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Soil Microbial Community Analysis using Terminal Restriction Fragment Length Polymorphisms

^a Department of Crop and Soil Sciences, Cornell Univ. Ithaca, NY 14853

View larger version (24K): [in this window] [in a new window]   Fig. 1. Number of refereed journal articles appearing in the ISI Web of Science Index between 1997 and December 2006 that describe the terminal restriction fragment length polymorphism (T-RFLP) method, report on its use for analyzing microbial communities in a variety of habitats, report pitfalls or improvements in the technique, or describe approaches to T-RFLP data analysis.

View larger version (24K): [in this window] [in a new window]   Fig. 2. Percentage of the articles enumerated in Fig. 1 that report results of terminal restriction fragment length polymorphism microbial community analyses from different environmental systems compared with descriptions of methods or data analysis (n = 525).

View larger version (25K): [in this window] [in a new window]   Fig. 3. Flow chart of the mechanics of the terminal restriction fragment length polymorphism procedure. Adapted from Theis (2007).

View larger version (39K): [in this window] [in a new window]   Fig. 4. Examples of terminal restriction fragment length polymorphism profiles: (A) and (B) (Marsh, 2005) show electropherograms from RsaI digestion of 16S rRNA genes amplified from DNA extracted from two different soil samples, the insert in (A) shows an expanded size range (50–100 bases) in the electropherogram; (C) and (D) (Cadillo-Quiroz et al., 2006) are electropherograms from archael 16S rRNA genes amplified from DNA extracted from two different acidic peat bogs in central New York. The archaeal groups represented by distinctive terminal restriction fragments are: Methanosarcinaceae (MS), Methanosaetaceae (MT), rice cluster-I (RC-I), rice cluster-II (RC-II), marine benthic group D (MBD) and Methanomicrobiales: group E1 (E1), group-E1' (E1'), group E2 (E2).