Paolo Ruisi

Advanced methods of plant disease detection. A review

Plant diseases are responsible for major economic losses in the agricultural industry worldwide. Monitoring plant health and detecting pathogen early are essential to reduce disease spread and facilitate effective management practices. DNA-based and serological methods now provide essential tools for accurate plant disease diagnosis, in addition to the traditional visual scouting for symptoms. Although DNA-based and serological methods have revolutionized plant disease detection, they are not very reliable at asymptomatic stage, especially in case of pathogen with systemic diffusion. They need at least 1–2 days for sample harvest, processing, and analysis. Here, we describe modern methods based on nucleic acid and protein analysis. Then, we review innovative approaches currently under development. Our main findings are the following: (1) novel sensors based on the analysis of host responses, e.g., differential mobility spectrometer and lateral flow devices, deliver instantaneous results and can effectively detect early infections directly in the field; (2) biosensors based on phage display and biophotonics can also detect instantaneously infections although they can be integrated with other systems; and (3) remote sensing techniques coupled with spectroscopy-based methods allow high spatialization of results, these techniques may be very useful as a rapid preliminary identification of primary infections. We explain how these tools will help plant disease management and complement serological and DNA-based methods. While serological and PCR-based methods are the most available and effective to confirm disease diagnosis, volatile and biophotonic sensors provide instantaneous results and may be used to identify infections at asymptomatic stages. Remote sensing technologies will be extremely helpful to greatly spatialize diagnostic results. These innovative techniques represent unprecedented tools to render agriculture more sustainable and safe, avoiding expensive use of pesticides in crop protection.

Influence of arbuscular mycorrhizae on biomass production and nitrogen fixation of berseem clover plants subjected to water stress.

Several studies, performed mainly in pots, have shown that arbuscular mycorrhizal symbiosis can mitigate the negative effects of water stress on plant growth. No information is available about the effects of arbuscular mycorrhizal symbiosis on berseem clover growth and nitrogen (N) fixation under conditions of water shortage. A field experiment was conducted in a hilly area of inner Sicily, Italy, to determine whether symbiosis with AM fungi can mitigate the detrimental effects of drought stress (which in the Mediterranean often occurs during the late period of the growing season) on forage yield and symbiotic N2 fixation of berseem clover. Soil was either left under water stress (i.e., rain-fed conditions) or the crop was well-watered. Mycorrhization treatments consisted of inoculation of berseem clover seeds with arbuscular mycorrhizal spores or suppression of arbuscular mycorrhizal symbiosis by means of fungicide treatments. Nitrogen biological fixation was assessed using the 15N-isotope dilution technique. Arbuscular mycorrhizal symbiosis was able to mitigate the negative effect of water stress on berseem clover grown in a typical semiarid Mediterranean environment. In fact, under water stress conditions, arbuscular mycorrhizal symbiosis resulted in increases in total biomass, N content, and N fixation, whereas no effect of crop mycorrhization was observed in the well-watered treatment.

Soil inoculation with symbiotic microorganisms promotes plant growth and nutrient transporter genes expression in durum wheat.

In a field experiment conducted in a Mediterranean area of inner Sicily, durum wheat was inoculated with plant growth-promoting rhizobacteria (PGPR), with arbuscular mycorrhizal fungi (AMF), or with both to evaluate their effects on nutrient uptake, plant growth, and the expression of key transporter genes involved in nitrogen (N) and phosphorus (P) uptake. These biotic associations were studied under either low N availability (unfertilized plots) and supplying the soil with an easily mineralizable organic fertilizer. Regardless of N fertilization, at the tillering stage, inoculation with AMF alone or in combination with PGPR increased the aboveground biomass yield compared to the uninoculated control. Inoculation with PGPR enhanced the aboveground biomass yield compared to the control, but only when N fertilizer was added. At the heading stage, inoculation with all microorganisms increased the aboveground biomass and N. Inoculation with PGPR and AMF+PGPR resulted in significantly higher aboveground P compared to the control and inoculation with AMF only when organic N was applied. The role of microbe inoculation in N uptake was elucidated by the expression of nitrate transporter genes. NRT1.1, NRT2, and NAR2.2 were significantly upregulated by inoculation with AMF and AMF+PGPR in the absence of organic N. A significant down-regulation of the same genes was observed when organic N was added. The ammonium (NH4+) transporter genes AMT1.2 showed an expression pattern similar to that of the NO3- transporters. Finally, in the absence of organic N, the transcript abundance of P transporters Pht1 and PT2-1 was increased by inoculation with AMF+PGPR, and inoculation with AMF upregulated Pht2 compared to the uninoculated control. These results indicate the soil inoculation with AMF and PGPR (alone or in combination) as a valuable option for farmers to improve yield, nutrient uptake, and the sustainability of the agro-ecosystem.

