Computer vision models enable mixed linear modeling to predict arbuscular mycorrhizal fungal colonization using fungal morphology.

The presence of Arbuscular Mycorrhizal Fungi (AMF) in vascular land plant roots is one of the most ancient of symbioses supporting nitrogen and phosphorus exchange for photosynthetically derived carbon. Here we provide a multi-scale modeling approach to predict AMF colonization of a worldwide crop from a Recombinant Inbred Line (RIL) population derived from Sorghum bicolor and S. propinquum. The high-throughput phenotyping methods of fungal structures here rely on a Mask Region-based Convolutional Neural Network (Mask R-CNN) in computer vision for pixel-wise fungal structure segmentations and mixed linear models to explore the relations of AMF colonization, root niche, and fungal structure allocation. Models proposed capture over 95% of the variation in AMF colonization as a function of root niche and relative abundance of fungal structures in each plant. Arbuscule allocation is a significant predictor of AMF colonization among sibling plants. Arbuscules and extraradical hyphae implicated in nutrient exchange predict highest AMF colonization in the top root section. Our work demonstrates that deep learning can be used by the community for the high-throughput phenotyping of AMF in plant roots. Mixed linear modeling provides a framework for testing hypotheses about AMF colonization phenotypes as a function of root niche and fungal structure allocations.

Production of bioethanol from sweet sorghum [Sorghum bicolor L] juice using yeast isolated from fermented sweet sorghum juice / Producción de bioetanol a partir de jugo de sorgo dulce [Sorghum bicolor L] utilizando levadura aislada de jugo de sorgo dulce fermentado

As a sugar-rich plant with no impact on global warming and food security, sweet sorghum can be exploited as an alternative source of renewable bioenergy. This study aimed to examine the potential of sweet sorghum juice for the generation of bioethanol using yeast isolated from the juice. The °Brix of sweet sorghum juice was measured using a digital refractometer. Additionally, 18 wild yeasts isolated from fermented sweet sorghum juice were subjected to various biochemical tests to describe them to identify potential yeast for ethanol production. The morphological and biochemical analyses of the yeasts revealed that all of the yeast isolates were most likely members of the genus Saccharomyces. The most ethanol-tolerant yeast isolate SJU14 was employed for sweet sorghum juice fermentation. A completely randomized factorial design was used with various fermentation parameters, primarily pH, temperature, and incubation period. Then ethanol content was determined using a potassium dichromate solution. According to the ANOVA, the highest ethanol content (18.765%) was produced at 30/26 °C, pH 4.5, and incubated for 96 h. Sweet sorghum juice was found to be an excellent source of potent yeasts, which have important industrial properties like the capacity to grow at high ethanol and glucose concentrations. Moreover, it can be utilized as a substitute substrate for the manufacturing of bioethanol production to lessen the environmental threat posed by fossil fuels. Further research is, therefore, recommended to develop strategically valuable applications of sweet sorghum for enhancing the food system and mitigating climate change.(AU)

Entomophthoralean and hypocrealean fungal pathogens of the sugarcane aphid, Melanaphis sacchari (Hemiptera: Aphididae), on sorghum in Georgia.

The sugarcane aphid, Melanaphis sacchari, is a widely distributed insect that attacks grasses in different genera including Miscanthus, Saccharum, and Sorghum. The invasive aphid superclone was first discovered in the U.S. attacking grain sorghum in Texas in 2013. Since then, it has been found in at least 25 states including Georgia. We conducted a survey of naturally occurring fungal pathogens of sugarcane aphids on five farms in Georgia, and identified a hypocrealean fungus, Akanthomyces dipterigenus, and two entomophthoralean fungi, Neoconidiobolus spp. From 2018 to 2020, fungal activity differed across farms but at one farm both major fungal species, A. dipterigenus and N. thromboides, were found each of the 3 years infecting sugarcane aphids, attacking adults, both alatae and apterae, and nymphs.

Effects of combined microplastic and cadmium pollution on sorghum growth, Cd accumulation, and rhizosphere microbial functions.

