Rhizosphere Of Common Bean Research Articles

Diversity of viruses and viroids in the rhizosphere of common bean cultivars differing in resistance to the fungal root pathogen Fusarium oxysporum

The rhizosphere microbiome plays a key role in plant protection against soil-borne pathogens. Plant breeding for resistance against soil-borne pathogens can alter the rhizosphere microbiome. However, most studies have focused on bacterial and fungal communities, leaving the role of the virus and viroids unassessed. Here, we tested the influence of resistance breeding on the composition of rhizosphere viruses and viroids. By analyzing metatranscriptomes from the rhizosphere of common bean (Phaseolus vulgaris) cultivars with varying resistance to the soil-borne pathogen Fusarium oxysporum, we recovered sequences representing 78 and 23 novel populations of viruses and viroids, respectively. We compared the abundances of these infectious agents across the different cultivars and found that the Fusarium-resistant cultivar harbored >1.2 times more viroids and a more different composition of viroids and viruses than less resistant plants. Given their role in interfering with host metabolism and their potential influence on plant-fungi associations, our study suggests that changes in the rhizosphere infectome are an important consideration in breeding for resistance against soil-borne pathogens.

Molecular Characterization and Mineralizing Potential of Phosphorus Solubilizing Bacteria Colonizing Common Bean (Phaseolus vulgaris L.) Rhizosphere in Western Kenya.

Phosphorus solubilizing bacteria (PSB) are a category of microbes that transform insoluble phosphates in soil into soluble forms that crops can utilize. Phosphorus in natural soils is abundant but poorly soluble. Hence, introducing PSB is a safer way of improving its solubility. The aim of this study was to genetically characterize and determine the mineralization capability of selected PSB colonizing rhizospheres of common beans in Western Kenya. Seven potential phosphorus solubilizing bacteria (PSB) were isolated from various subregions of Western Kenya. 16S ribosomal RNA gene sequencing and National Center for Biotechnology Information (NCBI), Basic Local Alignment Search Tool (BLAST) identified the isolates. The phosphate solubilization potential of the isolates was evaluated under agar and broth medium of National Botanical Research Institute's phosphate (NBRIP) supplemented with tricalcium calcium phosphate (TCP). Identified isolates were as follows: KK3 as Enterobacter mori, B5 (KB5) as Pseudomonas kribbensis, KV1 as Enterobacter asburiae, KB3 as Enterobacter mori, KK1 as Enterobacter cloacae, KBU as Enterobacter tabaci, and KB2 as Enterobacter bugandensis. The strains B5 and KV1 were the most effective phosphorus solubilizers with 4.16 and 3.64 indices, respectively. The microbes converted total soluble phosphate concentration in broth medium which was 1395 and 1471 P μg/mL, respectively. The least performing isolate was KBU with a 2.34 solubility index. Significant (p ≤ 0.05) differences in plant biomass for Rose coco and Mwitemania bean varieties were observed under inoculation with isolates B5 and KV1. PSB isolates found in common bean rhizospheres exhibited molecular variations and isolates B5 and KV1 are the potential in solving the insufficiency of phosphorus for sustainable crop production.

Impact of vermicompost derived from different substrates on soil carbon pools in Rhizosphere of common bean (Phaseolus vulgaris L.)

Impact of vermicompost derived from different substrates on soil carbon pools in Rhizosphere of common bean (Phaseolus vulgaris L.)

Harnessing the phosphate-solubilizing ability of Trichoderma strains to improve plant growth, phosphorus uptake and photosynthetic pigment contents in common bean (Phaseolus vulgaris)

A promising strategy for dissolving, mobilizing and enhancing the utilization of the complexed form of phosphorus (P) in soil-plant systems is the use of effective phosphate solubilizing microorganisms. In the present study, six strains of Trichoderma spp. previously obtained from the common bean rhizosphere were investigated for their ability to solubilize tricalcium phosphate (TCP) in NBRIP (National Botanical Research Institute Phosphate) broth medium. All six strains were able to solubilize TCP to various extents, with solubilization ranging from 66.9 μg/ml to 328.4 μg/ml. A significant negative linear correlation (r = - 0.94; p < 0.01) was found between solubilized P and the pH of the culture medium. The highest solubilization activity (328.4 μg/ml), fungal growth (87.21 mg/100 ml) and pH fluctuation (7.0–4.06) were achieved by Trichoderma gamsii It-62. Under pot conditions, inoculation with Trichoderma gamsii It-62 remarkably improved plant height, shoot and root weight, P uptake, photosynthetic pigments and total protein content compared with untreated common bean seedlings. These increases were significantly higher upon combined inoculation of the bioagent with TCP addition. The obtained results indicate that Trichoderma gamsii It-62 might be a promising alternative for the release of fixed forms of phosphates present in the soil, thereby increasing soil fertility.

