Preliminary evaluation of guava selections for guava wilt disease resistance in South Africa

Guava wilt disease (GWD), caused by Nalanthamala psidii, is a serious disease occurring in the guava-producing areas of the Mpumalanga and Limpopo provinces of South Africa. Two resistant guava rootstocks, TS-G1 and ‘TS-G2’, were developed by the ARC-ITSC in 1995. In 2009, a renewed outbreak of GWD was reported, which also affected the resistant ‘TS-G2’ cultivar, placing the guava industry under threat again. The aim of this study was to seek resistant guava selections by means of in vitro screening of guava seedlings and subsequently testing the most promising selections in inoculation studies with N. psidii. A culture filtrate of N. psidii was used to screen guava seedlings in vitro. Promising selections were multiplied in tissue culture, hardened-off and planted in bags before inoculation with the GWD fungus in a shadehouse trial. The number of plants surviving nine months after inoculation was recorded. Although none of the selections showed complete resistance, selection MS44 showed some tolerance against the G2 isolate of the pathogen obtained from diseased ‘TS-G2’ trees, whilst selection MS70 showed some tolerance against the G1 isolate obtained from diseased TS-G1 trees. These selections were also resistant to the original Fan Retief isolate of the pathogen.http://www.tandfonline.com/loi/tjps20hb201

Seed treatment with selected plant growth-promoting rhizobacteria increases maize yield in the field

Maize, Zea mays is the most important grain crop in South Africa and is a staple food in many African countries. The beneficial effects of plant growth-promoting rhizobacteria on crop growth and yield have been well documented, but obtaining reproducible results under field conditions is often difficult. In the current study, five selected rhizobacterial strains that showed plant growth-promoting activities in pilot studies were evaluated for potential enhancement of maize yield under field conditions. The five strains together with a commercial standard were assessed as seed treatments of maize over three seasons in four different soil types. The strains were identified on the basis of 16S rRNA sequencing as Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), Bacillus safensis (S7) Bacillus pumilus (A26) and Brevundimonas vesicularis (A40). The best yield increases in maize were obtained during the 2011/2012 and 2012/2013 seasons in the Shortlands ecotope with the rhizobacterial strains T19, T29 and S7, resulting in yield increases ranging from 24% to 34%. Strain T19 rendered the most consistent yield increases during the three successive field trials amounting to 33% and 24% in Shortlands ecotope and 12% in Clovalley ecotope, respectively. During 2013/2014 a consortium of three strains, viz. T19, S7 and A26 gave a 32% yield increase in Clovalley ecotope. All the rhizobacterial strains solubilised phosphate in vitro except T19. Strain T29 showed the best nitrogen-fixing activity in vitro, proliferating on a nitrogen-free substrate and also producing ammonia. All the strains tested positive for indole acetic acid production. The current study demonstrates the ability of rhizobacterial strains T19, T29, S7 and A26 applied as seed treatments to significantly enhance maize yield in the field, making development and commercialisation of these strains a viable option.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1744-73482018-09-30hj2017Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant PathologyPlant Production and Soil Scienc

Screening rhizobacteria for biological control of Fusarium root and crown rot of sorghum in Ethiopia

Fusarium oxysporum Schlectend causes root and crown rot in several crops including sorghum that results in low grain yield in Ethiopia and other East African countries. Seventy-eight bacterial isolates were obtained and subsequently tested both in vitro and in the greenhouse. Of the 78 isolates tested, 23 displayed between 30 and 66.3% inhibition of in vitro mycelial growth of F. oxysporum and also showed significant root colonization ability on sorghum seedlings. These isolates were further tested for their biocontrol ability against F. oxysporum in the greenhouse. Four isolates viz. KBE5-7, KBE5-1, KBE2-5 and NAE5-5 resulted in 100% disease suppression and no symptoms of root and crown rot were observed compared to the control. The complete suppression of F. oxysporum by these isolates was also confirmed by root plating on Fusarium-selective medium. The most effective isolates were identified by means of the API system as members of the Genus Bacillus including B. cereus, B. subtilis, B. circulans, B. licheniformis and B. stearothermophilus. Two other isolates, which colonized the sorghum rhizosphere and resulted in more than 70% disease suppression, have been identified as Chromobacterium violaceum. The study demonstrated effective biological control by the rhizobacterial isolates tested, thereby indicating the possibility of application of rhizobacteria for control of soilborne diseases of sorghum in Ethiopia and other countries

Efficacy of fungicides, plant resistance activators and biological control agents against guava wilt disease caused by Nalanthamala psidii