The interaction between microplastics (MPs) and cadmium (Cd) poses a threat to agricultural soil environments, and their effects on plant growth and rhizosphere microbial community functions are not yet clear. In this study, energy sorghum was used as a test plant to investigate the effects of two types of MPs, polystyrene (PS) and polyethylene (PE), at different particle sizes (13 µm, 550 µm) and concentrations (0.1%, 1% w/w), and Cd, as well as their interactions, on the growth of sorghum in a soil-cultivation pot experiment. The results showed that the combined effects of MP and Cd pollution on the dry weight and Cd accumulation rate in sorghum varied depending on the type, concentration, and particle size of the MPs, with an overall trend of increasing stress from combined pollution with increasing Cd content and accumulation. High-throughput sequencing analysis revealed that combined MP and Cd pollution increased bacterial diversity, and the most significant increase was observed in the abundance-based coverage estimator (ACE), Shannon, and Sobs indices in the 13 µm 1% PS+Cd treatment group. Metagenomic analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed that 19 groups of metabolic pathways, including microbial metabolism and methane metabolism, differed significantly under combined MP and Cd pollution. Hierarchical clustering results indicated that Cd treatment and combined MP and Cd treatment affected the abundances of sorghum rhizosphere soil nitrogen (N) and phosphorus (P) cycling genes and that the type of MP present was an important factor affecting N and P cycling genes. The results of this study provide a basis for exploring the toxic effects of combined MP and Cd pollution and for conducting soil environmental risk assessments.

The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection.

Sorghum bicolor is among the most important cereals globally and a staple crop for smallholder farmers in sub-Saharan Africa. Approximately 20% of sorghum yield is lost annually in Africa due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies are not singularly effective and integrated approaches are needed. Here, we demonstrate the functional potential of the soil microbiome to suppress Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation and with depletion of haustorium-inducing factors, compounds required for the initial stages of Striga infection. We further identify specific bacterial taxa that trigger the observed Striga-suppressive traits. Collectively, our study describes the importance of the soil microbiome in the early stages of root infection by Striga and pinpoints mechanisms of Striga suppression. These findings open avenues to broaden the effectiveness of integrated Striga management practices.

Analysis of the bacterial and fungal populations in South African sorghum beer (umqombothi) using full-length 16S rRNA amplicon sequencing.

There is a need to profile microorganisms which exist pre-and-post-production of umqombothi, to understand its microbial diversity and the interactions which subsequently influence the final product. Thus, this study sought to determine the relative microbial abundance in umqombothi and predict the functional pathways of bacterial and fungal microbiota present. Full-length bacterial 16S rRNA and internal transcribed spacer (ITS) gene sequencing using PacBio single-molecule, real-time (SMRT) technology was used to assess the microbial compositions. PICRUSt2 was adopted to infer microbial functional differences. A mixture of harmful and beneficial microorganisms was observed in all samples. The microbial diversity differed significantly between the mixed raw ingredients (MRI), customary beer brew (CB), and optimised beer brew (OPB). The highest bacterial species diversity was observed in the MRI, while the highest fungal species diversity was observed in the OPB. The dominant bacterial species in the MRI, CB, and OPB were Kosakonia cowanii, Apilactobacillus pseudoficulneus, and Vibrio alginolyticus, respectively, while the dominant fungal species was Apiotrichum laibachii. The predicted functional annotations revealed significant (p < 0.05) differences in the microbial pathways of the fermented and unfermented samples. The most abundant pathways in the MRI were the branched-chain amino acid biosynthesis super pathway and the pentose phosphate pathway. The CB sample was characterised by folate (vitamin B9) transformations III, and mixed acid fermentation. Biotin (vitamin B7) biosynthesis I and L-valine biosynthesis characterised the OPB sample. These findings can assist in identifying potential starter cultures for the commercial production of umqombothi. Specifically, A. pseudoficulneus can be used for controlled fermentation during the production of umqombothi. Likewise, the use of A. laibachii can allow for better control over the fermentation kinetics such as carbohydrate conversion and end-product characteristics, especially esters and aroma compounds.

Effects of Altering Three Steps of Monolignol Biosynthesis on Sorghum Responses to Stalk Pathogens and Water Deficit.

