Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum.

The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.IMPORTANCEThe development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

Assessment of Bacterial Inoculant Delivery Methods for Cereal Crops.

Despite growing evidence that plant growth-promoting bacteria can be used to improve crop vigor, a comparison of the different methods of delivery to determine which is optimal has not been published. An optimal inoculation method ensures that the inoculant colonizes the host plant so that its potential for plant growth-promotion is fully evaluated. The objective of this study was to compare the efficacy of three seed coating methods, seedling priming, and soil drench for delivering three bacterial inoculants to the sorghum rhizosphere and root endosphere. The methods were compared across multiple time points under axenic conditions and colonization efficiency was determined by quantitative polymerase chain reaction (qPCR). Two seed coating methods were also assessed in the field to test the reproducibility of the greenhouse results under non-sterile conditions. In the greenhouse seed coating methods were more successful in delivering the Gram-positive inoculant (Terrabacter sp.) while better colonization from the Gram-negative bacteria (Chitinophaga pinensis and Caulobacter rhizosphaerae) was observed with seedling priming and soil drench. This suggested that Gram-positive bacteria may be more suitable for the seed coating methods possibly because of their thick peptidoglycan cell wall. We also demonstrated that prolonged seed coating for 12 h could effectively enhance the colonization of C. pinensis, an endophytic bacterium, but not the rhizosphere colonizing C. rhizosphaerae. In the field only a small amount of inoculant was detected in the rhizosphere. This comparison demonstrates the importance of using the appropriate inoculation method for testing different types of bacteria for their plant growth-promotion potential.

Root exudates impact plant performance under abiotic stress.

Plant root exudates serve pivotal roles in supporting plant development and interactions with the physicochemical and biological factors in the rhizosphere. Under stress conditions, root exudation is involved in enhancing plant resource-use efficiency and facilitating the crosstalk between plant and soil microbes to ameliorate stress. Although there are a large number of root exudates that remain to be characterized, recent technological advancements have allowed for the function of many exudate compounds to be elucidated. In this review, we discuss current knowledge about the key root exudates that modulate plant resource-use efficiency under various abiotic stresses including drought, aluminum toxicity, phosphorus, nitrogen, and iron deficiency. The role that key root exudates play in shaping microbial communities in the rhizosphere under stress conditions is also an important consideration addressed in this review.

Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities.

The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.

The Sorghum bicolor Root Exudate Sorgoleone Shapes Bacterial Communities and Delays Network Formation.

Primary and secondary metabolites exuded from roots are key drivers of root-soil microbe interactions that contribute to the structure and function of microbial communities. Studies with model plants have begun to reveal the complex interactions between root exudates and soil microbes, but little is known about the influence of specialized exudates from crop plants. The aims of this work were to understand whether sorgoleone, a unique lipophilic secondary benzoquinone exuded only from the root hairs of sorghum, influences belowground microbial community structure in the field, to assess the effect of purified sorgoleone on the cultured bacteria from field soils, and to determine whether sorgoleone inhibits nitrification under field conditions. Studies were conducted comparing wild-type sorghum and lines with genetically reduced sorgoleone exudation. In the soil near roots and rhizosphere, sorgoleone influenced microbial community structure as measured by ß-diversity and network analysis. Under greenhouse conditions, the soil nitrogen content was an important factor in determining the impacts of sorgoleone. Sorgoleone delayed the formation of the bacterial and archaeal networks early in plant development and only inhibited nitrification at specific sampling times under field conditions. Sorgoleone was also shown to both inhibit and promote cultured bacterial isolate growth in laboratory tests. These findings provide new insights into the role of secondary metabolites in shaping the composition and function of the sorghum root-associated bacterial microbiomes. Understanding how root exudates modify soil microbiomes may potentially unlock an important tool for enhancing crop sustainability and yield in our changing environment.IMPORTANCE Plant roots exude a complex mixture of metabolites into the rhizosphere. Primary and secondary metabolites exuded from roots are key drivers of root-soil microbe interactions that contribute to the structure and function of microbial communities in agricultural and natural ecosystems. Previous work on plant root exudates and their influence on soil microbes has mainly been restricted to model plant species. Plant are a diverse group of organisms and produce a wide array of different secondary metabolites. Therefore, it is important to go beyond studies of model plants to fully understand the diverse repertoire of root exudates in crop plant species that feed human populations. Extending studies to a wider array of root exudates will provide a more comprehensive understanding of how the roots of important food crops interact with highly diverse soil microbial communities. This will provide information that could lead to tailoring root exudates for the development of more beneficial plant-soil microbe interactions that will benefit agroecosystem productivity.

