Evolution of the Crop Rhizosphere: Impact of Domestication on Root Exudates in Tetraploid Wheat (Triticum turgidum L.)

Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.

Multilab EcoFAB study shows highly reproducible physiology and depletion of soil metabolites by a model grass

There is a dynamic reciprocity between plants and their environment: soil physiochemical properties influence plant morphology and metabolism, and root morphology and exudates shape the environment surrounding roots. Here, we investigate the reproducibility of plant trait changes in response to three growth environments. We utilized fabricated ecosystem (EcoFAB) devices to grow the model grass Brachypodium distachyon in three distinct media across four laboratories: phosphate-sufficient and -deficient mineral media allowed assessment of the effects of phosphate starvation, and a complex, sterile soil extract represented a more natural environment with yet uncharacterized effects on plant growth and metabolism. Tissue weight and phosphate content, total root length, and root tissue and exudate metabolic profiles were consistent across laboratories and distinct between experimental treatments. Plants grown in soil extract were morphologically and metabolically distinct, with root hairs four times longer than with other growth conditions. Further, plants depleted half of the metabolites investigated from the soil extract. To interact with their environment, plants not only adapt morphology and release complex metabolite mixtures, but also selectively deplete a range of soil-derived metabolites. The EcoFABs utilized here generated high interlaboratory reproducibility, demonstrating their value in standardized investigations of plant traits.

A New Method to Correct for Habitat Filtering in Microbial Correlation Networks

Amplicon sequencing of 16S, ITS, and 18S regions of microbial genomes is a commonly used first step toward understanding microbial communities of interest for human health, agriculture, and the environment. Correlation network analysis is an emerging tool for investigating the interactions within these microbial communities. However, when data from different habitats (e.g., sampling sites, host genotype, etc.) are combined into one analysis, habitat filtering (co-occurrence of microbes due to habitat sampled rather than biological interactions) can induce apparent correlations, resulting in a network dominated by habitat effects and masking correlations of biological interest. We developed an algorithm to correct for habitat filtering effects in microbial correlation network analysis in order to reveal the true underlying microbial correlations. This algorithm was tested on simulated data that was constructed to exhibit habitat filtering. Our algorithm significantly improved correlation detection accuracy for these data compared to Spearman and Pearson correlations. We then used our algorithm to analyze a two real data sets of 16S variable region amplicon sequences that were expected to exhibit habitat filtering. Our algorithm was found to effectively reduce habitat effects, enabling the construction of consensus correlation networks from data sets combining multiple related sample habitats.

Metabolomics Provides Valuable Insight for the Study of Durum Wheat: A Review

Metabolomics is increasingly being applied in various fields offering a highly informative tool for high-throughput diagnostics. However, in plant sciences, metabolomics is underused, even though plant studies are relatively easy and cheap when compared to those on humans and animals. Despite their importance for human nutrition, cereals, and especially wheat, remain understudied from a metabolomics point of view. The metabolomics of durum wheat has been essentially neglected, although its genetic structure allows the inference of common mechanisms that can be extended to other wheat and cereal species. This review covers the present achievements in durum wheat metabolomics highlighting the connections with the metabolomics of other cereal species (especially bread wheat). We discuss the metabolomics data from various studies and their relationships to other "-omics" sciences, in terms of wheat genetics, abiotic and biotic stresses, beneficial microbes, and the characterization and use of durum wheat as feed, food, and food ingredient.

Root traits and root biomass allocation impact how wheat genotypes respond to organic amendments and earthworms

Plant-soil biological interactions are increasingly recognized as a key feature of agroecosystems, promoting both crop and soil health. However, the effectiveness of plant-soil synergies is likely modulated by both root system characteristics and soil management impacts on soil biological communities. To successfully manage for plant-soil interactions, we need to better understand how crops respond to changes in soil management, especially in terms of belowground investment. Specifically, crop genotypes that exhibit reduced plasticity in root growth and investment may not be able to take full advantage of changes in soil biological activity associated with soil health promoting practices. We hypothesized that genotypes with greater belowground investment respond more, in terms of plant growth and crop nitrogen (N) uptake, to compost and earthworm additions, agronomic factors commonly associated with soil health. We evaluated four spring wheat (Triticum aestivum) genotypes with distinct breeding and environmental histories, and one progenitor of wheat (Aegilops tauschii) under low soil fertility conditions in the greenhouse for differences in belowground root biomass and architecture. We then determined how these belowground traits influenced genotype response to additions of compost and earthworms. Measurements included plant growth, biomass, grain yield, root characteristics, plant N uptake, and soil N. Overall, in unamended soils, genotypes differed in above and belowground phenotypic traits. In general, Ae. tauschii had three times greater root: shoot (R:S) ratio, root length, and root biomass relative to wheat genotypes. We found that genotypes with higher R:S ratios responded more positively to compost additions compared to those with lower R:S ratios, particularly in terms of plant aboveground biomass, N uptake and soil N-cycling, and also exhibited greater plasticity in root morphology. Consequently, while higher R:S genotypes had relatively poorer yields in unamended soils, they outperformed lower R:S genotypes in total seed weight under compost treatments. Our findings suggest that genotypes with greater belowground investment may be better able to take advantage of soil health promoting practices, such as the use of organic amendments. These results highlight the need to consider soil management practices (and associated biological communities) in parallel with root phenotypic plasticity when evaluating wheat lines for improvements in plant-soil synergies.