The drought-resilient crop sorghum (Sorghum bicolor [L.] Moench) is grown worldwide for multiple uses, including forage or potential lignocellulosic bioenergy feedstock. A major impediment to biomass yield and quality are the pathogens Fusarium thapsinum and Macrophomina phaseolina, which cause Fusarium stalk rot and charcoal rot, respectively. These fungi are more virulent with abiotic stresses such as drought. Monolignol biosynthesis plays a critical role in plant defense. The genes Brown midrib (Bmr)6, Bmr12, and Bmr2 encode the monolignol biosynthesis enzymes cinnamyl alcohol dehydrogenase, caffeic acid O-methyltransferase, and 4-coumarate:CoA ligase, respectively. Plant stalks from lines overexpressing these genes and containing bmr mutations were screened for pathogen responses with controlled adequate or deficit watering. Additionally, near-isogenic bmr12 and wild-type lines in five backgrounds were screened for response to F. thapsinum with adequate and deficit watering. All mutant and overexpression lines were no more susceptible than corresponding wild-type under both watering conditions. The bmr2 and bmr12 lines, near-isogenic to wild-type, had significantly shorter mean lesion lengths (were more resistant) than RTx430 wild-type when inoculated with F. thapsinum under water deficit. Additionally, bmr2 plants grown under water deficit had significantly smaller mean lesions when inoculated with M. phaseolina than under adequate-water conditions. When well-watered, bmr12 in cultivar Wheatland and one of two Bmr2 overexpression lines in RTx430 had shorter mean lesion lengths than corresponding wild-type lines. This research demonstrates that modifying monolignol biosynthesis for increased usability may not impair plant defenses but can even enhance resistance to stalk pathogens under drought conditions.

Mycological and Multiple Mycotoxin Surveillance of Sorghum and Pearl Millet Produced by Smallholder Farmers in Namibia.

Mycological (mycotoxigenic Fusarium and aflatoxigenic Aspergillus spp.) and multiple mycotoxins [aflatoxin B1 (AFB1), fumonisin B (FB), deoxynivalenol and zearalenone] surveillance was conducted on raw whole grain sorghum (Sorghum bicolor) and pearl millet (Pennisetum glaucum) produced on smallholder farms, and processed products sold at open markets in northern Namibia. Fungal contamination was determined with morphological methods as well as with quantitative Real-Time PCR (qPCR). The concentrations of multiple mycotoxins in samples were determined with liquid chromatography tandem mass spectrometry. The incidence of mycotoxigenic Fusarium spp., Aspergillus flavus and A. parasiticus, as well as the concentrations of AFB1 and FB were significantly (P < 0.001) higher in the malts as compared to the raw whole grains, with Aspergillus spp. and AFB1 exhibiting the highest contamination (P < 0.001). None of the analysed mycotoxins were detected in the raw whole grains. Aflatoxin B1 above the regulatory maximum level set by the European Commission was detected in sorghum (2 of 10 samples; 20%; 3-11 µg/kg) and pearl millet (6 of 11 samples; 55%; 4-14 µg/kg) malts. Low levels of FB1 (6 of 10 samples; 60%; 15-245 µg/kg) were detected in sorghum malts and no FB was detected in pearl millet malts. Contamination possibly occurred postharvest, during storage, and/or transportation and processing. By critically monitoring the complete production process, the sources of contamination and critical control points could be identified and managed. Mycotoxin awareness and sustainable education will contribute to reducing mycotoxin contamination. This could ultimately contribute to food safety and security in northern Namibia where communities are exposed to carcinogenic mycotoxins in their staple diet.

Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex.

Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.

Enhancement of Biomass Conservation and Bioethanol Production of Sweet Sorghum Silage by Constructing Synergistic Microbial Consortia.

