This study evaluated the effects of lactic acid fermentation on the functional, nutritional, and microbial characteristics of a complementary food blend formulated from maize, soybean, and orange-fleshed sweet potato (OFSP). The blend was fermented for 24 h using Lactobacillus plantarum, Lactobacillus fermentum, and Lactococcus lactis, alongside a spontaneously fermented control. Samples were analysed for pH, viscosity, microbial load, proximate composition, and selected fermentation metabolites (organic acids, sugars, and ethanol) using validated chromatographic techniques. Fermentation significantly reduced pH (from 6.2 to < 4.0) and viscosity (from 2700 cPs to <1500 cPs), creating conditions unfavorable for spoilage organisms and improving product consistency for infant feeding. Although nutritional composition showed no major differences among fermentation treatments, the accumulation of lactic, acetic, and propionic acids and the concurrent reduction of fermentable sugars confirmed active microbial metabolism. Both starter culture and spontaneous fermentation produced microbiologically safe products, with comparable improvements in functional and safety attributes. These findings demonstrate that lactic acid fermentation can enhance the safety and suitability of maize-soybean-OFSP complementary foods. The comparable performance of spontaneous fermentation highlights its potential as a low-cost, culturally adaptable approach for improving infant nutrition in resource-limited settings.

Agronomic practices, including fertilizer and cropping systems, are employed to enhance soil nutrient content and biological properties to boost plant growth and development. However, little is known about the impact of these practices on the diversity and functional structure of endophytic microbes, which contribute to plant growth and health. Various studies have investigated endophytic microbes using in vitro experiments, limiting our knowledge of taxonomic and functional classification of microbial communities. Thus, this study assessed the endophytic bacteria of vegetables cultivated under organic and conventional fertilizers, using high throughput sequencing of the 16S rRNA gene and PICRUt2 pipeline for functional analysis. Taxonomic assignment showed the samples were colonized largely by Pseudomonas, Pantoea and Bacillus, which were differentially abundant across the plant species and farm types. The functional profile showed that endophytic bacteria possess key enzymes, primarily contributing to vitamin and amino acid biosynthesis and carbohydrate degradation. Differentially abundant pathways, including ppGpp and mycolate biosynthesis, which confer antibiotic resistance were prevalent in bacteria colonizing organically cultivated vegetables while taxadiene and L-isoleucine biosynthesis, contributing to physiological functions such as the human immune system, were predominant in bacteria from conventionally managed farms. Results showed that plants are colonized by diverse endophytic bacteria with vast functional profiles, which are significantly (P < 0.05) driven by plant species and fertilizer types. Predicted functional profiles suggest that endophytic bacteria contribute to human health, especially when vegetables are consumed raw. Overall, the study revealed a high genetic diversity of endophytic bacteria and their potential to contribute to human health.

Mucormycosis is a group of diseases that is increasing in frequency. A common opportunistic human fungal pathogen in this group is Rhizopus microsporus, which is a globally distributed species present in soil-associated environments. A subset of isolates in this species host endobacteria that are hypothesized to influence fungal pathogenicity in both clinical and environmental settings. We have limited understanding of how clinically and environmentally derived isolates are related or how physiological attributes, including thermotolerance and endosymbiosis, are correlated with population structure. Traditional molecular barcodes used to assess intraspecific relationships, such as ribosomal DNA internal transcribed spacer (ITS-rDNA)-based markers, do not provide species-level resolution, necessitating analyses of whole genome data. In this study, we generated novel whole genome sequencing data for six R. microsporus isolates and combined these data with publicly available whole genome sequences of 46 R. microsporus isolates. We evaluated these sequences to understand the evolutionary relationships among clinical and environmental isolates using phylogenomic and single nucleotide polymorphism (SNP)-based population genomics methods. We further studied their relationships by quantifying and comparing potential physiological differences and endosymbiont presence in a subset of 16 isolates with live cultures. We found that clinical isolates that originate from environmental settings contain higher molecular diversity than subpopulations isolated from clinical settings. We observed that environmental isolates grow faster than clinical isolates at temperatures between 22 and 37 C and that 7 of 16 (44%) contain endobacteria in the genus Mycetohabitans (Burkholderiales). Lastly, we observed that genome assembly size in R. microsporus is variable and that long-read sequencing technologies greatly enhance our ability to investigate the underlying genomic features. Our study provides a valuable backdrop for probing the basic biology and applied biomedical importance of Rhizopus and related fungi that cause mucormycosis.

