Computational protocol: Uranium (U)-Tolerant Bacterial Diversity from U Ore Deposit of Domiasiat in North-East India and Its Prospective Utilisation in Bioremediation

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Protocol publication

[…] The Basic Local Alignment Search Tool (BLAST) () programme was used to determine phylogenetic neighbours against the database of type strains with validly published prokaryotic names (21; available online: Molecular Evolutionary Genetics Analysis software (MEGA version 4) was used for phylogenetic analyses (). The sequences of identified phylogenetic neighbours were aligned with the sequences of the isolates using Clustal W inbuilt with MEGA 4. Deinococcus radiodurans (GenBank accession M21413) was used as the outgroup organism. The neighbor-joining method was employed to construct the phylogenetic tree with 1,000 bootstrap replications to assess nodal support in the tree. Based on high similarity (>98.7%) and clear phylogenetic clustering in the same branch, the isolates were assigned to a species.The number and frequency of phylotypes identified by ARDRA patterns were used to estimate the Shannon diversity index, Simpson’s index, and relative abundance of the three designated sites by using the Paleo-ecology statistics freeware package (PAST) (). The coverage index () as a percentage for each of the sites was assessed to determine how efficiently the sites described the complexity of a theoretical community as an original bacterial community. Various diversity indices were studied to understand the composition (types of bacteria), richness (number of types), and structure (frequency distribution) of the three designated sites. […]

Pipeline specifications

Software tools BLASTN, MEGA, Clustal W
Databases EzBioCloud
Application Phylogenetics
Diseases Sprains and Strains
Chemicals Uranium, Uranyl Nitrate