Community fingerprinting in a sequencing world.

Area of Science:

• Microbial Ecology
• Environmental Microbiology
• Molecular Ecology

Background:

• Large-scale microbial ecology studies using sequencing are costly and time-consuming, often leading to insufficient replication.
• This limits the ability to detect ecological patterns and understand microbial community structures.

Purpose of the Study:

• To compare the utility of two fingerprinting methods, automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (T-RFLP), against 454 pyrosequencing.
• To assess the ability of these methods to identify ecological patterns at local and global spatial scales using polar soil microbial communities.

Main Methods:

• Applied ARISA and T-RFLP to 225 polar soil samples from East Antarctica and the high Arctic.
• Compared results with 454 pyrosequencing data, analyzing microbial community structure and environmental correlations.
• Reduced pyrosequencing data to dominant operational taxonomic units (OTUs) to identify key drivers of observed patterns.

Main Results:

• Both ARISA and T-RFLP demonstrated similar capabilities to sequencing in separating samples by distance at local scales.
• Fingerprinting methods effectively correlated environmental variables with microbial community structure.
• Pyrosequencing offered higher resolution at global scales, but all methods differentiated polar sites.

Conclusions:

• Fingerprinting techniques (ARISA, T-RFLP) are legitimate, cost-effective, and rapid methods for generating large microbial ecology datasets.
• These methods can identify samples for subsequent taxonomic elucidation or diversity estimation via sequencing.
• Fingerprinting remains a valuable tool for microbial ecology research, especially when resources are limited.