Genetic diversity of elite rhizobial strains of subtropical and tropical legumes based on the 16S rRNA and glnII genes

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

BACKGROUND

The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].

RESULTS

At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27). At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%).

CONCLUSIONS

Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.

Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov

Agrobacterium strains are associated with soil, plants and animals, and known mainly by their pathogenicity. We studied 14 strains isolated from nodules of healthy soybean and common bean plants in Brazil, Mexico, Ecuador and Mozambique. Sequence analysis of the 16S rRNA gene positioned the strains as Agrobacterium, but with low phylogenetic resolution. Multilocus sequence analysis (MLSA) of three partial housekeeping genes (glnII, gyrB and recA) positioned the strains in four distinct clades, with Agrobacterium pusense, Agrobacterium deltaense, Agrobacterium radiobacter and Agrobacterium sp. genomospecies G1. Analysis by BOX-PCR revealed high intraspecies diversity. Genomic analysis of representative strains of the three clades indicated that they carry the protelomerase telA gene, and MLSA analysis with six complete housekeeping genes (atpD, glnII, gyrB, recA, rpoB and thrC), as well as average nucleotide identity (less than 90 % with closest species) and digital DNA-DNA hybridization (less than 41 % with closest species) revealed that strain CNPSo 675T and Agrobacterium sp. genomospecies G1 compose a new species. Other phenotypic and genotypic characteristics were determined for the new clade. Although not able to re-nodulate the host, we hypothesize that several strains of Agrobacterium are endophytes in legume nodules, where they might contribute to plant growth. Our data support the description of the CNPSo 675T and Agrobacterium sp. genomospecies G1 strains as a new species, for which the name Agrobacterium fabacearum is proposed. The type strain is CNPSo 675T (=UMR 1457T=LMG 31642T) and is also deposited in other culture collections.

Characterization of Bradyrhizobium strains indigenous to Western Australia and South Africa indicates remarkable genetic diversity and reveals putative new species

Bradyrhizobium are N₂-fixing microsymbionts of legumes with relevant applications in agricultural sustainability, and we investigated the phylogenetic relationships of conserved and symbiotic genes of 21 bradyrhizobial strains. The study included strains from Western Australia (WA), isolated from nodules of Glycine spp. the country is one genetic center for the genus and from nodules of other indigenous legumes grown in WA, and strains isolated from forage Glycine sp. grown in South Africa. The 16S rRNA phylogeny divided the strains in two superclades, of B. japonicum and B. elkanii, but with low discrimination among the species. The multilocus sequence analysis (MLSA) with four protein-coding housekeeping genes (dnaK, glnII, gyrB and recA) pointed out seven groups as putative new species, two within the B. japonicum, and five within the B. elkanii superclades. The remaining eleven strains showed higher similarity with six species, B. lupini, B. liaoningense, B. yuanmingense, B. subterraneum, B. brasilense and B. retamae. Phylogenetic analysis of the nodC symbiotic gene clustered 13 strains in three different symbiovars (sv. vignae, sv. genistearum and sv. retamae), while seven others might compose new symbiovars. The genetic profiles of the strains evaluated by BOX-PCR revealed high intra- and interspecific diversity. The results point out the high level of diversity still to be explored within the Bradyrhizobium genus, and further studies might confirm new species and symbiovars.

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.

Draft Genome Sequence of Agrobacterium deltaense Strain CNPSo 3391, Isolated from a Soybean Nodule in Mozambique

Agrobacterium deltaense strain CNPSo 3391 was isolated from a soybean nodule in Mozambique. Its genome size was estimated at 4,926,588 bp.

Agrobacterium deltaense strain CNPSo 3391 was isolated from a soybean nodule in Mozambique. Its genome size was estimated at 4,926,588 bp. This isolate carries several coding sequences for stress tolerance, but no identifiable nodulation or virulence genes. Possible ecological roles of bacteria isolated from legume nodules and closely related to Agrobacterium are discussed.

The Rhizobia-Lotus Symbioses: Deeply Specific and Widely Diverse

The symbiosis between Lotus and rhizobia has been long considered very specific and only two bacterial species were recognized as the microsymbionts of Lotus: Mesorhizobium loti was considered the typical rhizobia for the L. corniculatus complex, whereas Bradyrhizobium sp. (Lotus) was the symbiont for L. uliginosus and related species. As discussed in this review, this situation has dramatically changed during the last 15 years, with the characterization of nodule bacteria from worldwide geographical locations and from previously unexplored Lotus spp. Current data support that the Lotus rhizobia are dispersed amongst nearly 20 species in five genera (Mesorhizobium, Bradyrhizobium, Rhizobium, Ensifer, and Aminobacter). As a consequence, M. loti could be regarded an infrequent symbiont of Lotus, and several plant-bacteria compatibility groups can be envisaged. Despite the great progress achieved with the model L. japonicus in understanding the establishment and functionality of the symbiosis, the genetic and biochemical bases governing the stringent host-bacteria compatibility pairships within the genus Lotus await to be uncovered. Several Lotus spp. are grown for forage, and inoculation with rhizobia is a common practice in various countries. However, the great diversity of the Lotus rhizobia is likely squandered, as only few bacterial strains are used as inoculants for Lotus pastures in very different geographical locations, with a great variety of edaphic and climatic conditions. The agroecological potential of the genus Lotus can not be fully harnessed without acknowledging the great diversity of rhizobia-Lotus interactions, along with a better understanding of the specific plant and bacterial requirements for optimal symbiotic nitrogen fixation under increasingly constrained environmental conditions.

