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Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda’s indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda’s indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda’s goat genetic resources.

Plant fatty acids (FAs) and lipids are essential in storing energy and act as structural components for cell membranes and signaling molecules for plant growth and stress responses. Acyl carrier proteins (ACPs) are small acidic proteins that covalently bind the fatty acyl intermediates during the elongation of FAs. The Arabidopsis thaliana ACP family has eight members. Through reverse genetic, molecular, and biochemical approaches, we have discovered that ACP1 localizes to the chloroplast and limits the magnitude of pattern-triggered immunity (PTI) against the bacterial pathogen Pseudomonas syringae pv. tomato. Mutant acp1 plants have reduced levels of linolenic acid (18:3), which is the primary precursor for biosynthesis of the phytohormone jasmonic acid (JA), and a corresponding decrease in the abundance of JA. Consistent with the known antagonistic relationship between JA and salicylic acid (SA), acp1 mutant plants also accumulate a higher level of SA and display corresponding shifts in JA- and SA-regulated transcriptional outputs. Moreover, methyl JA and linolenic acid treatments cause an apparently enhanced decrease of resistance against P. syringae pv. tomato in acp1 mutants than that in WT plants. The ability of ACP1 to prevent this hormone imbalance likely underlies its negative impact on PTI in plant defense. Thus, ACP1 links FA metabolism to stress hormone homeostasis to be negatively involved in PTI in Arabidopsis plant defense. [Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Botrytis cinerea, the causative agent of gray mold disease (GMD), invades plants to obtain nutrients and disseminates through airborne conidia in nature. Bacillus amyloliquefaciens strain GD4a, a beneficial bacterium isolated from switchgrass, shows great potential in managing GMD in plants. However, the precise mechanism by which GD4a confers benefits to plants remains elusive. In this study, an A. thaliana-B. cinerea-B. amyloliquefaciens multiple-scale interaction model was used to explore how beneficial bacteria play essential roles in plant growth promotion, plant pathogen suppression, and plant immunity boosting. Arabidopsis Col-0 wild-type plants served as the testing ground to assess GD4a’s efficacy. Additionally, bacterial enzyme activity and targeted metabolite tests were conducted to validate GD4a’s potential for enhancing plant growth and suppressing plant pathogens and diseases. GD4a was subjected to co-incubation with various bacterial, fungal, and oomycete pathogens to evaluate its antagonistic effectiveness in vitro. In vivo pathogen inoculation assays were also carried out to investigate GD4a’s role in regulating host plant immunity. Bacterial extracellular exudate (BEE) was extracted, purified, and subjected to untargeted metabolomics analysis. Benzocaine (BEN) from the untargeted metabolomics analysis was selected for further study of its function and related mechanisms in enhancing plant immunity through plant mutant analysis and qRT-PCR analysis. Finally, a comprehensive model was formulated to summarize the potential benefits of applying GD4a in agricultural systems. Our study demonstrates the efficacy of GD4a, isolated from switchgrass, in enhancing plant growth, suppressing plant pathogens and diseases, and bolstering host plant immunity. Importantly, GD4a produces a functional bacterial extracellular exudate (BEE) that significantly disrupts the pathogenicity of B. cinerea by inhibiting fungal conidium germination and hypha formation. Additionally, our study identifies benzocaine (BEN) as a novel small molecule that triggers basal defense, ISR, and SAR responses in Arabidopsis plants. Bacillus amyloliquefaciens strain GD4a can effectively promote plant growth, suppress plant disease, and boost plant immunity through functional BEE production and diverse gene expression.

