Overview matrix of all sequences in the NTL-MO database:
          Overview by    Geographic region
          Overview by    Lake type
          Overview by    Thermal layer

Search for sequence data:
          Search by    Taxonomic characteristics of the Clone
          Search by    Ecological characteristics of the Sample
          Search by    Combination of ecological and taxonomic characteristics of the Sample

Look up sequences by (use wild card * to make more general queries):

Clone_id               

Accession Number

Sample_id             

Local BLAST against the NTL-MO database - (under development)

Overview
The NTL-MO Environmental Sequence Database represents our efforts to link microbial community composition and environmental data from north temperate lake ecosystems. Our dataset includes community fingerprints, 16S rDNA sequences, phylogenetic assignments, and environmental data collected using high-throughput techniques (overview of sample processing and analysis). The data are stored in a relational database that is fully integrated with the North Temperate Lakes LTER dataset, allowing us to link molecular data with ecological data.

Rationale
Microbial community "fingerprint" methods are often used to compare the diversity and composition of microbial assemblages. These methods are rapid, high-throughput approaches for assessment of microbial communities, but give limited phylogenetic resolution. In contrast, 16S rDNA clone libraries offer a high degree of phylogenetic resolution for culture-independent analyses, but are intractable for analysis of large numbers of samples generated by studies comparing microbial community variability over time or space. Our strategy leverages the advantages of both approaches, while exploiting the capabilities of relational database management and dynamic querying.

Approach
Community composition is rapidly assessed by automated ribosomal intergenic spacer analysis (ARISA). Phylogenetic assignments for individual ARISA fragments have been generated by high-throughput analysis of clone libraries that include both the 16S rRNA gene and the 16S-23S ribosomal intergenic spacer fragment from individual bacterial species. We have analyzed over 3900 clones obtained from 41 lakes that represent the range of trophic types found in temperate landscapes. The database containing these assignments forms the basis of the information management tool we have designed to rapidly infer the species composition of microbial assemblages from ARISA profiles.

Dynamic Query Architecture
We have in place a three-layered architecture for porting data to the web for public and/or restricted access. The database layer uses Oracle to store DNA sequence, community fingerprint, environmental and phylogenetic data collected using high-throughput techniques. Java is used to process the data from the Oracle tables and pass the output to a user-friendly web-based interface. This web interface offers the capacity to query phylogenetic or ecological information in our dataset. Advanced users can interface with Oracle directly to dynamically match ARISA fragments from community profiles and clones utilizing user-defined parameters. A combination of Oracle, Java, JSP, Servlets and Java Script modeled along the lines of MVC (Model View Control) architecture is the backbone of this system.

ARISA Protocol
Lake Microbial Community Protocol (ARISA)

Publications
Smith, D. J., B.J. Benson, and D. F. Balsiger. 2002. Designing web database applications for ecological research. In Proceedings of the 6th World Multiconference on Systemics, Cybernetics and Informatics. Vol VII: Informatics Systems Development II, July 14-18, 2002, Orlando, FL.

Angela D. Kent, Cheryan Jacob, Anthony C. Yannarell, Ryan J. Newton, Barbara J. Benson, Katherine D. McMahon. Linking fingerprints, phylogeny, and environmental data at the North Temperate Lakes Microbial Observatory, in preparation.