Guava wilt disease (GWD) caused by the fungus Nalanthamala psidii remains a major constraint to guava production in South Africa and South East Asia. In the current study, chemical and biological products as well as plant resistance activators were evaluated for control of GWD in shadehouse and glasshouse trials. In all trials, one-year-old ‘TS-G2’ guava plants were used. Plants were inoculated with a macerated culture suspension of a mixture of three isolates of N. psidii after artificial wounding of the roots. Products were applied as a soil drench or as a full cover spray. In trial 1 plants were evaluated according to a disease severity scale. In trial 2 and 3 data were recorded as number of dead plants at the termination of the trial. None of the chemical treatments caused a significant suppression of the disease. The best control was achieved with the combination of rhizobacterial strains Bacillus cereus S7 and Paenibacillus alvei T29 resulting in 53.4% and 50% disease control in trials 2 and 3 respectively. This treatment also seems to have a plant growth enhancing effect apart from disease suppression. This is to our knowledge the first report of control of GWD by means of bacterial antagonists.http://www.tandfonline.com/loi/tjps202017-11-30hb2017Microbiology and Plant Patholog

Towards developing a metabolic-marker based predictive model for Phytophthora nicotianae tolerance in citrus rootstocks

Root rot of citrus trees caused by Phytophthora nicotianae is responsible for severe economic losses in citriculture. Use of resistant rootstocks is an effective method of managing this problem, however, breeding and selection of new citrus rootstocks is a time-consuming undertaking. The objective was to develop a method for the rapid assessment of rootstocks for P. nicotianae tolerance, using a metabolomics approach to identify metabolic markers for the phenotypic trait of tolerance. Sixteen citrus rootstocks were inoculated with P. nicotianae in the greenhouse for determination of relative tolerance/susceptibility. Healthy citrus roots from four tolerant and four susceptible rootstocks were used for metabolite analysis with the objective of identifying potential biomarkers. Organic solvent extractions of the roots were prepared and analysed by mass-spectrometry based liquid chromatography, which produced 367 ion features (retention time and m/z). Orthogonal partial least squares discriminant analysis of peak abundance using MarkerLynx software allowed for the identification of ion features that differentiate tolerant and susceptible rootstocks. Using descriptive and inferential statistics based on the ion features of uninoculated tolerant vs. susceptible rootstocks, applying logistic regression, 14 top markers were identified and two of them (22.03_259.0975 and 22.21_313.1445: retention time (rt) and mass to charge ratio (m/z) were accepted as potential metabolic markers. A model that can potentially predict tolerance in citrus rootstocks with >98% accuracy is presented.The authors acknowledge financial support to conduct this research from Citrus Research International, South Africa. Supplementary funding was provided by the University of Pretoria (South Africa). We also thank Dr. Wilhelm Botha for the morphological and molecular characterisation of the pathogen (Pathogen Accession Number: Ph 453 PPRI 23883 Agricultural Research Council, Plant Protection Research Institute, Pretoria, South Africa).https://link.springer.com/journal/421612019-07-01am2019BiochemistryPlant ScienceStatistic

Bacterial community dynamics and functional profiling of soils from conventional and organic cropping systems

Soil microbiomes play an integral role in agricultural production systems. Understanding of the complex microbial community structure and responses to conventional compared to organic cropping systems is crucial for sustainable production and ecosystems health. This study investigated soil microbial community structure responses based on a four year long field experiment. Bacterial communities characterizing conventional and organic cropping systems were evaluated using Illumina MiSeq high-throughput sequencing targeting the V4-V5 variable region of the 16S rRNA gene. Soil bacterial community structure showed a cropping system dependant distribution, with nitrogen cycling taxa (Bacillus, Niastella, Kribbella, and Beijerinckia) dominant in conventional cropping systems, while carbon cycling taxa (Dokdonella, Caulobacter, Mathylibium, Pedobacter, Cellulomonas and Chthoniobacter and Sorangium) were abundant in organic cropping systems. Functional prediction of the bacterial biomes showed conventional cropping systems to harbour a community adapted to carbon-limited environments, with organic cropping systems dominated by those involved in the degradation of complex organic compounds. These findings suggest the existence of niche specific communities and functional specialization between cropping systems with potential use in soil management through selective promotion of organisms beneficial to soil health.This work forms part of the research of the Centre of Excellence (“CoE”) in Food Security sponsored by the Department of Science and Innovation, Republic of South Africa (“DSI”) and administered by the National Research Foundation (“NRF”).http://www.elsevier.com/locate/apsoilhj2022Plant Production and Soil Scienc

