Nicole Robinson

Plants can use protein as a nitrogen source without assistance from other organisms

Nitrogen is quantitatively the most important nutrient that plants acquire from the soil. It is well established that plant roots take up nitrogen compounds of low molecular mass, including ammonium, nitrate, and amino acids. However, in the soil of natural ecosystems, nitrogen occurs predominantly as proteins. This complex organic form of nitrogen is considered to be not directly available to plants. We examined the long-held view that plants depend on specialized symbioses with fungi (mycorrhizas) to access soil protein and studied the woody heathland plant Hakea actites and the herbaceous model plant Arabidopsis thaliana, which do not form mycorrhizas. We show that both species can use protein as a nitrogen source for growth without assistance from other organisms. We identified two mechanisms by which roots access protein. Roots exude proteolytic enzymes that digest protein at the root surface and possibly in the apoplast of the root cortex. Intact protein also was taken up into root cells most likely via endocytosis. These findings change our view of the spectrum of nitrogen sources that plants can access and challenge the current paradigm that plants rely on microbes and soil fauna for the breakdown of organic matter.

Nitrate paradigm does not hold up for sugarcane.

Modern agriculture is based on the notion that nitrate is the main source of nitrogen (N) for crops, but nitrate is also the most mobile form of N and easily lost from soil. Efficient acquisition of nitrate by crops is therefore a prerequisite for avoiding off-site N pollution. Sugarcane is considered the most suitable tropical crop for biofuel production, but surprisingly high N fertilizer applications in main producer countries raise doubt about the sustainability of production and are at odds with a carbon-based crop. Examining reasons for the inefficient use of N fertilizer, we hypothesized that sugarcane resembles other giant tropical grasses which inhibit the production of nitrate in soil and differ from related grain crops with a confirmed ability to use nitrate. The results of our study support the hypothesis that N-replete sugarcane and ancestral species in the Andropogoneae supertribe strongly prefer ammonium over nitrate. Sugarcane differs from grain crops, sorghum and maize, which acquired both N sources equally well, while giant grass, Erianthus, displayed an intermediate ability to use nitrate. We conclude that discrimination against nitrate and a low capacity to store nitrate in shoots prevents commercial sugarcane varieties from taking advantage of the high nitrate concentrations in fertilized soils in the first three months of the growing season, leaving nitrate vulnerable to loss. Our study addresses a major caveat of sugarcane production and affords a strong basis for improvement through breeding cultivars with enhanced capacity to use nitrate as well as through agronomic measures that reduce nitrification in soil.

The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application.

Diazotrophic bacteria potentially supply substantial amounts of biologically fixed nitrogen to crops, but their occurrence may be suppressed by high nitrogen fertilizer application. Here, we explored the impact of high nitrogen fertilizer rates on the presence of diazotrophs in field-grown sugarcane with industry-standard or reduced nitrogen fertilizer application. Despite large differences in soil microbial communities between test sites, a core sugarcane root microbiome was identified. The sugarcane root-enriched core taxa overlap with those of Arabidopsis thaliana raising the possibility that certain bacterial families have had long association with plants. Reduced nitrogen fertilizer application had remarkably little effect on the core root microbiome and did not increase the relative abundance of root-associated diazotrophs or nif gene counts. Correspondingly, low nitrogen fertilizer crops had lower biomass and nitrogen content, reflecting a lack of major input of biologically fixed nitrogen, indicating that manipulating nitrogen fertilizer rates does not improve sugarcane yields by enriching diazotrophic populations under the test conditions. Standard nitrogen fertilizer crops had improved biomass and nitrogen content, and corresponding soils had higher abundances of nitrification and denitrification genes. These findings highlight that achieving a balance in maximizing crop yields and minimizing nutrient pollution associated with nitrogen fertilizer application requires understanding of how microbial communities respond to fertilizer use.