Plant growth promoting and antagonistic Enterobacter sp. EPR4 from common bean rhizosphere of garhwal himalayan inhibits a soil-borne pathogen Sclerotinia sclerotiorum

Plant growth stimulating and antagonistic properties of 7 bacterial isolates of beneficial Enterobacter spp. (EPR1- EPR7) screened from the rhizospheric soil of Phaseolus vulgaris plants growing in Garhwal Himalaya, Uttarakhand, India was studied against soil borne phytopathogen Sclerotinia sclerotiorum causes root rots in various crops. Among the isolates, EPR4 showed 64.8% reduction in colony growth of the fungal pathogen in dual culture. All seven isolates are capable of producing Indole Acetic Acid (IAA), but EPR4 also produced cyanogens, solubilized inorganic and organic phosphate, siderophore, ACC (1-aminocyclopropane-1-carboxylic acid) deamininase, and extracellular enzymes like chitinase which inhibited the phytopathogen. For the EPR4 strain, 16S rRNA gene sequencing was followed by NCBI - BLAST similarity showed the maximum sequence similarity (100%) with the species of Enterobacter (available on NCBI data base), and recognized as Enterobacter sp. EPR4 (GenBank accession number JN225424). The Enterobacter sp. EPR4 has the potential to be used as a biocontrol agent against S. sclerotiorum as well as a good plant growth promoter for common bean and other crops grown in India's Garhwal Himalaya.

All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean (Phaseolus vulgaris) in Its Centre of Domestication.

Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing ‘at home’.

Plant parasitic nematodes and disease severity of common bean lines evaluated for reaction to root knot nematodes infestation

Plant parasitic nematodes are important pests in crop production in sub-Saharan Africa. The objective of this study was to identify the occurrence of nematodes associated with common bean (Phaseolus vulgaris L.) and evaluate breeding lines for their reaction to Meloidogyne spp. in Ghana. Common bean rhizosphere soil was sampled and processed using Modified Baermann Tray method. Five nematode genera, namely Meloidogyne, Pratylenchus, Rotylenchulus, Helicotylenchus and Trichodorus were extracted. The first four genera listed above were prevalent across locations, with Trichodorus present in 30% of the fields sampled. The highest nematode population density of 319 juveniles per 200 cubic centimeter of soil was recorded for Meloidogyne spp. compared to 45 juveniles per 200 cubic centimeter, for Trichodorus. Twelve breeding lines were evaluated by inoculating roots of two-weeks-old plants with 2000 infective-stage juveniles of Meloidogyne sp. Reactions of test lines to Meldogyne sp. infection were assessed by determining the number of egg masses and galling index (GI) on roots. Reproduction index (RI) was used to classify test lines as resistant or susceptible. Significant differences (P &lt; 0.05) were observed in the number of eggs, GI and RI among lines tested. No resistant line was identified; however, lines SEF 47, BFS 35 and BFS 60 were moderately resistant, with RI of 13.1, 17.4 and 23.7%, respectively. Line SEF 60, although classified as slightly resistant, recorded a 100 seed weight of 26.0 g, which was 60% higher than line SEF 53 with seed weight of 16.2 g. Moderately resistant common bean lines identified could be used in common bean improvement programmes to develop elite cultivars tolerant to root knot nematodes.

