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Exploring Viral Diversity in a Unique South African Soil Habitat.

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.

SUBMITTER: Segobola J

PROVIDER: S-EPMC5758573 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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Exploring Viral Diversity in a Unique South African Soil Habitat.

Segobola Jane J Adriaenssens Evelien E Tsekoa Tsepo T Rashamuse Konanani K Cowan Don D

Scientific reports 20180108 1

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 Gener ...[more]

PMID: 29311639

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Project description:The South American continent presents a great diversity of biomes, whose ecosystems are constantly threatened by the expansion of human activity. The emergence and re-emergence of viral populations with impact on the human population and ecosystem have shown increases in the last decades. In deference to the growing accumulation of genomic data, we explore the potential of South American-related public databases to detect signals that contribute to virosphere research. Therefore, our study aims to investigate public databases with emphasis on the surveillance of viruses with medical and ecological relevance. Herein, we profiled 120 "sequence read archives" metagenomes from 19 independent projects from the last decade. In a coarse view, our analyses identified only 0.38% of the total number of sequences from viruses, showing a higher proportion of RNA viruses. The metagenomes with the most important viral sequences in the analyzed environmental models were 1) aquatic samples from the Amazon River, 2) sewage from Brasilia, and 3) soil from the state of São Paulo, while the models of animal transmission were detected in mosquitoes from Rio Janeiro and Bats from Amazonia. Also, the classification of viral signals into operational taxonomic units (OTUs) (family) allowed us to infer from metadata a probable host range in the virome detected in each sample analyzed. Further, several motifs and viral sequences are related to specific viruses with emergence potential from Togaviridae, Arenaviridae, and Flaviviridae families. In this context, the exploration of public databases allowed us to evaluate the scope and informative capacity of sequences from third-party public databases and to detect signals related to viruses of clinical or environmental importance, which allowed us to infer traits associated with probable transmission routes or signals of ecological disequilibrium. The evaluation of our results showed that in most cases the size and type of the reference database, the percentage of guanine-cytosine (GC), and the length of the query sequences greatly influence the taxonomic classification of the sequences. In sum, our findings describe how the exploration of public genomic data can be exploited as an approach for epidemiological surveillance and the understanding of the virosphere.

Project description:GOALS OF THIS STUDY WERE TO: (1) develop distributional maps of modern rodent genera throughout the countries of South Africa, Lesotho, and Swaziland by georeferencing museum specimens; (2) assess habitat preferences for genera by cross-referencing locality position with South African vegetation; and (3) identify mean annual precipitation and temperature range where the genera are located. Conterminous South Africa including the countries of Lesotho and Swaziland Digital databases of rodent museum specimens housed in the Ditsong National Museum of Natural History, South Africa (DM), and the Division of Mammals, National Museum of Natural History, Smithsonian Institution, United States (NMNH), were acquired and then sorted into a subset of specimens with associated coordinate data. The coordinate data were then used to develop distributional maps for the rodent genera present within the study area. Percent habitat occupation and descriptive statistics for six climatic variables were then determined for each genus by cross-referencing locality positions with vegetation and climatic maps. This report presents a series of maps illustrating the distribution of 35 rodent genera based on 19,471 geo-referenced specimens obtained from two major collections. Inferred habitat use by taxon is provided for both locality and specimen percent occurrence at three hierarchical habitat levels: biome, bioregion, and vegetation unit. Descriptive statistics for six climatic variables are also provided for each genus based on locality and specimen percent incidence. As rodent faunas are commonly used in paleoenvironmental reconstructions, an accurate assessment of rodent environmental tolerance ranges is necessary before confidence can be placed in an actualistic model. While the data presented here represent only a subset of the modern geographic distributions for many of the taxa examined, a wide range of environmental regimes are observed, suggesting that more research is necessary in order to accurately reconstruct an environmental signature when these taxa are found in the fossil record.

Project description:MethodologyThis paper uses regression adjustment and entropy matching to achieve an appropriate balance between the two groups. Having achieved this balance any difference in the overall performance between the two groups can then be attributed directly to the new language policy that has been implemented. Our results indicate, after matching, that a significant difference in performance between the two groups occurs with Black African Zulu home language speakers in particular not performing as well as students from the other race and language groups. The data came from the University of KwaZulu-Natal and the study has been approved by the University Ethics committee and Research committee.Results and conclusionsUsing a weighted mean of marks to measure performance, the ATT estimates that result indicate that students in the treated group would all perform significantly better had they been allowed instead to enrol in the non-treated group. Furthermore, Zulu home language speakers, who are not actually forced to take this course, are significantly underperforming whether they have chosen to take this course in Zulu or not. Surprisingly, their underperformance is worse in the treated group. Because one would expect them to be scoring a higher mark for Zulu in this treated group, forfeiting the chance to take another course in their chosen area of study is clearly affecting the type of mark they could be getting for their other courses had they chosen to remain in the non-treated group. With English being the medium of instruction at this university, should the university not also consider introducing a compulsory course in English for these Zulu home language speakers? Females are doing better than males in both groups. The effect being stronger in the treated group suggests that females appear to cope better with the learning of a new language. Significant college effects are also being observed, suggesting that this new language rule possibly needs to be adjusted for the college a student wants to study in.

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Exploring Viral Diversity in a Unique South African Soil Habitat.

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Exploring Viral Diversity in a Unique South African Soil Habitat.

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