Microsymbionts of Phaseolus vulgaris in acid and alkaline soils of Mexico

The symbiovar mediterranense of Sinorhizobium meliloti nodulates Phaseolus vulgaris across Lanzarote (Canary Islands): A revision of this symbiovar supports a proposal to delimit symbiovars boundaries in Sinorhizobium and to define four new symbiovars

The symbiovar mediterranense of Sinorhizobium meliloti was initially found in Phaseolus vulgaris nodules in Tunisia and in an eastern location of Lanzarote (Canary Islands). Here we show that the symbiovar mediterranense of S. meliloti also nodulates P. vulgaris in two western locations of this Island. The analyses of the symbiotic nodA and nodC genes reveal the complexity of the symbiovar mediterranense which encompasses strains belonging to several phylogenetic lineages and clusters. The comparison of the nodA and nodC phylogenies showed that the nodC was the most resolutive phylogenetic marker for the delineation of Sinorhizobium symbiovars. Considering that the similarity of this gene within several symbiovars, particularly mediterranense, is around 95 %, the cut-off value for their differentiation should be lower. Considering that a nodC gene cut-off similarity value of around 92 % is accepted for the genus Bradyrhizobium and that the symbiovar concept is identical in all rhizobial genera, we propose to apply this value for symbiovars delineation within all these genera. Therefore, using this cut-off value for the nodC gene analysis of Sinorhizobium symbiovars, we propose to merge the symbiovars aegeanense and fredii into the single symbiovar fredii and to define four novel symbiovars with the names asiaense, culleni, sudanense and tunisiaense.

Rhizobium hidalgonense and Rhizobium redzepovicii as faba bean (Vicia faba L.) microsymbionts in Mexican soils

As a legume crop widely cultured in the world, faba bean (Vicia faba L.) forms root nodules with diverse Rhizobium species in different regions. However, the symbionts associated with this plant in Mexico have not been studied. To investigate the diversity and species/symbiovar affiliations of rhizobia associated with faba bean in Mexico, rhizobia were isolated from this plant grown in two Mexican sites in the present study. Based upon the analysis of recA gene phylogeny, two genotypes were distinguished among a total of 35 isolates, and they were identified as Rhizobium hidalgonense and Rhizobium redzepovicii, respectively, by the whole genomic sequence analysis. Both the species harbored identical nod gene cluster and the same phylogenetic positions of nodC and nifH. So, all of them were identified into the symbiovar viciae. As a minor group, R. hidalgonense was only isolated from slightly acid soil and R. redzepovicii was the dominant group in both the acid and neutral soils. In addition, several genes related to resistance to metals (zinc, copper etc.) and metalloids (arsenic) were detected in genomes of the reference isolates, which might offer them some adaptation benefits. As conclusion, the community composition of faba bean rhizobia in Mexico was different from those reported in other regions. Furthermore, our study identified sv. viciae as the second symbiovar in the species R. redzepovicii. These results added novel evidence about the co-evolution, diversification and biogeographic patterns of rhizobia in association with their host legumes in distinct geographic regions.

Prevalence, diversity and applications potential of nodules endophytic bacteria: a systematic review

Legumes are renowned for their distinctive biological characteristic of forming symbiotic associations with soil bacteria, mostly belonging to the Rhizobiaceae familiy, leading to the establishment of symbiotic root nodules. Within these nodules, rhizobia play a pivotal role in converting atmospheric nitrogen into a plant-assimilable form. However, it has been discerned that root nodules of legumes are not exclusively inhabited by rhizobia; non-rhizobial endophytic bacteria also reside within them, yet their functions remain incompletely elucidated. This comprehensive review synthesizes available data, revealing that Bacillus and Pseudomonas are the most prevalent genera of nodule endophytic bacteria, succeeded by Paenibacillus, Enterobacter, Pantoea, Agrobacterium, and Microbacterium. To date, the bibliographic data available show that Glycine max followed by Vigna radiata, Phaseolus vulgaris and Lens culinaris are the main hosts for nodule endophytic bacteria. Clustering analysis consistently supports the prevalence of Bacillus and Pseudomonas as the most abundant nodule endophytic bacteria, alongside Paenibacillus, Agrobacterium, and Enterobacter. Although non-rhizobial populations within nodules do not induce nodule formation, their presence is associated with various plant growth-promoting properties (PGPs). These properties are known to mediate important mechanisms such as phytostimulation, biofertilization, biocontrol, and stress tolerance, emphasizing the multifaceted roles of nodule endophytes. Importantly, interactions between non-rhizobia and rhizobia within nodules may exert influence on their leguminous host plants. This is particularly shown by co-inoculation of legumes with both types of bacteria, in which synergistic effects on plant growth, yield, and nodulation are often measured. Moreover these effects are pronounced under both stress and non-stress conditions, surpassing the impact of single inoculations with rhizobia alone.

