Determining the footprint of breeding in the seed microbiome of a perennial cereal.

BACKGROUND: Seed endophytes have a significant impact on plant health and fitness. They can be inherited and passed on to the next plant generation. However, the impact of breeding on their composition in seeds is less understood. Here, we studied the indigenous seed microbiome of a recently domesticated perennial grain crop (Intermediate wheatgrass, Thinopyrum intermedium L.) that promises great potential for harnessing microorganisms to enhance crop performance by a multiphasic approach, including amplicon and strain libraries, as well as molecular and physiological assays. RESULTS: Intermediate wheatgrass seeds harvested from four field sites in Europe over three consecutive years were dominated by Proteobacteria (88%), followed by Firmicutes (10%). Pantoea was the most abundant genus and Pantoea agglomerans was identified as the only core taxon present in all samples. While bacterial diversity and species richness were similar across all accessions, the relative abundance varied especially in terms of low abundant and rare taxa. Seeds from four different breeding cycles (TLI C3, C5, C704, C801) showed significant differences in bacterial community composition and abundance. We found a decrease in the relative abundance of the functional genes nirK and nifH as well as a drop in bacterial diversity and richness. This was associated with a loss of amplicon sequence variants (ASVs) in Actinobacteria, Alphaproteobacteria, and Bacilli, which could be partially compensated in offspring seeds, which have been cultivated at a new site. Interestingly, only a subset assigned to potentially beneficial bacteria, e.g. Pantoea, Kosakonia, and Pseudomonas, was transmitted to the next plant generation or shared with offspring seeds. CONCLUSION: Overall, this study advances our understanding of the assembly and transmission of endophytic seed microorganisms in perennial intermediate wheatgrass and highlights the importance of considering the plant microbiome in future breeding programs.

Water use efficiency and shoot biomass production under water limitation is negatively correlated to the discrimination against 13C in the C3 grasses Dactylis glomerata, Festuca arundinacea and Phalaris arundinacea.

Climate change impacts rainfall patterns which may lead to drought stress in rain-fed agricultural systems. Crops with higher drought tolerance are required on marginal land with low precipitation or on soils with low water retention used for biomass production. It is essential to obtain plant breeding tools, which can identify genotypes with improved drought tolerance and water use efficiency (WUE). In C3 plant species, the variation in discrimination against 13C (Δ13C) during photosynthesis has been shown to be a potential indicator for WUE, where discrimination against 13C and WUE were negatively correlated. The aim of this study was to determine the variation in the discrimination against 13C between species and cultivars of three perennial C3 grasses (Dactylis glomerata (cocksfoot), Festuca arundinacea (tall fescue) and Phalaris arundinacea (reed canary grass)) and test the relationships between discrimination against 13C, season-long water use WUEB, shoot and root biomass production in plants grown under well-watered and water-limited conditions. The grasses were grown in the greenhouse and exposed to two irrigation regimes, which corresponded to 25% and 60% water holding capacity, respectively. We found negative relationships between discrimination against 13C and WUEB and between discrimination against 13C and shoot biomass production, under both the well-watered and water-limited growth conditions (p < 0.001). Discrimination against 13C decreased in response to water limitation (p < 0.001). We found interspecific differences in the discrimination against 13C, WUEB, and shoot biomass production, where the cocksfoot cultivars showed lowest and the reed canary grass cultivars highest values of discrimination against 13C. Cocksfoot cultivars also showed highest WUEB, shoot biomass production and potential tolerance to water limitation. We conclude that discrimination against 13C appears to be a useful indicator, when selecting C3 grass crops for biomass production under drought conditions.

Soil disturbance alters plant community composition and decreases mycorrhizal carbon allocation in a sandy grassland.

We have studied how disturbance by ploughing and rotavation affects the carbon (C) flow to arbuscular mycorrhizal (AM) fungi in a dry, semi-natural grassland. AM fungal biomass was estimated using the indicator neutral lipid fatty acid (NLFA) 16:1ω5, and saprotrophic fungal biomass using NLFA 18:2ω6,9. We labeled vegetation plots with (13)CO(2) and studied the C flow to the signature fatty acids as well as uptake and allocation in plants. We found that AM fungal biomass in roots and soil decreased with disturbance, while saprotrophic fungal biomass in soil was not influenced by disturbance. Rotavation decreased the (13)C enrichment in NLFA 16:1ω5 in soil, but (13)C enrichment in the AM fungal indicator NLFA 16:1ω5 in roots or soil was not influenced by any other disturbance. In roots, (13)C enrichment was consistently higher in NLFA 16:1ω5 than in crude root material. Grasses (mainly Festuca brevipila) decreased as a result of disturbance, while non-mycorrhizal annual forbs increased. This decreases the potential for mycorrhizal C sequestration and may have been the main reason for the reduced mycorrhizal C allocation found in disturbed plots. Disturbance decreased the soil ammonium content but did not change the pH, nitrate or phosphate availability. The overall effect of disturbance on C allocation was that more of the C in AM fungal mycelium was directed to the external phase. Furthermore, the functional identity of the plants seemed to play a minor role in the C cycle as no differences were seen between different groups, although annuals contained less AM fungi than the other groups.