Changes in microbial and physicochemical properties under cover crop inclusion in a degraded common bean monoculture system

The expansion of the common bean monoculture system along with intensive agricultural practices focused on productivity has generated a misuse of natural resources, accompanied by a significant decline of the soil ecosystem services. The aim of this study was to analyze the short-term effect (3 years) of the inclusion of different cover crops (legumes, non-legumes and mixtures) on the physicochemical, biological properties and crop yield in a degraded common bean monoculture system in the north region of Argentina. The inclusion of legumes (vetch and melilotus) and non-legumes (oat and wheat) as sole cover crops over three consecutive years significantly increased the abundance of the main microbial groups, microbial biomass C and N (MBC and MBN) and the activity of the common bean rhizosphere microbial community, which resulted into a fast improvement of soil quality and rhizosphere microbiota compared with bean monoculture. However, mixed cover crops (oat + vetch) had a positive but lower impact on rhizosphere microbial community abundance compared to legume or non-legume cover crops when used as sole cover crops. The information generated in this study will contribute to the evaluation of the inclusion of specific cover crops as a conservation strategy to recover soil health and minimize soil degradation, while maintaining crop yields.

Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype

The full potential of managing microbial communities to support plant health is yet-unrealized, in part because it remains difficult to ascertain which members are most important for the plant. However, microbes that consistently associate with a plant species across varied field conditions and over plant development likely engage with the host or host environment. Here, we applied abundance-occupancy concepts from macroecology to quantify the core membership of bacterial/archaeal and fungal communities in the rhizosphere of the common bean (Phaseolus vulgaris). Our study investigated the microbiome membership that persisted over multiple dimensions important for plant agriculture, including major U.S. growing regions (Michigan, Nebraska, Colorado, and Washington), plant development, annual plantings, and divergent genotypes, and also included re-analysis of public data from beans grown in Colombia. We found 48 core bacterial taxa that were consistently detected in all samples, inclusive of all datasets and dimensions. This suggests reliable enrichment of these taxa to the plant environment and time-independence of their association with the plant. More generally, the breadth of ecologically important dimensions included in this work (space, time, host genotype, and management) provides an example of how to systematically identify the most stably-associated microbiome members, and can be applied to other hosts or systems.

Effects of Microplastics on Common Bean Rhizosphere Microbial Communities

Effects of Microplastics on Common Bean Rhizosphere Microbial Communities

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia

BackgroundModern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.ResultsHere, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil.ConclusionsCollectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.

Root architecture and rhizobial inoculation in relation to drought stress response in common bean (Phaseolus vulgaris l.)

The present study was aimed at assessing the root traits and rhizobial inoculation in relation to drought in common bean, Phaseolus vulgaris. Drought caused the largest decrease in shoot biomass followed by plant height, while an increase was recorded inroot/shoot ratio. Rhizobial inoculation caused largest increase in shoot biomass followed by root volume and root biomass and smallest increase in rooting depth. WB-216 and WB-185 had better rooting depth in all treatments. However, WB-83 (92.67) had highest rooting depth under irrigated conditions and SR-1 had highest rooting depth under irrigated conditions treated with rhizobium (108.50). Similarly, WB-216 had highest root/shoot ratio under drought (2.693) followed by WB-185 (1.285) while lowest value was recorded for Arka Anoop (0.373). In rhizobium treated drought condition, WB-216 recorded highest root/shoot ratio (5.540) followed by SFB-1 (1.967). Under irrigated conditions (both with and without rhizobium), WB-185 recorded highest root/shoot ratio while lowest was recorded for SR-1 (0.166). The mean squares due to root depth, root biomass and root volume were significant whereas the mean squares due to water and rhizobium were non-significant. Among interactions the genotype x water regime was significant for rooting depth (5 % level), genotype x rhizobia was significant for rooting depth and root volume (1 % level) and the interaction of genotype x water regime x rhizobium was significant for rooting depth, root biomass and root volume (1 % level). The results reinforce the need to further analyse the potential of other soil microbes in common bean rhizosphere in amelioration of the effects of water stress.