The Effect of Different Rhizobial Symbionts on the Composition and Diversity of Rhizosphere Microorganisms of Chickpea in Different Soils

BACKGROUND

Chickpea (Cicer arietinum L.) is currently the third most important legume crop in the world. It could form root nodules with its symbiotic rhizobia in soils and perform bio-nitrogen fixation. Mesorhizobium ciceri is a prevalent species in the world, except China, where Mesorhizobium muleiense is the main species associated with chickpea. There were significant differences in the competitive ability between M. ciceri and M. muleiense in sterilized and unsterilized soils collected from Xinjiang, China, where chickpea has been grown long term. In unsterilized soils, M. muleiense was more competitive than M. ciceri, while in sterilized soils, the opposite was the case. In addition, the competitive ability of M. ciceri in soils of new areas of chickpea cultivation was significantly higher than that of M. muleiense. It was speculated that there might be some biological factors in Xinjiang soils of China that could differentially affect the competitive nodulation of these two chickpea rhizobia. To address this question, we compared the composition and diversity of microorganisms in the rhizosphere of chickpea inoculated separately with the above two rhizobial species in soils from old and new chickpea-producing regions.

RESULTS

Chickpea rhizosphere microbial diversity and composition varied in different areas and were affected significantly due to rhizobial inoculation. In general, eight dominant phyla with 34 dominant genera and 10 dominant phyla with 47 dominant genera were detected in the rhizosphere of chickpea grown in soils of Xinjiang and of the new zones, respectively, with the inoculated rhizobia. Proteobacteria and Actinobacteria were dominant at the phylum level in the rhizosphere of all soils. Pseudomonas appeared significantly enriched after inoculation with M. muleiense in soils from Xinjiang, a phenomenon not found in the new areas of chickpea cultivation, demonstrating that Pseudomonas might be the key biological factor affecting the competitive colonization of M. muleiense and M. ciceri there.

CONCLUSIONS

Different chickpea rhizobial inoculations of M. muleiense and M. ciceri affected the rhizosphere microbial composition in different sampling soils from different chickpea planting areas. Through high throughput sequencing and statistical analysis, it could be found that Pseudomonas might be the key microorganism influencing the competitive nodulation of different chickpea rhizobia in different soils, as it is the dominant non-rhizobia community in Xinjiang rhizosphere soils, but not in other areas.

Diversity of common bean rhizobia in blackland of northeastern China and their symbiotic compatibility with two host varieties

The common bean (Phaseolus vulgaris L.) is an important crop in the world that forms root nodules with diverse rhizobia. Aiming to learn the rhizobial communities associated with the common bean in the black soil of Northeast China, 79 rhizobia were isolated from root nodules of two host varieties (Cuican and Jiadouwang) grown in two sites of blackland and were characterized by comparative sequence analyses of 16S rRNA, recA, atpD, nodC, and nifH genes, and whole genome. As a result, Rhizobium indigoferae, R. anhuiense, and R. croatiense as minor groups and three dominant novel Rhizobium species were identified based on their average nucleotide identity and DNA-DNA hybridization values to the type strains of relative species. This community composition of rhizobia associated with the common bean in the tested black soils was unique. Despite their different species affiliations, all of them were identified into the symbiovar phaseoli according to the phylogenies of symbiotic genes, nodC and nifH. While the phylogenetic discrepancies found in nodC, nifH evidenced that the evolutions of nodulation (nod) and nitrogen fixation (nif ) genes were partially independent. In addition, only one dominant rhizobial species was shared by the two common bean varieties grown in the two soil samples, implying that both the plant variety and the soil characteristics affected the compatibility between rhizobia and their hosts. These findings further enlarged the spectrum of common bean-nodulating rhizobia and added more information about the interactions among the soil factors, rhizobial species, and host plants in the symbiosis.

Genetic characterization at the species and symbiovar level of indigenous rhizobial isolates nodulating Phaseolus vulgaris in Greece

