Exploring Viral Diversity in a Unique South African Soil Habitat

Jane Segobola,Tsepo Tsekoa,Evelien Adriaenssens,Don Cowan,Konanani Rashamuse

doi:10.1038/s41598-017-18461-0

Jane Segobola, Tsepo Tsekoa + Show 3 more

Open Access

https://doi.org/10.1038/s41598-017-18461-0

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Abstract

The Kogelberg Biosphere Reserve in the Cape Floral Kingdom in South Africa is known for its unique plant biodiversity. The potential presence of unique microbial and viral biodiversity associated with this unique plant biodiversity led us to explore the fynbos soil using metaviromic techniques. In this study, metaviromes of a soil community from the Kogelberg Biosphere Reserve has been characterised in detail for the first time. Metaviromic DNA was recovered from soil and sequenced by Next Generation Sequencing. The MetaVir, MG-RAST and VIROME bioinformatics pipelines were used to analyse taxonomic composition, phylogenetic and functional assessments of the sequences. Taxonomic composition revealed members of the order Caudovirales, in particular the family Siphoviridae, as prevalent in the soil samples and other compared viromes. Functional analysis and other metaviromes showed a relatively high frequency of phage-related and structural proteins. Phylogenetic analysis of PolB, PolB2, terL and T7gp17 genes indicated that many viral sequences are closely related to the order Caudovirales, while the remainder were distinct from known isolates. The use of single virome which only includes double stranded DNA viruses limits this study. Novel phage sequences were detected, presenting an opportunity for future studies aimed at targeting novel genetic resources for applied biotechnology.

Highlights

The Cape Floristic Region situated in the Western Cape province of South Africa is one of five Mediterranean-type ecosystems in the world[1] and is recognized as one of the world’s biodiversity hotspots[2]
Analysis of the morphology of viruses identified in Kogelberg Biosphere Reserve fynbos soil was carried out by transmission electron microscopy (TEM)
This high percentage of bacterial sequences in metaviromes may be due to the presence of unknown prophages in bacterial genomes, phages carrying host genes, relatively large size of bacterial genomes compared to viral genomes and larger size of the microbial genome database which is statistically increasing the chance of matching bacterial sequences

Summary

South African Soil Habitat

Jane Segobola[1,2], Evelien Adriaenssens 2, Tsepo Tsekoa[1], Konanani Rashamuse1 & Don Cowan[2]. There is evidence that above-ground floral communities are implicated in shaping microbial communities[12,13], and that some microbial clades show a high level of plant–host specificity[10] This is consistent with the general concept of the mutualistic relationships between the plants and the microbial communities in fynbos soils[14]. The difficulty of culturing viruses, which are absolutely dependent on a cell host to provide the apparatus for replication and production of progeny virions, presents a barrier to fully accessing viral biodiversity This is a particular issue in poorly studied habitats, such as fynbos soil, where the true microbial. Features #Pre-QC Sequence reads #Pre-QC sequence in base pairs #post-QC average read length #contigs #contigs/reads in bp CLC 7,019,527 1,488,462,918 212.05 13,595 28,526,478 bp

Database used for CDS annotation

Results and Discussion

Relative abundance of taxa

Conclusion

Additional Information