Aims: The rhizosphere microbiome substantially affects plant health, yet comparatively little is known regarding the foliar community dynamics. Here, we examine the relationship between the microbiota and their response to natural infection by pathogens.Methods: We established an experimental system using a set of sorghum recombinant inbred lines (RILS). These RILS included four models denoted as resistant, moderately resistant, susceptible and highly susceptible. A combination of 16S rRNA and ITS gene amplicon approaches was used to assess bacteria and fungi, respectively, in foliar samples.Results: We show that the foliar microbiome differs substantially in asymptomatic and symptomatic RILs subsequent to natural infection by pathogens. A significant association was found between plant health and microbial community structure. Our analyses revealed several distinct fungal and bacterial pathogens. These pathogens includedGibberellaandPantoeagenera, which were associated with the highly susceptible group. In addition to these pathogens, we also found signatures forAscochyta, a known plant pathogenic genus. Members of the bacterial genusMethylorubrumand the fungal genusHannaella,both known to exhibit plant growth-promoting (PGP) traits, were associated with the resistant and moderately resistant groups. These data also reveal numerous highly diverse fungal and bacterial taxa in RILs that did not show symptoms. We also found taxonomic differences between the microbiota hosted by the symptomatic and asymptomatic RILs.Conclusions: Together, these data suggest that pathogen infection may result in distinct microbiota. These results suggest that highly diverse microbiome may promote the plants ability to resist the effects of pathogens potentially contributing to plant health.

Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, the field of metagenomics has emerged as a powerful tool for studying the microbial communities associated with cereal crops and their impact on plant health and growth. This chapter aims to provide a comprehensive overview of cereal metagenomics and its role in enhancing food security through the exploration of beneficial and pathogenic microbial interactions. Furthermore, we will examine how the integration of metagenomics with other tools can effectively address the adverse effects on food security. For this purpose, we discuss the integration of metagenomic data and machine learning in providing novel insights into the dynamic interactions shaping plant-microbe relationships. We also shed light on the potential applications of leveraging microbial diversity and epigenetic modifications in improving crop resilience and yield sustainability. Ultimately, cereal metagenomics has revolutionized the field of food security by harnessing the potential of beneficial interactions between cereals and their microbiota, paving the way for sustainable agricultural practices.

The aim of this present study was to optimize the fermentation conditions (time and temperature) of amasi (a Southern African fermented dairy product) using response surface methodology (RSM), and to determine the physicochemical properties, as well as the microbial composition, using next generation sequencing. Fermentation time and temperature were optimized to produce different amasi samples and different parameters, including pH, total soluble solids (TSS), total titratable acids (TTA), and consistency. All the variables studied were found to show significant (p ≤ 0.05) changes with increasing fermentation time and temperature. Numerical optimization was used to obtain the optimal fermentation conditions for amasi; based on RSM, it was 32 °C for 140 h, while with k-means clustering, it was 25 °C for 120 h. Under both conditions for the optimal samples, the pH reduced from 6.64 to 3.99, TTA increased from 0.02 to 0.11 (% lactic acid), TSS decreased from 9.47 to 6.67 °Brix, and the consistency decreased from 23 to 15.23 cm/min. Most of the identified bacteria were linked to lactic acid bacteria, with the family Lactobacillaceae being the most predominant in amasi, while in raw milk, Prevotellaceae was the most abundant. The fermentation conditions (time and temperature) had a significant influence on the parameters investigated in this study. Results of this study could provide information for the commercialization of quality amasi.

Amidst the rapid degradation of the environment, protected areas act as a buffer for sensitive species against drivers of change. The Kruger National Park, in the Zambezian Lowveld Freshwater Ecoregion, encompasses two critical transboundary river basins, which are threatened by overexploitation, climate change and nonnative invasive species. We complete an assessment of the abundance, distribution, spread and potential impacts of the invasive redclaw crayfish on community assemblages throughout the five main rivers of the Kruger National Park and compare them to other invasive populations in Southern Africa. Redclaw crayfish have established populations in the Crocodile River and the Sabie‐Sand River and are spreading at a rate of 7–8 km/year downstream and 3 km/year upstream. Abundance is lower than the more established invasions, but based on other trajectories, we can expect a tenfold increase in the next 5 years. No impact of crayfish presence or abundance was detected on fish or macroinvertebrate community assemblages. This suggests that as crayfish abundance is still relatively low, there may be a window of opportunity for targeted management. Management options in the rivers of the Kruger National Park are fraught with practical issues due to dangerous megafauna, but further understanding of the role of environmental flows on the establishment capacity of redclaw crayfish may hold some potential. Preventing new incursions into the protected area from watersheds originating outside of the park will need strategic multiorganisational collaboration.