Bacteria consortium optimization improves nutrient uptake, nodulation, disease suppression and growth of the common bean (Phaseolus vulgaris) in both pot and field studies

Several plant growth promoting bacteria (PGPB) were isolated from the nodules and rhizosphere of common bean and evaluated for their potential to improve its growth and yield. Among these, 86% isolates produced IAA and siderophore whereas almost all (95%) were able to solubilize inorganic phosphate, only 4.54% isolates were able to produce ACC deaminase. Among all isolates three had superior growth promoting characteristics. These three were identified by 16S rRNA sequence homology as belonging to Bacillus sp., Pseudomonas sp., and Rhizobium leguminosarum. All three isolates strongly inhibited several plant pathogens in vitro. Efficiency of these three strain and their consortia was evaluated in pot assay as well as in a field study. In both pot and field studies the three strains, singly or in consortia, increased germination, plant height and weight and nodulation compared to controls. Our results show that consortia were more efficient at growth promotion and disease suppression than the strains applied individually. The number of pods per plant, seeds per pod, grain yield, stover yield, biological yield, and harvest index were increased the most in consortium-3, followed by consortium-2, consortium-1, then the bacteria used singly. Therefore, the utilization of the bacterial consortium comprised of strains RPN5, BPR7 and PPR8 could be beneficial to maximize growth and grain yield of crop in field.

Bacterial capacities to mineralize phytate increase in the rhizosphere of nodulated common bean (Phaseolus vulgaris) under P deficiency

Phytate (a form of Inositol phosphate), which is one of the most abundant sources of organic phosphorus (Po) in soils, needs to be mineralized by microbial phosphatases to become available for plants. Phytases are the most active phosphatases for the dephosphorylation of phytate but the ecology of the phytate mineralising bacteria (PMB) remains poorly understood. The aim of this work was to determine if PMB represent an important component of the rhizosphere of legumes and if their density and their activities depend upon the soil-P availability. In this work the density, activity and phylogenetic affiliation of the PMB were characterized in the nodulated rhizosphere of a legume (Phaseolus vulgaris) grown in two soils with contrasting Low-P or P-sufficient content. Screened on solid medium, the density of PMB was higher in the rhizosphere of common bean than in the bulk soil only when plants were cultured on the low-P soil. In liquid culture, half of the rhizosphere isolates were able to use phytate as the sole P source and to release free inorganic P in the medium at rates much higher when bacterial strains were isolated from low-P than from P-sufficient soil. Enzymatic activity confirmed the ability of these rhizosphere isolates to mineralize phytate. Whatever the soil P level, the PMB belonged to the same genera Pseudomonas, Pantoae, Enterobacter and Salmonella, but not Bacillus. Our work demonstrates that low soil P availability increases both PMB density in the rhizosphere compared to the bulk soil and the activities of PMB populations through different growth patterns.

Bacillus strains isolated from rhizosphere showed plant growth promoting and antagonistic activity against phytopathogens

Seven bacterial isolates screened from rhizosphere of common bean growing at Uttarakhand Himalaya showed potential plant growth promoting (PGP) and antagonistic activities. Based on 16S rRNA gene sequence the isolate BPR7 was identified as Bacillus sp. BPR7. The strain BPR7 produced IAA, siderophore, phytase, organic acid, ACC deaminase, cyanogens, lytic enzymes, oxalate oxidase, and solubilized various sources of organic and inorganic phosphates as well as potassium and zinc. Strain BPR7 strongly inhibited the growth of several phytopathogens such as Macrophomina phaseolina, Fusarium oxysporum, F. solani, Sclerotinia sclerotiorum, Rhizoctonia solani and Colletotricum sp. in vitro. Cell-free culture filtrate of strain BPR7 also caused colony growth inhibition of all test pathogens. PGP and antifungal activities of Bacillus sp. BPR7 suggest that it may be exploited as a potential bioinoculant agent for P. vulgaris.

Survival of Pseudomonas extremorientalis TSAU20 and P. chlororaphis TSAU13 in the rhizosphere of common bean (Phaseolus vulgaris) under saline conditions

The abilities of Pseudomonas extremorientalis TSAU20 and P. chlororaphis TSAU13 to colonise and survive in the rhizosphere of common bean under saline conditions were studied. Four salinity levels (5.0, 7.5, 10.0, and 12.5 dS/m) were maintained in the gnotobiotic system using NaCl salt. Results showed that with increasing salt content root-tip colonization of both bacterial strains was reduced. Both bacterial treatments used in the study increased root and/or shoot length compared to non-treated plants at each NaCl concentration tested, whereas shoot growth was not stimulated at high saline condition (12.5 dS/m). In conclusion, the results of this study indicated that P. extremorientalis TSAU20 and P. chlororaphis TSAU 13 have the ability to survive in ecologically stressed conditions, such as saline and nitrogen deficient soils, and may positively effect on plant growth of bean. High salinity inhibited their colonisation in the rhizosphere of bean and thus their stimulatory effect on plants was also reduced.

