Abstract:
:Terminal-restriction fragment length polymorphism (T-RFLP) analysis is widely used in microbial ecology studies. In the present study, T-RFLP analysis of PCR products digested by five restriction enzymes (AluI, HaeIII, MspI, Sau3AI and TaqI) was applied for 20 samples from three contrasting coastal environments to assess the biases associated with the choice of enzyme digestion and T-RF analysis. The five enzyme digestions produced highly variable species richness (in terms of number of T-RFs). Analysis of peak areas with a threshold of 0.5% of the total peak area, which recovered 92-96% of the total peak area, revealed different diversity indexes from the five enzyme digestions. Multidimensional scaling, based on matrices that were generated by scoring peak presence/absence and area, revealed similar bacterial community structure patterns among the 20 samples, regardless of the choice of restriction enzymes. Our results strongly argue that the choice of different digestion enzymes in the T-RFLP technique generated valid and consistent bacterial community structures but highly variable species richness and diversity indices. The biases associated with the choice of digestion enzymes needs to be evaluated carefully or at least to be addressed when using T-RFLP analysis.
journal_name
FEMS Microbiol Ecoljournal_title
FEMS microbiology ecologyauthors
Zhang R,Thiyagarajan V,Qian PYdoi
10.1111/j.1574-6941.2008.00493.xsubject
Has Abstractpub_date
2008-07-01 00:00:00pages
169-78issue
1eissn
0168-6496issn
1574-6941pii
FEM493journal_volume
65pub_type
杂志文章abstract::Extreme acidophiles (microorganisms with pH optima of < 3) can colonize and exploit subterranean environments, such as abandoned metal sulfide mines, that have the potential for developing widespread or isolated pockets of acidity. Although acidophiles can utilize a wide range of electron donors, inorganic materials (...
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pub_type: 杂志文章
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pub_type: 杂志文章
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pub_type: 杂志文章
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pub_type: 评论,信件
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pub_type: 杂志文章
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