MicroRNAs (miRNAs) are a class of small non-coding RNAs that have recently emerged as important regulators of gene expression, mainly through cleavage and/or translation inhibition of the target mRNAs during or after transcription. miRNAs play important roles by regulating a multitude of biological processes in plants which include maintenance of genome integrity, development, metabolism, and adaptive responses towards environmental stresses. The increasing population of the world and their food demands requires focused efforts for the improvement of crop plants to ensure sustainable food production. Manipulation of mRNA transcript abundance via miRNA control provides a unique strategy for modulating differential plant gene expression and miRNAs are thus emerging as the next generation targets for genetic engineering for improvement of the agronomic properties of crops. However, a deeper understanding of its potential and the mechanisms involved will facilitate the design of suitable strategies to obtain the desirable traits with minimum trade-offs in the modified crops. In this regard, this review highlights the diverse roles of conserved and newly identified miRNAs in various food and industrial crops and recent advances made in the uses of miRNAs to improve plants of agronomically importance so as to significantly enhance crop yields and increase tolerance to various environmental stress agents of biotic - or abiotic origin.

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.

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.

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.

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.

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.