Forage production, N uptake, N2 fixation, and N recovery of berseem clover grown in pure stand and in mixture with annual ryegrass under different managements

In Mediterranean countries, forage grasses and legumes are commonly grown in mixture because of their ability to increase herbage yield and quality compared with monocrop systems. However, the benefits of intercropping over a monocrop system are not always realized because the efficiency of a grass–legume mixture is strongly affected by agronomic factors. The present study evaluated productivity, N2 fixation, N transfer, and N recovery of berseem clover (Trifolium alexandrinum) grown in pure stand and in mixture with annual ryegrass (Lolium multiflorum) under high or low defoliation frequencies and varying plant arrangements (sowing in the same row or in alternating rows). On average, the berseem–ryegrass mixtures resulted in a greater yield and N yield than the monocrops. When mixed together, ryegrass was more efficient than berseem at absorbing soil N, increasing the reliance of berseem on N2 fixation. Both defoliation management and plant arrangement affected forage yield and the quality of the mixture, modifying the proportion of the two components, the N content of the forage, and the symbiotic N2 fixation of the legume. Reducing the proximity between plants of the two species may benefit the weaker component of the mixture. No apparent transfer of fixed N from berseem to ryegrass was detected.

Metabolomics Suggests That Soil Inoculation with Arbuscular Mycorrhizal Fungi Decreased Free Amino Acid Content in Roots of Durum Wheat Grown under N-Limited, P-Rich Field Conditions

Arbuscular mycorrhizal fungi (AMF) have a major impact on plant nutrition, defence against pathogens, a plant’s reaction to stressful environments, soil fertility, and a plant’s relationship with other microorganisms. Such effects imply a broad reprogramming of the plant’s metabolic activity. However, little information is available regarding the role of AMF and their relation to other soil plant growth—promoting microorganisms in the plant metabolome, especially under realistic field conditions. In the present experiment, we evaluated the effects of inoculation with AMF, either alone or in combination with plant growth–promoting rhizobacteria (PGPR), on the metabolome and changes in metabolic pathways in the roots of durum wheat (Triticum durum Desf.) grown under N-limited agronomic conditions in a P-rich environment. These two treatments were compared to infection by the natural AMF population (NAT). Soil inoculation with AMF almost doubled wheat root colonization by AMF and decreased the root concentrations of most compounds in all metabolic pathways, especially amino acids (AA) and saturated fatty acids, whereas inoculation with AMF+PGPR increased the concentrations of such compounds compared to inoculation with AMF alone. Enrichment metabolomics analyses showed that AA metabolic pathways were mostly changed by the treatments, with reduced amination activity in roots most likely due to a shift from the biosynthesis of common AA to γ-amino butyric acid. The root metabolome differed between AMF and NAT but not AMF+PGPR and AMF or NAT. Because the PGPR used were potent mineralisers, and AMF can retain most nitrogen (N) taken as organic compounds for their own growth, it is likely that this result was due to an increased concentration of mineral N in soil inoculated with AMF+PGPR compared to AMF alone.

Nitrogen uptake and nitrogen fertilizer recovery in old and modern wheat genotypes grown in the presence or absence of interspecific competition

Choosing genotypes with a high capacity for taking up nitrogen (N) from the soil and the ability to efficiently compete with weeds for this nutrient is essential to increasing the sustainability of cropping systems that are less dependent on auxiliary inputs. This research aimed to verify whether differences exist in N uptake and N fertilizer recovery capacity among wheat genotypes and, if so, whether these differences are related to a different competitive ability against weeds of wheat genotypes. To this end, 12 genotypes, varying widely in morphological traits and year of release, were grown in the presence or absence of interspecific competition (using Avena sativa L. as a surrogate weed). Isotopic tracer 15N was used to measure the fertilizer N uptake efficiencies of the wheat genotypes and weed. A field experiment, a split-plot design with four replications, was conducted during two consecutive growing seasons in a typical Mediterranean environment. In the absence of interspecific competition, few differences in either total N uptake (range: 98–112 kg N ha−1) or the 15N fertilizer recovery fraction (range: 30.0–36.7%) were observed among the wheat genotypes. The presence of competition, compared to competitor-free conditions, resulted in reductions in grain yield (49%), total N uptake (29%), and an 15N fertilizer recovery fraction (32%) that were on average markedly higher in modern varieties than in old ones. Both biomass and grain reductions were strongly related to the biomass of the competitor (correlation coefficients > 0.95), which ranged from 135 to 573 g m−2. Variations in both grain and biomass yield due to interspecific competition were significantly correlated with percentage of soil cover and leaf area at tillering, plant height at heading, and total N uptake, thus highlighting that the ability to take up N from the soil played a certain role in determining the different competitive abilities against weed of the genotypes.