Dynamics of phosphorus fractions in the rhizosphere of common bean (Phaseolus vulgaris L.) and durum wheat (Triticum turgidum durum L.) grown in monocropping and intercropping systems

The main objective of the present study was to investigate phosphorus (P) dynamics in the rhizosphere of durum wheat (Triticum turgidum durum L.) and common bean (Phaseolus vulgaris L.) grown in monocropping and intercropping systems with nitrate supply. Wheat and common bean were grown either alone or in association in a cropping device with a thin (1 mm) soil layer sandwiched between large root mats. Wheat intercropped with common bean exhibited a 33% increase in shoot biomass and a 22% increased root biomass, without significantly affecting common bean growth. After 12 days of culture, rhizosphere pH decreased by 1.66 and 1.13 units in monocropping system of common bean and intercropping system, respectively. Wheat increased intercropped common bean proton release by 36% compared with monocropped beans. Common bean and wheat exhibited different behaviors in rhizosphere P dynamics. Monocropped wheat decreased Resin-P, NaHCO3-P and NaOH-P in its rhizosphere by 24, 96 and 10%, respectively. However, NaHCO3-P and NaOH-P were increased by 61 and 10% in the rhizosphere of intercropping. Almost all values about P fraction in intercropping system were between those in monocropped common bean and monocropped wheat. Through taping different P fraction, different plants species possibly can alleviate competition for phosphorus in intercropping system.

Prey range characterization, ribotyping, and diversity of soil and rhizosphere Bdellovibrio spp. isolated on phytopathogenic bacteria.

Thirty new Bdellovibrio strains were isolated from an agricultural soil and from the rhizosphere of plants grown in that soil. Using a combined molecular and culture-based approach, we found that the soil bdellovibrios included subpopulations of organisms that differed from rhizosphere bdellovibrios. Thirteen soil and seven common bean rhizosphere Bdellovibrio strains were isolated when Pseudomonas corrugata was used as prey; seven and two soil strains were isolated when Erwinia carotovora subsp. carotovora and Agrobacterium tumefaciens, respectively, were used as prey; and one tomato rhizosphere strain was isolated when A. tumefaciens was used as prey. In soil and in the rhizosphere, depending on the prey cells used, the concentrations of bdellovibrios were between 3 x 10(2) to 6 x 10(3) and 2.8 x 10(2) to 2.3 x 10(4) PFU g(-1). A prey range analysis of five soil and rhizosphere Bdellovibrio isolates performed with 22 substrate species, most of which were plant-pathogenic and plant growth-enhancing bacteria, revealed unique utilization patterns and differences between closely related prey cells. An approximately 830-bp fragment of the 16S rRNA genes of all of the Bdellovibrio strains used was obtained by PCR amplification by using a Bdellovibrio-specific primer combination. Soil and common bean rhizosphere strains produced two and one restriction patterns for this PCR product, respectively. The 16S rRNA genes of three soil isolates and three root-associated isolates were sequenced. One soil isolate belonged to the Bdellovibrio stolpii-Bdellovibrio starrii clade, while all of the other isolates clustered with Bdellovibrio bacteriovorus and formed two distantly related, heterogeneous groups.

Production of plant growth promoting substances by Rhizosphere Microorganisms

Summary Different microorganisms belonging to the genera Azotobacter, Bacillus and Streptomyces, isolated from the rhizosphere of common bean and tomato plants, were used to investigate their ability to synthesize plant growth substances. The supernatant of the bacterial cultures showed the presence of a compound with Rf 0.92 which corresponds to indole acetic acid together with unidentified derivatives. These organisms also secreted gibberellins having different Rf values. The spectrum of indoles and gibberellins differed between tested bacterial strains. The elutes of different spots of indoles and gibberellins showed stimulatory effect on the length and dry weight of excised barley roots. The highest response was in the case of indoles having Rf 0.99 and gibberellins having Rf 0.54.