This study investigated the nutritional changes and bacterial community dynamics occurring during spontaneous and backslopping fermentation of a complementary food blend formulated from maize, soybean, and orange-fleshed sweet potato. The blend was fermented for over 48 h, and samples were analysed for pH, proximate composition, and microbial counts. Bacterial communities were analysed using culture-dependent and culture-independent techniques, employing 16S rRNA gene sequencing. Fermentation significantly improved the nutritional quality, with protein increasing from 15.00 % to 19.45 % and crude fibre decreasing from 4.25 % to 3.95 %. Similarly, carbohydrate and fat content also decreased. The final pH dropped significantly to 4.25, thus enhancing the microbial safety of the samples. A total of 212 amplicon sequence variants (ASVs) were detected. Firmicutes and Proteobacteria were identified as the dominant phyla, while lactic acid bacteria (LAB), such as Lactococcus and Enterococcus, were among the dominant genera observed, especially in the backslopped samples. The presence of other genera, including opportunistic pathogens such as Serratia, Enterobacter, and Paenibacillus, raises safety concerns, emphasizing the necessity of strictly adhering to hygiene practices and microbial quality measures during food processing. Alpha diversity was higher in backslopped samples compared to the spontaneous samples, suggesting that selective pressure favored the dominance of specific taxa such as Lactococcus. The Principal Coordinate Analysis (PCoA) revealed distinct clustering of the flour samples from the fermented samples, reflecting fermentation-driven microbial shifts. These findings highlight backslopping fermentation as a practical and scalable method to improve complementary food quality using locally available crops. The study provides essential baseline information for optimising low-cost fermentation processes in household or small-scale food production, supporting infant nutrition and food safety.

Rhizopus rot is considered one of the most common diseases influencing global production and yield of horticulture commodities. However, the factors contributing to this pattern of prevalence are uncertain. Here, we focused on R. microsporus, which is known to rely on its endosymbiotic bacterium, Mycetohabitans, to produce toxins that interfere with plant development and inhibit the growth of other fungi. We assessed the impact of the symbiotic R. microsporus harboring its endosymbiont as well as the fungus cured of it on: (1) the magnitude of spoilage in tomato fruits, as evaluated by Koch's postulate for pathogenicity, (2) the shifts in native communities of endophytic fungi inhabiting these fruits, as examined by ITS rRNA gene metabarcoding and (3) secondary metabolites generated by these communities, as analyzed using multi-analyte LC-MS/MS. The pathogenicity test showed that the symbiotic endobacterium-containing R. microsporus W2-50 was able to cause tomato fruit spoilage. This was accompanied by decreased relative abundance of Alternaria spp. and an increase in the relative abundance of Penicillium spp. that may have facilitated the observed spoilage. In conclusion, symbiotic W2-50 appeared to facilitate fruit spoilage, possibly through successful colonization or toxin production by its endosymbiont.

Durum and bread wheat are widely planted cereal crops that contribute immensely to global food security. To maintain and improve on crop yields, fertilizers are applied including nitrogenous fertilizers. However, there is limited research focusing on the effect of nitrogen application rate on observed and estimated durum and bread wheat yields in dryland environments. This study investigated the application of unmanned aerial vehicle (UAV) multispectral bands and vegetation indices using artificial neural networks (ANN) and multiple linear regression (MLR) models to estimate yields of durum and bread under different nitrogen fertilizer application rates. The ratio vegetation index (r = 0.29; P < 0.05) and normalized difference vegetation index (r = 0.26; P < 0.05) showed a low, but significant correlation with bread yield under 48 kg/ha nitrogen application. The ANN model outperformed MLR for yield prediction under all nitrogen rates and produced highest accuracy of R² = 0.7753, RMSE = 0.0825 t/ha under 24 kg/ha nitrogen application for durum. The key findings from this study highlight that UAV datasets and ANN models can be used to predict durum and bread yields in real-time which is beneficial for crop nutrient management. The methods from this study should be explored with more robust machine learning and larger datasets for optimal crop yield estimation.

