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Coupling 16S‐ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series
Author(s) -
Brown Mark V.,
Schwalbach Michael S.,
Hewson Ian,
Fuhrman Jed A.
Publication year - 2005
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/j.1462-2920.2005.00835.x
Subject(s) - prochlorococcus , biology , ribosomal intergenic spacer analysis , 16s ribosomal rna , ribosomal rna , actinobacteria , abundance (ecology) , ribosomal dna , ecology , evolutionary biology , computational biology , genetics , cyanobacteria , phylogenetics , bacteria , gene , internal transcribed spacer , synechococcus
Summary We outline an approach to simultaneously assess multilevel microbial diversity patterns utilizing 16S‐ITS rDNA clone libraries coupled with automated ribosomal intergenic spacer analysis (ARISA). Sequence data from 512 clones allowed estimation of ARISA fragment lengths associated with bacteria in a coastal marine environment. We matched 92% of ARISA peaks (each comprising > 1% total amplified product) with corresponding lengths from clone libraries. These peaks with putative identification accounted for an average of 83% of total amplified community DNA. At 16S rDNA similarities < 98%, most taxa displayed differences in ARISA fragment lengths > 10 bp, readily detectable and suggesting ARISA resolution is near the ‘species’ level. Prochlorococcus abundance profiles from ARISA were strongly correlated ( r 2 = 0.86) to Prochlorococcus cell counts, indicating ARISA data are roughly proportional to actual cell abundance within a defined taxon. Analysis of ARISA profiles for 42 months elucidated patterns of microbial presence and abundance providing insights into community shifts and ecological niches for specific organisms, including a coupling of ecological patterns for taxa within the Prochlorococcus , the Gamma Proteobacteria and Actinobacteria. Clade‐specific ARISA protocols were developed for the SAR11 and marine cyanobacteria to resolve ambiguous identifications and to perform focused studies. 16S‐ITS data allowed high‐resolution identification of organisms by ITS sequence analysis, and examination of microdiversity.