The efficient storage of materials before bioethanol production could be key to improving pretreatment protocol and facilitating biodegradation, in turn improving the cost-effectiveness of biomass utilization. Biological inoculants were investigated for their effects on ensiling performance, biodegradability of silage materials, and final bioethanol yield from sweet sorghum. Two cellulolytic microbial consortia (CF and PY) were used to inoculate silages of sweet sorghum, with and without combined lactic acid bacteria (Xa), for up to 60 days of ensiling. We found that the consortia notably decreased pH and ammonia nitrogen content while increasing lactic acid/acetic acid ratios. The microbes also functioned in synergy with Xa, significantly reducing lignocellulose content and improving biomass preservation. First-order exponential decay models captured the kinetics of nonstructural carbohydrates and suggested high water-soluble carbohydrate (grams per kilogram dry matter [DM]) preservation potential in PY-Xa (33.48), followed by CF-Xa (30.51). Combined addition efficiently improved enzymatic hydrolysis and enhanced bioethanol yield, and sweet sorghum treated with PY-Xa had the highest ethanol yield (28.42 g L-1). Thus, combined bioaugmentation of synergistic microbes provides an effective method of improving biomass preservation and bioethanol production from sweet sorghum silages. IMPORTANCE Ensiling is an effective storage approach to ensure stable year-round supply for downstream biofuel production; it offers combined facilities of storage and pretreatment. There are challenges in ensiling sweet sorghum due to its coarse structure and high fiber content. This study provides a meaningful evaluation of the effects of adding microbial consortia, with and without lactic acid bacteria, on changes in key properties of sweet sorghum. This study highlighted the bioaugmented ensiling using cellulolytic synergistic microbes to outline a cost-effective strategy to store and pretreat sweet sorghum for bioethanol production.

Characterization of a Host-Specific Toxic Activity Produced by Bipolaris cookei, Causal Agent of Target Leaf Spot of Sorghum.

Target leaf spot (TLS) of sorghum, caused by the necrotrophic fungus Bipolaris cookei, can cause severe yield loss in many parts of the world. We grew B. cookei in liquid culture and observed that the resulting culture filtrate (CF) was differentially toxic when infiltrated into the leaves of a population of 288 diverse sorghum lines. In this population, we found a significant correlation between high CF sensitivity and susceptibility to TLS. This suggests that the toxin produced in culture may play a role in the pathogenicity of B. cookei in the field. We demonstrated that the toxic activity is light sensitive and, surprisingly, insensitive to pronase, suggesting that it is not proteinaceous. We identified the two sorghum genetic loci most associated with the response to CF in this population. Screening seedlings with B. cookei CF could be a useful approach for prescreening germplasm for TLS resistance.

Diurnal Variation of Epiphytic Microbiota: an Unignorable Factor Affecting the Anaerobic Fermentation Characteristics of Sorghum-Sudangrass Hybrid Silage.

Forage epiphytic microbiota exhibits pronounced changes in composition and function throughout the day. However, the effects of these changes on silage fermentation are rarely explored. Here, we transplanted the epiphytic microbiota of sorghum-sudangrass hybrid (SSG) harvested at 7:00 h (AM), 12:00 h (M), and 17:00 h (PM) to sterilized SSG to evaluate the effects of diurnal variation of epiphytic microbiota on fermentation characteristics. During fermentation, remarkable differences in bacterial community successions were observed between silages inoculated with AM and M microbiota. Compared to AM microbiota, M microbiota inoculation increased the proportions of Pantoea dispersa, Leuconostoc lactis, Enterobacter, and Klebsiella variicola, whereas it decreased the proportions of Weissella cibaria and Lactobacillus plantarum during fermentation. This led to the most rapid pH declines and organic acid production in AM silage and the slowest in M silage. Both M and PM microbiota affected the bacterial cooccurrence patterns, indicated by decreased complexity and stability in the community structures of M and PM silages compared to that of AM silage. The predicted functions indicated that some key carbohydrate metabolism pathways related to lactic acid synthesis were downregulated, while some competing pathways (ascorbate and aldarate metabolism and C5-branched dibasic acid metabolism) were upregulated in M silage compared to AM silage after 3 days of fermentation. Correlation analysis revealed positive correlations between competing pathways and enterobacterial species. The current study highlights the importance of diurnal variation of epiphytic microbiota in affecting the silage bacterial community, potentially providing an effective strategy to improve silage quality by optimizing harvest time. IMPORTANCE Ensiling is a way to preserve wet biomass for animal and bioenergy production worldwide. The fermentation quality of silage is largely dependent on the epiphytic microbiota of the material. Plant epiphytic microbiota exhibit diurnal changes in composition and function. However, the effects of these changes on silage fermentation are rarely explored. The results presented here demonstrated that diurnal variation of epiphytic microbiota could affect the fermentation characteristics and bacterial community during SSG fermentation. Marked bacterial community differences were observed between AM and M silages during the initial 3 days of fermentation. The dominance rate of Lactobacillus plantarum was highest in AM silage, whereas enterobacterial species were more abundant in M silage. The predicted function revealed downregulated lactic acid synthesis pathways and upregulated competing pathways in M silage compared to those in AM silage. This study provides clues for technological-parameter optimization of the fermentation process by the selection of harvest time.