The use of plant growth-promoting (PGP) bacteria is an emerging strategy for sustainable agriculture, offering alternatives to chemical fertilisers and pesticides. Here, we report the draft genome sequence and functional characterization of Lysinibacillus capsici NAVL5D isolated from the leaf of ready-to-eat lettuce plant grown in South Africa. The genome generated using the Illumina NovaSeq 6000 had a size of 4,631,824 bp, with 22 contigs and a G + C content of 37.3

Soil microbial communities are key drivers of plant health and productivity, influencing nutrient cycling and energy flow. This study investigated the impact of environmental variables on the bacterial communities within the rhizospheres of maize and soybean, two economically important crops, across contrasting South African climates with identical agricultural practices. Using 16S rRNA amplicon sequencing, we conducted a comparative analysis of rhizosphere bacterial communities in the semi-arid steppe of Free State and the subtropical region of Mpumalanga. In the semi-arid steppe, Actinobacteriota (36.5%), Pseudomonadota (24.4%), and Chloroflexi (12.8%) were dominant, while the subtropical region had higher proportions of Actinobacteriota (34.8%), Pseudomonadota (27.6%), and Acidobacteriota (12.6%). Our findings indicate that while a core bacterial community persists across regions, environmental factors significantly influence the diversity of non-core taxa. For instance, in Mpumalanga, correlation analysis suggested that the abundance of families like Burkholderiaceae and Symbiobacteraceae were influenced by moisture and minimum daily temperature while in Free State, families such as WS2 and Legionellaceae were influenced by maximum daily temperature, soil pH, and texture. These findings underscore the influence of climate and soil properties on the rhizosphere microbiome and highlight the importance of understanding these patterns for enhancing crop production in changing environmental conditions.

The high phosphorus (P) containing in swine wastewater (SW) presents as both an environmental hazard and a potential source of high-value phosphorus resource. This study presents a biomineralization-driven Fe-P crystals (FePs) metabolism to facilitate simultaneous pollutant removal, energy recovery, and membrane fouling mitigation in SW treatment. The approach enhanced methane production from 0.20 ± 0.05 to 0.29 ± 0.02 L CH4/g COD while achieving 96.8 ± 1.7 % TP removal. Our result is explained by the proposed concept that included the facilitation of partial Fe3+ reduction to Fe2+ by Clostridiaceae. In addition, the concurrent upregulation of key phosphorus metabolism genes (ppk, phoA, and phnP) that enhanced extracellular phosphorus hydrolysis, leading to the release of PO43- was also reported. The released phosphate then participates in biomineralization along with Fe2+, forming high-value vivianite (Fe3(PO4)2·8H2O) during organic degradation. After PO43- is fixed, its free concentration decreases, resulting in the inhibition of PO43- uptake by microorganisms, thus having a positive impact on the expression of Ugp. Microorganisms turned to sn-glycerol 3-phosphate and other phosphorus compounds to meet their P needs. Concurrently, vivianite contributed to membrane fouling mitigation through hydrodynamic flushing and extracellular polymeric substances (EPS) degradation on the membrane surface. Archaea such as Peptostreptococcaceae and Anaerolineaceae were enriched on the membrane, which also promoted the degradation of membrane organic fouling. This innovative strategy advances the paradigm of wastewater treatment by transforming conventional pollutant removal processes into integrated resource recovery systems, offering both technical and economic advantages for sustainable SW management.

