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1.
J Appl Microbiol ; 134(4)2023 Apr 03.
Article in English | MEDLINE | ID: mdl-37012225

ABSTRACT

AIMS: This study evaluated the red clover (Trifolium pratense) root-associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites. METHODS AND RESULTS: 16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence were analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium, and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys, and Tetracladium fungal genera known for endophytic, saprotrophic, and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms. CONCLUSIONS: We showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the Rhizobiumleguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study.


Subject(s)
Microbiota , Trifolium , Trifolium/genetics , Trifolium/microbiology , Farms , Medicago/genetics , Medicago/microbiology , RNA, Ribosomal, 16S/genetics , Microbiota/genetics
2.
Nat Prod Res ; 37(6): 981-984, 2023 Mar.
Article in English | MEDLINE | ID: mdl-35762366

ABSTRACT

The possibility of modifying terpene production in plants is a defensive strategy that has been studied in conjunction with their biosynthetic pathways. A biotic factor such as Arbuscular Mycorrhizal Fungi (AMF) could modify terpene production in Trifolium pratense L. In this work, the enzymatic production of monoterpenes in Superqueli INIA cultivar with two AMF was evaluated via HeadSpace-Gas Chromatography (HS-GC). A significant increase of (S)-limonene was found in plants inoculated with Claroideoglomus claroideum as well as with the AMF mix (genera Scutellospora, Acaulospora and Glomus). Moreover, significant increases in other monoterpenes such as (-)-ß-pinene, myrcene, linalool, were observed. Results showed higher monoterpene production capacities in the Superqueli-INIA cultivar, suggesting the participation of monoterpene synthases (MTS). The significant rise of (S)-limonene in red clover plants inoculated with AMF suggests this strategy could be implemented in an agronomical manage for controlling the H. obscurus, the primary pest.


Subject(s)
Mycorrhizae , Trifolium , Mycorrhizae/metabolism , Trifolium/metabolism , Trifolium/microbiology , Monoterpenes , Limonene , Fungi/metabolism , Terpenes/metabolism , Plants/metabolism , Pest Control
3.
Sci Rep ; 12(1): 12144, 2022 07 15.
Article in English | MEDLINE | ID: mdl-35840628

ABSTRACT

Rhizobia are soil-borne bacteria forming symbiotic associations with legumes and fixing atmospheric dinitrogen. The nitrogen-fixation potential depends on the type of host plants and microsymbionts as well as environmental factors that affect the distribution of rhizobia. In this study, we compared genetic diversity of bacteria isolated from root nodules of Trifolium pratense grown in two geographical regions (Tromsø, Norway and Lublin, Poland) located in distinct climatic (subpolar and temperate) zones. To characterize these isolates genetically, three PCR-based techniques (ERIC, BOX, and RFLP of the 16S-23S rRNA intergenic spacer), 16S rRNA sequencing, and multi-locus sequence analysis of chromosomal house-keeping genes (atpD, recA, rpoB, gyrB, and glnII) were done. Our results indicate that a great majority of the isolates are T. pratense microsymbionts belonging to Rhizobium leguminosarum sv. trifolii. A high diversity among these strains was detected. However, a lower diversity within the population derived from the subpolar region in comparison to that of the temperate region was found. Multi-locus sequence analysis showed that a majority of the strains formed distinct clusters characteristic for the individual climatic regions. The subpolar strains belonged to two (A and B) and the temperate strains to three R. leguminosarum genospecies (B, E, and K), respectively.


Subject(s)
Rhizobium leguminosarum , Rhizobium , Trifolium , DNA, Bacterial/genetics , Phylogeny , Polymorphism, Restriction Fragment Length , RNA, Ribosomal, 16S/genetics , Rhizobium/genetics , Rhizobium leguminosarum/genetics , Root Nodules, Plant/microbiology , Sequence Analysis, DNA , Symbiosis/genetics , Trifolium/genetics , Trifolium/microbiology
4.
J Microbiol Methods ; 195: 106455, 2022 04.
Article in English | MEDLINE | ID: mdl-35367471

