Microbial Community Analysis using RDP II (Ribosomal Database Project II):Methods, Tools and New Advances

Abstract

Microorganisms play an important role in the geochemical cycles, industry, environmental cleanup, and biotechnology among other fields. Given the high microbial diversity, identification of the microorganism is essential in understanding and managing the processes. One of the most popular and powerful method for microbial identification is comparative 16S rRNA gene analysis. Due to the highly conserved nature of this essential gene, sequencing and later comparison of it against known rRNA databases can provide assignment of the bacteria into the taxonomy, and the identity of its closest relatives. Isolation and sequencing of 16S rRNA genes directly from natural environments (either from DNA or RNA) can also be used to study the structure of the whole microbial community. Nowadays, novel sequencing technologies with massive outputs are giving researchers worldwide the chance to study the microbial world with a depth that was previously too expensive to achieve. In this article we describe commonly used research approaches for the study of individual microorganisms and microbial communities using the tools provided by Ribosomal Database Project website.

Novel Biphenyl-Oxidizing Bacteria and Dioxygenase Genes from a Korean Tidal Mudflat

“…Gene-targeted pyrosequencing was performed by Macrogen, Inc. (Seoul, South Korea), using a 454/Roche GS-FLX titanium instrument (Roche, Nutley, NJ). The microbial community structure was analyzed with the pyrosequencing pipeline provided by the Ribosomal Database Project (RDP) (2,5). Operational taxonomic units (OTUs) were clustered at 97% sequence identity, and the median sequence of the cluster was used to determine taxonomy and percent identity to the nearest neighbor in Greengenes (6).…”

Characterization of microbial community structure and population dynamics of tetrachloroethene-dechlorinating tidal mudflat communities

“…Sequence alignment and complete linkage clustering from 0 to 10% dissimilarity were performed using the Ribosomal Database Project II (RDP) pyrosequencing pipeline (http://rdp.cme.msu.edu/) (Cole et al 2009;Cardenas et al 2009). The number of clusters was considered as Operational Taxonomic Units (OTUs) for generating rarefaction curves analysis and for calculating diversity indices.…”

Speculation on the Identity of Bacteria Named TFOs Occurring in the Inefficient P-Removal Phase of a Biological Phosphorus Removal System

“…and the W-5 clone were 100 and 98% respectively. Historically, the genus Acinetobacter, known as strict aerobes [16], has also been thought to be a primary P remover prior to the introduction of molecular techniques for the analysis of bacterial community structures in sludges and several ecosystems [17]. This suggests that an alternation to the aerobic-anaerobic regime, especially in the SBR system, where bacteria must suffer from the changes in dissolved oxygen (DO), might cause the occurrence of TFOs.…”