Correlations Between Root Metabolomics and Bacterial Community Structures in the Phragmites australis Under Acid Mine Drainage-Polluted Wetland Ecosystem.

Despite root microecology playing critical role in plant growth and fidelity, relatively few studies have focused on the link between the microbial communities and root metabolome in the aquatic macrophytes under heavy metal (HM) pollution. Using high-throughput metagenomic sequencing, targeted metabolomics and community-level physiological profile analyses, we investigated the symbiotic associations between Phragmites australis with rhizospheric bacterial communities under differing acid mine drainage (AMD) pollution. Results indicated that AMD pollution and root localization significantly affected root metabolome profiles. Higher accumulation of adenosine monophosphate, inosine, methionine, carnitine and dimethylglycine were observed in the rhizosphere under AMD than non-AMD habitat. Overall, the bacterial diversity and richness, and functional (metabolic) diversity were lower under high-AMD pollution. While non-AMD site was enriched with members of phylum Firmicutes, Proteobacteria were the most abundant taxa in the rhizosphere and endosphere under AMD-polluted sites. Further, plant growth promoting rhizobacteria (Rhizobium, Delftia, Bradyrhizobium, and Mesorhizobium) and metal-tolerant bacteria (Bacillus, Arthrobacter, Massilia and Methylocystis) were most abundant in AMD-polluted than non-AMD habitat. Finally, pH, TDS (total dissolved solids), Cu, Cr, Fe, and Zn content were the key environmental factors that strongly contributed to the spatial perturbation of rhizospheric metabolites, proteobacterial and acidobacterial taxa. Overall, the study linked the differential endospheric and rhizospheric bacterial community and metabolite profiles in P. australis under AMD environment and provided insights into HM adaptability and phytoremediation potential.

Acetaldehyde suppresses growth, changes conidia morphology and reduces the production of adenosine 3',5'-cyclic monophosphate in a dose dependent manner in Alternaria alternata.

One-day-old cultures of the plant pathogenic fungus Alternaria alternata were exposed to 0%, 5% and 10% acetaldehyde mixed with distilled water. Fungal growth data showed that, overall, the 5% and the 10% acetaldehyde treatments significantly inhibited the growth of A. alternata, and that acetyldehyde also facilitated maturity and multicellularity of fungal conidia. The increase of the acetyldehyde dose also caused correlated decrease of adenosine 3',5'-cyclic monophosphate produced by A. alternata.

Chlorinated organic compounds produced by Fusarium graminearum.

Fusarium graminearum, a pathogen of wheat and maize, not only reduces grain yield and degrades quality but also produces mycotoxins in the infected grain. Focus has been on mycotoxins because of the human and animal health hazards associated with them. In addition to work done on mycotoxins, chemical profiling of F. graminearum to identify other compounds produced by this fungus remains critical. With chemical profiling of F. graminearum the entire chemistry of this fungus can be understood. The focus of this work was to identify chlorinated compounds produced by F. graminearum. Various chlorinated compounds were detected and their role in F. graminearum is yet to be understood.

Benzene derivatives produced by Fusarium graminearum - Short communication.

Using NMR spectroscopy benzene derivatives were detected in mycelia of Fusarium graminearum, a pathogen of wheat and maize. In previous studies F. graminearum was found to cause cancer to humans and benzene derivatives were detected in breath of cancer sufferers. Surprisingly, no study found benzene derivatives to be the cancerous agents in F. graminearum. In this study we detected benzene derivatives in F. graminearum and propose to study their role as cancer agents.

A data catalogue of alcohol dehydrogenases in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa.

Alcohol dehydrogenases (ADHs) catalyze the oxidation of alcohols and reduction of aldehydes and ketones. Primarily ADHs mitigate aldehydes and alcohol toxicity but they may also perform other functions. we listed all ADHs in the genome of strain BD163 of P. brasiliense submitted in www.ncbi.nlm.nih.gov. In total, 11 ADHs or alcohol dehydrogenase catalytic domain-containing proteins from the 4897858-length genome sequence of strain BD163 of P. brasiliense (GenBank JAKNTB000000000.1) were extracted, and when comparing with other strains, it was found that other P. brasiliense strains have similar or slightly different alcohol dehydrogenase capability. Still, other species had varying numbers of ADHs.

Relationship between different physiological processes of Tomato seedlings exposed to acid mine water Uncovered using correlation analysis.

