Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions

Background When maize (Zea mays L.) is grown in the Northern hemisphere, its development is heavily arrested by chilling temperatures, especially at the juvenile phase. As some endophytes are beneficial for plants under stress conditions, we analyzed the impact of chilling temperatures on the root microbiome and examined whether microbiome-based analysis might help to identify bacterial strains that could promote growth under these temperatures. Results We investigated how the maize root microbiome composition changed by means of 16S rRNA gene amplicon sequencing when maize was grown at chilling temperatures in comparison to ambient temperatures by repeatedly cultivating maize in field soil. We identified 12 abundant and enriched bacterial families that colonize maize roots, consisting of bacteria recruited from the soil, whereas seed-derived endophytes were lowly represented. Chilling temperatures modified the root microbiome composition only slightly, but significantly. An enrichment of several chilling-responsive families was detected, of which the Comamonadaceae and the Pseudomonadaceae were the most abundant in the root endosphere of maize grown under chilling conditions, whereas only three were strongly depleted, among which the Streptomycetaceae. Additionally, a collection of bacterial strains isolated from maize roots was established and a selection was screened for growth-promoting effects on juvenile maize grown under chilling temperatures. Two promising strains that promoted maize growth under chilling conditions were identified that belonged to the root endophytic bacterial families, from which the relative abundance remained unchanged by variations in the growth temperature. Conclusions Our analyses indicate that chilling temperatures affect the bacterial community composition within the maize root endosphere. We further identified two bacterial strains that boost maize growth under chilling conditions. Their identity revealed that analyzing the chilling-responsive families did not help for their identification. As both strains belong to root endosphere enriched families, visualizing and comparing the bacterial diversity in these communities might still help to identify new PGPR strains. Additionally, a strain does not necessarely need to belong to a high abundant family in the root endosphere to provoke a growth-promoting effect in chilling conditions

An evaluation of alternative methods of P application for increased maize production under smallholder farmers' conditions in Kenya

Smallholder farmers in sub-Saharan Africa are confronted by low crop production due to phosphorus deficiency and a limited investment capacity in P inputs. Alternative P fertilizer types are being commercialized which aim at improved P use efficiency through specialized formulations. These products include, amongst others, leaf sprays, seed coatings and conditioners with humic acids. We evaluated these products in pot trials under greenhouse conditions and in multi-locational participatory field trials with farmer groups in three distinct agro-ecological zones in Kenya. The products were applied in conjunction with TSP fertilizer at half the recommended economic rate, as the P supplied through these products was insufficient to attain adequate crop yields. P response was assessed by including treatments without P addition, and TSP applied at half and full recommended rate. In the pot trial, none of the products significantly (P<0.05) increased the shoot dry matter yield of 6-weeks old maize. Seed coating, however, resulted in increased root yield and root-shoot ratio. In the field trials, responses to TSP application were observed in two agro-ecologies, with maize yield increases in the order of 1.4 – 2.6 t ha-1. However, none of the treatments with the different products significantly increased maize yields. Leaf spraying tended to result in yield penalties, particularly when rainfall was insufficient after application of the spray. Correlation analysis revealed that seed treatment has a small positive effect on yield when control yields are low, but not necessarily when response to P fertilizer was large, suggesting that the effect of the treatment way not be directly related to P nutrition. Possibly, seed treatment may have stimulated root development during early stages, which could entail benefits in drought-prone areas and will be further investigated. Our findings indicate that alternative methods of P application have limited benefits for maize production under smallholder farmers' conditions. (Texte intégral

Biostimulant Effects of Seed-Applied Sedaxane Fungicide: Morphological and Physiological Changes in Maize Seedlings

Most crops are routinely protected against seed-born and soil-borne fungal pathogens through seed-applied fungicides. The recently released succinate dehydrogenase inhibitor (SDHI), sedaxane®, is a broad-spectrum fungicide, used particularly to control Rhizoctonia spp., but also has documented growth-enhancement effects on wheat. This study investigates the potential biostimulant effects of sedaxane and related physiological changes in disease-free maize seedlings (3-leaf stage) at increasing application doses (25, 75 and 150 μg a.i. seed-1) under controlled sterilized conditions. We show sedaxane to have significant auxin-like and gibberellin-like effects, which effect marked morphological and physiological changes according to an approximate saturation dose-response model. Maximum benefits were attained at the intermediate dose, which significantly increased root length (+60%), area (+45%) and forks (+51%), and reduced root diameter as compared to untreated controls. Sedaxane enhanced leaf and root glutamine synthetase (GS) activity resulting in greater protein accumulation, particularly in the above-ground compartment, while glutamate synthase (GOGAT) activity remained almost unchanged. Sedaxane also improved leaf phenylalanine ammonia-lyase (PAL) activity, which may be responsible for the increase in shoot antioxidant activity (phenolic acids), mainly represented by p-coumaric and caffeic acids. We conclude that, in addition to its protective effect, sedaxane can facilitate root establishment and intensify nitrogen and phenylpropanoid metabolism in young maize plants, and may be beneficial in overcoming biotic and abiotic stresses in early growth stages