This study evaluated the diversity and functional structure of endophytic bacterial communities residing within four common leafy vegetables: Brassica oleracea, Lactuca sativa, Allium cepa, and Spinacia oleracea, cultivated under organic (OF) and conventional (CF) farming systems. Utilizing high-throughput 16S rRNA gene sequencing and the PICRUSt2 pipeline, the research assessed the influence of plant species, organ (leaf/root), and fertilizer type on these microbial communities. Findings revealed that plant species and organ type significantly shaped endophytic bacterial community composition and diversity. Onion communities were distinct, and roots exhibited higher diversity and richness compared to leaves. Fertilizer type significantly impacted overall bacterial diversity, with CF farms showing higher diversity than OF. Microbial network analysis identified keystone taxa, including network hubs like Serratia and Streptomyces, and module hubs like Solirubrobacter, Corynebacterium, and Mycobacterium. Functional predictions indicated diverse metabolic capabilities, with organ type significantly affecting pathway abundance (leaves enriched in carbohydrate degradation, roots in nutrient metabolism/degradation). OF farms showed higher predicted abundance of some potential virulence pathways, while CF farms had higher abundance of certain biotechnological pathways. Vegetable nutrient content significantly correlated with both bacterial community composition and predicted metabolic pathways. This study highlights the complex interplay between farming practices, plant factors, endophytic microbiomes, and their functional potential, underscoring implications for vegetable microbiological quality and potential human health.

Knowledge of the arbuscular mycorrhizal (AM) fungal diversity in semi-arid soils is crucial to understanding the ecological functions of AM fungi, exploiting their potential for plant and ecosystem sustainability, and informing effective conservation actions. However, in South Africa, the biodiversity of AM fungi in the soil and influencing factors are understudied. Thus, we assessed the AM fungal diversity and community composition and their association with edaphic factors in rhizospheric soils of eleven indigenous legume species occurring in two South African provinces with contrasting elevations, Gauteng and Mpumalanga. High-throughput sequence analysis of the 18S rRNA gene detected 322 and 335 AM fungal amplicon sequence variants in Gauteng and Mpumalanga, respectively; Glomus was the dominant genus, accounting for a mean relative abundance of approximately 72%-90 % across provinces. AM fungal richness and diversity varied significantly among the different legume species. There was no marked compositional difference in AM fungal communities among legumes and between provinces, but available phosphorus and soil texture significantly influenced the community composition. The data contribute to the knowledge of biodiversity and likely ecological drivers of the AM fungal community structure in semi-arid soils and suggest no host specificity and altitudinal-induced effects on rhizosphere AM fungal diversity in indigenous legumes of South Africa.

Strains of the Gram-negative, facultatively anaerobic, rod-shaped Serratia genus are plant endophytes. Here, we described three draft genome sequences of Serratia liquefaciens isolated in South Africa from the leaves of tomatoes and lettuce.

Beneficial microbes, including endophytic bacteria, are widely used in bioformulation to improve crop productivity. However, the microbes are rarely assessed for their virulence properties. Thus, this study evaluates bacterial endophytes from vegetables for their hemolytic, antibiotic, cytotoxic activity, and ability to colonise and promote spinach (Spinacia oleracea) growth. Colonisation was assessed by visualising mCherry plasmid-tagged endophytic bacteria within plant tissues using a confocal microscope. Results showed that endophytic Pseudomonas azotoformans, Enterobacter bugandensis, Bacillus cereus and Serratia marcescens were non-hemolytic, sensitive to antibiotics, with high antibacterial and very slow cytotoxic activity, suggesting their nonvirulence and biocontrol potential. These bacteria had the highest and fastest rate of promoting seed germination and colonised the spinach leaves in a greenhouse experiment, as revealed by the visualised red fluorescence of the mCherry-plasmid transformed endophytes. Spinach inoculated with E. bugandensis and S. marcescens had higher total chlorophyll, but lower growth parameters compared to P. azotoformans and B. cereus. The root length, fresh weight and dry weight were higher in plants inoculated with P. azotoformans compared to the control and other endophytes. While endophytes with virulence potential may present health implications when consumed by humans, the nonvirulent and plant growth-promoting endophytes have applications in microbial formulation. Overall, beneficial endophytes present valuable resources in inoculum production for sustainable crop production.