This study was conducted to assess the correlation between growth response, phytoaccumulation factor of different tissues, and elemental composition in tomato seedlings exposed to acid mine water (AMW). In pairwise correlation determinations values of plant height, stem diameter, seed germination indices (radicle length, final germination percentage (FGP), emergency rate index (ERI), vigour index (VI), germination percentage (G%) and germination rate index (GRI)) and the elemental compositions (Cd, Cr, Cu, Ni and Zn) in the different plant tissues, root (root accumulation factor = RAF), stem (stem translocation factor = STF) and leaves (leaf translocation factor = LTF) were selected for the relationship determinations. Pearson correlation coefficients were calculated and revealed the relationships between the paired parameters. The study concluded that the strongly correlated physiological parameters were jointly co-ordinated in tomato seedlings exposed to AMW.

Sustainable Applications of Endophytic Bacteria and Their Physiological/Biochemical Roles on Medicinal and Herbal Plants: Review.

Bacterial endophytes reside within the tissues of living plant species without causing any harm or disease to their hosts. These endophytes can be isolated, identified, characterized, and used as biofertilizers. Moreover, bacterial endophytes increase the plants' resistance against diseases, pests, and parasites, and are a promising source of pharmaceutically important bioactives. For instance, the production of antibiotics, auxins, biosurfactants, cytokinin's, ethylene, enzymes, gibberellins, nitric oxide organic acids, osmolytes, and siderophores is accredited to the existence of various bacterial strains. Thus, this manuscript intends to review the sustainable applications of endophytic bacteria to promote the growth, development, and chemical integrity of medicinal and herbal plants, as well as their role in plant physiology. The study of the importance of bacterial endophytes in the suppression of diseases in medicinal and herbal plants is crucial and a promising area of future investigation.

Draft genome assemblies of 12 Enterobacter hormaechei strains isolated from the North West province of South Africa.

We present draft genome sequences of 12 Enterobacter hormaechei strains from feces isolated from cow rectums in the North West province, South Africa. The genome sizes ranged from 4.43 to 5.02Mb, with G + C contents of 55.5-56%, and contained 16-262 contigs. These data will contribute to our knowledge of the ecology and diversity of this species in South Africa.

Draft Genome Sequence of Pectobacterium brasiliense Isolated from Potato in South Africa.

This study reports a draft genome of a phytopathogenic bacterium, Pectobacterium brasiliense, isolated from potato in South Africa. The total reported length of the genome is 4,897,858 bp, contained in 172 contigs with 4,378 genes. The GC content of the genome is 51.6%.

Gibberellic acid improves growth and reduces heavy metal accumulation: A case study in tomato (Solanum lycopersicum L.) seedlings exposed to acid mine water.

This study investigated the effect of gibberellic acid (GA3) on the growth of tomato seedlings and heavy metal accumulation within seedlings tissue irrigated with acid mine water (AMW). Three experimental treatments were administered using a completely randomized design with five replicates. The experimental treatments included were gibberellic acid + acid mine water (GA3 + AMW), acid mine water (AMW), and tap water. Seedlings were irrigated directly in pots with 400 mL of 100% AMW at two-day intervals 21 days after planting. Drenching of the seedlings with GA3 was done every 24 h for eight consecutive days from 28 days after planting. Results on the physicochemical analysis showed high concentrations of heavy metals (HMs) in AMW compared to tap water and the experimental treatment significantly affected the measured plant growth parameters. Tomato plants irrigated with AMW alone were shorter (4.00 cm) than plants irrigated with tap water (14.00 cm), while plants treated with AMW and GA3 were much taller (16.50 cm) than the latter (control). Moreover, HM accumulation differed among the three treatments. Seedlings that received AMW with no GA3 accumulated more HMs (Cd, Cr, Cu, Ni, and Zn) in their roots, stems, and leaves while plants treated with GA3 had a decrease in the accumulation and distribution of HMs in the different plant tissues (roots, stems, and leaves) relative to AMW alone and the plants irrigated with tap water alone. The study revealed that GA3 boosted the growth of tomato seedlings irrigated with AMW and also altered HM accumulation with the tissues of the seedlings.

The Differential Effects of Tuta absoluta Infestations on the Physiological Processes and Growth of Tomato, Potato, and Eggplant.

