Identifying abnormalities in symbiotic development between Trifolium spp. and Rhizobium leguminosarum bv. trifolii leading to sub-optimal and ineffective nodule phenotypes

BACKGROUND AND AIMS

Legumes overcome nitrogen limitations by entering into a mutualistic symbiosis with N(2)-fixing bacteria (rhizobia). Fully compatible associations (effective) between Trifolium spp. and Rhizobium leguminosarum bv. trifolii result from successful recognition of symbiotic partners in the rhizosphere, root hair infection and the formation of nodules where N(2)-fixing bacteroids reside. Poorly compatible associations can result in root nodule formation with minimal (sub-optimal) or no (ineffective) N(2)-fixation. Despite the abundance and persistence of strains in agricultural soils which are poorly compatible with the commercially grown clover species, little is known of how and why they fail symbiotically. The aims of this research were to determine the morphological aberrations occurring in sub-optimal and ineffective clover nodules and to determine whether reduced bacteroid numbers or reduced N(2)-fixing activity is the main cause for the Sub-optimal phenotype.

METHODS

Symbiotic effectiveness of four Trifolium hosts with each of four R. leguminosarum bv. trifolii strains was assessed by analysis of plant yields and nitrogen content; nodule yields, abundance, morphology and internal structure; and bacteroid cytology, quantity and activity.

KEY RESULTS

Effective nodules (Nodule Function 83-100 %) contained four developmental zones and N(2)-fixing bacteroids. In contrast, Sub-optimal nodules of the same age (Nodule Function 24-57 %) carried prematurely senescing bacteroids and a small bacteroid pool resulting in reduced shoot N. Ineffective-differentiated nodules carried bacteroids aborted at stage 2 or 3 in differentiation. In contrast, bacteroids were not observed in Ineffective-vegetative nodules despite the presence of bacteria within infection threads.

CONCLUSIONS

Three major responses to N(2)-fixation incompatibility between Trifolium spp. and R. l. trifolii strains were found: failed bacterial endocytosis from infection threads into plant cortical cells, bacteroid differentiation aborted prematurely, and a reduced pool of functional bacteroids which underwent premature senescence. We discuss possible underlying genetic causes of these developmental abnormalities and consider impacts on N(2)-fixation of clovers.

Isolation and characterization of rhizosphere bacteria with potential for biological control of weeds in vineyards

AIMS

Deleterious rhizosphere inhabiting bacteria (DRB) have potential to suppress plant growth. This project focuses on the isolation of DRB with potential for development as commercial products for weed control.

METHODS AND RESULTS

Bacteria were isolated from the rhizosphere, rhizoplane, and endorhizosphere of seedlings and mature plants of wild radish (Raphanus raphanistrum), annual ryegrass (Lolium rigidum) and capeweed (Arctotheca calendula) growing in vineyards in the Swan Valley, Western Australia. A majority (81.5%) of the 442 strains was obtained from either rhizospheres or rhizoplanes. Rapid screening techniques were developed to evaluate in the laboratory and glasshouse the effects of bacteria on plants. Strains were screened in the glasshouse for deleterious effects on annual ryegrass, wild radish, grapevine rootlings (Vitis vinifera) and the legume cover crop subterranean clover (Trifolium subterraneum). Three strains were identified using the Biolog system and 16S rRNA gene sequencing as two strains of Pseudomonas fluorescens (WSM3455 and WSM3456) and one strain of Alcaligenes xylosoxidans (WSM3457). One of the P. fluorescens (WSM3455) strain produced hydrogen cyanide, an inhibitor of plant roots and a broad-spectrum antimicrobial compound.

CONCLUSIONS

Three strains specifically inhibited wild radish but had no significant deleterious effects on either grapevine rootlings or subterranean clover.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study suggested manipulation of the weed seedling rhizosphere using identified DRB as a potential biocontrol agent for wild radish.