Phaseolus vulgaris (L.), commonly known as bean or common bean, is considered a promiscuous legume host since it forms nodules with diverse rhizobial species and symbiovars. Most of the common bean nodulating rhizobia are mainly affiliated to the genus Rhizobium, though strains belonging to Ensifer, Pararhizobium, Mesorhizobium, Bradyrhizobium, and Burkholderia have also been reported. This is the first report on the characterization of bean-nodulating rhizobia at the species and symbiovar level in Greece. The goals of this research were to isolate and characterize rhizobia nodulating local common bean genotypes grown in five different edaphoclimatic regions of Greece with no rhizobial inoculation history. The genetic diversity of the rhizobial isolates was assessed by BOX-PCR and the phylogenetic affiliation was assessed by multilocus sequence analysis (MLSA) of housekeeping and symbiosis-related genes. A total of fifty fast-growing rhizobial strains were isolated and representative isolates with distinct BOX-PCR fingerpriniting patterns were subjected to phylogenetic analysis. The strains were closely related to R. anhuiense, R. azibense, R. hidalgonense, R. sophoriradicis, and to a putative new genospecies which is provisionally named as Rhizobium sp. I. Most strains belonged to symbiovar phaseoli carrying the α-, γ-a and γ-b alleles of nodC gene, while some of them belonged to symbiovar gallicum. To the best of our knowledge, it is the first time that strains assigned to R. sophoriradicis and harbored the γ-b allele were found in European soils. All strains were able to re-nodulate their original host, indicating that they are true microsymbionts of common bean.

Genetic Diversity and Characterization of Symbiotic Bacteria Isolated from Endemic Phaseolus Cultivars Located in Contrasting Agroecosystems in Venezuela

Phaseolus vulgaris is a grain cultivated in vast areas of different countries. It is an excellent alternative to the other legumes in the Venezuelan diet and is of great agronomic interest due to its resistance to soil acidity, drought, and high temperatures. Phaseolus establishes symbiosis primarily with Rhizobium and Ensifer species in most countries, and this rhizobia-legume interaction has been studied in Asia, Africa, and the Americas. However, there is currently no evidence to show that rhizobia nodulate the endemic cultivars of P. vulgaris in Venezuela. Therefore, we herein investigated the phylogenetic diversity of plant growth-promoting and N2-fixing nodulating bacteria isolated from the root nodules of P. vulgaris cultivars in a different agroecosystem in Venezuela. In comparisons with other countries, higher diversity was found in isolates from P. vulgaris nodules, ranging from α- and β-proteobacteria. Some isolates belonging to several new phylogenetic lineages within Bradyrhizobium, Ensifer, and Mesorhizobium species were also specifically isolated at some topographical regions. Additionally, some isolates exhibited tolerance to high temperature, acidity, alkaline pH, salinity stress, and high Al levels; some of these characteristics may be related to the origin of the isolates. Some isolates showed high tolerance to Al toxicity as well as strong plant growth-promoting and antifungal activities, thereby providing a promising agricultural resource for inoculating crops.

Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean

Rhizobia-legume symbiosis is an important type of plant-microbe mutualism; however, the establishment of this association is complicated and can be affected by many factors. The soybean rhizosphere has a specific microbial community, yet whether these organisms affect rhizobial nodulation has not been well investigated. Here, we analyzed the compositions and relationships of soybean rhizocompartment microbiota in three types of soil. First, we found that the rhizosphere community composition of soybean varied significantly in different soils, and the association network between rhizobia and other rhizosphere bacteria was examined. Second, we found that some rhizosphere microbes were correlated with the composition of bradyrhizobia and sinorhizobia in nodules. We cultivated 278 candidate Bacillus isolates from alkaline soil. Finally, interaction and nodulation assays showed that the Bacillus cereus group specifically promotes and suppresses the growth of sinorhizobia and bradyrhizobia, respectively, and alleviates the effects of saline-alkali conditions on the nodulation of sinorhizobia as well as affecting its colonization in nodules. Our findings demonstrate a crucial role of the bacterial microbiota in shaping rhizobia-host interactions in soybean, and provide a framework for improving the symbiotic efficiency of this system of mutualism through the use of synthetic bacterial communities.

Characterization of Pisum sativum and Vicia faba microsymbionts in Morocco and definition of symbiovar viciae in Rhizobium acidisoli

In this work, we analyzed the diversity of seventy-six bacteria isolated from Pea and faba bean nodules in two regions of Morocco. The molecular diversity was realized using the analysis of the sequences of 16S rRNA and six housekeeping genes (recA, glnII, atpD, dnaK, rpoB and gyrB) and two symbiotic genes (nodA and nodC). The phylogeny of the 16S rRNA gene sequences revealed that all strains belong to the genus Rhizobium, being related to the type strains of R. leguminosarum, R. laguerreae, R. indigoferae, R. anhuiense and R. acidisoli. The housekeeping genes phylogenies showed that some strains formed a subclade distinct from the rhizobial species that usually nodulate Vicia faba and Pisum sativum which are closely related to R. acidisoli FH23 with sequence similarity of 98.3%. Analysis of the PGPR activities of the different isolates showed that the strains related to R. laguerreae were able to solubilize phosphates and to produce siderophores and auxin phytohormone. However, R. acidisoli strain F40D2 was unable to solubilize phosphates although they produce siderophores and IAA. The phylogenetic analysis of the nodA and nodC sequences showed that all isolated strains were closely related with the strains of symbiovar viciae. The nodulation tests confirmed the ability to nodulate V. faba and P. sativum but not Cicer arietinum or Phaseolus vulgaris. Hence, in Morocco P. sativum is nodulated by R. laguerreae; whereas V. faba is nodulated by R. laguerreae and the symbiovar viciae of R. acidisoli which has been not previously described in this species.