High-resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities.

Much effort has been placed on developing microbial inoculants to replace or supplement fertilizers to improve crop productivity and environmental sustainability. However, many studies ignore the dynamics of plant-microbe interactions and the genotypic specificity of the host plant on the outcome of microbial inoculation. Thus, it is important to study temporal plant responses to inoculation in multiple genotypes within a single species. With the implementation of high-throughput phenotyping, the dynamics of biomass and nitrogen (N) accumulation of four sorghum genotypes with contrasting N-use efficiency were monitored upon the inoculation with synthetic microbial communities (SynComs) under high and low-N. Five SynComs comprising bacteria isolated from field grown sorghum were designed based on the overall phylar composition of bacteria and the enriched host compartment determined from a field-based culture independent study of the sorghum microbiome. We demonstrated that the growth response of sorghum to SynCom inoculation is genotype-specific and dependent on plant N status. The sorghum genotypes that were N-use inefficient were more susceptible to the colonization from a diverse set of inoculated bacteria as compared to the N-use efficient lines especially under low-N. By integrating high-throughput phenotyping with sequencing data, our findings highlight the roles of host genotype and plant nutritional status in determining colonization by bacterial synthetic communities.

The Effects of Soil Depth on the Structure of Microbial Communities in Agricultural Soils in Iowa, USA.

This study investigated the differences in microbial community abundance, composition and diversity throughout the depth profiles in soils collected from corn and soybean fields in lowa, USA using 16S rRNA amplicon sequencing. The results revealed decreased richness and diversity in microbial communities at increasing soil depth. Soil microbial community composition differed due to crop type only in the top 60 cm and due to location only in the top 90 cm. While the relative abundance of most phyla decreased in deep soils, the relative abundance of the phylum Proteobacteria increased and dominated agricultural soils below the depth of 90 cm. Although soil depth was the most important factor shaping microbial communities, edaphic factors including soil organic matter, soil bulk density and the length of time that deep soils were saturated with water were all significant factors explaining the variation in soil microbial community composition. Soil organic matter showed the highest correlation with the exponential decrease in bacterial abundance with depth. A greater understanding of how soil depth influences the diversity and composition of soil microbial communities is vital for guiding sampling approaches in agricultural soils where plant roots extend beyond the upper soil profile. In the long term a greater knowledge of the influence of depth on microbial communities should contribute to new strategies that enhance the sustainability of soil which is a precious resource for food security.IMPORTANCE Determining how microbial properties change across different soils and within the soil depth profile, will be potentially beneficial to understanding the long-term processes that are involved in the health of agricultural ecosystems. Most literature on soil microbes has been restricted to the easily accessible surface soils. However, deep soils are important in soil formation, carbon sequestration, and in providing nutrients and water for plants. In the most productive agricultural systems in the USA where soybean and corn are grown, crop plant roots extend into the deeper regions of soils (> 100 cm), but little is known about the taxonomic diversity or the factors that shape deep soil microbial communities. The findings reported here highlight the importance of soil depth in shaping microbial communities, provide new information about edaphic factors that influence the deep soil communities and reveal more detailed information on taxa that exist in deep agricultural soils.