Arabidopsis and Lobelia anceps access small peptides as a nitrogen source for growth

While importance of amino acids as a nitrogen source for plants is increasingly recognised, other organic N sources including small peptides have received less attention. We assessed the capacity of functionally different species, annual and nonmycorrhizal Arabidopsis thaliana (L.) Heynh. (Brassicaceae) and perennial Lobelia anceps L.f. (Campanulaceae), to acquire, metabolise and use small peptides as a N source independent of symbionts. Plants were grown axenically on media supplemented with small peptides (2-4 amino acids), amino acids or inorganic N. In A. thaliana, peptides of up to four amino acid residues sustained growth and supported up to 74% of the maximum biomass accumulation achieved with inorganic N. Peptides also supported growth of L. anceps, but to a lesser extent. Using metabolite analysis, a proportion of the peptides supplied in the medium were detected intact in root and shoot tissue together with their metabolic products. Nitrogen source preferences, growth responses and shoot-root biomass allocation were species-specific and suggest caution in the use of Arabidopsis as the sole plant model. In particular, glycine peptides of increasing length induced effects ranging from complete inhibition to marked stimulation of root growth. This study contributes to emerging evidence that plants can acquire and metabolise organic N beyond amino acids.

Nitrogen fertilizer dose alters fungal communities in sugarcane soil and rhizosphere

Fungi play important roles as decomposers, plant symbionts and pathogens in soils. The structure of fungal communities in the rhizosphere is the result of complex interactions among selection factors that may favour beneficial or detrimental relationships. Using culture-independent fungal community profiling, we have investigated the effects of nitrogen fertilizer dosage on fungal communities in soil and rhizosphere of field-grown sugarcane. The results show that the concentration of nitrogen fertilizer strongly modifies the composition but not the taxon richness of fungal communities in soil and rhizosphere. Increased nitrogen fertilizer dosage has a potential negative impact on carbon cycling in soil and promotes fungal genera with known pathogenic traits, uncovering a negative effect of intensive fertilization.

Sugarcane genotypes differ in internal nitrogen use efficiency

The large amounts of nitrogen (N) fertiliser applied to most cropping systems support high yields but cause N pollution. More efficient use of N in cropping systems can be achieved through improved N management practices combined with genetic improvement of the crop. The magnitude of genetic variation in sugarcane (Saccharum officinarum L.) for internal nitrogen use efficiency (iNUE, biomass produced per unit tissue N) was investigated as this could provide a basis for breeding varieties with reduced N demand. Genotypes of a mapping population were examined for biomass production and physiological variables under low or high N supply in controlled conditions. Key findings were: (i) genotypic variation for biomass production and iNUE was up to 3-fold greater under low than high N supply, (ii) elite parent Q165 was among the best performing genotypes for biomass and iNUE at high N but not at low N supply, and (iii) several genotypes had high iNUE at both N supplies. While glutamine synthetase (GS; EC 6.3.1.2) activity has been linked with grain yield in other crops, no direct relationship was observed between whole tissue GS activity and vegetative biomass or iNUE in sugarcane genotypes. Soluble protein content was negatively correlated with iNUE and biomass production. This study demonstrates that there is considerable genetic variation for iNUE in sugarcane, which can be exploited for breeding. It is proposed that breeding programs should assess genotypes not only at high N, but also at low N supply rates to select genotypes that produce high biomass with low and high N supply.

Nitrogen fluxes at the root-soil interface show a mismatch of nitrogen fertilizer supply and sugarcane root uptake capacity

Globally only ≈50% of applied nitrogen (N) fertilizer is captured by crops, and the remainder can cause pollution via runoff and gaseous emissions. Synchronizing soil N supply and crop demand will address this problem, however current soil analysis methods provide little insight into delivery and acquisition of N forms by roots. We used microdialysis, a novel technique for in situ quantification of soil nutrient fluxes, to measure N fluxes in sugarcane cropping soils receiving different fertilizer regimes, and compare these with N uptake capacities of sugarcane roots. We show that in fertilized sugarcane soils, fluxes of inorganic N exceed the uptake capacities of sugarcane roots by several orders of magnitude. Contrary, fluxes of organic N closely matched roots’ uptake capacity. These results indicate root uptake capacity constrains plant acquisition of inorganic N. This mismatch between soil N supply and root N uptake capacity is a likely key driver for low N efficiency in the studied crop system. Our results also suggest that (i) the relative contribution of inorganic N for plant nutrition may be overestimated when relying on soil extracts as indicators for root-available N, and (ii) organic N may contribute more to crop N supply than is currently assumed.

