Microbiology Research - Academic Journals

Table 3. Advantages and disadvantages of common fingerprinting methods used in the analysis of soil microbial communities.
Methods Advantages Disadvantages References
DGGE∗/TGGE
SSCP
T-RFLP
Provides full sequences that can be subject to further
analysis technically; obtain an overview of the dominant
species
Provides full sequences that can be subject to further
analysis technically; obtain an overview of the dominant
species
Technically simple and reproducible; high discrimination
power (number of types/analysis);
ARDRA Technically simple and convenient
LH-PCR/ARISA
FISH
PLFA
Microarrays
Technically simple; replicate profiles are highly
reproducible; it can quickly evaluate community changes
Direct analysis without extraction of nucleic acid;
generally quantitative;
No bias due to PCR; cover whole communities across
kingdoms; quantitative description of the community
No bias due to PCR; simultaneously analyze about ten
thousand samples; high sample throughput expensive
equipment parallel analysis of different parameters
16SrDNA library Technically simple, can evaluate the community overall
∗See text for the explanation of abbreviations.
Only short sequences < 400 bp can be analyzed;
DNA fragments of different species might have
similar electrophoretic mobility
Only short sequences < 200 bp can be analyzed
Loss of some variability (sequences not cleaved or
cleaved near to primer); low phylogenetic
specificity of terminal restriction sites;
Affected by PCR biases and the choice of the
enzyme;
Low discrimination power; amplicon distributions
are sometimes difficult to resolve with the current
software; one amplicon can represent more than
one taxon
Low fluorescent intensity cannot be detected; its
rRNA sequence must be known (if the probe has
not yet been published);
Low taxonomic separation limited to community
composition analysis; not a good choice as a
standard alone method
Detects only sequences corresponding to probes;
detection limit lower than in PCR-based methods;
impossible discover a new species;
Only detected the absence or exist between to
samples; PCR biases; selected clone numbers
Wang et al. 5083
Sanz and Köchling (2007),
Muyzer et al. (1993) and
Nannipieri et al. (2003).
Lee et al. (1996), Dohrmann and
Tebbe (2004) and Sanz and
Köchling (2007).
Liu et al. (1997) and Nannipieri
et al. (2003).
Ranjard et al. (2000).
Fisher and Triplett (1999) and
Mills et al. (2007).
Dahllof (2002) and Sanz and
Köchling (2007).
Findlay et al. (1989) and Sanz
and Köchling (2007).
Shalon et al. (1996) and Ranjard
et al. (2000).
Li et al. (2007).
Forestry University (500017) and Ornamental Plant and Horticulture key lab of Yunnan Province, Southwest Forestry University (000703).