The promiscuity of Phaseolus vulgaris L. (common bean) for nodulation with rhizobia: a review

Phaseolus vulgaris L. (common bean) is a legume indigenous to American countries currently cultivated in all continents, which is nodulated by different rhizobial species and symbiovars. Most of species able to nodulate this legume worldwide belong to the genus Rhizobium, followed by those belonging to the genera Ensifer (formerly Sinorhizobium) and Pararhizobium (formerly Rhizobium) and minority by species of the genus Bradyrhizobium. All these genera belong to the phylum alpha-Proteobacteria, but the nodulation of P. vulgaris has also been reported for some species belonging to Paraburkholderia and Cupriavidus from the beta-Proteobacteria. Several species nodulating P. vulgaris were originally isolated from nodules of this legume in American countries and are linked to the symbiovars phaseoli and tropici, which are currently present in other continents probably because they were spread in their soils together with the P. vulgaris seeds. In addition, this legume can be nodulated by species and symbiovars originally isolated from nodules of other legumes due its high promiscuity, a concept currently related with the ability of a legume to be nodulated by several symbiovars rather than by several species. In this article we review the species and symbiovars able to nodulate P. vulgaris in different countries and continents and the challenges on the study of the P. vulgaris endosymbionts diversity in those countries where they have not been studied yet, that will allow to select highly effective rhizobial strains in order to guarantee the success of P. vulgaris inoculation.

Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts

Background

Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC) of these rhizobia can be different within each genus and among distinct genera. Little information is available about the symbiotic structure of indigenous Rhizobium strains nodulating introduced bean plants or the emergence of a symbiotic ability to associate with bean plants in Bradyrhizobium and Ensifer strains. Here, we sequenced the genomes of 29 representative bean microsymbionts (21 Rhizobium, four Ensifer, and four Bradyrhizobium) and compared them with closely related reference strains to estimate the origins of symbiosis genes among these Chinese bean microsymbionts.

Results

Comparative genomics demonstrated horizontal gene transfer exclusively at the plasmid level, leading to expanded diversity of bean-nodulating Rhizobium strains. Analysis of vertically transferred genes uncovered 191 (out of the 2654) single-copy core genes with phylogenies strictly consistent with the taxonomic status of bacterial species, but none were found on symbiosis plasmids. A common symbiotic region was wholly conserved within the Rhizobium genus yet different from those of the other two genera. A single strain of Ensifer and two Bradyrhizobium strains shared similar gene content with soybean microsymbionts in both chromosomes and symbiotic regions.

Conclusions

The 19 native bean Rhizobium microsymbionts were assigned to four defined species and six putative novel species. The symbiosis genes of R. phaseoli, R. sophoriradicis, and R. esperanzae strains that originated from Mexican bean-nodulating strains were possibly introduced alongside bean seeds. R. anhuiense strains displayed distinct host ranges, indicating transition into bean microsymbionts. Among the six putative novel species exclusive to China, horizontal transfer of symbiosis genes suggested symbiosis with other indigenous legumes and loss of originally symbiotic regions or non-symbionts before the introduction of common bean into China. Genome data for Ensifer and Bradyrhizobium strains indicated symbiotic compatibility between microsymbionts of common bean and other hosts such as soybean.

Novel putative Mesorhizobium and Ensifer genomospecies together with a novel symbiovar psoraleae nodulate legumes of agronomic interest grown in Tunisia