Differential metabolic reprogramming in paenibacillus alvei-primed sorghum bicolor seedlings in response to fusarium pseudograminearum infection

Metabolic changes in sorghum seedlings in response to Paenibacillus alvei (NAS-6G6)-induced systemic resistance against Fusarium pseudograminearum crown rot were investigated by means of untargeted ultra-high performance liquid chromatography-high definition mass spectrometry (UHPLC-HDMS). Treatment of seedlings with the plant growth-promoting rhizobacterium P. alvei at a concentration of 1 × 108 colony forming units mL- 1 prior to inoculation with F. pseudograminearum lowered crown rot disease severity significantly at the highest inoculum dose of 1 × 106 spores mL-1. Intracellular metabolites were subsequently methanol-extracted from treated and untreated sorghum roots, stems and leaves at 1, 4 and 7 days post inoculation (d.p.i.) with F. pseudograminearum. The extracts were analysed on an UHPLC-HDMS platform, and the data chemometrically processed to determine metabolic profiles and signatures related to priming and induced resistance. Significant treatment-related differences in primary and secondary metabolism post inoculation with F. pseudograminearum were observed between P. alvei-primed versus naïve S. bicolor seedlings. The differential metabolic reprogramming in primed plants comprised of a quicker and/or enhanced upregulation of amino acid-, phytohormone-, phenylpropanoid-, flavonoid- and lipid metabolites in response to inoculation with F. pseudograminearum.Supplementary Materials: Figure S1. (A) Microscopic identification of F. pseudograminearum at 400 × magnification. (B) Conidial morphology of F. pseudograminearum taken from Aoki et al. [65]. Figure S2. UHPLC-HDMS BPI chromatograms of ESI-positive data indicating the metabolomic profiles of untreated (black), naïve infected (blue) and primed infected (green) stems obtained at 1 d.p.i. with F. pseudograminearum. Figure S3. UHPLC-HDMS BPI chromatograms of ESI-positive data indicating the metabolomic profiles of untreated (black), naïve infected (blue) and primed infected (green) leaves obtained at 1 d.p.i. with F. pseudograminearum. Figure S4. PCA score/scatter plot of stem samples computed from ESI-positive data. Figure S5. PCA score/scatter plot of leaf samples computed from ESI-positive data. Figure S6. PCA score/scatter plot of root samples computed from ESI-negative data. Figure S7. PCA score/scatter plot of stems samples computed from ESI-negative data. Figure S8. PCA score/scatter plot of leaves samples computed from ESI-negative data. Figure S9. OPLS-DA modelling and variable/feature selection ESI-positive data (stem samples). Figure S10. OPLS-DA modelling and variable/feature selection ESI-positive data (leaf samples). Table S1. Summary of the description and validation of all the generated OPLS-DA models separating naïve versus primed S. bicolor plants. Figure S11. Summary of pathway analysis with MetPA. Figure S12. Venn diagram comparing the number of metabolites shown in Table 2 that were significantly upregulated at 1 d.p.i. (blue), 4 d.p.i. (yellow) and 7 d.p.i. (green) with F. pseudograminearum in primed versus naïve S. bicolor seedlings.https://www.mdpi.com/journal/metaboliteshj2020Plant Production and Soil Scienc