Pseudomonas syringae and Botrytis cinerea cause destructive bacterial speck and grey mold diseases in many plant species, leading to substantial economic losses in agricultural production. Our study discovered that the application of Bacillus proteolyticus strain OSUB18 as a root-drench enhanced the resistance of Arabidopsis plants against P. syringae and B. cinerea through activating Induced Systemic Resistance (ISR). The underlying mechanisms by which OSUB18 activates ISR were studied. Our results revealed that the Arabidopsis plants with OSUB18 root-drench showed the enhanced callose deposition and ROS production when inoculated with Pseudomonas syringae and Botrytis cinerea pathogens, respectively. Also, the increased salicylic acid (SA) levels were detected in the OSUB18 root-drenched plants compared with the water root-drenched plants after the P. syringae infection. In contrast, the OSUB18 root-drenched plants produced significantly higher levels of jasmonyl isoleucine (JA-Ile) than the water root-drenched control after the B. cinerea infection. The qRT-PCR analyses indicated that the ISR-responsive gene MYC2 and the ROS-responsive gene RBOHD were significantly upregulated in OSUB18 root-drenched plants upon both pathogen infections compared with the controls. Also, twenty-four hours after the bacterial or fungal inoculation, the OSUB18 root-drenched plants showed the upregulated expression levels of SA-related genes (PR1, PR2, PR5, EDS5, and SID2) or JA-related genes (PDF1.2, LOX3, JAR1 and COI1), respectively, which were consistent with the related hormone levels upon these two different pathogen infections. Moreover, OSUB18 can trigger ISR in jar1 or sid2 mutants but not in myc2 or npr1 mutants, depending on the pathogen’s lifestyles. In addition, OSUB18 prompted the production of acetoin, which was reported as a novel rhizobacterial ISR elicitor. In summary, our studies discover that OSUB18 is a novel ISR inducer that primes plants’ resistance against bacterial and fungal pathogens by enhancing the callose deposition and ROS accumulation, increasing the production of specific phytohormones and other metabolites involved in plant defense, and elevating the expression levels of multiple defense genes.

The isolation of B. proteolyticus OSUB18 from switchgrass unveiled its significant potential in both the enhancement of plant growth and the suppression of plant diseases in our previous study. The elucidation of the related mechanisms governing this intricate plant–microbe interaction involved the utilization of the model plant Arabidopsis thaliana. In our comprehensive study on Arabidopsis, OSUB18 treatment was found to significantly alter root architecture and enhance plant growth under various abiotic stresses. An RNA-seq analysis revealed that OSUB18 modified gene expression, notably upregulating the genes involved in glucosinolate biosynthesis and plant defense, while downregulating those related to flavonoid biosynthesis and wound response. Importantly, OSUB18 also induces systemic resistance in Arabidopsis against a spectrum of bacterial and fungal pathogens and exhibits antagonistic effects on phytopathogenic bacteria, fungi, and oomycetes, highlighting its potential as a beneficial agent in plant stress management and pathogen resistance. Overall, our findings substantiate that OSUB18 exerts a stimulatory influence on plant growth and health, potentially attributed to the remodeling of root architecture, defense signaling, and the comprehensive mitigation of various biotic and abiotic stresses.

The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.

Plants have a diverse endophytic microbiome that is functionally important for their growth, development, and health. In this study, the diversity and specificity of culturable endophytic fungal communities were explored in one of the most important biofuel crops, switchgrass plants (Panicum virgatum L.), which have been cultivated on a reclaimed coal-mining site for more than 20 years. The endophytic fungi were isolated from the surface-sterilized shoot (leaf and stem), root, and seed tissues of switchgrass plants and then cultured for identification. A total of 1339 fungal isolates were found and 22 operational taxonomic units (OTUs) were sequence identified by internal transcribed spacer (ITS) primers and grouped into 7 orders and 4 classes. Although a diverse range of endophytic fungi associated with switchgrass were documented, the most abundant class, order, and species were Sordariomycetes, Hypocreales, and Fusarium spp. respectively. About 86% of the isolated endophytic fungi were able to enhance the heights of the shoots; 69% could increase the shoot fresh weights; and 62% could improve the shoot dry weights after being reintroduced back into the switchgrass plants, which illustrated their functional importance. Through the Shannon Diversity Index analysis, we observed a gradation of species diversity, with shoots and roots having the similar values and seeds having a lesser value. It was observed that the switchgrass plants showing better growth performance displayed higher endophytic fungal species diversity and abundance. It was also discovered that the rhizosphere soil organic matter content was positively correlated with the fungal species diversity. All these data demonstrate the functional association of these beneficial endophytic fungi with switchgrass and their great potential in improving the switchgrass growth and biomass to benefit the biofuel industry by reducing chemical inputs and burden to the environment.