Enhancing Mechanisms of the Plant Growth-Promoting Bacterial Strain Brevibacillus sp. SR-9 on Cadmium Enrichment in Sweet Sorghum by Metagenomic and Transcriptomic Analysis.

To explore the mechanism by which the plant growth-promoting bacterium Brevibacillus sp. SR-9 improves sweet sorghum tolerance and enriches soil cadmium (Cd) under pot conditions, the effect of strain SR-9 inoculation on the microbial community of sorghum rhizosphere soil was analyzed by metagenomics. Gene expression in sweet sorghum roots was analyzed using transcriptomics. The results showed that strain SR-9 promoted the growth of sweet sorghum and improved the absorption and enrichment of Cd in the plants. Compared with the uninoculated treatment, the aboveground part and root dry weight in strain SR-9 inoculated with sorghum increased by 21.09% and 17.37%, respectively, and the accumulation of Cd increased by 135% and 53.41%, respectively. High-throughput sequencing showed that strain SR-9 inoculation altered the rhizosphere bacterial community, significantly increasing the relative abundance of Actinobacteria and Firmicutes. Metagenomic analysis showed that after inoculation with strain SR-9, the abundance of genes involved in amino acid transport metabolism, energy generation and conversion, and carbohydrate transport metabolism increased. KEGG functional classification showed that inoculation with strain SR-9 increased the abundance of genes involved in soil microbial metabolic pathways in the rhizosphere soil of sweet sorghum and the activity of soil bacteria. Transcriptome analysis identified 198 upregulated differentially expressed genes in sweet sorghum inoculated with strain SR-9, including those involved in genetic information processing, biological system, metabolism, environmental information processing, cellular process, and human disease. Most of the annotated differentially expressed genes were enriched in the metabolic category and were related to pathways such as signal transduction, carbohydrate metabolism, amino acid metabolism, and biosynthesis of other secondary metabolites. This study showed that plant growth-promoting bacteria can alter the rhizosphere bacterial community composition, increasing the activity of soil bacteria and upregulating gene expression in sweet sorghum roots. The findings enhance our understanding of the microbiological and botanical mechanisms by which plant growth-promoting bacterial inoculation improves the remediation of heavy metals by sorghum.

Dynamic Changes in Fermentation Quality and Structure and Function of the Microbiome during Mixed Silage of Sesbania cannabina and Sweet Sorghum Grown on Saline-Alkaline Land.

Protein-rich Sesbania cannabina and sugar-rich sweet sorghum [Sorghum dochna (Forssk.) Snowden] are characterized by their higher tolerance to saline-alkaline stresses and simultaneous harvests. They could be utilized for coensiling because of their nutritional advantages, which are crucial to compensate protein-rich forage in saline-alkaline regions. The current study investigated the fermentation quality, microbial community succession, and predicted microbial functions of Sesbania cannabina and sweet sorghum in mixed silage during the fermentation process. Before ensiling, the mixtures were treated with compound lactic acid bacteria (LAB) inoculants followed by 3, 7, 14, 30, and 60 days of fermentation. The results revealed that the inoculated homofermentative species Lactobacillus plantarum and Lactobacillus farciminis dominated the early phase of fermentation, and these shifted to the heterofermentative species Lactobacillus buchneri and Lactobacillus hilgardii in the later phase of fermentation. As a result, the pH of the mixed silages decreased significantly, accompanied by the growth of acid-producing microorganisms, especially L. buchneri and L. hilgardii, which actively influenced the bacterial community structure and metabolic pathways. Moreover, the contents of lactic acid, acetic acid, 1,2-propanediol, and water-soluble carbohydrates increased, while the contents of ammonia-N and fiber were decreased, with increasing ratios of sweet sorghum in the mixed silage. Overall, coensiling Sesbania cannabina with >30% sweet sorghum is feasible to attain high-quality silage, and the relay action between homofermentative and heterofermentative LAB species could enhance fermentation quality and conserve the nutrients of the mixed silage. IMPORTANCE The coensiling of Sesbania cannabina and sweet sorghum is of great practical importance in order to alleviate the protein-rich forage deficiency in saline-alkaline regions. Furthermore, understanding the microbial community's dynamic changes, interactions, and metabolic pathways during ensiling will provide the theoretical basis to effectively regulate silage fermentation. Here, we established that coensiling Sesbania cannabina with >30% sweet sorghum was effective at ensuring better fermentation quality and preservation of nutrients. Moreover, the different fermentation types of LAB strains played a relay role during the fermentation process. The homofermentative species L. plantarum and L. farciminis dominated in the early phase of fermentation, while the heterofermentative species L. buchneri and L. hilgardii dominated in the later phase of fermentation. Their relay action in Sesbania cannabina-sweet sorghum mixed silage may help to improve fermentation quality and nutrient preservation.

