No abstract

Soil microorganisms play crucial roles in soil fertility, e.g., through decomposing organic matter, cycling nutrients or through beneficial interactions with plants. Actinomycetes are a major component of soil inhabitants; they are prolific producers of specialized metabolites, among which many antibiotics. Here we report the isolation and characterization of 175 Actinomycetes from rhizosphere and bulk soil samples collected in 18 locations in Sudan. We evaluated the strains’ metabolic potential for plant protection by testing their ability to inhibit the mycelial growth of the oomycete Phytophthora infestans, which is one of the most devastating plant pathogens worldwide. Most strains significantly reduced the oomycete’s growth in direct confrontational in vitro assays. A significant proportion of the tested strains (15%) were able to inhibit P. infestans to more than 80%, 23% to 50%–80%, while the remaining 62% had inhibition percentages lesser than 50%. Different morphologies of P. infestans mycelial growth and sporangia formation were observed upon co-inoculation with some of the Actinomycetes isolates, such as the production of fewer, thinner hyphae without sporangia leading to a faint growth morphology, or on the contrary, of clusters of thick-walled hyphae leading to a bushy, or “frozen” morphology. These morphologies were caused by strains differing in activity levels but phylogenetically closely related with each other. To evaluate whether the isolated Actinomycetes could also inhibit the pathogen’s growth in planta, the most active strains were tested for their ability to restrict disease progress in leaf disc and full plant assays. Five of the active strains showed highly significant protection of potato leaves against the pathogen in leaf disc assays, as well as substantial reduction of disease progress in full plants assays. Using cell-free filtrates instead of the bacterial spores also led to full protection against disease on leaf discs, which highlights the strong crop protective potential of the secreted metabolites that could be applied as leaf spray. This study demonstrates the strong anti-oomycete activity of soil- and rhizosphere-borne Actinomycetes and highlights their significant potential for the development of sustainable solutions based on either cell suspensions or cell-free filtrates to safeguard potatoes from their most damaging pathogen.

Fungi are one of the most diverse groups of organisms and considered as one of the least-explored biodiversity resources. Soil fungal community was investigated in two agricultural sites in Khartoum state, Sudan, during two seasons. A total of 42 soil samples were collected, their physicochemical properties were determined, then subjected to metabarcoding and metagenomic analyses. fungal community composition, diversity and microbial trophic modes were determined utilizing R software packages. From both sites, a total of 15 different phyla were detected, out of them, 11 were the most abundant and frequent. Ascomycota was the dominant phylum (86.54% total abundance), followed by the Basidiomycota (8.29%). The dominant class was Sordariomycetes (41.02%), followed by Dothideomycetes (19.80%). Aspergillus (6.2%), Curvularia (6.0%), Neurospora (5.8%) and Fusarium (4.9%) were the most abundant genera. Deniquelata for the first time being recorded in Sudan. Apha diversity measures revealed sample richness ranging from 71 to 361 ASVs, and Shannon index ranging from 2.794 to 5.087. The two sites had significantly different alpha diversity. Land-use types were also significantly different in their diversity regardless of site. Season had no effect on alpha diversity of soil fungal communities. Beta diversity analysis indicated significant differences between the two sites and the different land-use types. No significant differences in the community structure recorded between the two seasons. The dominant trophic mode among the assigned ASVs in soil mycobiome was saprotroph mode (22.11%). Results of this study reveals that fungal community structure is affected by site and land-use type. It gives a comprehensive database for the mycobiome of the agricultural soil in Khartoum state.

Background Enteric fever has a persistently great impact on public health. It is caused by Salmonella enterica associated with malaria during the rainy season; the bacterium is seldom detected in wastewater of stabilisation stations due to treatment processes. The aim of this study is to evaluate the recent state of antibiotics susceptibility of Salmonella typhi with special attention to multidrug-resistant strains and predict the emergence of new resistance patterns. Methods S. typhi isolates were recovered from 128 wastewater samples collected from ponds at Soba Stabilization Station and Omdurman Hospital Stabilization Station. The isolates were identified using standard Salmonella identification guidelines and their susceptibility to seven antibiotics was determined. Minimum inhibitory concentration (MIC) of ciprofloxacin and minimum bactericidal concentrations (MBC) were also determined. Statistical predictions for the resistance emergence were done using logistic regression and forecasting linear equations. Results A total of 12 S. typhi isolated strains were recovered from 128 samples of wastewater; they were resistant to antibiotics except Ciprofloxacin. Current patterns of ciprofloxacin breakpoints interpretations were in susceptible ranges by disc diffusion (S≥20 mm), minimum inhibitory concentration was recorded as (I=16 mg/ml) and minimum bactericidal concentration=(R≥32 mg/ml). The probability of an isolate to develop resistance was plotted for MBCs; the rate of resistance solved by (y=0.0235×−0.0411). The predictive patterns of resistance were spontaneously solved using exponential trend (y=n e x ) for each isolate at 16 mg/ml and 32 mg/ml of ciprofloxacin in certain period and the high values of coefficient R 2 >0.5 indicate the incidence rates of bacterial resistance. Conclusions The current sensitivity patterns of S. typhi isolates against ciprofloxacin were acceptable, but the probability of emerging multidrug resistance to ciprofloxacin was observed in sensitivity which had begun to decline according to frequent consuming, drug policy and bacterial genetic mutations.