ABSTRACT

The purpose of developing this high throughput assay was to determine whether there was evidence of pH adaptation in strains of rhizobia which nodulate subterranean clover (SC) and white clover (WC), and whether this was related to the pH of the soil of origin. pH is a first-order factor influencing the niche preferences of soil microorganisms and has been convincingly shown to be a key driver of soil bacterial communities. Naturalised strains of Rhizobium spp. that are pH-adapted may have the potential to better compete and/or persist in acidic or alkaline soils compared with introduced commercial strains. Three pilot studies were conducted to design the optimised bioassay. This bioassay tested the effect of pH-amended yeast mannitol broth (seven pH values from pH 4.5-9.0), across three time points, on the in vitro growth of 299 Rhizobium strains isolated from the nodules of SC and WC. The media pH where strains demonstrated fastest growth was related to the pH of the soil that strains were isolated from. However, the correlation between media pH and soil pH was strongly influenced by the growth of strains from alkaline soils (alkaline adaptation), especially in strains isolated from SC nodules.


Subject(s)
Rhizobium , Trifolium , Biological Assay , Hydrogen-Ion Concentration , Phylogeny , Soil , Symbiosis , Trifolium/microbiology
5.
Theor Appl Genet ; 135(1): 125-143, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34628514

ABSTRACT

KEY MESSAGE: Accurate genomic prediction of yield within and across generations was achieved by estimating the genetic merit of individual white clover genotypes based on extensive genetic replication using cloned material. White clover is an agriculturally important forage legume grown throughout temperate regions as a mixed clover-grass crop. It is typically cultivated with low nitrogen input, making yield dependent on nitrogen fixation by rhizobia in root nodules. Here, we investigate the effects of clover and rhizobium genetic variation by monitoring plant growth and quantifying dry matter yield of 704 combinations of 145 clover genotypes and 170 rhizobium inocula. We find no significant effect of rhizobium variation. In contrast, we can predict yield based on a few white clover markers strongly associated with plant size prior to nitrogen fixation, and the prediction accuracy for polycross offspring yield is remarkably high. Several of the markers are located near a homolog of Arabidopsis thaliana GIGANTUS 1, which regulates growth rate and biomass accumulation. Our work provides fundamental insight into the genetics of white clover yield and identifies specific candidate genes as breeding targets.


Subject(s)
Genes, Plant , Nitrogen Fixation , Rhizobium leguminosarum/physiology , Trifolium/genetics , Genetic Variation , Genotype , Models, Genetic , Plant Development/genetics , Rhizobium leguminosarum/classification , Rhizobium leguminosarum/isolation & purification , Trifolium/growth & development , Trifolium/metabolism , Trifolium/microbiology
6.
Microbiologyopen ; 10(4): e1217, 2021 08.
Article in English | MEDLINE | ID: mdl-34459547

ABSTRACT

The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison with the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonizing each plant compartment were predicted using FUNGuild, FAPROTAX, and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonized by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilization (nitrogen fixation, phosphorus solubilization, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion but also to ecosystem sustainability.


Subject(s)
Acclimatization/genetics , Bacteria/genetics , Climate Change , Fungi/genetics , Trifolium/growth & development , Trifolium/microbiology , Bacteria/classification , Fungi/classification , Germany , Indoleacetic Acids/metabolism , Microbiota/genetics , Mycobiome/genetics , Nitrogen Fixation/physiology , Phosphorus/metabolism , Plant Roots/microbiology , Rhizosphere , Siderophores/biosynthesis , Soil Microbiology
7.
Methods Mol Biol ; 2309: 75-89, 2021.
Article in English | MEDLINE | ID: mdl-34028680

ABSTRACT

Strigolactones (SLs) are components of root exudates as a consequence of active release from the roots into the soil. Notably, they have been described as stimulants of seed germination in parasitic plants and of the presymbiotic growth in arbuscular mycorrhizal (AM) fungi, which are a crucial component of the plant root beneficial microbiota. SLs have therefore the potential to influence other microbes that proliferate in the soil around the roots and may interact with plants. A direct effect of SL analogs on the in vitro growth of a number of saprotrophic or plant pathogenic fungi was indeed reported.Here we describe a standardized method to evaluate the effect of SLs or their synthetic analogs on AM and filamentous fungi. For AM fungi, we propose a spore germination assay since it is more straightforward than the hyphal branching assay and it does not require deep expertise and skills. For filamentous fungi that can grow in axenic cultures, we describe the assay based on SLs embedded in the solid medium or dissolved in liquid cultures where the fungus is inoculated to evaluate the effect on growth, hyphal branching or conidia germination. These assays are of help to test the activity of natural SLs as well as of newly designed SL analogs for basic and applied research.