Forty rhizobial strains were isolated from Lotus creticus, L. pusillus and Bituminaria bituminosa endemic to Tunisia, and they belonged to the Mesorhizobium and Ensifer genera based on 16S rDNA sequence phylogeny. According to the concatenated recA and glnII sequence-based phylogeny, four Bituminaria isolates Pb5, Pb12, Pb8 and Pb17 formed a monophyletic group with Mesorhizobium chacoense ICMP14587^T, whereas four other strains Pb1, Pb6, Pb13 and Pb15 formed two separate lineages within the Ensifer genus. Among the L. pusillus strains, Lpus9 and Lpus10 showed a 96% identical nucleotide with Ensifer meliloti CCBAU83493^T; whereas six other strains could belong to previously undescribed Mesorhizobium and Ensifer species. For L. creticus strains, Lcus37, Lcus39 and Lcus44 showed 98% sequence identity with Ensifer aridi JNVU TP6, and Lcus42 shared a 96% identical nucleotide with Ensifer meliloti CCBAU83493^T; whereas another four strains were divergent from all the described Ensifer and Mesorhizobium species. The analysis of the nodC gene-based phylogeny identified four symbiovar groups; Mesorhizobium sp. sv. anthyllidis (Lpus3 and Lpus11 from L. pusillus, Lcus43 from L. creticus), Ensifer medicae sv. meliloti (four strains from L. creticus and two strains from L. pusillus), E. meliloti sv. meliloti (four from L. creticus, four from L. pusillus and four from B. bituminosa). In addition, four B. bituminosa strains (Pb5, Pb8, Pb12, and Pb17) displayed a distinctive nodC sequence distant from those of other symbiovars described to date. According to their symbiotic gene sequences and host range, the B. bituminosa symbionts (Pb5, Pb8, Pb12 and Pb17) would represent a new symbiovar of M. chacoense for which sv. psoraleae is proposed.

Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov

In northern Mexico, aridity, salinity and high temperatures limit areas that can be cultivated. To investigate the nature of nitrogen-fixing symbionts of Phaseolus filiformis, an adapted wild bean species native to this region, their phylogenies were inferred by MLSA. Most rhizobia recovered belong to the proposed new species Ensifer aridi. Phylogenetic analyses of nodC and nifH show that Mexican isolates carry symbiotic genes acquired through horizontal gene transfer that are divergent from those previously characterized among bean symbionts. These strains are salt tolerant, able to grow in alkaline conditions, high temperatures, and capable of utilizing a wide range of carbohydrates and organic acids as carbon sources for growth. This study improves the knowledge on diversity, geographic distribution and evolution of bean-nodulating rhizobia in Mexico and further enlarges the spectrum of microsymbiont with which Phaseolus species can interact with, including cultivated bean varieties, notably under stressed environments. Here, the species Ensifer aridi sp. nov. is proposed as strain type of the Moroccan isolate LMR001^T (= LMG 31426^T; = HAMBI 3707^T) recovered from desert sand dune.

Phylogenetic diversity of rhizobia nodulating Phaseolus vulgaris in Croatia and definition of the symbiovar phaseoli within the species Rhizobium pisi

Phaseolus vulgaris is a legume indigenous to America which is currently cultivated in Europe including countries located at the Southeast of this continent, such as Croatia, where several local landraces are cultivated, most of them of Andean origin. In this work we identify at species and symbiovar levels several fast-growing strains able to form effective symbiosis with P. vulgaris in different Croatian soils. The identification at species level based on MALDI-TOF MS and core gene sequence analysis showed that most of these strains belong to the species R. leguminosarum, R. hidalgonense and R. pisi. In addition, several strains belong to putative new species phylogenetically close to R. ecuadorense and R. sophoriradicis. All Croatian strains belong to the symbiovar phaseoli and harbour the α and γ nodC alleles typical for American strains of this symbiovar. Nevertheless, most of Croatian strains harboured the γ nodC gene allele supporting its Andean origin since it is also dominant in other European countries, where Andean cultivars of P. vulgaris are traditionally cultivated, as occurs in Spain. The only strains harbouring the α nodC allele belong to R. hidalgonense and R. pisi, this last only containing the symbiovars viciae and trifolii to date. This is the first report about the presence in Europe of the species R. hidalgonense, the nodulation of P. vulgaris by R. pisi and the existence of the symbiovar phaseoli within this species. These results significantly increase the knowledge of the biogeography of Rhizobium-P. vulgaris symbiosis.

Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive phylogenomic position and chromid

Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI). CCGE531 and CCGE532 had common phenotypic characteristics with tropici type B rhizobial symbionts. Genome synteny analysis and ANI showed that P. dumosus isolates had different chromids and our analysis suggests that chromids have independently evolved in different lineages of the Rhizobium genus. Finally, we considered that P. dumosus and Phaseolus vulgaris plants belong to the same cross-inoculation group since they have conserved symbiotic affinites for rhizobia.

