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Permanent URI for this collectionhttp://ir-dev.dut.ac.za/handle/10321/213

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Subject: search.filters.subject.06 Biological Sciences

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    A metagenomic investigation of the faecal RNA virome structure of asymptomatic chickens obtained from a commercial farm in Durban, KwaZulu-Natal province, South Africa.
    (Springer Science and Business Media LLC, 2024-06) Nwokorogu, Vivian C.; Pillai, Santhosh; San, James E.; Pillay, Charlene; Nyaga, Martin M.; Sabiu, Saheed
    Virome studies on birds, including chickens are relatively scarce, particularly from the African continent. Despite the continuous evolution of RNA viruses and severe losses recorded in poultry from seasonal viral outbreaks, the information on RNA virome composition is even scantier as a result of their highly unstable nature, genetic diversity, and difficulties associated with characterization. Also, information on factors that may modulate the occurrence of some viruses in birds is limited, particularly for domesticated birds. Viral metagenomics through advancements in sequencing technologies, has enabled the characterization of the entire virome of diverse host species using various samples.

    Methods

    The complex RNA viral constituents present in 27 faecal samples of asymptomatic chickens from a South African farm collected at 3-time points from two independent seasons were determined, and the impact of the chicken's age and collection season on viral abundance and diversity was further investigated. The study utilized the non-invasive faecal sampling method, mRNA viral targeted enrichment steps, a whole transcriptome amplification strategy, Illumina sequencing, and bioinformatics tools.

    Results

    The results obtained revealed a total of 48 viral species spanning across 11 orders, 15 families and 21 genera. Viral RNA families such as Coronaviridae, Picornaviridae, Reoviridae, Astroviridae, Caliciviridae, Picorbirnaviridae and Retroviridae were abundant, among which picornaviruses, demonstrated a 100% prevalence across the three age groups (2, 4 and 7 weeks) and two seasons (summer and winter) of the 27 faecal samples investigated. A further probe into the extent of variation between the different chicken groups investigated indicated that viral diversity and abundance were significantly influenced by age (P = 0.01099) and season (P = 0.00099) between chicken groups, while there was no effect on viral shedding within samples in a group (alpha diversity) for age (P = 0.146) and season (P = 0.242).

    Conclusion

    The presence of an exceedingly varied chicken RNA virome, encompassing avian, mammalian, fungal, and dietary-associated viruses, underscores the complexities inherent in comprehending the causation, dynamics, and interspecies transmission of RNA viruses within the investigated chicken population. Hence, chickens, even in the absence of discernible symptoms, can harbour viruses that may exhibit opportunistic, commensal, or pathogenic characteristics.
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    Bioaugmentation efficiency of diesel degradation by Bacillus pumilus JLB and Acinetobacter calcoaceticus LT1 in contaminated soils
    (2010-10-11) Pillay, Charlene; Lin, Johnson
    The abilities of diesel-degrading Bacillus pumilus JLB and Acinetobacter calcoaceticus LT1 were tested in contaminated soils. The effect of nutrient supplementation on bioaugmented samples was also examined. The results show that bio-augmentation and biostimulation accelerated significantly (p < 0.05) the diesel degradation in the contaminated loam soil and sea sand. Supplementing fertilizers to the augmented loam samples did not result in a significantly higher degradation rate. Furthermore, A. calcoaceticus LT1 alone failed to stimulate higher degradation rates in sea sand unless further supplementation of fertilizer. The results from environmental scanning electron microscopy demonstrate the population increases, then decreases in augmented samples corresponding to the level of diesel degradation. Fungi-like microorganisms became dominant in contaminated loam soil at the end of the study but not in sea sand. The study shows that it is critical not only to understand the physiology of the inoculum but also how it affects microbial community structure and function before the microorganism being introduced in the contaminated soil.