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa

Understanding complex interactions among plant genotypes, environmental conditions and microbiome structure provides crucial information for sustainable farming practices towards disease control in agriculture. In this study, fungal diversity and composition in wheat rhizosphere and non-rhizosphere soils were investigated. Special emphasis was placed on pathogenic and beneficial genera. Wheat rhizosphere and non-rhizosphere soil from three different wheat growing regions were analyzed using Illumina high-throughput sequencing. The analysis showed a significant decline in the fungal diversity and richness from non-rhizosphere to rhizosphere soils. Ascomycota and Basidiomycota were the dominant fungal phyla detected in both rhizosphere and non-rhizosphere soils across the three test sites. Genera known to include wheat pathogens detected included Fusarium, Phoma and Colletotrichum genera while, beneficial groups included Trichoderma, Aureobasidium and Acaulospora. The presence of Fusarium was observed to be inversely proportional to that of Aureobasidium, a well-known antagonist of the Fusarium spp. This information could provide new opportunities to explore the potential of manipulating natural fungal antagonistic microorganisms for use in controlling soil-borne pathogenic fungi in wheat.Supplementary Table A1. Permutational multivariate analysis of variance (PERMANOVA) of main factors tested and their interactions for wheat rhizosphere and non-rhizosphere soil from the same field sites.Supplementary Table A2. Descriptive statistics on OUT richness (Chao 1) and species diversity (Shannon-Weaver).Supplementary Fig. A1. Overall relative abundance of fungal class on SST88 and Kariega rhizosphere (R), and non-rhizosphere (NR) soil at Site A, Kariega rhizosphere (R) and non-rhizosphere soil at site B and Eland rhizosphere and non-rhizosphere soil at Site C wheat growing area. SST88_A, SST88 rhizosphere soil at Site A; Kariega_A, Kariega rhizosphere soil at Site A; NR_A, Non- rhizosphere soil at Site A; Kariega_B, Kariega rhizosphere soil at Site B; NR_B, Non- rhizosphere soil at Site B; Eland_C, Eland rhizosphere soil at Site C; NR_C, Non- rhizosphere soil at Site C.Supplementary Fig. A2. Overall relative abundance of fungal order on cv. SST88 wheat rhizosphere (R) at site A.Supplementary Fig. A3. Overall relative abundance of fungal order on cv. Kariega wheat rhizosphere (R) at site A.The National Research Foundation (NRF) and the Centre of Excellence (“CoE”) in Food Security sponsored by the Department of Science, Technology and Innovation and administered by the NRF.http://www.elsevier.com/locate/apsoil2021-07-01hj2020Plant Production and Soil Scienc

Effects of soil drenching of water-soluble potassium silicate on commercial avocado (Persea americana Mill.) orchard trees infected with Phytophthora cinnamomi Rands on root density, canopy health, induction and concentration of phenolic compounds

Please read abstract in the article.The National Research Foundation of South Africa and by the South African Avocado Growers Association.http://www.tandfonline.com/loi/tjps202015-07-31hb201

Unravelling the metabolic reconfiguration of the post-challenge primed state in Sorghum bicolor responding to Colletotrichum sublineolum infection

Priming is a natural phenomenon that pre-conditions plants for enhanced defence against a wide range of pathogens. It represents a complementary strategy, or sustainable alternative that can provide protection against disease. However, a comprehensive functional and mechanistic understanding of the various layers of priming events is still limited. A non-targeted metabolomics approach was used to investigate metabolic changes in plant growth-promoting rhizobacteria (PGPR)-primed Sorghum bicolor seedlings infected with the anthracnose-causing fungal pathogen, Colletotrichum sublineolum, with a focus on the post-challenge primed state phase. At the 4-leaf growth stage, the plants were treated with a strain of Paenibacillus alvei at 108 cfu mL1. Following a 24 h PGPR application, the plants were inoculated with a C. sublineolum spore suspension (106 spores mL1), and the infection monitored over time: 1, 3, 5, 7 and 9 days post-inoculation. Non-infected plants served as negative controls. Intracellular metabolites from both inoculated and non-inoculated plants were extracted with 80% methanol-water. The extracts were chromatographically and spectrometrically analysed on an ultra-high performance liquid chromatography (UHPLC) system coupled to high-definition mass spectrometry. The acquired multidimensional data were processed to create data matrices for chemometric modelling. The computed models indicated time-related metabolic perturbations that reflect primed responses to the fungal infection. Evaluation of orthogonal projection to latent structure-discriminant analysis (OPLS-DA) loading shared and unique structures (SUS)-plots uncovered the di erential stronger defence responses against the fungal infection observed in primed plants. These involved enhanced levels of amino acids (tyrosine, tryptophan), phytohormones (jasmonic acid and salicylic acid conjugates, and zeatin), and defence-related components of the lipidome. Furthermore, other defence responses in both naïve and primed plants were characterised by a complex mobilisation of phenolic compounds and de novo biosynthesis of the flavones, apigenin and luteolin and the 3-deoxyanthocyanidin phytoalexins, apigeninidin and luteolinidin, as well as some related conjugates.Supplementary Material: Figure S1: Evaluation of disease symptoms in Colletotrichum sublineolum infected sorghum plants; Figure S2: Representative BPI MS chromatograms of ESI(+) data (3 d.p.i.); Figure S3: Unsupervised chemometric modelling of ESI(-) data; Figure S4: OPLS-DA modelling and variable/feature selection. Table S1: Annotated (MSI-level 2) metabolites reported in Table 1, with fragmentation information.The South African National Research Foundation (NRF)http://www.mdpi.com/journal/metabolitesam2020Plant Production and Soil Scienc