Diversity and metabolism of marine bacteria cultivated on dissolved DNA

Abstract

Dissolved DNA (dDNA) is a potentially important source of energy and nutrients in aquatic ecosystems. However, little is known about the identity, metabolism, and interactions of the microorganisms capable of consuming dDNA. Bacteria from Eel Pond (Woods Hole, MA) were cultivated on low-molecular-weight (LMW) or high-molecular-weight (HMW) dDNA, which served as the primary source of carbon, nitrogen, and phosphorus. Cloning and sequencing of 16S rRNA genes revealed that distinct bacterial assemblages with comparable levels of taxon richness developed on LMW and HMW dDNA. Since the LMW and HMW dDNA used in this study were stoichiometrically identical, the results confirm that the size alone of dissolved organic matter can influence bacterial community composition. Variation in the growth and metabolism of isolates provided insight into mechanisms that may have generated differences in bacterial community composition. For example, bacteria from LMW dDNA enrichments generally grew better on LMW dDNA than on HMW dDNA. In contrast, bacteria isolated from HMW dDNA enrichments were more effective at degrading HMW dDNA than bacteria isolated from LMW dDNA enrichments. Thus, marine bacteria may experience a trade-off between their ability to compete for LMW dDNA and their ability to access HMW dDNA via extracellular nuclease production. Together, the results of this study suggest that dDNA turnover in marine ecosystems may involve a succession of microbial assemblages with specialized ecological strategies.

FIG. 1.

Unrooted phylogenetic tree for 16S rRNA gene sequences from bacterial assemblages that developed on LMW and HMW dDNA. The numbers in parentheses are the numbers of clones in clades.

FIG. 2.

CFUs from enrichments containing no added DNA (i.e., control), HMW dDNA, and LMW dDNA. The data are means ± standard errors of the means. The P value was determined by a one-way ANOVA.

FIG. 3.

Representative growth curves for some of the major groups of marine bacteria enriched on dDNA. Bacterial strains were originally isolated from LMW dDNA enrichments and then inoculated into either LMW or HMW dDNA liquid medium. The data are means ± standard errors of the means. The P values were determined by repeated-measures ANOVA. Note that the scales on the y axes are different in different panels. OD 600, optical density at 600 nm.

FIG. 4.

Ethidium bromide assay used to document HMW dDNA degradation. (A) Negative control stained with ethidium bromide; (B) positive control with a 50-μl drop of DNase I spotted in the middle of the plate, followed by ethidium bromide staining; (C) bacterial activity resulting in 13% HMW dDNA degradation; (D) bacterial activity resulting in 65% HMW dDNA degradation. The images in panels C and D were obtained after ethidium bromide staining of HMW dDNA plates which had incubated for 10 days following spotting of a cell suspension in the center of each plate.

FIG. 5.

Rates of HMW dDNA degradation determined by the ethidium bromide assay for strains originally isolated from LMW and HMW dDNA enrichments. The P value was determined by a t test.