Genome sequence of Colletotrichum karsti isolated from rose leaves exhibiting anthracnose symptoms in Potchefstroom, South Africa.

We present the genome sequence of Colletotrichum karsti isolated from rose leaves exhibiting anthracnose symptoms. The genome was assembled to 53.2 Mbp organized into 753 scaffolds having an N50 of 582,313 kbp and a GC content of 52.5%. The genome had an estimated 99.4% of the core Ascomycota genes.

The effects of irrigation on the survival of Clostridium sporogenes in the phyllosphere and soil environments of lettuce.

This study aimed to address the gap in knowledge regarding the fate of foodborne pathogens within agro-ecosystems. It specifically focused on the surrogate microorganism Clostridium sporogenes, which was introduced into lettuce-producing environments via surface and spray irrigation methods, respectively. The concentration of C. sporogenes in the rhizosphere, phyllosphere, and non-rhizosphere soil was quantified by quantitative polymerase chain reaction (qPCR) over a 42-day trial. The surface irrigation method exhibited a more noticeable contamination effect on the soil environments, compared to the phyllosphere. The results indicated a noticeable increase in C. sporogenes concentrations during the initial 22 days, with a 10.4-fold rise (0.39-4.05 log copy numbers/g soil) in the rhizosphere and 1.9-fold increase (2.97-5.59 log copy numbers/g soil) in the non-rhizosphere. However, concentrations in both soil environments subsequently decreased, falling below the initial inoculum concentration by the end of the trial. In contrast, the spray irrigation method resulted in most of the contamination being localised on the lettuce phyllosphere, with a high C. sporogenes concentration of 9.09 log copy numbers/g leaves on day 0. This concentration exponentially decreased to a minimal 0.019 log copy numbers/g leaves by day 32. Although concentrations in both soil environments decreased over time, trace concentrations of C. sporogenes were detectable at the end of the trial, posing a potential hazard to the microbiological safety of postharvest produce. These findings shed light on the dynamics of C. sporogenes in agro-ecosystems and underscore the importance of irrigation practices that ensure the safety of those who consume fresh produce. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-04069-5.

Draft genome sequences of Weissella cibaria GM93m3, a promising probiotic strain from raw goat milk.

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%.

Carbon flow, energy metabolic intensity and metagenomic characteristics of a Fe (III)-enhanced anerobic digestion system during treating swine wastewater.

Deep treatment and bioenergy recovery of swine wastewater (SW) are beneficial for constructing a low-carbon footprint and resource-recycling society. In this study, Fe (III) addition from 0 to 600 mg/L significantly increased the methane (CH4) content of the recovered biogas from 61.4 ± 2.0 to 89.3 ± 2.0 % during SW treatment in an anaerobic membrane digestion system. The specific methane yields (SMY) also increased significantly from 0.20 ± 0.05 to 0.29 ± 0.02 L/g COD. Fe (III) and its bio-transformed products which participated in establishing direct interspecific electron transfer (DIET), upregulated the abundance of e-pili and Nicotinamide adenine dinucleotide (NADH), enriched electroactive bacteria. The increase in cellular adenosine triphosphate (cATP) from 6583 to 14,518 ng/gVSS and electron transport system (ETS) from 1468 to 1968 mg/(g·h) promoted the intensity of energy flow and electron flow during anaerobic digestion of SW. Moreover, Fe (III) promoted the hydrolysis and acidification of organic matters, and strengthened the acetoacetic methanogenesis pathway. This study established an approach for harvesting high quality bioenergy from SW and revealed the effects and mechanisms from the view of carbon flow, energy metabolic intensity and metagenomics.

Nanoparticle applications in agriculture: overview and response of plant-associated microorganisms.

Globally, food security has become a critical concern due to the rise in human population and the current climate change crisis. Usage of conventional agrochemicals to maximize crop yields has resulted in the degradation of fertile soil, environmental pollution as well as human and agroecosystem health risks. Nanotechnology in agriculture is a fast-emerging and new area of research explored to improve crop productivity and nutrient-use efficiency using nano-sized agrochemicals at lower doses than conventional agrochemicals. Nanoparticles in agriculture are applied as nanofertilizers and/or nanopesticides. Positive results have been observed in terms of plant growth when using nano-based agricultural amendments. However, their continuous application may have adverse effects on plant-associated rhizospheric and endospheric microorganisms which often play a crucial role in plant growth, nutrient uptake, and disease prevention. While research shows that the application of nanoparticles has the potential to improve plant growth and yield, their effect on the diversity and function of plant-associated microorganisms remains under-explored. This review provides an overview of plant-associated microorganisms and their functions. Additionally, it highlights the response of plant-associated microorganisms to nanoparticle application and provides insight into areas of research required to promote sustainable and precision agricultural practices that incorporate nanofertilizers and nanopesticides.

Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production.

Introduction: Rhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types. Methods: Rhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline. Results: Overall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH4, PO4, pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms. Discussion: Module hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces, Bacillus and Nocardioides. The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices.

Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants.

Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.

Convergent reductive evolution and host adaptation in Mycoavidus bacterial endosymbionts of Mortierellaceae fungi.

Intimate associations between fungi and intracellular bacterial endosymbionts are becoming increasingly well understood. Phylogenetic analyses demonstrate that bacterial endosymbionts of Mucoromycota fungi are related either to free-living Burkholderia or Mollicutes species. The so-called Burkholderia-related endosymbionts or BRE comprise Mycoavidus, Mycetohabitans and Candidatus Glomeribacter gigasporarum. These endosymbionts are marked by genome contraction thought to be associated with intracellular selection. However, the conclusions drawn thus far are based on a very small subset of endosymbiont genomes, and the mechanisms leading to genome streamlining are not well understood. The purpose of this study was to better understand how intracellular existence shapes Mycoavidus and BRE functionally at the genome level. To this end we generated and analyzed 14 novel draft genomes for Mycoavidus living within the hyphae of Mortierellomycotina fungi. We found that our novel Mycoavidus genomes were significantly reduced compared to free-living Burkholderiales relatives. Using a genome-scale phylogenetic approach including the novel and available existing genomes of Mycoavidus, we show that the genus is an assemblage composed of two independently derived lineages including three well supported clades of Mycoavidus. Using a comparative genomic approach, we shed light on the functional implications of genome reduction, documenting shared and unique gene loss patterns between the three Mycoavidus clades. We found that many endosymbiont isolates demonstrate patterns of vertical transmission and host-specificity, but others are present in phylogenetically disparate hosts. We discuss how reductive evolution and host specificity reflect convergent adaptation to the intrahyphal selective landscape, and commonalities of eukaryotic endosymbiont genome evolution.

Corrigendum to "Development of a GIS-based knowledge hub for contaminants of emerging concern in South African water resources using open-source software: Lessons learnt" [Heliyon 9 (1) (January 2023) Article e13007].

[This corrects the article DOI: 10.1016/j.heliyon.2023.e13007.].

Bioaugmentation potential of inoculum derived from anaerobic digestion feedstock for enhanced methane production using water hyacinth.

The utilisation of water hyacinth for production of biogas is considered to be a solution to both its control and the global renewable energy challenge. In this instance, an investigation was conducted to evaluate the potential of water hyacinth inoculum to enhance methane production during anaerobic digestion (AD). Chopped whole water hyacinth (10% (w/v)) was digested to prepare an inoculum consisting mainly of water hyacinth indigenous microbes. The inoculum was incorporated in the AD of freshly chopped whole water hyacinth to set up different ratios of water hyacinth inoculum and water hyacinth mixture with appropriate controls. The results of batch tests with water hyacinth inoculum showed a maximal cumulative volume of 211.67 ml of methane after 29 days of AD as opposed to 88.6 ml of methane generated from the control treatment without inoculum. In addition to improving methane production, inclusion of water hyacinth inoculum reduced the electrical conductivity (EC) values of the resultant digestate, and, amplification of nifH and phoD genes in the digestate accentuates it as a potential soil ameliorant. This study provides an insight into the potential of water hyacinth inoculum to enhance methane production and contribute to the feasibility of the digestate as a soil fertility enhancer.

Bacteriological Quality and Biotoxin Profile of Ready-to-Eat Foods Vended in Lagos, Nigeria.

A comprehensive study of bacterial and biotoxin contaminants of ready-to-eat (RTE) foods in Nigeria is yet to be reported. Hence, this study applied 16S rRNA gene sequencing and a dilute-and-shoot LC-MS/MS method to profile bacteria and biotoxins, respectively, in 199 RTE food samples comprising eko (n = 30), bread (n = 30), shawarma (n = 35), aadun (n = 35), biscuits (n = 34), and kokoro (n = 35). A total of 631 bacterial isolates, clustered into seven operational taxonomic units, namely Acinetobacter, Bacillus, Klebsiella, Proteus and Kosakonia, Kurthia, and Yokenella, that are reported for the first time were recovered from the foods. One hundred and eleven metabolites comprising mycotoxins and other fungal metabolites, phytoestrogenic phenols, phytotoxins, and bacterial metabolites were detected in the foods. Aflatoxins, fumonisins, and ochratoxins contaminated only the artisanal foods (aadun, eko, and kokoro), while deoxynivalenol and zearalenone were found in industrially-processed foods (biscuit, bread, and shawarma), and citrinin was present in all foods except eko. Mean aflatoxin (39.0 µg/kg) in artisanal foods exceeded the 10 µg/kg regulatory limit adopted in Nigeria by threefold. Routine surveillance, especially at the informal markets; food hygiene and safety education to food processors and handlers; and sourcing of high-quality raw materials are proposed to enhance RTE food quality and safeguard consumer health.