Subject(s)
Biological Assay , Fungi/drug effects , Heterocyclic Compounds, 3-Ring/pharmacology , Lactones/pharmacology , Mycorrhizae/drug effects , Plant Growth Regulators/pharmacology , Seeds/microbiology , Spores, Fungal/drug effects , Trifolium/microbiology , Fungi/growth & development , Heterocyclic Compounds, 3-Ring/chemical synthesis , Lactones/chemical synthesis , Mycorrhizae/growth & development , Plant Growth Regulators/chemical synthesis , Spores, Fungal/growth & development
8.
Arch Microbiol ; 203(7): 3839-3849, 2021 Sep.
Article in English | MEDLINE | ID: mdl-34003331

ABSTRACT

High concentrations of heavy metals in mine soil disturb the interactions between legumes and microorganisms leading to select strains adapted to these specific conditions. In this work, we analyzed the diversity of fifty strains isolated from Trifolium sp. nodules growing on Pb-Zn mine soil, in the Northeastern of Algeria and highlighted their potential symbiotic traits. The phylogeny of the 16S rRNA gene sequences revealed a high bacterial diversity with a predominance of non-rhizobial endophytes. The identified isolates belong to the thirteen following genera Cupriavidus, Pseudomonas, Bacillus, Acinetobacter, Enterobacter, Roseomonas, Paracoccus, Frondihabitans, Microbacterium, Kocuria, Providencia, Micrococcus and Staphylococcus. Regarding rhizobial strains, only isolates affiliated to Rhizobium genus were obtained. The symbiotic gene nodC and the nitrogen fixation gene nifH present showed that Rhizobium isolates belonged to the symbiovar trifolii. In addition to bacterial, one yeast strain was isolated and identified as Rhodotorula mucilaginosa by sequencing the internal transcribed spacer (ITS) region.


Subject(s)
Biodiversity , Endophytes , Lead , Rhizobium , Trifolium , Zinc , Algeria , Endophytes/classification , Endophytes/drug effects , Endophytes/genetics , Environmental Pollutants/toxicity , Lead/toxicity , Mining , Phylogeny , RNA, Ribosomal, 16S/genetics , Rhizobium/classification , Rhizobium/drug effects , Rhizobium/genetics , Rhodotorula/genetics , Rhodotorula/isolation & purification , Root Nodules, Plant/microbiology , Symbiosis , Trifolium/microbiology , Zinc/toxicity
9.
Int J Mol Sci ; 22(6)2021 Mar 10.
Article in English | MEDLINE | ID: mdl-33802057

ABSTRACT

Heavy metals polluting the 100-year-old waste heap in Boleslaw (Poland) are acting as a natural selection factor and may contribute to adaptations of organisms living in this area, including Trifolium repens and its root nodule microsymbionts-rhizobia. Exopolysaccharides (EPS), exuded extracellularly and associated with bacterial cell walls, possess variable structures depending on environmental conditions; they can bind metals and are involved in biofilm formation. In order to examine the effects of long-term exposure to metal pollution on EPS structure and biofilm formation of rhizobia, Rhizobium leguminosarum bv. trifolii strains originating from the waste heap area and a non-polluted reference site were investigated for the characteristics of the sugar fraction of their EPS using gas chromatography mass-spectrometry and also for biofilm formation and structural characteristics using confocal laser scanning microscopy under control conditions as well as when exposed to toxic concentrations of zinc, lead, and cadmium. Significant differences in EPS structure, biofilm thickness, and ratio of living/dead bacteria in the biofilm were found between strains originating from the waste heap and from the reference site, both without exposure to metals and under metal exposure. Received results indicate that studied rhizobia can be assumed as potentially useful in remediation processes.


