Evaluating rRNA as an indicator of microbial activity in environmental communities: limitations and uses

Abstract

Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the 'active' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population's growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.

Figure 1

Microorganism metabolic states and their contribution to ecosystem functioning. Viable microorganisms exist in one of three general metabolic states that are all subject to mortality. Definitions of terms: Growing—cells are actively dividing, Active—cells are measurably metabolizing (catabolic and/or anabolic processes) but are not necessarily dividing, Dormant—cells are not measurably dividing or metabolizing, Deceased—cells are not metabolically active or capable of becoming metabolically active in the future, but intact macromolecules may persist.

Figure 2

From ribosome cycling to microbial activity: factors that affect ribosome quantities and their relationship to microbial activities. Life strategy is defined here as the potential physiological responses, hardwired via DNA into an organism or population, toward two competing goals: surviving and reproducing.