The draft genome of a previously documented potential probiotic Weissella cibaria strain GM93m3 from raw goat milk in Nigeria is reported. The total genome size was 2,447,229 with 46 contigs and G+C content of 44.86%.

Abstract Background Cow milk, which is sometimes consumed raw, hosts a plethora of microorganisms, some of which are beneficial, while others raise food safety concerns. In this study, the draft genome of an extended-spectrum β-lactamase-producing Klebsiella pneumoniae subsp. pneumoniae strain Cow102, isolated from raw cow milk used to produce traditional foods in Nigeria, is reported. Result The genome has a total length of 5,359,907 bp, with 70 contigs and a GC content of 57.35%. A total of 5,244 protein coding sequences were detected with 31% mapped to a subsystem, and genes coding for amino acids and derivatives being the most prevalent. Multilocus sequence typing revealed that the strain had new allelic profile assigned to the novel 6914 sequence type possessing capsular and lipopolysaccharide antigen K locus 122 with an unknown K type (KL122) and O locus O1/O2v2 with type O2afg, respectively. A total of 28 resistance-related genes, 98 virulence-related genes, two plasmids and five phages were identified in the genome. The resistance genes oqxA, oqxB and an IS3 belonging to cluster 204 were traced to bacteriophage Escher 500,465. Comparative analysis predicted one strain specific orthologous group comprising three genes. Conclusion This report of a novel sequence type (ST6914) in K. pneumoniae presents a new allelic profile, indicating ongoing evolution and diversification within the species. Its uniqueness suggests it may represent a locally evolved lineage, although further sampling would be necessary to confirm this hypothesis. The strain’s multidrug resistance, virulence gene repertoire, and isolation from animal milk render it a potentially significant public health concern, underscoring the importance of genomic surveillance in non-clinical settings to detect emerging strains. Further research is required to fully characterise the capsular K type of ST6914.