Subject(s)
Biofilms , Metals, Heavy/metabolism , Polysaccharides, Bacterial/metabolism , Rhizobium leguminosarum/physiology , Soil Pollutants/metabolism , Trifolium/microbiology , Biofilms/drug effects , Biofilms/growth & development
10.
Chemosphere ; 263: 127918, 2021 Jan.
Article in English | MEDLINE | ID: mdl-32822944

ABSTRACT

Some rhizosphere bacteria could colonize on the root surface of plants, or even form biofilm to promote plant growth, enhance plant resistance to harsh external environments and block the soil contamination. In this study, to explore the effects of pyrene-degrading bacterium on root surface on plant uptake of pyrene, a pyrene-degrading bacterium Mycolicibacterium sp. Pyr9 was isolated from the root surface of Eleusine indica L. Gaertn. in PAH-contaminated fields; after antibiotic labeling, it was colonized onto the root surface of white clover (Trifolium repens L.), and its distribution and performance were monitored under different levels of pyrene contamination. Strain Pyr9 could degrade 98% of pyrene (with an initial concentration of 50 mg L-1) in culture solution within 8 d; it also owns a variety of plant growth promoting characteristics and appreciable tolerance to harsh environments. The transcription of pyrene catabolic genes in Pyr9 enhanced obviously when induced by pyrene. Pyr9 colonized and grew well on the root surface of white clover via root inoculation; some cells could even enter into the root tissues and move to the shoots. Compared with the Pyr9-free treatment, the pyrene contents in the roots and shoots of Pyr9-inoculated white clover decreased by 25%-30% and 33%-42%, respectively. Correspondingly, the pyrene accumulation and translocation factors in white clover decreased as well. These results indicate that Pyr9 would be a good potential to circumvent plant pyrene pollution. This research may provide a theoretical basis and technical support for the safety of agricultural products and human health in PAH-contaminated sites.


Subject(s)
Biodegradation, Environmental , Pyrenes/metabolism , Soil Pollutants/metabolism , Trifolium/metabolism , Bacteria/metabolism , Humans , Medicago/metabolism , Plant Roots/metabolism , Soil Pollutants/analysis , Trifolium/growth & development , Trifolium/microbiology
11.
Mol Plant Microbe Interact ; 34(1): 131-134, 2021 Jan.
Article in English | MEDLINE | ID: mdl-33021882

ABSTRACT

Rhizobium leguminosarum symbiovar trifolii strains TA1 and CC275e are nitrogen-fixing microsymbionts of Trifolium spp. and have been used as commercial inoculant strains for clovers in pastoral agriculture in Australia and New Zealand. Here we present the complete genome sequences of both strains, resolving their multipartite genome structures and allowing for future studies using genomic approaches.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.


Subject(s)
Genome, Bacterial , Rhizobium leguminosarum , Trifolium , Genome, Bacterial/genetics , Genomics , Rhizobium leguminosarum/genetics , Symbiosis/genetics , Trifolium/microbiology
12.
Syst Appl Microbiol ; 44(1): 126156, 2021 Jan.
Article in English | MEDLINE | ID: mdl-33232849

ABSTRACT

Berseem clover (T. alexandrinum) is the main forage legume crop used as animal feed in Egypt. Here, eighty rhizobial isolates were isolated from root nodules of berseem clover grown in different regions in Egypt and were grouped by RFLP-16S rRNA ribotyping. Representative isolates were characterized using phylogenetic analyses of the 16S rRNA, rpoB, glnA, pgi, and nodC genes. We also investigated the performance of these isolates using phenotypic tests and nitrogen fixation efficiency assays. The majority of strains (<90%) were closely related to Rhizobium aegyptiacum and Rhizobium aethiopicum and of the remaining strains, six belonged to the Rhizobium leguminosarum genospecies complex and only one strain was assigned to Agrobacterium fabacearum. Despite their heterogeneous chromosomal background, most of the strains shared nodC gene alleles corresponding to symbiovar trifolii. Some of the strains closely affiliated to R. aegyptiacum and R. aethiopicum had superior nodulation and nitrogen fixation capabilities in berseem clover, compared to the commercial inoculant (Okadein®) and N-added treatments. R. leguminosarum strain NGB-CR 17 that harbored a nodC allele typical of symbiovar viciae, was also able to form an effective symbiosis with clover. Two strains with nodC alleles of symbiovar trifolii, R. aegyptiacum strains NGB-CR 129 and 136, were capable of forming effective nodules in Phaseolus vulgaris in axenic greenhouse conditions. This adds the symbiovar trifolii which is well-established in the Egyptian soils to the list of symbiovars that form nodules in P. vulgaris.


