Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time - PubMed (original) (raw)

Microbial biogeography along an estuarine salinity gradient: combined influences of bacterial growth and residence time

Byron C Crump et al. Appl Environ Microbiol. 2004 Mar.

Abstract

Shifts in bacterioplankton community composition along the salinity gradient of the Parker River estuary and Plum Island Sound, in northeastern Massachusetts, were related to residence time and bacterial community doubling time in spring, summer, and fall seasons. Bacterial community composition was characterized with denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S ribosomal DNA. Average community doubling time was calculated from bacterial production ([(14)C]leucine incorporation) and bacterial abundance (direct counts). Freshwater and marine populations advected into the estuary represented a large fraction of the bacterioplankton community in all seasons. However, a unique estuarine community formed at intermediate salinities in summer and fall, when average doubling time was much shorter than water residence time, but not in spring, when doubling time was similar to residence time. Sequencing of DNA in DGGE bands demonstrated that most bands represented single phylotypes and that matching bands from different samples represented identical phylotypes. Most river and coastal ocean bacterioplankton were members of common freshwater and marine phylogenetic clusters within the phyla Proteobacteria, Bacteroidetes, and ACTINOBACTERIA: Estuarine bacterioplankton also belonged to these phyla but were related to clones and isolates from several different environments, including marine water columns, freshwater sediments, and soil.

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Figures

FIG. 1.

FIG. 1.

Map of Plum Island Sound with subsections indicated.

FIG. 2.

FIG. 2.

Salinity profile along main stem of estuary at mean high tide (A) and average residence time of water in each subsection (B) on summer, fall, and spring sampling dates.

FIG. 3.

FIG. 3.

Bacterial production rate (A) and average community doubling time (B) along main stem of estuary on spring, summer, and fall sampling dates.

FIG. 4.

FIG. 4.

DGGE gel of PCR-amplified 16S rDNA genes from samples collected along the salinity gradient on 28 September 2000. Bands from which DNA was sequenced are marked and numbered, corresponding to band numbers in Table 3.

FIG. 5.

FIG. 5.

Multidimensional scaling diagrams (with stress values) of Dice distance matrices calculated from DGGE banding patterns of samples collected in spring (A), summer (B), and fall (C). Solid symbols represent real DGGE banding patterns. Open symbols represent artificial banding patterns from which estuarine bands were removed. Symbols representing unfiltered water samples are connected with lines according to the salinity gradient. Symbols representing 1-μm- screened samples are either the closest symbols to the unfiltered samples or are connected to the unfiltered samples with a line. Salinity of samples is indicated.

FIG. 6.

FIG. 6.

DGGE gel of select samples from three sampling series indicating bands from which DNA was sequenced. Parentheses indicate bands containing DNA with sequence identical to a previously sequenced band. Numbers correspond to the band numbers in Table 3.

FIG. 7.

FIG. 7.

Minimum evolution trees showing phylogenetic positions of organisms within α-Proteobacteria (A), β- and γ-Proteobacteria (B), Bacteroidetes (C), Actinobacteria (D), and cyanobacteria and chloroplasts (E). Sequences from this study are in boldface type, with origin indicated. Labels on square brackets indicate the phylogenetic cluster (11, 47) and environmental sources of clones and isolates. Each set of identical sequences (100% similarity) was treated as a single sequence during analyses. Bootstrap values for distance and parsimony estimations are shown when both values are greater than 50. Analyses were based on alignments of 133 to 157 bp, including the hypervariable region in helix 18 (40).

FIG. 7.

FIG. 7.

Minimum evolution trees showing phylogenetic positions of organisms within α-Proteobacteria (A), β- and γ-Proteobacteria (B), Bacteroidetes (C), Actinobacteria (D), and cyanobacteria and chloroplasts (E). Sequences from this study are in boldface type, with origin indicated. Labels on square brackets indicate the phylogenetic cluster (11, 47) and environmental sources of clones and isolates. Each set of identical sequences (100% similarity) was treated as a single sequence during analyses. Bootstrap values for distance and parsimony estimations are shown when both values are greater than 50. Analyses were based on alignments of 133 to 157 bp, including the hypervariable region in helix 18 (40).

References

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