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.qPCR | seed bank | SAR11 | microbial observatory | kill the winner

Vertical Distribution of Functional Potential and Active Microbial Communities in Meromictic Lake Kivu

“…The experimental evaluation suggests that the quantification of functional genes by qPCR was mostly in agreement with the pyrosequencing of complex microbial communities. This study showed that rare taxa (mainly specialists), especially in the anoxic zone, cannot solely be characterized as a seed bank or dormant cells in Lake Kivu but that a significant portion of the rare community is potentially active, which supports the results of various studies conducted in freshwater and marine environments [13,14]. However, the impact of environmental parameters measuredwas stronger for the generalists (mainly abundant taxa), which indicates the presence of different ecological rules for different groups.…”

“…In contrast, rare OTUs were detected in a high proportion exclusively in either bulk or potentially active bacterial communities. As suggested for estuarine and coastal ocean waters, the metabolically active rare biosphere of Lake Kivu might be potentially important for the functioning and the temporal dynamics of microbial communities as they shift between seasons [13][14][15].…”

“…Even though potential biases can be introduced during DNA and RNA extraction, complementary DNA (cDNA) synthesis, and PCR amplification [12], parallel comparisons of DNA-and RNA-based pyrosequencing approaches can help differentiate whether abundant taxa are active or whether rare but active taxa exist. In addition, stronger evidence on the links between biogeochemical processes and microbial communities might be obtained if active communities are monitored rather than bulk communities [13][14][15][16].…”

Deciphering associations between dissolved organic molecules and bacterial communities in a pelagic marine system

“…A Mantel test confirmed strong correlations between DNA and RNA-based BC compositions at all phylogenetic levels (Po0.01; Supplementary Table S4), similar to a previous report on samples collected off the US-American east coast (Campbell et al, 2011). Bacteria of the orders Flavobacteriales and Rhodobacterales were the most abundant taxa.…”

“…Calculated rarefaction curves, as well as diversity indices (data not shown), revealed that our surveying effort discovered the majority of-yet not all-the bacterial species and phyla (480%) at 3% and 20% genetic distance. The active community yielded a higher number of OTUs than the total BC, resulting in a DNA/RNA ratio of OTU richness ranging from 0.76 to 0.88 and denoting that a significant portion of the rare taxa may be proportionally more active (Jones and Lennon, 2010;Campbell et al, 2011;Wilhelm et al, 2014). The percentage of OTUs that appeared in both, the RNA …”