Distinct biogeographic patterns of rhizobia and non-rhizobial endophytes associated with soybean nodules across China

Both rhizobia and non-rhizobial endophytes (NRE) are inhabitants of legume nodules. The biogeography of rhizobia has been well investigated, but little is known about the spatial distribution and community assemblage of NRE. By using high-throughput sequencing, we compared biogeographic patterns of rhizobial and non-rhizobial subcommunities and investigated their bacterial co-occurrence patterns in nodules collected from 50 soybean fields across China. Dispersal probability was lower in NRE than in rhizobia, as revealed by a significant distance-decay relationship found in NRE, but not in rhizobia, in addition to a significant occupancy-abundance relationship in the entire community. Rhizobial and NRE subcommunities were significantly influenced by different environmental and spatial variables. Moreover, the rhizobial subcommunities were grouped into Ensifer- and Bradyrhizobium-dominated clusters that were significantly related to soil pH. The non-rhizobial subcommunities were grouped into Proteobacteria- and Firmicutes-dominated clusters that were more influenced by climatic than by edaphic factors. These results demonstrated that rhizobial and non-rhizobial subcommunities are characterized by distinct biogeographic patterns. Network analysis showed rhizobia and NRE as separately grouped and uncorrelated with each other, suggesting they did not share niche space in soybean nodules. In sum, these results broaden our knowledge of how bacteria are distributed and assemble as a community in root nodules.

Influence of Altered Microbes on Soil Organic Carbon Availability in Karst Agricultural Soils Contaminated by Pb-Zn Tailings

Soil organic carbon (SOC) availability is determined via a complex bio-mediated process, and Pb-Zn tailings are toxic to the soil microbes that are involved in this process. Here, Pb-Zn-tailings- contaminated karst soils with different levels (paddy field > corn field > citrus field > control group) were collected to explore the intrinsic relationship between Pb-Zn tailings and microbes due to the limited microbial abundance in these soils. The SOC concentration in the paddy fields is the highest. However, based on the soil microbial diversity and sole-carbon-source utilization profiles, the rate of SOC availability, McIntosh index, Shannon-Wiener diversity index, Simpson's diversity index and species richness are the lowest in the rice paddy soils. According to the results of Illumina sequencing of the 16S rRNA gene, Acidobacteria and Proteobacteria are the dominant phyla in all samples, accounting for more than 70% of the reads, while the majority of the remaining reads belong to the phyla Verrucomicrobia, Chloroflexi, Actinobacteria, Bacteroidetes, and Nitrospirae. We also observed that their class, order, family, genus and operational taxonomic units (OTUs) were dependent on SOC availability. Pearson correlation analysis reveals that L-asparagine utilization profiles show significant positive correlation with OTUs 24, 75, and 109 (r = 0.383, 0.350, and 0.292, respectively), and malic acid utilization profiles show significant positive correlation with OTUs 4, 5, 19, 27 (Bradyrhizobium), 32 (Burkholderia), 75 and 109 (r = 0.286, 0.361, 0.387, 0.384, 0.363, 0.285, and 0.301, respectively), as also evidenced by the redundancy analysis (RDA) biplot and heat map. These results indicate that the most abundant groups of bacteria, especially the uncultured facultative Deltaproteobacteria GR-WP33-30 (OTU 24), after long-term acclimation in heavy metal-contaminated soil, are associated with the variance of labile carbon source such as L-asparagine and may have considerable control over the stability of the vast SOC pool in karst surface soils with different agricultural land-use practices. These findings can expand our understanding of global soil-carbon sequestration and storage via changes in microbial community structure of the most abundant species.

Genomic insight into the taxonomy of Rhizobium genospecies that nodulate Phaseolus vulgaris

Due to the wide cultivation of bean (Phaseolus vulgaris L.), rhizobia associated with this plant have been isolated from many different geographical regions. In order to investigate the species diversity of bean rhizobia, comparative genome sequence analysis was performed in the present study for 69 Rhizobium strains mainly isolated from root nodules of bean and clover (Trifolium spp.). Based on genome average nucleotide identity, digital DNA:DNA hybridization, and phylogenetic analysis of 1,458 single-copy core genes, these strains were classified into 28 clusters, consistent with their species definition based on multilocus sequence analysis (MLSA) of atpD, glnII, and recA. The bean rhizobia were found in 16 defined species and nine putative novel species; in addition, 35 strains previously described as Rhizobium etli, Rhizobium phaseoli, Rhizobium vallis, Rhizobium gallicum, Rhizobium leguminosarum and Rhizobium spp. should be renamed. The phylogenetic patterns of symbiotic genes nodC and nifH were highly host-specific and inconsistent with the genomic phylogeny. Multiple symbiovars (sv.) within the Rhizobium species were found as a common feature: sv. phaseoli, sv. trifolii and sv. viciae in Rhizobium anhuiense; sv. phaseoli and sv. mimosae in Rhizobium sophoriradicis/R. etli/Rhizobium sp. III; sv. phaseoli and sv. trifolii in Rhizobium hidalgonense/Rhizobium acidisoli; sv. phaseoli and sv. viciae in R. leguminosarum/Rhizobium sp. IX; sv. trifolii and sv. viciae in Rhizobium laguerreae. Thus, genomic comparison revealed great species diversity in bean rhizobia, corrected the species definition of some previously misnamed strains, and demonstrated the MLSA a valuable and simple method for defining Rhizobium species.