Bradyrhizobium tropiciagri sp. nov. and Bradyrhizobium embrapense sp. nov., nitrogen-fixing symbionts of tropical forage legumes

Biological nitrogen fixation is a key process for agricultural production and environmental sustainability, but there are comparatively few studies of symbionts of tropical pasture legumes, as well as few described species of the genus Bradyrhizobium, although it is the predominant rhizobial genus in the tropics. A detailed polyphasic study was conducted with two strains of the genus Bradyrhizobium used in commercial inoculants for tropical pastures in Brazil, CNPSo 1112T, isolated from perennial soybean (Neonotonia wightii), and CNPSo 2833T, from desmodium (Desmodium heterocarpon). Based on 16S-rRNA gene phylogeny, both strains were grouped in the Bradyrhizobium elkanii superclade, but were not clearly clustered with any known species. Multilocus sequence analysis of three (glnII, gyrB and recA) and five (plus atpD and dnaK) housekeeping genes confirmed that the strains are positioned in two distinct clades. Comparison with intergenic transcribed spacer sequences of type strains of described species of the genus Bradyrhizobium showed similarity lower than 93.1 %, and differences were confirmed by BOX-PCR analysis. Nucleotide identity of three housekeeping genes with type strains of described species ranged from 88.1 to 96.2 %. Average nucleotide identity of genome sequences showed values below the threshold for distinct species of the genus Bradyrhizobium ( < 90.6 %), and the value between the two strains was also below this threshold (91.2 %). Analysis of nifH and nodC gene sequences positioned the two strains in a clade distinct from other species of the genus Bradyrhizobium. Morphophysiological, genotypic and genomic data supported the description of two novel species in the genus Bradyrhizobium, Bradyrhizobium tropiciagri sp. nov. (type strain CNPSo 1112T = SMS 303T = BR 1009T = SEMIA 6148T = LMG 28867T) and Bradyrhizobium embrapense sp. nov. (type strain CNPSo 2833T = CIAT 2372T = BR 2212T = SEMIA 6208T = U674T = LMG 2987).

Genetic diversity of Rhizobia isolates from Amazon soils using cowpea (Vigna unguiculata) as trap plant

The aim of this work was to characterize rhizobia isolated from the root nodules of cowpea (Vigna unguiculata) plants cultivated in Amazon soils samples by means of ARDRA (Amplified rDNA Restriction Analysis) and sequencing analysis, to know their phylogenetic relationships. The 16S rRNA gene of rhizobia was amplified by PCR (polymerase chain reaction) using universal primers Y1 and Y3. The amplification products were analyzed by the restriction enzymes HinfI, MspI and DdeI and also sequenced with Y1, Y3 and six intermediate primers. The clustering analysis based on ARDRA profiles separated the Amazon isolates in three subgroups, which formed a group apart from the reference isolates of Bradyrhizobium japonicum and Bradyrhizobium elkanii. The clustering analysis of 16S rRNA gene sequences showed that the fast-growing isolates had similarity with Enterobacter, Rhizobium, Klebsiella and Bradyrhizobium and all the slow-growing clustered close to Bradyrhizobium.

Multilocus sequence analysis (MLSA) of Bradyrhizobium strains: revealing high diversity of tropical diazotrophic symbiotic bacteria

Symbiotic association of several genera of bacteria collectively called as rhizobia and plants belonging to the family Leguminosae (=Fabaceae) results in the process of biological nitrogen fixation, playing a key role in global N cycling, and also bringing relevant contributions to the agriculture. Bradyrhizobium is considered as the ancestral of all nitrogen-fixing rhizobial species, probably originated in the tropics. The genus encompasses a variety of diverse bacteria, but the diversity captured in the analysis of the 16S rRNA is often low. In this study, we analyzed twelve Bradyrhizobium strains selected from previous studies performed by our group for showing high genetic diversity in relation to the described species. In addition to the 16S rRNA, five housekeeping genes (recA, atpD, glnII, gyrB and rpoB) were analyzed in the MLSA (multilocus sequence analysis) approach. Analysis of each gene and of the concatenated housekeeping genes captured a considerably higher level of genetic diversity, with indication of putative new species. The results highlight the high genetic variability associated with Bradyrhizobium microsymbionts of a variety of legumes. In addition, the MLSA approach has proved to represent a rapid and reliable method to be employed in phylogenetic and taxonomic studies, speeding the identification of the still poorly known diversity of nitrogen-fixing rhizobia in the tropics.