Subject(s)
Phylogeny , Rhizobium/classification , Root Nodules, Plant/microbiology , Trifolium/microbiology , Bacterial Typing Techniques , DNA, Bacterial/genetics , Egypt , Genes, Bacterial , Nitrogen Fixation , RNA, Ribosomal, 16S/genetics , Rhizobium/isolation & purification , Sequence Analysis, DNA , Symbiosis
13.
Int J Mol Sci ; 21(20)2020 Oct 20.
Article in English | MEDLINE | ID: mdl-33092221

ABSTRACT

Rhizobium leguminosarum bv. trifolii produces exopolysaccharide (EPS) composed of glucose, glucuronic acid, and galactose residues at a molar ratio 5:2:1. A majority of genes involved in the synthesis, modification, and export of exopolysaccharide are located in the chromosomal Pss-I region. In the present study, a ΔpssJ deletion mutant was constructed and shown to produce EPS lacking terminal galactose in the side chain of the octasaccharide subunit. The lack of galactose did not block EPS subunit translocation and polymerization. The in trans delivery of the pssJ gene restored the production of galactose-containing exopolysaccharide. The mutant was compromised in several physiological traits, e.g., motility and biofilm production. An impact of the pssJ mutation and changed EPS structure on the symbiotic performance was observed as improper signaling at the stage of molecular recognition, leading to formation of a significant number of non-infected empty nodules. Terminal galactosyltransferase PssJ was shown to display a structure typical for the GT-A class of glycosyltransferases and interact with other GTs and Wzx/Wzy system proteins. The latter, together with PssJ presence in soluble and membrane protein fractions indicated that the protein plays its role at the inner membrane interface and as a component of a larger complex.


Subject(s)
Bacterial Proteins/genetics , Galactosyltransferases/genetics , Mutation , Polysaccharides, Bacterial/metabolism , Rhizobium leguminosarum/genetics , Bacterial Proteins/metabolism , Biofilms , Galactose/chemistry , Galactose/metabolism , Galactosyltransferases/metabolism , Host-Pathogen Interactions , Plant Root Nodulation/genetics , Polysaccharides, Bacterial/chemistry , Rhizobium leguminosarum/enzymology , Rhizobium leguminosarum/physiology , Root Nodules, Plant/genetics , Root Nodules, Plant/microbiology , Symbiosis/genetics , Trifolium/microbiology
14.
Ecotoxicol Environ Saf ; 202: 110958, 2020 Oct 01.
Article in English | MEDLINE | ID: mdl-32800230

ABSTRACT

Phytoremediation is an effective way to repair heavy metal contaminated soil and rhizosphere microorganisms play an important role in plant regulation. Nevertheless, little information is known about the variation of microbial metabolic activities and community structure in rhizosphere during phytoremediation. In this study, the rhizosphere soil microbial metabolic activities and community structure of Trifolium repensL. during Cd-contaminated soil phytoremediation, were analyzed by Biolog EcoPlate™ and high-throughput sequencing. The uptake in the roots of Trifolium repensL. grown in 5.68 and 24.23 mg/kg Cd contaminated soil was 33.51 and 84.69 mg/kg respectively, causing the acid-soluble Cd fractions decreased 7.3% and 5.4%. Phytoremediation significantly influenced microbial community and Trifolium repensL. planting significantly increased the rhizosphere microbial population, diversity, the relative abundance of plant growth promoting bacteria (Kaistobacter and Flavisolibacter), and the utilization of difficultly metabolized compounds. The correlation analysis among substrate utilization and microbial communities revealed that the relative abundance increased microorganisms possessed stronger carbon utilization capacity, which was beneficial to regulate the stability of plant-microbial system. Collectively, the results of this study provide fundamental insights into the microbial metabolic activities and community structure during heavy metal contaminated soil phytoremediation, which may aid in the bioregulation of phytoremediation.