Genetic diversity and symbiotic effectiveness of Phaseolus vulgaris-nodulating rhizobia in Kenya

Phaseolus vulgaris (common bean) was introduced to Kenya several centuries ago but the rhizobia that nodulate it in the country remain poorly characterised. To address this gap in knowledge, 178 isolates recovered from the root nodules of P. vulgaris cultivated in Kenya were genotyped stepwise by the analysis of genomic DNA fingerprints, PCR-RFLP and 16S rRNA, atpD, recA and nodC gene sequences. Results indicated that P. vulgaris in Kenya is nodulated by at least six Rhizobium genospecies, with most of the isolates belonging to Rhizobium phaseoli and a possibly novel Rhizobium species. Infrequently, isolates belonged to Rhizobium paranaense, Rhizobium leucaenae, Rhizobium sophoriradicis and Rhizobium aegyptiacum. Despite considerable core-gene heterogeneity among the isolates, only four nodC gene alleles were observed indicating conservation within this gene. Testing of the capacity of the isolates to fix nitrogen (N₂) in symbiosis with P. vulgaris revealed wide variations in effectiveness, with ten isolates comparable to Rhizobium tropici CIAT 899, a commercial inoculant strain for P. vulgaris. In addition to unveiling effective native rhizobial strains with potential as inoculants in Kenya, this study demonstrated that Kenyan soils harbour diverse P. vulgaris-nodulating rhizobia, some of which formed phylogenetic clusters distinct from known lineages. The native rhizobia differed by site, suggesting that field inoculation of P. vulgaris may need to be locally optimised.

Natural rhizobial diversity helps to reveal genes and QTLs associated with biological nitrogen fixation in common bean

Common bean is one of the most important crops for human feed, and the most important legume for direct consumption by millions of people, especially in developing countries. It is a promiscuous host legume in terms of nodulation, able to associate with a broad and diverse range of rhizobia, although the competitiveness for nodulation and the nitrogen fixation capacity of most of these strains is generally low. As a result, common bean is very inefficient for symbiotic nitrogen fixation, and nitrogen has to be supplied with chemical fertilizers. In the last years, symbiotic nitrogen fixation has received increasing attention as a sustainable alternative to nitrogen fertilizers, and also as a more economic and available one in poor countries. Therefore, optimization of nitrogen fixation of bean-rhizobia symbioses and selection of efficient rhizobial strains should be a priority, which begins with the study of the natural diversity of the symbioses and the rhizobial populations associated. Natural rhizobia biodiversity that nodulates common bean may be a source of adaptive alleles acting through phenotypic plasticity. Crosses between accessions differing for nitrogen fixation may combine alleles that never meet in nature. Another way to discover adaptive genes is to use association genetics to identify loci that common bean plants use for enhanced biological nitrogen fixation and, in consequence, for marker assisted selection for genetic improvement of symbiotic nitrogen fixation. In this review, rhizobial biodiversity resources will be discussed, together with what is known about the loci that underlie such genetic variation, and the potential candidate genes that may influence the symbiosis' fitness benefits, thus achieving an optimal nitrogen fixation capacity in order to help reduce reliance on nitrogen fertilizers in common bean.

Alkalinity of Lanzarote soils is a factor shaping rhizobial populations with Sinorhizobium meliloti being the predominant microsymbiont of Lotus lancerottensis

Lotus lancerottensis is an endemic species that grows widely throughout Lanzarote Island (Canary Is.). Characterization of 48 strains isolated from root nodules of plants growing in soils from eleven locations on the island showed that 38 isolates (79.1%) belonged to the species Sinorhizobium meliloti, whereas only six belonged to Mesorhizobium sp., the more common microsymbionts for the Lotus. Other genotypes containing only one isolate were classified as Pararhizobium sp., Sinorhizobium sp., Phyllobacterium sp. and Bradyrhizobium-like. Strains of S. meliloti were distributed along the island and, in most of the localities they were exclusive or major microsymbionts of L. lancerottensis. Phylogeny of the nodulation nodC gene placed the S. meliloti strains within symbiovar lancerottense and the mesorhizobial strains with the symbiovar loti. Although strains from both symbiovars produced effective N₂-fixing nodules, S. meliloti symbiovar lancerottense was clearly the predominant microsymbiont of L. lancerottensis. This fact correlated with the better adaptation of strains of this species to the alkaline soils of Lanzarote, as in vitro characterization showed that while the mesorhizobial strains were inhibited by alkaline pH, S. meliloti strains grew well at pH 9.