Microbiome of rehydrated corn and sorghum grain silages treated with microbial inoculants in different fermentation periods.

Due to the co-evolved intricate relationships and mutual influence between changes in the microbiome and silage fermentation quality, we explored the effects of Lactobacillus plantarum and Propionibacterium acidipropionici (Inoc1) or Lactobacillus buchneri (Inoc2) inoculants on the diversity and bacterial and fungal community succession of rehydrated corn (CG) and sorghum (SG) grains and their silages using Illumina Miseq sequencing after 0, 3, 7, 21, 90, and 360 days of fermentation. The effects of inoculants on bacterial and fungal succession differed among the grains. Lactobacillus and Weissella species were the main bacteria involved in the fermentation of rehydrated corn and sorghum grain silage. Aspergillus spp. mold was predominant in rehydrated CG fermentation, while the yeast Wickerhamomyces anomalus was the major fungus in rehydrated SG silages. The Inoc1 was more efficient than CTRL and Inoc2 in promoting the sharp growth of Lactobacillus spp. and maintaining the stability of the bacterial community during long periods of storage in both grain silages. However, the bacterial and fungal communities of rehydrated corn and sorghum grain silages did not remain stable after 360 days of storage.

Transcriptome Analysis Reveals Contrasting Plant Responses of Sorghum bicolor upon Colonization by Two Formae Speciales of Sporisorium reilianum.

The biotrophic fungus Sporisorium reilianum exists in two host-adapted formae speciales that cause head smut in maize (S. reilianum f. sp. zeae; SRZ) and sorghum (S. reilianum f. sp. reilianum; SRS). In sorghum, the spread of SRZ is limited to the leaves. To understand the plant responses to each forma specialis, we determined the transcriptome of sorghum leaves inoculated either with SRS or SRZ. Fungal inoculation led to gene expression rather than suppression in sorghum. SRZ induced a much greater number of genes than SRS. Each forma specialis induced a distinct set of plant genes. The SRZ-induced genes were involved in plant defense mainly at the plasma membrane and were associated with the Molecular Function Gene Ontology terms chitin binding, abscisic acid binding, protein phosphatase inhibitor activity, terpene synthase activity, chitinase activity, transmembrane transporter activity and signaling receptor activity. Specifically, we found an upregulation of the genes involved in phospholipid degradation and sphingolipid biosynthesis, suggesting that the lipid content of the plant plasma membrane may contribute to preventing the systemic spread of SRZ. In contrast, the colonization of sorghum with SRS increased the expression of the genes involved in the detoxification of cellular oxidants and in the unfolded protein response at the endoplasmic reticulum, as well as of the genes modifying the cuticle wax and lipid composition through the generation of alkanes and phytosterols. These results identified plant compartments that may have a function in resistance against SRZ (plasma membrane) and susceptibility towards SRS (endoplasmic reticulum) that need more attention in the future.

Genome-wide association study of Senegalese sorghum seedlings responding to a Texas isolate of Colletotrichum sublineola.