Subject(s)
Cadmium/toxicity , Microbiota/drug effects , Rhizosphere , Soil Microbiology , Soil Pollutants/toxicity , Soil/chemistry , Trifolium/drug effects , Biodegradation, Environmental , Cadmium/metabolism , Plant Roots/drug effects , Plant Roots/growth & development , Plant Roots/metabolism , Plant Roots/microbiology , Soil Pollutants/metabolism , Trifolium/growth & development , Trifolium/metabolism , Trifolium/microbiology
15.
Article in English | MEDLINE | ID: mdl-32784849

ABSTRACT

This study aimed to evaluate the impact of co-inoculation Rhizobium sp. and Azospirillum sp. on plant (Trifolium pratense L.) growth in the presence of polycyclic aromatic hydrocarbon (PAH) contamination (anthracene, phenanthrene, and pyrene). Eight strains from the genus Rhizobium leguminosarum bv. trifolii were selected for biotest analysis. Two methods of inoculation were used in the chamber experiment: (1) R. leguminosarum alone and (2) a combined inoculant (R. leguminosarum and Azospirillum brasilense). For comparison, non-contaminated controls were also used. The results demonstrated that co-inoculation of plants with Rhizobium and Azospirillum resulted in more root and shoot biomass than in plants inoculated with R. leguminosarum alone. The results indicated that application of a co-inoculation of bacteria from Rhizobium and Azospirillum species had a positive effect on clover nodulation and growth under the condition of PAH contamination.


Subject(s)
Azospirillum brasilense , Polycyclic Aromatic Hydrocarbons , Rhizobium leguminosarum , Soil Pollutants , Trifolium , Polycyclic Aromatic Hydrocarbons/toxicity , Soil Pollutants/toxicity , Trifolium/microbiology
16.
Appl Environ Microbiol ; 86(18)2020 09 01.
Article in English | MEDLINE | ID: mdl-32651206

ABSTRACT

Establishment of the symbiotic relationship that develops between rhizobia and their legume hosts is contingent upon an interkingdom signal exchange. In response to host legume flavonoids, NodD proteins from compatible rhizobia activate expression of nodulation genes that produce lipochitin oligosaccharide signaling molecules known as Nod factors. Root nodule formation commences upon legume recognition of compatible Nod factor. Rhizobium leguminosarum was previously considered to contain one copy of nodD; here, we show that some strains of the Trifolium (clover) microsymbiont R. leguminosarum bv. trifolii contain a second copy designated nodD2. nodD2 genes were present in 8 out of 13 strains of R. leguminosarum bv. trifolii, but were absent from the genomes of 16 R. leguminosarum bv. viciae strains. Analysis of single and double nodD1 and nodD2 mutants in R. leguminosarum bv. trifolii strain TA1 revealed that NodD2 was functional and enhanced nodule colonization competitiveness. However, NodD1 showed significantly greater capacity to induce nod gene expression and infection thread formation. Clover species are either annual or perennial and this phenological distinction is rarely crossed by individual R. leguminosarum bv. trifolii microsymbionts for effective symbiosis. Of 13 strains with genome sequences available, 7 of the 8 effective microsymbionts of perennial hosts contained nodD2, whereas the 3 microsymbionts of annual hosts did not. We hypothesize that NodD2 inducer recognition differs from NodD1, and NodD2 functions to enhance competition and effective symbiosis, which may discriminate in favor of perennial hosts.IMPORTANCE Establishment of the rhizobium-legume symbiosis requires a highly specific and complex signal exchange between both participants. Rhizobia perceive legume flavonoid compounds through LysR-type NodD regulators. Often, rhizobia encode multiple copies of nodD, which is one determinant of host specificity. In some species of rhizobia, the presence of multiple copies of NodD extends their symbiotic host-range. Here, we identified and characterized a second copy of nodD present in some strains of the clover microsymbiont Rhizobium leguminosarum bv. trifolii. The second nodD gene contributed to the competitive ability of the strain on white clover, an important forage legume. A screen for strains containing nodD2 could be utilized as one criterion to select strains with enhanced competitive ability for use as inoculants for pasture production.