Many endophytic bacteria have plant growth promoting attributes that could improve agricultural yield as well as resistance to various types of stress and disease. Detection of such attributes usually involves in vitro screening and the subsequent testing of the isolates on the plants for specific or combined effects on germination, seedling growth and yield. Despite many studies in this field, there is a knowledge gap on the influence of endophytes on early growth of certain economically important plants such as medicinal plants. In the present study, we evaluated the in vitro capabilities of bacterial endophytes isolated from Lessertia frutescens (L.) Goldblatt & J.C.Manning (syn. Sutherlandia frutescens (L.) W.T.Aiton) for plant growth promotion and their effect on initial seedling growth. Using a culture-dependent approach, plant samples of Lessertia frutes cens were screened for bacterial endophytes. The isolated bacterial endophytes were subsequently evaluated for their plant growth-promoting attributes along with their ability to produce hydrolytic enzymes. Molecular identification of selected endophytic bacteria based on the 16S rRNA genes of strains that tested negative in the hemolysis test was conducted. The two most promising isolates were evaluated for their ability to promote Lessertia frutescens seedling growth in a two-month pot trial study. The obtained results revealed that many of the bacterial endophytes had potential to promote plant growth. Specifically, 86% of the endophytes possessed nitrogen-fixing, phosphate solubilizing, and IAA-producing abilities, while approximately 71 % were able to exhibit siderophore-producing capabilities. The endophytes exhibited significant production of essential hydrolytic enzymes, including amylase (86 %), gelatinase (86 %), protease (29 %), lipase (43 %), and D-nase (57 %). The two best isolates were identified as relatives of Bacillus spp. (Bacillus licheniformis BaDB06 and Bacillus velezensis strain SM-95). Their plant growth-promoting properties such as their ability to enhance plant height and their ability to be used as bio-agent were further confirmed in the pot trial study as they enhanced the growth of Lessertia frutescens seedlings compared to the control. This study provides insights into the functional roles of endophytic bacteria of Lessertia frutescens in seedling growth and their potential plant growth enhancement, highlighting their potential for sustainable agriculture and ecosystem management. (c) 2024 The Author(s). Published by Elsevier B.V. on behalf of SAAB. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Maize (Zea mays L.), a key staple crop in Sub-Saharan Africa, is particularly vulnerable to concurrent drought and heat stress, which threatens crop yield and food security. Plant growth-promoting rhizobacteria (PGPR) have shown potential as biofertilizers to enhance plant resilience under such abiotic stresses. This study aimed to (1) identify PGPR isolates tolerant to drought and heat, (2) assess their capacity to mitigate the effects of these stresses on early maize growth, and (3) analyze maize gene expression changes associated with PGPR-induced tolerance. Rhizobacteria were isolated and screened for drought and heat tolerance, alongside key plant growth-promoting (PGP) traits, including phosphorus solubilization, nitrogen fixation, and indole acetic acid production. In vitro and pot trials evaluated the effects of selected isolates on maize growth under stress, using indicators such as shoot length, root and shoot biomass (wet and dry), and leaf water content. Quantitative reverse transcription PCR (qRT-PCR) was employed to profile maize stress response genes. The identified PGPR isolates included Bacillus cereus (11MN1), Bacillus pseudomycoides (21MN1B), Lelliottia amnigena (33MP1), and Leclercia adecarboxylata (36MP8). Greenhouse trials demonstrated that L. amnigena 33MP1, L. adecarboxylata 36MP8, and a mixed culture of isolates (11MN1, 21MN1B, 33MP1, 36MP8) effectively alleviated the adverse effects of concurrent drought and heat stress in maize. Notably, qRT-PCR analysis indicated that PGPR-induced tolerance may involve the modulation of stress response genes CAT2 (catalase 2) and DHN2 (dehydrin 2), which play roles in oxidative stress management and cellular protection. The PGPR isolates identified in this study represent promising bioinoculants for enhancing maize resilience under climate-induced stresses, offering a sustainable approach to improve maize productivity, conserve water, and reduce irrigation needs in drought-prone regions.

AbstractAloe species are often used interchangeably for medicinal and cosmeceutical applications, presenting a challenge to the biological efficacy consistency of some herbal preparations. Sustainable production of high-quality commonly used medicinal plants remains a limitation for commercialisation. Thus, this study investigated the potential for plant substitution by examining bacterial endophytes capable of producing similar host plant secondary metabolites. The metabolite profiles and endophytic bacterial communities of endangered Aloe lettyae were compared with those of Aloe longibracteata using nuclear magnetic resonance spectroscopy and 16 S rRNA gene sequencing. Only 15 metabolites were significantly different between A. lettyae and A. longibracteata based on metabolite concentrations. However, both plants’ functionality and potential application remain comparable. Phytohormones, including indole-3-acetate and 5-hydroxyindole-3-acetate, were more concentrated in A. lettyae than A. longibracteata. Metabolites such as tyrosine, allantoin, and myo-inositol, with human health benefits, were annotated in both species. Aloe lettyae harboured a phylogenetically diverse bacteria community compared to A. longibracteata, with a higher richness of bacterial species, indicating a likelihood of diverse metabolic capabilities among the bacteria. Dominant endophytes, including Bacillus, Comamonas, and Pseudomonas, possess enzymes contributing to various metabolic pathways. The enzymes have the potential to impact the synthesis, or breakdown of plant metabolites, consequently influencing the overall metabolic composition of the host plant. Therefore, this study supports the interchangeability of A. lettyae and A. longibracteata due to their ability to produce similar metabolites, and although the Aloe species exhibit phylogenetically diverse endophytic communities, the feasibility of utilizing their endophytes as producers of secondary metabolites remains viable. Graphical abstract