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PMID: 17827330 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Phylogenetic ecology of the freshwater Actinobacteria acI lineage.

Applied and environmental microbiology ·Vol. 73 ·No. 22 ·2007-11-00 ·Pages 7169-76

Newton RJ, Jones SE, Helmus MR, McMahon KD

Abstract

The acI lineage of freshwater Actinobacteria is a cosmopolitan and often numerically dominant member of lake bacterial communities. We conducted a survey of acI 16S rRNA genes and 16S-23S rRNA internal transcribed spacer regions from 18 Wisconsin lakes and used standard nonphylogenetic and phylogenetic statistical approaches to investigate the factors that determine acI community composition at the local scale (within lakes) and at the regional scale (across lakes). Phylogenetic reconstruction of 434 acI 16S rRNA genes revealed a well-defined and highly resolved phylogeny. Eleven previously unrecognized monophyletic clades, each with > or =97.9% within-clade 16S rRNA gene sequence identity, were identified. Clade community similarity positively correlated with lake environmental similarity but not with geographic distance, implying that the lakes represent a single biotic region containing environmental filters for communities that have similar compositions. Phylogenetically disparate clades within the acI lineage were most abundant at the regional scale, and local communities were comprised of more closely related clades. Lake pH was a strong predictor of the community composition, but only when lakes with a pH below 6 were included in the data set. In the remaining lakes (pH above 6) biogeographic patterns in the landscape were instead a predictor of the observed acI community structure. The nonrandom distribution of the newly defined acI clades suggests potential ecophysiological differences between the clades, with acI clades AI, BII, and BIII preferring acidic lakes and acI clades AII, AVI, and BI preferring more alkaline lakes.

MeSH Terms
Actinobacteria/classification,genetics DNA, Bacterial/chemistry,genetics DNA, Ribosomal Spacer Ecology Fresh Water/microbiology Hydrogen-Ion Concentration Molecular Sequence Data Phylogeny RNA, Ribosomal, 16S/genetics RNA, Ribosomal, 23S/genetics Sequence Analysis, DNA Wisconsin
Chemicals
DNA, Bacterial DNA, Ribosomal Spacer RNA, Ribosomal, 16S RNA, Ribosomal, 23S
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Newton Ryan J
Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA.
Jones Stuart E
Helmus Matthew R
McMahon Katherine D
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Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/AEM.00794-07
Published
2007-11-00
Epub
2007-00-07
Pages
7169-76
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC2168227
Subset
IM
Grants
PHS HHS · 5 T32 G08349 · United States
Databases
GENBANK
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PubMed source DOI: 10.1128/AEM.00794-07 PMC Full Text View journal details
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