Interspecific differences in aluminium tolerance in relation to root cation-exchange capacity

Genotypic differences in aluminium (Al) tolerance hold considerable promise in overcoming an important limitation to plant growth in acid soils. Little is known, however, about the biochemical basis of such differences. Extracellular properties, particularly low root cation-exchange capacity (CEC), have been associated with Al tolerance, since roots of low CEC adsorb less Al than do those of high CEC. A solution culture study was conducted in which 12 plant species (monocots and dicots) were grown in solution culture of low ionic strength (ca 2 mM) for 8 d at four Al concentrations (0, 16, 28 and 55 μM). The species differed significantly in Al tolerance as shown by differences in root length. Root length relative to that of the same species grown in the absence of Al varied from 6 to 117% at 16 μM Al, and from 6 to 75% at 28 μM Al. Species tolerance of Al was not closely associated with differences in root CEC. Although in some species Al sensitivity was associated with high adsorption of Al during a 10- or 40-min exposure to Al (expressed on a fresh mass or root length basis), this was not a good predictor of Al tolerance across all species studied.

Amino acids are a nitrogen source for sugarcane

Organic forms of nitrogen (ON) represent potential N sources for crops and an alternative to inorganic N (IN, ammonium nitrate). Sugarcane soils receive organic harvest residues (~40-100kg ON ha-1), but it is unknown whether ON is a direct N source for crops. We investigated whether sugarcane can use organic monomers in the form of amino acids and whether the use of amino acids as a N source results in distinct metabolic or morphological change when compared with use of inorganic N (IN). Plantlets cultivated in sterile culture and young plants grown in non-sterile soil culture were supplied with IN, ON (five amino acids present in sugarcane soils), or combined IN and ON. All treatments resulted in similar biomass and N content indicating that sugarcane has a well developed capacity to use ON and confirms findings in other species. ON-supplied plants in axenic culture had increased total branch root length per unit primary root axis which has not been reported previously. In both experimental systems, ON supplied plants had increased asparagine concentrations suggesting altered N metabolism. Root of ON-supplied soil-grown plants had significantly reduced nitrate concentrations. We interpret the shift from nitrate to asparagine as indicative of N form use other than or in addition to nitrate by sugarcane. N metabolite profiling could advance knowledge of crop N sources and this will aid in development of N efficient cropping systems with a reduced N pollution footprint.

A quantitative genetics approach to nitrogen use efficiency in sugarcane

The economic and environmental consequences of inefficient use of nitrogen (N) fertiliser in agricultural crops is of concern worldwide, so new crop varieties with improved nitrogen use efficiency (NUE) are sought. Here, we report the first study of mapping quantitative trait loci (QTL) for nitrogen physiology traits in sugarcane. QTL analysis was undertaken for each parent of a segregating bi-parental sugarcane mapping population. We grew 168 progeny under limiting (0.2mM NH(4)NO(3)) and non-limiting (5.0mM NH(4)NO(3)) N supplies in two glasshouse experiments. Significant marker-trait associations (MTA) were detected in each treatment for shoot dry weight, root dry weight, total shoot N, shoot internal NUE (iNUE; measured as units shoot dry weight per unit N), leaf protein content and glutamine synthetase (GS) activity. MTA for GS activity did not co-locate with other traits except leaf protein content, indicating that variation in GS activity is not linked to plant size or iNUE during early growth. Under high N, there were no significant MTA for iNUE among markers from the male parent, Q165, an Australian commercial cultivar, but six MTA were found for markers inherited from the female parent, IJ76-514, a Saccharum officinarum ancestral variety. The results indicate that variation for iNUE under high N may be lower in commercial varieties than unimproved genotypes. Further, four MTA were consistent with previous field-based research on sugar and biomass production. Our study provides initial evidence that QTL may be incorporated in sugarcane breeding programs targeting improved NUE.