Evidence of selection for effective nodulation in the Trifolium spp. symbiosis with Rhizobium leguminosarum biovar trifolii

The pasture-breeding program to improve production in the natural grasslands in Uruguay has acknowledged that indigenous Rhizobium strains are incompatible with introduced Mediterranean clovers. In an attempt to understand and overcome this problem, a cross-row experiment was set up in 1999 in a basaltic, acid soil in Glencoe, Uruguay, to follow the survival and performance of 9 exotic strains of Rhizobium leguminosarum bv. trifolii. This paper reports on the ability of the introduced strains to compete for nodule occupancy of Mediterranean clover hosts and impacts of the introduced strains on the productivity of the indigenous Uruguayan clover Trifolium polymorphum. Strain WSM1325 was a superior inoculant and remained highly persistent and competitive for the effective symbiosis with the Mediterranean hosts, T. purpureum and T. repens, in the Uruguayan environment in the third year of the experiment. The Mediterranean hosts (T. purpureum and T. repens) nodulated with the introduced strains but did not nodulate with any indigenous R. leguminosarum bv. trifolii typed from nodules of T. polymorphum. Conversely, there were no nodules on the Uruguayan host T. polymorphum that contained introduced R. leguminosarum bv. trifolii. These results reveal the establishment of effective symbioses between strains of R. leguminosarum bv. trifolii and clover even though the soil contained ineffective R. leguminosarum bv. trifolii for all hosts. We believe our results are the first reported example of ‘selective’ nodulation for an effective symbiosis in situ with annual and perennial clovers in acid soils.

The interactions of Rhizobium leguminosarum biovar trifolii in nodulation of annual and perennial Trifolium spp. from diverse centres of origin

The release of effective inocula for new perennial clovers into cropping zones where subterranean clover is important might compromise N2 fixation by this valuable annual clover if symbiosis between the new inoculants and subterranean clover is not optimal. To assist our understanding of the interactions between clovers and their microsymbionts, rhizobial strains and clovers from South and equatorial Africa, North and South America, and the Euro–Mediterranean regions were tested. Glasshouse-based studies of the cross-inoculation characteristics of 38 strains of Rhizobium leguminosarum bv. trifolii associated with 38 genotypes of annual and perennial Trifolium spp. from these world centres of diversity were undertaken. Less than 7.5% of the perennial clover symbioses were effective whereas 40% of associations were effective for many of the annual clover species of Euro–Mediterranean origin. There was substantial specificity within the African clovers for effective nodulation. Rhizobial strains from the South American perennial T. polymorphum or from the African clovers were unable to nodulate subterranean clover effectively. Also, 7 of the 17 strains from these regions were unable to form nodules with the less promiscuous Mediterranean annual clovers, T. glanduliferum and T. isthmocarpum. Fifty-three of about 400 cross-inoculation treatments examined, which included annual and perennial clovers, were incapable of forming nodules, while only 65 formed effective nodules. There are 2 barriers to effective nodulation: a ‘geographic’ barrier representing the broad centres of clover diversity, across which few host-strain combinations were effective; and, within each region, a significant ‘phenological’ barrier between annual and perennial species. Clovers and their rhizobia from within the Euro–Mediterranean region of diversity were more able to cross the phenological barrier than genotypes from the other regions. It appears that only the relatively promiscuous clovers, whether annual or perennial, have been commercialised to date. The data indicate that, for perennial clovers, it will be a substantial challenge to develop inocula that do not adversely affect N2 fixation by subterranean clover and other annual clovers available commercially, especially if the perennial clovers were originally from Africa or America. Some future strategies for development of inoculants for clovers are proposed.

Root and root hair mechanisms that confer symbiotic competence for nodulation in acidic soils within Medicago species: a holistic model