Subject(s)
Bacterial Proteins/genetics , Microbial Interactions , Plant Root Nodulation , Rhizobium leguminosarum/physiology , Trifolium/microbiology , Bacterial Proteins/metabolism , Plant Roots/microbiology
17.
Microb Genom ; 6(4)2020 04.
Article in English | MEDLINE | ID: mdl-32176601

ABSTRACT

Rhizobia supply legumes with fixed nitrogen using a set of symbiosis genes. These can cross rhizobium species boundaries, but it is unclear how many other genes show similar mobility. Here, we investigate inter-species introgression using de novo assembly of 196 Rhizobium leguminosarum sv. trifolii genomes. The 196 strains constituted a five-species complex, and we calculated introgression scores based on gene-tree traversal to identify 171 genes that frequently cross species boundaries. Rather than relying on the gene order of a single reference strain, we clustered the introgressing genes into four blocks based on population structure-corrected linkage disequilibrium patterns. The two largest blocks comprised 125 genes and included the symbiosis genes, a smaller block contained 43 mainly chromosomal genes, and the last block consisted of three genes with variable genomic location. All introgression events were likely mediated by conjugation, but only the genes in the symbiosis linkage blocks displayed overrepresentation of distinct, high-frequency haplotypes. The three genes in the last block were core genes essential for symbiosis that had, in some cases, been mobilized on symbiosis plasmids. Inter-species introgression is thus not limited to symbiosis genes and plasmids, but other cases are infrequent and show distinct selection signatures.


Subject(s)
Bacterial Proteins/genetics , Plasmids/genetics , Rhizobium leguminosarum/genetics , Trifolium/microbiology , Whole Genome Sequencing/methods , Genetic Introgression , Haplotypes , High-Throughput Nucleotide Sequencing , Linkage Disequilibrium , Phylogeny , Plant Roots/microbiology , Rhizobium leguminosarum/classification , Selection, Genetic , Symbiosis
18.
Chemosphere ; 246: 125766, 2020 May.
Article in English | MEDLINE | ID: mdl-31901662

ABSTRACT

Lead (Pb+2) is a heavy metal and one of the main environmental pollutant, toxic to plants, animals and humans. Present study was conducted to evaluate ten plant growth promoting bacteria strains (B1-10) for biofilm production and their effect on growth indices, physiology, yield, antioxidant profile and lead uptake in rapeseed (Brassica napus) and clover (Trifolium repens) in lead polluted soil under nutrient broth medium and pot condition. Three pre-characterized biofilm forming lead tolerant growth promoting strains (B3: Pseudomonas fluorescens), B6: Pseudomonas putida and (B8: Bacillus safensis) were used to inoculate rapeseed and clover growing in the soil polluted with different levels (400, 800 and 1200 mg kg-1) of Pb arranged in completely randomized design with factorial arrangement. Results from screening experiment exhibited that more biofilm was produced by B3, B6 and B8 under highest level of lead contamination (1200 mg kg-1). Further, lead contamination decreased rapeseed and clover growth, physiology and yield at all levels of lead stress. But biofilm forming lead tolerant growth promoting bacteria application in lead contaminated soil enhanced rapeseed and clover growth, physiology, yield, antioxidant profile, proline and decreased malanodialdehyde content (which was decreased by different strains application under lead stress) of rapeseed and clover over no inoculation. Inoculation with all strains also increased the lead uptake in roots, shoots and decreased lead uptake in seeds of rapeseed and clover than plants in lead stress without inoculation.


