dna viral fractions  (Thermo Fisher)

Journal: Applied and Environmental Microbiology

Article Title: Seasonal patterns of viromes in urban aquatic environments of Manitoba

doi: 10.1128/aem.00408-24

Figure Lengend Snippet: Taxonomic families of DNA viruses (inclusive of those unclassified) during the Spring, Summer, and Fall of 2021 that were identified from BLASTp v.2.15.0 against NCBI Viral RefSeq database and geNomad v.1.8.0. Host range of DNA viral families: Autographiviridae : bacteria (Gammaproteobacteria); Chaseviridae : bacteria (Gammaproteobacteria); Circoviridae : vertebrates and invertebrates (Cyclovirus); Demerecviridae : bacteria (multiple strains of Salmonella and E. coli , Erwiniaceae ), Drexleviridae : plants (monocots and dicots); Kyanoviridae : bacteria and archaea ( Cyanobacteriota , Pseudomonadota , and Actinomycetota ); Mimiviridae : amoebae, protists, and algae; Straboviridae : gram-negative bacteria.

Article Snippet: For DNA viral fractions, this step was not required, as quantifiable amounts were observed after the addition of Ambion RNase III enzyme to degrade ribosomal rRNA.

Techniques: Bacteria, Algae

Journal: Applied and Environmental Microbiology

Article Title: Seasonal patterns of viromes in urban aquatic environments of Manitoba

doi: 10.1128/aem.00408-24

Figure Lengend Snippet: Factor analysis of viral DNA and RNA families and environmental variables observed at each sample collection site (1–11) during the Spring (blue dots), Summer (orange dots), and Fall (red dots) of 2021. Factor 1 represents the influence of agricultural activities from rural environments, while factor 2 represents the effect of urbanization and industrialization practices on aquatic environments.

Article Snippet: For DNA viral fractions, this step was not required, as quantifiable amounts were observed after the addition of Ambion RNase III enzyme to degrade ribosomal rRNA.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Seasonal patterns of viromes in urban aquatic environments of Manitoba

doi: 10.1128/aem.00408-24

Figure Lengend Snippet: Correlogram of viral DNA and RNA families and environmental variables observed at each sample collection site (1–11). Correlation coefficients range from +1 to −1 and are represented by circles colored blue to red. DO, dissolved oxygen; River TEM, temperature of the river water; cBOD 5 , carbonaceous biochemical oxygen demand; BOD 5 , biochemical oxygen demand; NH 4 -N, ammonia, PO 4 , ortho-phosphorus; E. coli (MPN/100 mL), E. coli colony forming unit counts. The following viruses were assessed through quantitative analyses (GCN per 100 mL), HAdV, crAssphage, PMMoV, and RoV, while the remaining viruses were assessed metagenomically.

Article Snippet: For DNA viral fractions, this step was not required, as quantifiable amounts were observed after the addition of Ambion RNase III enzyme to degrade ribosomal rRNA.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Seasonal patterns of viromes in urban aquatic environments of Manitoba

doi: 10.1128/aem.00408-24

Figure Lengend Snippet: Assessment of the beta diversity among DNA viral communities present in aquatic samples 1–11 collected during the Spring (blue dots), Summer (orange dots), and Fall (red dots) 2021. The Bray-Curtis dissimilarity (beta diversity) index was calculated using the k-mer tables generated by MerCat2 with factoextra and MASS packages in RStudio.

Article Snippet: For DNA viral fractions, this step was not required, as quantifiable amounts were observed after the addition of Ambion RNase III enzyme to degrade ribosomal rRNA.

Techniques: Generated