Activity of abundant and rare bacteria in a coastal ocean

Abstract

The surface layer of the oceans and other aquatic environments contains many bacteria that range in activity, from dormant cells to those with high rates of metabolism. However, little experimental evidence exists about the activity of specific bacterial taxa, especially rare ones. Here we explore the relationship between abundance and activity by documenting changes in abundance over time and by examining the ratio of 16S rRNA to rRNA genes (rDNA) of individual bacterial taxa. The V1-V2 region of 16S rRNA and rDNA was analyzed by tag pyrosequencing in a 3-y study of surface waters off the Delaware coast. Over half of the bacterial taxa actively cycled between abundant and rare, whereas about 12% always remained rare and potentially inactive. There was a significant correlation between the relative abundance of 16S rRNA and the relative abundance of 16S rDNA for most individual taxa. However, 16S rRNA:rDNA ratios were significantly higher in about 20% of the taxa when they were rare than when abundant. Relationships between 16S rRNA and rDNA frequencies were confirmed for five taxa by quantitative PCR. Our findings suggest that though abundance follows activity in the majority of the taxa, a significant portion of the rare community is active, with growth rates that decrease as abundance increases.

Fig. 1.

Classification of bacterial OTUs and variation over 3 y. The OTUs were divided into three categories: mostly abundant (occurring >50% of the time), cycling (<50% of the time), and always rare (<1% abundance in all samples). (A) Percentage of OTUs in the three groups and the percentage of sequences within each group. (B) Phylogenetic classification of bacterial OTUs found in Delaware coastal waters.

Fig. 2.

Relationships between 16S rRNA and 16S rDNA frequencies of bacterial OTUs defined in the pyrosequence dataset. The points are paired 16S rRNA and rDNA frequencies for each individual OTU and time point. Circled points are discussed in the main text. The dotted line is the 1:1 line.

Fig. 3.

Relative abundance of 16S rRNA vs. rDNA for selected dominant taxa over 3 y. SAR11 (A) and Rhodobacteriaceae (B). Solid lines were determined by linear regression, and the dashed lines are 1:1 relationships.

Fig. 4.

Relationship between 16S rRNA and 16S rDNA for selected OTUs as indicated by the tag dataset (A) and by quantitative PCR (B).