Tuta absoluta (Meyrick, 1917) (Lepidoptera: Gelechiidae) is a destructive insect pest toward crops and belongs to the Solanaceae family. Since it was first recorded in South Africa in 2016, the pest has spread extensively and caused tremendous damage to field and tunnel-grown tomato crops. This study aimed to investigate how T. absoluta affects the growth and physiology of three Solanaceae plant species: tomato, potato, and eggplant. These three crops were infested with L1 instar larvae, and their growth and physiology were assessed during insect feeding. The damage to the infested tomato host plant was severe, with T. absoluta destroying 100% of the plants. The tomato plants were distorted 15 days after infestation, that is, before the fruit set. For potato, the defoliation was moderate, but the infested plants produced fewer tubers compared to the uninfested host plants. Eggplant had fewer visible signs of feeding, resulting in no significant difference between the infested and uninfested host plants in terms of growth and physiological functions. Infested tomato and potato plants had stagnant growth, fewer and damaged leaves, a reduced chlorophyll content, a reduced photosynthesis rate, a poor transpiration rate, poor water conductance, and poor intercellular carbon dioxide concentrations. This study closes the knowledge gap on the morphological (growth) and physiological responses of different Solanaceae species to T. absoluta infestation, and it also demonstrates the differential risk of T. absoluta infestations in the production of tomato, potato, and eggplant.

Fungal and metabolome diversity of the rhizosphere and endosphere of Phragmites australis in an AMD-polluted environment.

Symbiotic associations with rhizospheric microbial communities coupled with the production of metabolites are key adaptive mechanisms by metallophytes to overcome metal stress. However, little is known about pseudometallophyte Phragmites australis interactions with fungal community despite commonly being applied in wetland phytoremediation of acid mine drainage (AMD). In this study, fungal community diversity and metabolomes production by rhizosphere and root endosphere of P. australis growing under three different AMD pollution gradient were analyzed. Our results highlight the following: 1) Ascomycota and Basidiomycota were dominant phyla, but the diversity and richness of taxa were lower within AMD sites with Penicillium, Candida, Saccharomycetales, Vishniacozyma, Trichoderma, Didymellaceae, and Cladosporium being enriched in the root endosphere and rhizosphere in AMD sites than non-AMD site; 2) non-metric multidimensional scaling (NMDS) of 73 metabolomes revealed spatially defined metabolite exudation by distinct root parts (rhizosphere vs endosphere) rather than AMD sites, with significant variability occurring within the rhizosphere correlating to pH, TDS, Fe, Cr, Cu and Zn content changes; 3) canonical correspondence analysis (CCA) confirmed specific rhizospheric fungal taxonomic changes are driven by pH, TDS, heavy metals, and stress-related metabolomes produced. This is the first report that gives a snapshot on the complex endophytic and rhizospheric fungal community structure and metabolites perturbations that may be key in the adaptability and metal phytoremediation by P. australis under AMD environment.

Proteomic analysis of the phytogenic fungus Sclerotinia sclerotiorum.

Sclerotinia sclerotiorum is a necrotrophic phytopathogen that has been the subject of several scientific research efforts. Despite the numerous research efforts its proteome remains understudied. This study aimed to identify proteins produced by S. sclerotiorum, thereby increasing the current proteomic knowledge base. Total proteins were extracted from mycelia scraped from five-day old cultures of S. sclerotiorum. The extracted proteins were separated by sodium dodecyl polyacrylamide gel electrophoresis (SDS-PAGE) and were annotated using the AB Sciex TripleToF 6600 mass spectrometer. Exactly 1471 proteins were reproducibly present in all three replicates. All proteins detected were classified based on their molecular and biological functions. To the knowledge of the authors, this is the most comprehensive proteomic study on S. sclerotiorum (judging by the high number of proteins identified).

Breeding Wheat for Durable Leaf Rust Resistance in Southern Africa: Variability, Distribution, Current Control Strategies, Challenges and Future Prospects.

Leaf or brown rust of wheat caused by Puccinia triticina (Pt) is one of the most damaging diseases globally. Considerable progress has been made to control leaf rust through crop protection chemicals and host plant resistance breeding in southern Africa. However, frequent changes in the pathogen population still present a major challenge to achieve durable resistance. Disease surveillance and monitoring of the pathogen have revealed the occurrence of similar races across the region, justifying the need for concerted efforts by countries in southern Africa to develop and deploy more efficient and sustainable strategies to manage the disease. Understanding the genetic variability and composition of Pt is a pre-requisite for cultivar release with appropriate resistance gene combinations for sustainable disease management. This review highlights the variability and distribution of the Pt population, and the current control strategies, challenges and future prospects of breeding wheat varieties with durable leaf rust resistance in southern Africa. The importance of regular, collaborative and efficient surveillance of the pathogen and germplasm development across southern Africa is discussed, coupled with the potential of using modern breeding technologies to produce wheat cultivars with durable resistance.

