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Applied and Environmental Microbiology, September 2006, p. 5982-5989, Vol. 72, No. 9
0099-2240/06/$08.00+0     doi:10.1128/AEM.01361-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Comparison of Two Fingerprinting Techniques, Terminal Restriction Fragment Length Polymorphism and Automated Ribosomal Intergenic Spacer Analysis, for Determination of Bacterial Diversity in Aquatic Environments

R. Danovaro,1* G. M. Luna,1 A. Dell'Anno,1 and B. Pietrangeli2

Department of Marine Sciences, Marine Biology Section, Faculty of Science, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy,1 Istituto Superiore Sicurezza sul Lavoro, Dipartimento Insediamenti Produttivi ed Interazione con l'Ambiente, Rome, Italy2

Received 14 June 2006/ Accepted 19 June 2006

We investigated bacterial diversity in different aquatic environments (including marine and lagoon sediments, coastal seawater, and groundwater), and we compared two fingerprinting techniques (terminal restriction fragment length polymorphism [T-RFLP] and automated ribosomal intergenic spacer analysis [ARISA]) which are currently utilized for estimating richness and community composition. Bacterial diversity ranged from 27 to 99 phylotypes (on average, 56) using the T-RFLP approach and from 62 to 101 genotypes (on average, 81) when the same samples were analyzed using ARISA. The total diversity encountered in all matrices analyzed was 144 phylotypes for T-RFLP and 200 genotypes for ARISA. Although the two techniques provided similar results in the analysis of community structure, bacterial richness and diversity estimates were significantly higher using ARISA. These findings suggest that ARISA is more effective than T-RFLP in detecting the presence of bacterial taxa accounting for <5% of total amplified product. ARISA enabled also distinction among aquatic bacterial isolates of Pseudomonas spp. which were indistinguishable using T-RFLP analysis. Overall, the results of this study show that ARISA is more accurate than T-RFLP analysis on the 16S rRNA gene for estimating the biodiversity of aquatic bacterial assemblages.

* Corresponding author. Mailing address: Dept. of Marine Science, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy. Phone: 39 71 220 4654. Fax: 39 71 220 4650. E-mail: r.danovaro{at}univpm.it.

Applied and Environmental Microbiology, September 2006, p. 5982-5989, Vol. 72, No. 9
0099-2240/06/$08.00+0     doi:10.1128/AEM.01361-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



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