Low-P tolerance by maize (Zea mays L.) genotypes: Significance of root growth, and organic acids and acid phosphatase root exudation

We investigated some mechanisms, which allow maize genotypes to adapt to soils which are low in available P. Dry matter production, root/shoot-ratio, root length and root exudation of organic acids and acid phosphatase were investigated in four maize genotypes grown under P-deficient and P-sufficient conditions in sterile hydroponic culture. A low-P tolerant, an acid-tolerant and a low-P susceptible genotype of maize were compared with a Swiss commercial cultivar. The study found increased root development and increased exudation of acid phosphatase under P-deficient conditions in all maize genotypes, except for the Swiss cultivar. Effects on root formation and acid phosphatase were greater for the low-P tolerant than for the low-P susceptible, and the acid soil tolerant genotypes. Organic acid contents in root tissues were increased under P deficiency and related to increased PEPC activity. However, the increase in contents was associated with an increase in exudation for the low-P tolerant genotype only. The low-P susceptible genotype was characterized by high organic acid content in roots and low organic acid exudation. The organic acids content in the phloem exudates of shoots was related to root exudation under different P supply, to the difference between lines in organic acids root content, but not to the low-P tolerance or susceptibility of maize genotype

Cloning and characterisation of a maize carotenoid cleavage dioxygenase (ZmCCD1) and its involvement in the biosynthesis of apocarotenoids with various roles in mutualistic and parasitic interactions

Colonisation of maize roots by arbuscular mycorrhizal (AM) fungi leads to the accumulation of apocarotenoids (cyclohexenone and mycorradicin derivatives). Other root apocarotenoids (strigolactones) are involved in signalling during early steps of the AM symbiosis but also in stimulation of germination of parasitic plant seeds. Both apocarotenoid classes are predicted to originate from cleavage of a carotenoid substrate by a carotenoid cleavage dioxygenase (CCD), but the precursors and cleavage enzymes are unknown. A Zea mays CCD (ZmCCD1) was cloned by RT-PCR and characterised by expression in carotenoid accumulating E. coli strains and analysis of cleavage products using GC¿MS. ZmCCD1 efficiently cleaves carotenoids at the 9, 10 position and displays 78% amino acid identity to Arabidopsis thaliana CCD1 having similar properties. ZmCCD1 transcript levels were shown to be elevated upon root colonisation by AM fungi. Mycorrhization led to a decrease in seed germination of the parasitic plant Striga hermonthica as examined in a bioassay. ZmCCD1 is proposed to be involved in cyclohexenone and mycorradicin formation in mycorrhizal maize roots but not in strigolactone formatio

Root anatomical traits contribute to deeper rooting of maize under compacted field conditions

© The Author(s) 2020. To better understand the role of root anatomy in regulating plant adaptation to soil mechanical impedance, 12 maize lines were evaluated in two soils with and without compaction treatments under field conditions. Penetrometer resistance was 1–2 MPa greater in the surface 30 cm of the compacted plots at a water content of 17–20% (v/v). Root thickening in response to compaction varied among genotypes and was negatively associated with rooting depth at one field site under non-compacted plots. Thickening was not associated with rooting depth on compacted plots. Genotypic variation in root anatomy was related to rooting depth. Deeper-rooting plants were associated with reduced cortical cell file number in combination with greater mid cortical cell area for node 3 roots. For node 4, roots with increased aerenchyma were deeper roots. A greater influence of anatomy on rooting depth was observed for the thinner root classes. We found no evidence that root thickening is related to deeper rooting in compacted soil; however, anatomical traits are important, especially for thinner root classes

Autecology of the biocontrol strain Pseudomonas fluorescens CHA0 in the rhizosphere and inside roots at later stages of plant development

A spontaneous rifampicin-resistant mutant of the biocontrol agent Pseudomonas fluorescens CHA0 was released as soil inoculant in large outdoor lysimeters and its ability to colonise the roots of winter wheat, spring wheat (grown after Phacelia) and maize at the later stages of plant development was investigated by colony counts. The inoculant (i.e. CHA0-Rif) colonised the rhizosphere and the interior of the roots of both wheat varieties but CFUs at ripening were about 2 log (g root)−1 or lower. In contrast, the roots of maize were colonised poorly by the pseudomonad at flowering, but the latter was found at 3 or more log CFU (g root)−1 on and inside the roots in late ripening stage. Furthermore, CHA0-Rif was recovered at more than 5 log CFU (g root)−1 from the interior of several maize root samples. Whereas most cells of CHA0-Rif in soil were small and did not respond to Kogure's viability test, the pseudomonad was present as viable, unusually large (7 mm long) rods inside maize roots. In a microcosm experiment performed with similar sandy-loam soil, the CFUs of maize root-associated CHA0-Rif were higher where the shoots of the plant had been cut off, confirming that older and/or decaying maize roots represent a favourable niche for the inoculant. Overall, the results indicate that Pseudomonas inoculants have the potential to colonise the roots of certain crops (e.g. maize but not wheat for strain CHA0-Rif) at later stages of plant developmen