Colletotrichum sublineola is a destructive fungal pathogen that causes anthracnose in sorghum. Senegalese sorghum germplasm is currently being considered as an option of sources for genetic resistance. In a recent study, Senegalese sorghum accessions were evaluated for response to a mixture of Texas isolates of C. sublineola at the 8-leaf stage in the greenhouse. As a comparison, 159 Senegalese sorghum accessions at the 1-leaf developmental stage were evaluated against a single Texas isolate of C. sublineola (FSP53) using an excised-leaf assay. A genome-wide association study (GWAS) was conducted based on the phenotypic data acquired to discover genetic variation associated with response to C. sublineola using 193,727 single nucleotide polymorphisms (SNPs) throughout the genome. Sorghum seedlings tended to be more resistant when compared with sorghum plants inoculated at the 8-leaf stage in the greenhouse in previous experiments. Based on the highest score evaluated in the 1-leaf developmental stage excised leaf assay for each accession, 16 accessions were labeled as susceptible. GWAS identified the SNP locus S01_72868925 that is associated with protein kinase domain // Leucine rich repeat N-terminal domain at a level of confidence that surpassed Bonferroni correction. Along with the SNP locus S01_72868925, other top SNP loci were also associated with genes that are known to play critical roles in plant defense or plant stress responses.

Metaprofiling of the bacterial community in sorghum silages inoculated with lactic acid bacteria.

AIMS: To characterize the fermentation process and bacterial diversity of sorghum silage inoculated with Lactiplantibacillus plantarum LpAv, Pediococcus pentosaceus PpM and Lacticaseibacillus paracasei LcAv. METHODS AND RESULTS: Chopped sorghum was ensiled using the selected strains. Physicochemical parameters (Ammonia Nitrogen/Total Nitrogen, Dry Matter, Crude Protein, Acid Detergent Fibre, Neutral Detergent Fibre, Acid Detergent Lignin, Ether Extract and Ashes), bacterial counts, cell cytometry and 16sRNA sequencing were performed to characterize the ensiling process and an animal trial (BALB/c mice) was conducted in order to preliminary explore the potential of sorghum silage to promote animal gut health. After 30 days of ensiling, the genus Lactobacillus comprised 68.4 ± 2.3% and 73.5 ± 1.8% of relative abundance, in control and inoculated silages respectively. Richness (Chao1 index) in inoculated samples, but not in control silages, diminished along ensiling, suggesting the domination of fermentation by the inoculated LAB. A trend in conferring enhanced protection against Salmonella infection was observed in the mouse model used to explore the potential to promote gut health of sorghum silage. CONCLUSIONS: The LAB strains used in this study were able to dominate sorghum fermentation. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report using metaprofiling of 16sRNA to characterize sorghum silage, showing a microbiological insight where resident and inoculated LAB strains overwhelmed the epiphytic microbiota, inhibiting potential pathogens of the genus Klebsiella.

Genetic mapping of sorghum resistance to an Illinois isolate of Colletotrichum sublineola.

Anthracnose leaf blight (ALB) is an economically important disease of sorghum [Sorghum bicolor (L.) Moench] caused by the fungal pathogen Colletotrichum sublineola Henn. ex Sacc. & Trotter. Although qualitative and quantitative resistance have been identified for ALB, the usefulness of resistance loci differs depending on the pathogen pathotype. Identifying resistance effective against unique pathogen pathotypes is critical to managing ALB, as the disease is managed primarily through the deployment of host resistance. We isolated C. sublineola from ALB-infected leaves collected in Illinois and found that the strain was a novel pathotype, as it produced a unique combination of virulence against a set of differential lines. Using this isolate, we inoculated 579 temperate-adapted sorghum conversion lines in 2019 and 2020. We then conducted a genome-wide association study (GWAS) and a metabolic pathway analysis using the Pathway Associated Study Tool (PAST). We identified 47 significant markers distributed across all chromosomes except chromosome 8. We identified 32 candidate genes based on physical proximity with significant markers, some of which have a known role in host defense. We identified 47 pathways associated with ALB resistance, indicating a role for secondary metabolism in defense to ALB. Our results are important to improve the understanding of the genetic basis of ALB resistance in sorghum and highlight the importance of developing durable resistance to ALB.

Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons.

Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.