Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter

Abstract

We used a method that combines microautoradiography with hybridization of fluorescent rRNA-targeted oligonucleotide probes to whole cells (MICRO-FISH) to test the hypothesis that the relative contributions of various phylogenetic groups to the utilization of dissolved organic matter (DOM) depend solely on their relative abundance in the bacterial community. We found that utilization of even simple low-molecular-weight DOM components by bacteria differed across the major phylogenetic groups and often did not correlate with the relative abundance of these bacterial groups in estuarine and coastal environments. The Cytophaga-Flavobacter cluster was overrepresented in the portion of the assemblage consuming chitin, N-acetylglucosamine, and protein but was generally underrepresented in the assemblage consuming amino acids. The amino acid-consuming assemblage was usually dominated by the alpha subclass of the class Proteobacteria, although the representation of alpha-proteobacteria in the protein-consuming assemblages was about that expected from their relative abundance in the entire bacterial community. In our experiments, no phylogenetic group dominated the consumption of all DOM, suggesting that the participation of a diverse assemblage of bacteria is essential for the complete degradation of complex DOM in the oceans. These results also suggest that the role of aerobic heterotrophic bacteria in carbon cycling would be more accurately described by using three groups instead of the single bacterial compartment currently used in biogeochemical models.

FIG. 1

Micrograph of bacteria assayed by MICRO-FISH. (A) DAPI-stained bacteria (UV excitation). Dark spots surrounding cells are silver grains deposited in photographic emulsion around cells that took up a mixture of tritiated free amino acids. Less than 0.6% of cells in formaldehyde-killed controls had silver grains. (B) Bacteria hybridized with Cy3-labeled oligonucleotide probe Eub338 for eubacteria (green excitation). Cells with bound probe fluoresce yellow. Magnification, ×1,350.

FIG. 2

Community composition and consumption of chitin, NAG, protein, and amino acids by the major phylogenetic groups of bacterioplankton in the Roosevelt Inlet, assayed by MICRO-FISH. (A) Composition of bacterioplankton communities in incubations containing tritiated compounds. (B) Relative abundance of phylogenetic groups of bacteria consuming various tritiated compounds. Less than 3% of the cells were gram positive. Cells binding none of the group-specific probes are indicated (Not identified). Percentages were calculated relative to total bacteria counted by using DAPI, although the eubacterial probe (Eub338) detected on average 80% of bacterial abundance. proteobact., proteobacteria; Flavobact., Flavobacter.

FIG. 3

Community composition and consumption of chitin, NAG, protein, and amino acids by the major phylogenetic groups of bacterioplankton in the Indian River Inlet, assayed by MICRO-FISH. (A) Composition of bacterioplankton communities in incubations containing tritiated compounds. (B) Relative abundance of phylogenetic groups of bacteria consuming various tritiated compounds. Less than 3% of the cells were gram positive. Cells binding none of the group-specific probes are indicated (Not identified). Percentages were calculated relative to total bacteria counted by using DAPI, although the eubacterial probe (Eub338) detected on average 80% of the bacterial abundance.

FIG. 4

Relationship among the phylogenetic classifications of bacteria consuming chitin (A), NAG (B), protein (C), and amino acids (D) versus phylogenetic classification of cells identified as eubacteria. Bacteria were classified by using rRNA-binding oligonucleotide probes specific for α-proteobacteria (α), β-proteobacteria (β), γ-proteobacteria (γ), and the Cytophaga-Flavobacter group (C). Data points falling above the 1:1 line indicate phylogenetic groups enriched in the portion of the assemblage consuming the compound. Results are from coastal (Fig. 2) and estuarine (Fig. 3) environments. Percentages were calculated relative to the numbers of cells identified as eubacteria with the Eub338 probe.