses with rhizobial bacteria. Rhizobial diversity in tropical legumes has been studied, but it is considered that the enormous diversity of rhizobia in the tropics remains largely unknown, as do the molecular mechanisms of their symbioses. Analyses of the nodule bacteria from Phaseolus vulgaris bean plants have revealed several new species. Current knowledge suggests that there is not a high degree of specificity in tropical symbioses, and hence many tropical legumes have been classified as promiscuous. This promiscuity has consequences for the use of rhizobia as inoculants for tropical legumes. Rhizobial inoculants have been successfully used for over 100 years in many places, but inoculation in the tropics has only been successful in a few cases. New interest in biofuels has raised interest in tropical legumes with high oil content, such as Pongamia pinnata, which is now being studied for its symbiotic nitrogen-fixing potential.

Short-Term Evolution of Rhizobial Strains Toward Sustainability in Agriculture

Some rhizobial strains are widely used as biofertilizers substituting inorganic nitrogen fertilization, mainly for legumes. The successful use of rhizobia in agriculture derives from appropriate selection of strains with high capacities to fix nitrogen. However, the selection of more efficient rhizobia is from a limited number of plant growth conditions. In other environments, inoculant strains may exhibit low competitiveness or low nitrogen fixation. We argue here that rhizobial strains are continuously evolving in plants and therefore recommend an approach inspired on experimental evolution studies where strains adapted to particular conditions may be selected. The selection and detection of efficient rhizobial strains should take place under local field conditions in order to obtain superior nitrogen-fixing symbionts. To support our recommendation, we reviewed different examples of experimental evolution in bacteria and summarized results on rhizobial co-inoculation with different microbes.