Exploring Viral Diversity in a Unique South African Soil Habitat

Segobola, Jane; Adriaenssens, Evelien M.; Tsekoa, Tsepo L.; Rashamuse, Konanani; Cowan, Don A.

doi:10.1038/s41598-017-18461-0

Cited by 25 publications

(17 citation statements)

References 75 publications

(108 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Paired-end reads were assembled using the MetaSPADES-3.7.1 assembler 75 . Based on the denovo assembly, contigs with length >=300 bp were first aligned against the Refseq bacterial genome database and the unaligned contigs were aligned against NCBI RefSeq viral genome sequences (release version 80) using GBLASTN with 80% sequence identity and 85% average query coverage with an E-value cutoff of 10 −5 for taxonomic classification 41 , 76 , 77 . The unaligned sequences against viruses were further aligned against archeal and fungal Refseq genome sequences downloaded from NCBI with the same release version and with similar cutoff parameters to ensure that only viral sequences were considered for analysis.…”

Section: Materials and Methodologymentioning

confidence: 99%

Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India

Jasna

Parvathi

Dash³

2018

Sci Rep

View full text Add to dashboard Cite

The present study illustrates the genetic diversity of four uncultured viral communities from the surface waters of Cochin Estuary (CE), India. Viral diversity inferred using Illumina HiSeq paired-end sequencing using a linker-amplified shotgun library (LASL) revealed different double-stranded DNA (dsDNA) viral communities. The water samples were collected from four stations PR1, PR2, PR3, and PR4, during the pre-monsoon (PRM) season. Analysis of virus families indicated that the Myoviridae was the most common viral community in the CE followed by Siphoviridae and Podoviridae. There were significant (p < 0.05) spatial variations in the relative abundance of dominant families in response to the salinity regimes. The relative abundance of Myoviridae and Podoviridae were high in the euryhaline region and Siphoviridae in the mesohaline region of the estuary. The predominant phage type in CE was phages that infected Synechococcus. The viral proteins were found to be involved in major functional activities such as ATP binding, DNA binding, and DNA replication. The study highlights the genetic diversity of dsDNA viral communities and their functional protein predictions from a highly productive estuarine system. Further, the metavirome data generated in this study will enhance the repertoire of publicly available dataset and advance our understanding of estuarine viral ecology.

show abstract

Section: Materials and Methodologymentioning

confidence: 99%

Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India

Jasna

Parvathi

Dash³

2018

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Consequently, to desorb virions, various chemical reagents with different charges and physical methods are employed [5]. Virus desorption methods in particular should be tailored to specific soil types [35,[153][154][155]. We therefore first suggest characterizing a soil to understand its anion/cation-exchange capacity (a measure of how many ions can be retained on soil particle surfaces [156]) and, separately, the diversity of the associated microbial community (e.g., via 16S rRNA gene surveys).…”

Section: The Challenge Of Separating Virions From Soilsmentioning

confidence: 99%

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

et al. 2020

View full text Add to dashboard Cite

The study of soil viruses, though not new, has languished relative to the study of marine viruses. This is particularly due to challenges associated with separating virions from harboring soils. Generally, three approaches to analyzing soil viruses have been employed: (1) Isolation, to characterize virus genotypes and phenotypes, the primary method used prior to the start of the 21st century. (2) Metagenomics, which has revealed a vast diversity of viruses while also allowing insights into viral community ecology, although with limitations due to DNA from cellular organisms obscuring viral DNA. (3) Viromics (targeted metagenomics of virus-like-particles), which has provided a more focused development of ‘virus-sequence-to-ecology’ pipelines, a result of separation of presumptive virions from cellular organisms prior to DNA extraction. This separation permits greater sequencing emphasis on virus DNA and thereby more targeted molecular and ecological characterization of viruses. Employing viromics to characterize soil systems presents new challenges, however. Ones that only recently are being addressed. Here we provide a guide to implementing these three approaches to studying environmental viruses, highlighting benefits, difficulties, and potential contamination, all toward fostering greater focus on viruses in the study of soil ecology.

show abstract

“…In Kogelberg Biosphere Reserve in South Africa, the unique plant viral biodiversity was explored in a vegetation in the western province using metaviromic technique. The recovered DNA from the soil samples was sequenced under the Illumina Platform with some bioinformatics analysis carried out which detected biodiversity among the Caudovirales group [ 224 ].…”

Section: Metagenomics and Its Application In Africamentioning

confidence: 99%

Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes

Osunmakinde

Selvarajan

Sibanda

et al. 2018

Viruses

View full text Add to dashboard Cite

There has been an increase in the quest for metagenomics as an approach for the identification and study of the diversity of human viruses found in aquatic systems, both for their role as waterborne pathogens and as water quality indicators. In the last few years, environmental viral metagenomics has grown significantly and has enabled the identification, diversity and entire genome sequencing of viruses in environmental and clinical samples extensively. Prior to the arrival of metagenomics, traditional molecular procedures such as the polymerase chain reaction (PCR) and sequencing, were mostly used to identify and classify enteric viral species in different environmental milieu. After the advent of metagenomics, more detailed reports have emerged about the important waterborne viruses identified in wastewater treatment plant effluents and surface water. This paper provides a review of methods that have been used for the concentration, detection and identification of viral species from different environmental matrices. The review also takes into consideration where metagenomics has been explored in different African countries, as well as the limitations and challenges facing the approach. Procedures including sample processing, experimental design, sequencing technology, and bioinformatics analysis are discussed. The review concludes by summarising the current thinking and practices in the field and lays bare key issues that those venturing into this field need to consider and address.

show abstract

Exploring Viral Diversity in a Unique South African Soil Habitat

Cited by 25 publications

References 75 publications

Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India

Genetic and functional diversity of double-stranded DNA viruses in a tropical monsoonal estuary, India

Coming-of-Age Characterization of Soil Viruses: A User’s Guide to Virus Isolation, Detection within Metagenomes, and Viromics

Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes

Contact Info

Product

Resources

About