Pathogenicity and Virulence Factors of Fusarium graminearum Including Factors Discovered Using Next Generation Sequencing Technologies and Proteomics.

Fusarium graminearum is a devasting mycotoxin-producing pathogen of grain crops. F. graminearum has been extensively studied to understand its pathogenicity and virulence factors. These studies gained momentum with the advent of next-generation sequencing (NGS) technologies and proteomics. NGS and proteomics have enabled the discovery of a multitude of pathogenicity and virulence factors of F. graminearum. This current review aimed to trace progress made in discovering F. graminearum pathogenicity and virulence factors in general, as well as pathogenicity and virulence factors discovered using NGS, and to some extent, using proteomics. We present more than 100 discovered pathogenicity or virulence factors and conclude that although a multitude of pathogenicity and virulence factors have already been discovered, more work needs to be done to take advantage of NGS and its companion applications of proteomics.

Gene expression responses of tomato inoculated with Pectobacterium carotovorum subsp. carotovorum.

Defense responses of tomato (Solanum lycopersicum L.) against attack by Pectobacterium carotovorum subsp. carotovorum (Pcc), the causal agent of soft rot diseases, were studied. The expression of some tomato defense genes were evaluated by real-time PCR quantification analysis, 24 and 72 hr after actively growing tomato plants were inoculated with Pcc. These included: MYB transcriptor factor, ethylene response element-binding protein, suppressor of the G2 allele of Skp1, cytochrome P450, small Sar1 GTPase, hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase, pathogenesis-related protein 1a, endo-1,3-beta-glucanase, chitinase, proteinase inhibitor, defensin, CC-NBS-LRR resistance protein, and phenylalanine ammonia lyase. The results showed dynamic transcriptomic changes, with transcripts exhibiting different expression kinetics at 24 and 72 hr to confer resistance to tomato against Pcc infection.

Gene expression and evidence of coregulation of the production of some metabolites of chilli pepper inoculated with Pectobacterium carotovorum ssp. carotovorum.

Chilli pepper (Capsicum annuum L.) is susceptible to Pectobacterium carotovorum subsp. carotovorum (Pcc), the causal agent of soft rot disease in crops. Understanding the molecular principles of systemic acquired resistance, which is poorly understood in chilli pepper, represents an important step towards understanding inducible defence responses and can assist in designing appropriate intervention strategies for crop disease management. Accordingly, we investigated (via real-time PCR and metabolomics profiling) the molecular response of chilli pepper to Pcc by characterisation of the crucial metabolic regulators involved in the establishment of defence response. We profiled 13 key inducible defence response genes, which included MYB transcriptor factor, ethylene response element-binding protein, suppressor of the G2 allele of Skp1, cytochrome P450, small Sar1 (GTPase), hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase, pathogenesis-related protein 1a, endo-1,3-ß-glucanase, chitinase, proteinase inhibitor, defensin, coiled-coil-nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) resistance and phenylalanine ammonia lyase. In addition, we determined metabolomic shifts induced by Pcc in pepper. The PCR results revealed a significant induction of the selected plant defence-related genes in response to Pcc inoculation; the metabolomic profiling showed that of 99 primary metabolites profiled the quantities of acetylcarnitine, adenosine, adenosine 3',5' cyclic monophosphate, guanosine 3',5' cyclic monophosphate and inosine decreased in pepper leaves inoculated with Pcc.

The Mode of Action of Bacillus Species against Fusarium graminearum, Tools for Investigation, and Future Prospects.

Fusarium graminearum is a pervasive plant pathogenic fungal species. Biological control agents employ various strategies to weaken their targets, as shown by Bacillus species, which adopt various mechanisms, including the production of bioactive compounds, to inhibit the growth of F. graminearum. Various efforts to uncover the antagonistic mechanisms of Bacillus against F. graminearum have been undertaken and have yielded a plethora of data available in the current literature. This perspective article attempts to provide a unified record of these interesting findings. The authors provide background knowledge on the use of Bacillus as a biocontrol agent as well as details on techniques and tools for studying the antagonistic mechanism of Bacillus against F. graminearum. Emphasizing its potential as a future biological control agent with extensive use, the authors encourage future studies on Bacillus as a useful antagonist of F. graminearum and other plant pathogens. It is also recommended to take advantage of the newly invented analytical platforms for studying biochemical processes to understand the mechanism of action of Bacillus against plant pathogens in general.