Genetic diversity and community structure of rhizobia nodulating Sesbania cannabina in saline-alkaline soils

Sesbania cannabina is a plant that grows naturally along the seashores in Rudong County, China (RDC) and it has been introduced into the Yellow River Delta (YRD) as a pioneer plant to improve the saline-alkaline soils. In order to investigate the diversity of S. cannabina rhizobia in these soils, a total of 198 rhizobial isolates were characterized and phylogenetic trees were constructed based on data from multilocus sequence analysis (MLSA) of the housekeeping genes recA, atpD and glnII, as well as 16S rRNA. Symbiotic features were also studied by establishing the phylogeny of the symbiotic genes nodA and nifH, and by performing nodulation assays. The isolates had highly conserved symbiotic genes and were classified into nine genospecies belonging to the genera Ensifer, Agrobacterium, Neorhizobium and Rhizobium. A unique community structure was detected in the rhizobia associated with S. cannabina in the saline-alkaline soils that was characterized by five novel genospecies and four defined species. In addition, Ensifer sp. I was the predominant rhizobia in YRD, whereas Ensifer meliloti and Neorhizobium huautlense were the dominant species in RDC. Therefore, the study demonstrated for the first time that this plant strongly selected the symbiotic gene background but not the genomic background of its microsymbionts. In addition, biogeographic patterns existed in the rhizobial populations associated with S. cannabina, which were mainly correlated with pH and salinity, as well as the mineral nutrient contents. This study provided novel information concerning the interaction between soil conditions, host plant and rhizobia, in addition to revealing the diversity of S. cannabina rhizobia in saline-alkaline soils.

Genetic diversity and distribution of rhizobia associated with the medicinal legumes Astragalus spp. and Hedysarum polybotrys in agricultural soils

With the increasing cultivation of medicinal legumes in agricultural fields, the rhizobia associated with these plants are facing new stresses, mainly from fertilization and irrigation. In this study, investigations on the nodulation of three cultivated medicinal legumes, Astragalus mongholicus, Astragalus membranaceus and Hedysarum polybotrys were performed. Bacterial isolates from root nodules of these legumes were subjected to genetic diversity and multilocus sequence analyses. In addition, the distribution of nodule bacteria related to soil factors and host plants was studied. A total 367 bacterial isolates were obtained and 13 genospecies were identified. The predominant microsymbionts were identified as Mesorhizobium septentrionale, Mesorhizobium temperatum, Mesorhizobium tianshanense, Mesorhizobium ciceri and Mesorhizobium muleiense. M. septentrionale was found in most root nodules especially from legumes grown in the barren soils (with low available nitrogen and low organic carbon contents), while M. temperatum was predominant in nodules where the plants were grown in the nitrogen-rich fields. A. mongholicus tended to be associated with M. septentrionale, M. temperatum and M. ciceri in different soils, while A. membranaceus and H. polybotrys tended to be associated with M. tianshanense and M. septentrionale, respectively. This study showed that soil fertility may be the main determinant for the distribution of rhizobia associated with these cultured legume plants.

Rhizobial Diversity and Nodulation Characteristics of the Extremely Promiscuous Legume Sophora flavescens

In present study, we report our extensive survey on the diversity and biogeography of rhizobia associated with Sophora flavescens, a sophocarpidine (matrine)-containing medicinal legume. We additionally investigated the cross nodulation, infection pattern, light and electron microscopies of root nodule sections of S. flavescens infected by various rhizobia. Seventeen genospecies of rhizobia belonging to five genera with seven types of symbiotic nodC genes were found to nodulate S. flavescens in natural soils. In the cross-nodulation tests, most representative rhizobia in class α-Proteobacteria, whose host plants belong to different cross-nodulation groups, form effective indeterminate nodules, while representative rhizobia in class β-Proteobacteria form ineffective nodules on S. flavescens. Highly host-specific biovars of Rhizobium leguminosarum (bv. trifolii and bv. viciae) and Rhizobium etli bv. phaseoli could establish symbioses with S. flavescens, providing further evidence that S. flavescens is an extremely promiscuous legume and it does not have strict selectivity on either the symbiotic genes or the species-determining housekeeping genes of rhizobia. Root-hair infection is found as the pattern that rhizobia have gained entry into the curled root hairs. Electron microscopies of ultra-thin sections of S. flavescens root nodules formed by different rhizobia show that the bacteroids are regular or irregular rod shape and nonswollen types. Some bacteroids contain poly-β-hydroxybutyrate (PHB), while others do not, indicating the synthesis of PHB in bacteroids is rhizobia-dependent. The extremely promiscuous symbiosis between S. flavescens and different rhizobia provide us a basis for future studies aimed at understanding the molecular interactions of rhizobia and legumes.