Three experiments were undertaken to investigate the mechanisms used by the annual medic species, Medicago murex (Murex medic) to achieve nodulation more rapidly in acidic soils than the perennial species Medicago sativa (lucerne). In experiment 1, numbers and locations of root hairs on the primary roots of medic and lucerne were determined from plants grown in soil of pH 4.3 and 7.0. Experiment 2 enumerated the numbers of Sinorhizobium medicae (rhizobia) associated with the roots of medic and lucerne when grown in an acidic soil. Experiment 3 used a GFP-marked strain of rhizobia to determine the localised distribution of rhizobia along various zones of the primary roots of medic and lucerne in soil of pH 4.3 and 7.0. When grown in an acidic soil, medic produced 60% more root hairs/mm root along the primary root axis compared with lucerne, from 7 days after sowing. In soil of low pH, medic also had higher numbers of rhizobia associated with its entire root system than lucerne, with about 103 cfu/cm root throughout the 24-day period of the experiment, compared with lucerne for which rhizobial numbers decreased from 102 to 11 cfu/cm root over the same time period. When the intensity of fluorescence emitted by a GFP-marked transconjugant of rhizobia was measured at localised zones along the primary root of medic and lucerne grown in the acidic soil, it was 1.8-fold higher from the roots of medic than lucerne at 7 days after sowing, indicating higher numbers of rhizobia along medic roots. Hence, the numbers of rhizobia associated with the entire root system, and those colonised on localised zones of the primary root of medic were both higher than that of lucerne. These fundamental differences between the 2 species, combined with the earlier finding that lucerne tends to acidify its rhizosphere more than medic, allowed us to construct conceptual models that attempt to explain the increased symbiotic competency of medic compared with lucerne, and the different nodulation responses between medic and lucerne at low pH.

Phylogenetic relationships of three bacterial strains isolated from the pasture legume Biserrula pelecinus L

Three bacterial strains (WSM 1283, WSM 1284, WSM 1497) isolated from root nodules of the pasture legume Biserrula pelecinus L. growing in Morocco, Italy and Greece, respectively, were studied in order to determine their phylogenetic relationship to the other members of the family Rhizobiaceae. A polyphasic approach, which included analyses of morphological and physiological characteristics, plasmid profiles, symbiotic performance and 16S rRNA gene sequencing, indicated that these strains belong to the genus Mesorhizobium.

Nutritional constraints on root nodule bacteria affecting symbiotic nitrogen fixation: a review

Root nodule bacteria require access to adequate concentrations of mineral nutrients for metabolic processes to enable their survival and growth as free-living soil saprophytes, and in their symbiotic relationship with legumes. Essential nutrients, with a direct requirement in metabolism of rhizobia are carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, potassium, calcium, magnesium, iron, manganese, copper, zinc, molybdenum, nickel, cobalt and selenium. Boron does not seem to be required by rhizobia, but is essential for the establishment of effective legume symbioses. Nutrient constraints can affect both free-living and symbiotic forms of root nodule bacteria, but whether they do is a function of a complex series of events and interactions. Important physiological characteristics of rhizobia involved in, or affected by, their mineral nutrition include nutrient uptake, growth rate, gene regulation, nutrient storage, survival, genetic exchange and the viable non-culturable state. There is considerable variation between genera, species and strains of rhizobia in their response to nutrient deficiency. The effects of nutrient deficiencies on free-living rhizobia in the soil are poorly understood. Competition between strains of rhizobia for limiting phosphorus and iron in the rhizosphere may affect their ability to nodulate legumes. Processes in the development of some legume symbioses specifically require calcium, cobalt, copper, iron, potassium, molybdenum, nickel, phosphorus, selenium, zinc and boron. Limitations of phosphorus, calcium, iron and molybdenum in particular, can reduce legume productivity by affecting nodule development and function. The effects of nutrient deficiencies on rhizobia–legume signalling are not understood. The supply of essential inorganic nutrients to bacteroids in relation to nutrient partitioning in nodule tissues and nutrient transport to the symbiosome may affect effectiveness of nitrogen fixation. An integration of molecular approaches with more traditional biochemical, physiological and field-based studies is needed to improve understanding of the agricultural importance of rhizobia response to nutrient stress.

The adaptive acid tolerance response in root nodule bacteria and Escherichia coli