Diversity, Co-occurrence and Implications of Fungal Communities in Wastewater Treatment Plants.

Three wastewater treatment plants (WWTPs) located in Gauteng province in South Africa were investigated to determine the diversity, co-occurrence and implications of their fungal communities using illumina sequencing platform and network analysis. Phylogenetic taxonomy revealed that members of the fungal communities were assigned to 6 phyla and 361 genera. Basidiomycota and Ascomycota were the most abundant phyla, dominated by the genera Naumovozyma, Pseudotomentella, Derxomyces, Ophiocordyceps, Pulchromyces and Paecilomyces. Phylogenetic analysis revealed the existence of fungal OTUs related to class lineages such as Agaricomycetes, Eurotiomycetes and Sordariomycetes indicating new fungal diversity in WWTPs. Dominant and rare fungal genera that can potentially be used in bioremediation such as Trichoderma, Acremonium, Talaromyces, Paecilomyces, cladophialophora and Saccharomyces were detected. Conversely, genera whose members are known to be pathogenic to human and plant such as Olpidium, Paecilomyces, Aspergillus, Rhodotorula, Penicillium, Candida, Synchytrium, Phyllosticta and Mucor were also detected in all WWTPs. Phylotype analysis confirmed that some fungal phylotypes were highly similar to the reported fungal pathogens of concern. Co-occurrence network analysis revealed that the fungal genera such as Minimedusa, Glomus, Circinella, Coltricia, Caloplaca, Phylosticta, Peziza, Candida, and Hydnobolites were the major networking hub in the WWTPs. The overall results in this study highlighted that WWTPs represent a potential source of beneficial fungi for bioremediation of pollutants in the ecosystem and the need to consider human and plant fungal pathogens during safety evaluation of treated wastewater for reuse.

Effect of Salicylic Acid on the Growth and Chemical Responses of Pectobacterium carotovorum subsp. carotovorum.

BACKGROUND AND OBJECTIVE: Salicylic acid is a signal molecule which activates plant defense against plant pathogens such as the soft rot enterobacterium Pectobacterium carotovorum subsp. carotovorum. The objectives of study were to determine bactericidal effects of salicylic acid on the growth of P. carotovorum subsp. carotovorum and secondly, assess chemical responses of P. carotovorum subsp. carotovorum to salicylic acid. MATERIALS AND METHODS: Pectobacterium carotovorum subsp. carotovorum was grown in lysogeny broth amended with salicylic acid at concentrations of 0, 100, 200, 400, 800 and 1200 mg L-1. The P. carotovorum subsp. carotovorum cultures were incubated at 25°C and sampled at two time points, 0 h (sampled before incubation) and 24 h. Bacterial counts were done at the onset of the incubation (0 h) and after the 24 h incubation. The set which was incubated for 24 h was split into two, one subset was centrifuged and the other was not. From the centrifuged subset the supernatant was recovered and was, together with all the other samples (0 and 24 h not centrifuged), analyzed with1H nuclear magnetic resonance and gas chromatography. RESULTS: Bacterial counts done before and after incubation showed that the lower concentrations of salicylic acid, 0, 100, 200 and 400 mg L-1, supported the growth of P. carotovorum subsp. carotovorum whereas the higher concentrations of 800 and 1200 mg L-1 inhibited the growth of the bacterium completely. Nuclear magnetic resonance results showed either slight or no differences in the metabolite profiles and gas chromatography showed different responses without a clearly defined pattern among the experimental treatments. However, methanethiol was detected by both nuclear magnetic resonance and gas chromatography in all the treatments and was probably formed as a result of the breakdown of lysogeny broth. CONCLUSION: From the results obtained it was concluded that salicylic acid promotes the growth of P. carotovorum subsp. carotovorum at lower concentrations of 0-400 mg L-1 but higher concentrations of salicylic acid of 800 and 1200 mg L-1 inhibit bacterial growth. All the tested salicylic acid concentrations (0-1200 mg L-1) cause only slight chemical shifts in the bacterial culture. Methanethiol was detected in all treatments and it is probably formed from the breakdown of lysogeny broth.