Subject(s)
Biodegradation, Environmental , Biofilms/growth & development , Lead/toxicity , Soil Pollutants/toxicity , Bacteria/drug effects , Brassica napus/microbiology , Brassica napus/physiology , Brassica rapa , Environmental Pollution , Medicago , Metals, Heavy/pharmacology , Plant Roots/growth & development , Soil , Soil Pollutants/analysis , Trifolium/microbiology , Trifolium/physiology
19.
Int J Mol Sci ; 20(21)2019 Nov 02.
Article in English | MEDLINE | ID: mdl-31684086

ABSTRACT

Plant-rhizobia symbiosis can activate key genes involved in regulating nodulation associated with biological nitrogen fixation (BNF). Although the general molecular basis of the BNF process is frequently studied, little is known about its intraspecific variability and the characteristics of its allelic variants. This study's main goals were to describe phenotypic and genotypic variation in the context of nitrogen fixation in red clover (Trifolium pretense L.) and identify variants in BNF candidate genes associated with BNF efficiency. Acetylene reduction assay validation was the criterion for selecting individual plants with particular BNF rates. Sequences in 86 key candidate genes were obtained by hybridization-based sequence capture target enrichment of plants with alternative phenotypes for nitrogen fixation. Two genes associated with BNF were identified: ethylene response factor required for nodule differentiation (EFD) and molybdate transporter 1 (MOT1). In addition, whole-genome population genotyping by double-digest restriction-site-associated sequencing (ddRADseq) was performed, and BNF was evaluated by the natural 15N abundance method. Polymorphisms associated with BNF and reflecting phenotype variability were identified. The genetic structure of plant accessions was not linked to BNF rate of measured plants. Knowledge of the genetic variation within BNF candidate genes and the characteristics of genetic variants will be beneficial in molecular diagnostics and breeding of red clover.


Subject(s)
Genes, Plant/genetics , Nitrogen Fixation/genetics , Polymorphism, Genetic , Sequence Analysis, DNA/methods , Trifolium/genetics , Alleles , Genotype , Host Microbial Interactions , Phenotype , Plant Roots/genetics , Plant Roots/microbiology , Rhizobium/physiology , Symbiosis/genetics , Trifolium/microbiology
20.
Sci Rep ; 9(1): 13907, 2019 09 25.
Article in English | MEDLINE | ID: mdl-31554862

ABSTRACT

Primary infection of legumes by rhizobia involves the controlled localized enzymatic breakdown of cell walls at root hair tips. Previous studies determined the role of rhizobial CelC2 cellulase in different steps of the symbiotic interaction Rhizobium leguminosarum-Trifolium repens. Recent findings also showed that CelC2 influences early signalling events in the Ensifer meliloti-Medicago truncatula interaction. Here, we have monitored the root hair phenotypes of two legume plants, T. repens and M. sativa, upon inoculation with strains of their cognate and non-cognate rhizobial species, R. leguminosarum bv trifolii and E. meliloti, (over)expressing the CelC2 coding gene, celC. Regardless of the host, CelC2 specifically elicited 'hole-on-the-tip' events (Hot phenotype) in the root hair apex, consistent with the role of this endoglucanase in eroding the noncrystalline cellulose found in polarly growing cell walls. Overproduction of CelC2 also increased root hair tip redirections (RaT phenotype) events in both cognate and non-cognate hosts. Interestingly, heterologous celC expression also induced non-canonical alterations in ROS (Reactive Oxygen Species) homeostasis at root hair tips of Trifolium and Medicago. These results suggest the concurrence of shared unspecific and host-related plant responses to CelC2 during early steps of symbiotic rhizobial infection. Our data thus identify CelC2 cellulase as an important determinant of events underlying early infection of the legume host by rhizobia.


Subject(s)
Cellulase/metabolism , Fabaceae/metabolism , Fabaceae/microbiology , Host-Pathogen Interactions/physiology , Rhizobium leguminosarum/metabolism , Symbiosis/physiology , Cell Wall/metabolism , Cell Wall/microbiology , Gram-Negative Bacterial Infections/microbiology , Medicago truncatula/metabolism , Medicago truncatula/microbiology , Phenotype , Plant Roots/metabolism , Plant Roots/microbiology , Root Nodules, Plant/metabolism , Root Nodules, Plant/microbiology , Trifolium/metabolism , Trifolium/microbiology
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