Root nodule bacteria and Escherichia coli show an adaptive acid tolerance response when grown under mildly acidic conditions. This is defined in terms of the rate of cell death upon exposure to acid shock at pH 3.0 and expressed in terms of a decimal reduction time, D. The D values varied with the strain and the pH of the culture medium. Early exponential phase cells of three strains of Rhizobium leguminosarum (WU95, 3001 and WSM710) had D values of 1, 6 and 5 min respectively when grown at pH 7.0; and D values of 5, 20 and 12 min respectively when grown at pH 5.0. Exponential phase cells of Rhizobium tropici UMR1899, Bradyrhizobium japonicum USDA110 and peanut Bradyhizobium sp. NC92 were more tolerant with D values of 31, 35 and 42 min when grown at pH 7.0; and 56, 86 and 68 min when grown at pH 5.0. Cells of E. coli UB1301 in early exponential phase at pH 7.0 had a D value of 16 min, whereas at pH 5.0 it was 76 min. Stationary phase cells of R. leguminosarum and E. coli were more tolerant (D values usually 2 to 5-fold higher) than those in exponential phase. Cells of R. leguminosarum bv. trifolii 3001 or E. coli UB1301 transferred from cultures at pH 7.0 to medium at pH 5.0 grew immediately and induced the acid tolerance response within one generation. This was prevented by the addition of chloramphenicol. Acid-adapted cells of Rhizobium leguminosarum bv. trifolii WU95 and 3001; or E. coli UB1301, M3503 and M3504 were as sensitive to UV light as those grown at neutral pH.

Cloning, characterization, and complementation of lesions causing acid sensitivity in Tn5-induced mutants of Rhizobium meliloti WSM419

Four Tn5-induced mutants of Rhizobium meliloti WSM419 were unable to grow or maintain intracellular pH at an external pH of 5.6. Restriction analysis of DNA fragments carrying Tn5 and flanking sequences cloned from these mutants indicated that all four cloned mutations are unique and that the two strains (TG1-6 and TG1-11) carry Tn5 insertions which are within 4.4 kilobases of each other on a single EcoRI fragment. Southern analysis of total mutant DNA indicated a single copy of Tn5 in each mutant. A limited cosmid gene bank of wild-type WSM419 DNA was probed for homology to mutant DNA cloned from the acid-sensitive mutants. Dot hybridization experiments identified one cosmid element within this bank carrying wild-type DNA sequences corresponding to DNA implicated in acid tolerance. This cosmid was able to complement defects in growth and intracellular pH maintenance in TG1-11 but not TG1-6.

Iron-deficiency specifically limits nodule development in peanut inoculated with Bradyrhizobium sp

Severely iron-deficient peanuts (Arachis hypogaaea L.) grown on calcareous soils in central Thailand failed to nodulate until given foliar iron applications. Glasshouse experiments were conducted on two cultivars (Tainan 9 and Robut 33-1) to identify which stage of the nodule symbiosis was most sensitive to iron-deficiency. Iron-deficiency did not limit growth of soil or rhizosphere populations of peanut liradyrhizobium. Similar numbers of root nodule initials formed in the roots of both control and iron-sprayed plants, showing that iron-deficiency did not directly affect root infection and nodule initiation. Plants sprayed with iron produced greater numbers of excisable nodules and carried a greater nodule mass than untreated plants. Five days after iron application, nodules on sprayed plants of CV. Tainan 9 contained 200-fold higher bacteroid numbers per unit weight and 14-fold higher concentrations of leghaemoglobain. The onset of nitrogenase activity was also delayed by iron deficiency in both cultivars. Tainan 9 appeared more sensitive to iron-deficiency than Robut 33-1 in terms of nodule mass produced, but both cultivars showed the same effect of iron-deficiency on nitrogenase activity per plant. It is concluded that the failure of the infecting rhizobia to obtain adequate amounts of iron from the plant results in arrested nodule development and a failure of nitrogen fixation.

Effect of inoculation of Zea mays with Azospirillum brasilense strains under temperate conditions

Seven strains of Azospirillum brasilense were compared for their effect on the growth of Zea mays grown under temperate conditions in sand--vermiculite pot cultures. Inoculation with all seven strains tested, including Fix(-) mutant strains, increased dry weight and total nitrogen content of shoots, but nitrogen concentrations were unaffected. Low and variable rates of acetylene reduction activity were observed from excised roots of inoculated plants without preincubation. Estimates of N2-fixing A. brasilense associated with inoculated roots showed differences between strains in establishing themselves in the rhizosphere and endorhizosphere. In some strains enrichment in the endorhizosphere of roots occurred following inoculation, but the relative numbers and location of the strains did not appear to affect the yield response.