Development of a GIS-based knowledge hub for contaminants of emerging concern in South African water resources using open-source software: Lessons learnt.

With population growth and dwindling freshwater sources, protecting such sources has come to the forefront of water resource management. Historically, society's response to a problem is based on funding availability, current threat, and public outcry. Achieving this is largely dependent on the knowledge of the factors that are resulting in compromised water sources. These factors are constantly changing as novel contaminants are introduced into surface water sources. As we are in the information age, the interest in contaminants of emerging concern (CEC) is gaining ground. Whilst research is being conducted to identify contaminants in South African water sources, the research outputs and available information is not collated and presented to the science community and stakeholders in readily available formats and platforms. Current research outcomes need to be made known to regulators in order to develop environmental laws. By using fourth industrial revolution technology, we were able to collate available data in literature and display these in a user-friendly online format to regulatory bodies as well as researchers. A standardized excel spreadsheet was developed and uploaded to a PostgreSQL, running a PostGIS extension and was then processed in the GeoServer to allow for visualization on an interactive map which can be continuously updated. The near real-time access to information will reduce the possibility of duplication of research efforts, enhance collaboration in the discipline, and act as a CEC early warning system.

Bacterial and yeast communities in raw milk from three dairy animal species in Nigeria.

The present study aimed to reveal the microbial (bacteria and yeast) composition of raw milk from dairy camel (n = 10), cow (n = 10) and goat (n = 10) in North-western Nigeria. High-throughput DNA metabarcoding was used to compare microbial compositions in raw milk among the three species. Although the three species had similar dominant bacterial (Firmicutes and Proteobacteria) and yeast (Ascomycota and Basidiomycota) phyla, their microbial compositions at the genus level were noticeably different. The top differentially abundant bacterial and yeast genera (percentage abundance) were Lactobacillus (36%), Streptococcus (34%), Enterococcus (12%), Kluyveromyces (28%), Saccharomyces (24%), and Candida (18%), respectively. Principal coordinate analysis based on unweighted UniFrac values revealed significant differences in the structure of bacterial communities and no differences in yeast communities in milk samples from the three species. This study provides insight into the rich and diverse bacterial and yeast communities in raw animal milk consumed in Nigeria, which could play beneficial roles or pose health threats to consumers. However, further research on the economic significance of the microbial community in animal milk consumed in Nigeria is required.

Probiotic Potentials of Lactic Acid Bacteria and Yeasts from Raw Goat Milk in Nigeria.

Probiotic microorganisms are incorporated in foods due to their numerous health benefits. We investigated lactic acid bacteria (LAB) and yeasts isolated from goat milk in Nigeria for novel probiotic strains. In this study, a total of 27 LAB and 23 yeast strains were assessed for their probiotic potentials. Only six LAB strains (Weissella cibaria GM 93m3, Weissella confusa GM 92m1, Pediococcus acidilactici GM 18a, Pediococcus pentosaceus GM 23d, Lactiplantibacillus pentosus GM 102s4, Limosilactobacillus fermentum GM 30m1) and four yeast strains (Candida tropicalis 12a, C. tropicalis 33d, Diutina rugosa 53b, and D. rugosa 77a) identified using partial 16S and 26S rDNA sequencing, respectively, showed survival at pH 2.5, 0.3% bile salt, and simulated gastrointestinal conditions and possessed auto-aggregative and hydrophobic properties, thus satisfying key in vitro criteria as probiotics. All LAB strains showed coaggregation properties and antimicrobial activities against pathogens. Pediococcus pentosaceus GM 23d recorded the strongest coaggregation percentage (34-94%) against 14 pathogens, while W. cibaria GM 93m3 showed the least (6-57%) against eight of the 14 pathogens. The whole cell and extracellular extracts of LAB and yeast strains, with the exception of D. rugosa 77a, had either 2,2-diphenyl-1-picryl-hydrazyl and/or hydroxyl radical scavenging activity. In conclusion, all six LAB and four yeast strains are important probiotic candidates that can be further investigated for use as functional starter cultures.

Bambara Groundnut Rhizobacteria Antimicrobial and Biofertilization Potential.