Biostimulant Effects of Seed-Applied Sedaxane Fungicide: Morphological and Physiological Changes in Maize Seedlings

Most crops are routinely protected against seed-born and soil-borne fungal pathogens through seed-applied fungicides. The recently released succinate dehydrogenase inhibitor (SDHI), sedaxane\uae, is a broad-spectrum fungicide, used particularly to control Rhizoctonia spp., but also has documented growth-enhancement effects on wheat. This study investigates the potential biostimulant effects of sedaxane and related physiological changes in disease-free maize seedlings (3-leaf stage) at increasing application doses (25, 75 and 150 \u3bcg a.i. seed-1) under controlled sterilized conditions. We show sedaxane to have significant auxin-like and gibberellin-like effects, which effect marked morphological and physiological changes according to an approximate saturation dose-response model. Maximum benefits were attained at the intermediate dose, which significantly increased root length (+60%), area (+45%) and forks (+51%), and reduced root diameter as compared to untreated controls. Sedaxane enhanced leaf and root glutamine synthetase (GS) activity resulting in greater protein accumulation, particularly in the above-ground compartment, while glutamate synthase (GOGAT) activity remained almost unchanged. Sedaxane also improved leaf phenylalanine ammonia-lyase (PAL) activity, which may be responsible for the increase in shoot antioxidant activity (phenolic acids), mainly represented by p-coumaric and caffeic acids. We conclude that, in addition to its protective effect, sedaxane can facilitate root establishment and intensify nitrogen and phenylpropanoid metabolism in young maize plants, and may be beneficial in overcoming biotic and abiotic stresses in early growth stages

A soil-free root observation system for the study of root-microorganism interactions in maize

Background and aims: The root surface of a plant usually exceeds the leaf area and is constantly exposed to a variety of soil-borne microorganisms. Root pathogens and pests, as well as belowground interactions with beneficial microbes, can significantly influence a plants' performance. Unfortunately, the analysis of these interactions is often limited because of the arduous task of accessing roots growing in soil. Here, we present a soil-free root observation system (SF-ROBS) designed to grow maize (Zea mays) plants and to study root interactions with either beneficial or pathogenic microbes. Methods: The SF-ROBS consists of pouches lined with wet filter paper supplying nutrient solution. Results: The aspect of maize grown in the SF-ROBS was similar to soil-grown maize; the plant growth was similar for the shoot but different for the roots (biomass and length increased in the SF-ROBS). SF-ROBS-grown roots were successfully inoculated with the hemi-biotrophic maize fungal pathogen Colletotrichum graminicola and the beneficial rhizobacteria Pseudomonas putida KT2440. Thus, the SF-ROBS is a system suitable to study two major belowground phenomena, namely root fungal defense reactions and interactions of roots with beneficial soil-borne bacteria. Conclusions: This system contributes to a better understanding of belowground plant microbe interactions in maize and most likely also in other crop

RACINE2: A software application for processing spatial distribution of root lenght density from intersections on trench profiles

A field method has been developed to quantify root length density (RLD) from root intersection density (RID) measured on a trench-profile, using modelling RID-RLD relationships. For 2D spatial distribution mapping of RID (at 5-cm scale for example), the large amount of data is processed and converted into RLD and root distances (ARD) through modeling. Calculations and RLD mapping can be performed quickly using a new freeware: RACINE2, tailored to this field method. The software also allows a simple modeling of potential root exploration ratio in the soil (PRER) taking ARD into account. The software contains published models calculating RLD from RID for several crops (maize, sorghum, sugarcane, rice), ARD from RLD and PRER from RD. Models may be changed or added into RACINE2. RLD, ARD and PRER are calculated for each spatial unit. They can be mapped. Data can be exported to a spreadsheet or a surface mapping software for further analysis. It is also possible to import data into RACINE2 from a spreadsheet. RACINE2 thus makes studies about root-soil interactions, root growth and root uptake easier. Some examples of field results calculated by RACINE2 are presented (RLD, ARD and RER profiles and maps). They point out differences of PRER when taking (or not taking) into account 2D spatial root distribution. Taking into account spatial variability of root system in relation with soil characteristics may be important for root water and nutrient uptake in field conditions. (Résumé d'auteur