The Critical Period of Weed Control in Faba Bean and Chickpea in Mediterranean Areas

Abstract Weeds are often the major biological constraint to growing legume crops successfully, and an understanding of the critical period of weed control (CPWC) is important for developing environmentally sustainable weed management practices to prevent unacceptable yield loss. Therefore, we carried out two field experiments to identify the CPWC for two grain legume crops traditionally grown in Mediterranean areas: chickpea and faba bean. The experiments were conducted at two sites both located in the Sicilian inland (Italy). In chickpea, when weeds were left to compete with the crop for the whole cycle, the grain yield reduction was on average about 85% of the weed-free yield, whereas in faba bean the reduction was less severe (on average about 60% of the weed-free yield). The onset of the CPWC at a 5% yield loss level varied by species, occurring later in faba bean than in chickpea (on average, 261 and 428 growing degree days after emergence for chickpea and faba bean, respectively). In both species, the end of the CPWC occurred at the early full-flowering stage when the canopy of each crop enclosed the interrow space. On the whole, the CPWC at a 5% yield loss level ranged from 50 to 69 d in chickpea and from 28 to 33 d in faba bean. The results highlight the fact that faba bean has a higher competitive ability against weeds than chickpea. This could be attributable both to more vigorous early growth and to the plants greater height, both factors related to a greater shading ability and, consequently, to a better ability to suppress weeds. Nomenclature: Faba bean, Vicia faba L. var. minor; chickpea, Cicer arietinum L.

Pheno-morphological, agronomic and genetic diversity among natural populations of sulla (Hedysarum coronarium L.) collected in Sicily, Italy

Sulla (Hedysarum coronarium L.) is a short-lived perennial forage legume that plays a key role in cereal-based systems in semi-arid Mediterranean regions, particularly in organic production and low-input oriented agriculture. In Sicily, the species is widespread both as a wild and cultivated plant. The present study assessed the phenotypic and genetic variation among natural populations of sulla collected from different environments throughout Sicily and analysed how the patterns of phenotypic diversity varied according to the environmental parameters of each collection site. Two commercial varieties and two Sicilian agro-ecotypes were also included in the study as controls. Principal components analysis (PCA) was performed on the sites using geographic, climatic, and pedological data to assess the differences in types of collection sites. PCA was also performed on the accessions (using pheno-morphological and agronomic data) to establish the importance of different traits in explaining multivariate polymorphisms. The results showed a large degree of genetic diversity (based on ISSR markers) and variability in pheno-morphological and agronomic traits. PCA did not clearly differentiate the accessions according to their habitats of origin, but in some cases accessions from the same habitat had a tendency to group together. The agronomic attributes of several populations were more pronounced than those of the controls. The observed variability may be valuable when selecting for H. coronarium varieties suitable for various uses (e.g., hay production, grazing, soil protection).

Variation in pheno-morphological and agronomic traits among burr medic (Medicago polymorpha L.) populations collected in Sicily, Italy.

The present study assessed the diversity of pheno-morphological and agronomic traits among 31 natural populations of burr medic (Medicago polymorpha L.) from different environments throughout Sicily, and analysed the patterns of phenotypic diversity in relation to the environmental parameters of each collection site. Three commercial cultivars (Cavalier, Santiago, and Anglona) were also included in the study as check cultivars. Two field experiments were performed in 2005–06 in a hilly area of the Sicilian inland. Principal components analysis (PCA) was performed on the sites using geographic, climatic, and pedological data to assess the differences in types of collection sites. PCA was also performed on the accessions using pheno-morphological and agronomic data to establish the importance of different traits in explaining multivariate polymorphisms. Sicilian burr medic populations showed highly significant inter-population differences for all of the recorded pheno-morphological and agronomic traits, and several populations had agronomic attributes that were more pronounced than those of the check cultivars. PCA did not clearly differentiate the accessions according to their habitats of origin, but in some cases, accessions from the same habitat had a tendency to stay together. Populations from drier and warmer habitats flowered earlier and were less productive than those from wetter and colder ones. The large variability in both pheno-morphological and agronomic traits among Sicilian populations may be valuable when searching for suitable M. polymorpha material to exploit in pastures and crop–livestock farming systems in the Mediterranean region.

An assessment of factors controlling N2O and CO2 emissions from crop residues using different measurement approaches

Management of plant residues plays an important role in maintaining soil quality and nutrient availability for plants and microbes. However, there is considerable uncertainty regarding the factors controlling residue decomposition and their effects on greenhouse gas (GHG) emissions from the soil. This uncertainty is created both by the complexity of the processes involved and limitations in the methodologies commonly used to quantify GHG emissions. We therefore investigated the addition of two soil residues (durum wheat and faba bean) with similar C/N ratios but contrasting fibres, lignin and cellulose contents on nutrient dynamics and GHG emission from two contrasting soils: a low-soil organic carbon (SOC), high pH clay soil (Chromic Haploxerert) and a high-SOC, low pH sandy-loam soil (Eutric Cambisol). In addition, we compared the effectiveness of the use of an infrared gas analyser (IRGA) and a photoacoustic gas analyser (PGA) to measure GHG emissions with more conventional gas chromatography (GC). There was a strong correlation between the different measurement techniques which strengthens the case for the use of continuous measurement approaches involving IRGA and PGA analyses in studies of this type. The unamended Cambisol released 286% more CO2 and 30% more N2O than the Haploxerert. Addition of plant residues increased CO2 emissions more in the Haploxerert than Cambisol and N2O emission more in the Cambisol than in the Haploxerert. This may have been a consequence of the high N stabilization efficiency of the Haploxerert resulting from its high pH and the effect of the clay on mineralization of native organic matter. These results have implication management of plant residues in different soil types.