Bambara groundnut, an underutilized crop has been proved to be an indigenous crop in Africa with the potential for food security. The rhizosphere of Bambara groundnut contains Rhizobacteria, with the ability to grow, adapt, and colonize their surroundings even in unfavorable conditions and have not been explored for their plant growth-promoting properties. The aim of this research was to determine the potential of rhizobacteria from Bambara groundnut soil samples as either biofertilizers or biocontrol agents or both to help provide sustainable agriculture in Africa and globally. Bambara groundnut rhizospheric soil samples were collected and analyzed for their chemical composition. Rhizobacteria isolates were cultured from the soil samples. Plant growth-promoting, antifungal activities and phylogenetic analysis using 16S rRNA were carried out on the isolates to identify the rhizobacteria. A 2-year field study planting was carried out to determine the effect of these rhizobacteria as biofertilizers for Bambara groundnut (Vigna subterranean). The study was carried out in a complete randomized block experimental design with three replications. All the isolates were able to produce ammonia and 1-aminocyclopropane-1-carboxylate, while 4.65, 12.28, and 27.91% produced hydrogen cyanide, indole acetic acid, and solubilized phosphate, respectively, making them important targets as biocontrol and biofertilizer agents. The field results revealed that treatment with rhizobacteria had significant results compared with the control. Characterization of selected isolates reveals their identity as B. amyloliquefaciens, B. thuringiensis, and Bacillus sp. These Bacillus isolates have proved to be plant growth-promoting agents that can be used as biofertilizers to enhance the growth of crops and consequent improved yield. This is the first time the rhizobacteria from the Bambara groundnut rhizosphere are applied as biofertilizer.

Draft Genome Sequences of Multidrug-Resistant Shiga Toxin-Producing Escherichia coli O116:H25 Strains from Ready-to-Eat Foods Sold in Lagos, Nigeria.

Draft genomes of multidrug-resistant Shiga toxin-producing Escherichia coli (STEC) strains IPK9(1) and IKS1(2), which were isolated from ready-to-eat foods (kokoro and shawarma) sold in Lagos, Nigeria, are reported. The genomes possessed genetic determinants for virulence and the antibiotic resistance gene for macrolide-associated resistance mdf(A). Ready-to-eat foods increase public health threats in Nigeria.

Prospects in the bioremediation of petroleum hydrocarbon contaminants from hypersaline environments: A review.

Hypersaline environments are underappreciated and are frequently exposed to pollution from petroleum hydrocarbons. Unlike other environs, the high salinity conditions present are a deterrent to various remediation techniques. There is also production of hypersaline waters from oil-polluted ecosystems which contain toxic hydrophobic pollutants that are threat to public health, environmental protection, and sustainability. Currently, innovative advances are being proposed for the remediation of oil-contaminated hypersaline regions. Such advancements include the exploration and stimulation of native microbial communities capable of utilizing and degrading petroleum hydrocarbons. However, prevailing salinity in these environments is unfavourable for the growth of non-halophylic microorganisms, thus limiting effective bioremediation options. An in-depth understanding of the potentials of various remediation technologies of hydrocarbon-polluted hypersaline environments is lacking. Thus, we present an overview of petroleum hydrocarbon pollution in hypersaline ecosystems and discuss the challenges and prospects associated with several technologies that may be employed in remediation of hydrocarbon pollution in the presence of delimiting high salinities. The application of biological remediation technologies including the utilization of halophilic and halotolerant microorganisms is also discussed.

Draft Genome Sequences of Three Identified Rhizobacteria Associated with Maize Rhizosphere.

In this study, we sequenced the entire genomes of three identified rhizobacterial strains associated with maize plantation. Genome annotation of the sequenced data revealed several putative growth-promoting proteins associated with the production of indoleacetic acids and siderophore, the assimilation of nitrogen, and phosphorus solubilization.

Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity.

Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host-microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy-molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant-pathogen interactions and in the enhancement of plant innate immunity.

Insights into organic loading rates of anaerobic digestion for biogas production: a review.

Anaerobic digestion (AD) for biogas production is affected by many factors that includes organic loading rate (OLR). This OLR appears to be closely linked to various other factors and understanding these linkages would therefore allow the sole use of OLR for process performance monitoring, control, as well as reactor design. This review's objective is to collate the various AD factor specific studies, then relate these factors' role in OLR fluctuations. By further analyzing the influence of OLR on the AD performance, it would then be possible, once all the other factors have been determined and fixed, to manage an AD plant by monitoring and controlling OLR only. Decisions on reactor design, process kinetics, biogas yield and process stability can then be made much more quickly and with minimal troubleshooting steps.