Central role of the cell in microbial ecology

Abstract

Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.

FIG. 1.

Microbial growth can be directly determined without the use of molecular biology techniques. Methods used to determine optical density or cell numbers vary in their sensitivity. (A) Visualizing the turbidity of a culture with the naked eye allows detection of ∼10⁵ cells/ml. (B) Observing cells under the microscope allows detection of ∼10³ cells/ml. (C) The use of a flow cytometer in combination with encapsulation of cells detects up to 10¹ cells total. (D) Growth (division) of single microbial cells can be monitored by microscopy, and cells can subsequently be isolated using microfluidic and micromanipulation devices. In addition to microscopy, flow cytometry also allows for detection and isolation of individual cells.

FIG. 2.

A combinatorics example illustrates the vast number of medium combinations possible by variation of its components. Starting with a standard medium containing 33 components (plus water) and changing one component at a time (gray line) led to 33 different media. Accounting for variants in concentrations (increasing or decreasing concentration for each component [black line]) resulted in 66 different medium combinations. Depending on the total number of components in the medium that will be varied to account for inhibitory effects, the potential number of combinations will reach over 10⁹ (for one component at a time [gray line]) and 10¹⁴ (to account for two variations in concentration).

FIG. 3.

Two growth curves of E. coli (optical density [OD] at 660 nm [red line]) and a methanogenic consortium (gas production in ml [black line]) plotted in the same graph over time (days) illustrate two extremes in microbial growth rates. Successful cultivation of microorganisms depends on the growth stage of the organisms and the correct timing of isolation. After 2 years of cultivation, the methanogenic consortium exhibited exponential growth, while viable cells from the E. coli culture could no longer be recovered. (Adapted from reference by permission from Macmillan Publishers Ltd., copyright 1999.)

FIG. 4.

Top-down and bottom-up approaches in microbial ecology, spanning orders of magnitude in spatial resolution. Top-down approaches (including but not limited to biodiversity assessments, rate measurements, isotope signature determination, and various “-omics” studies) utilize data sets which are in general not organism (individual) specific. Interpretation of these data often relies on previous knowledge (e.g., in the form of a molecular biology database). Bottom-up approaches (e.g., cultivation or single-cell techniques and various “-omics” methods) focus on single organisms. Knowledge gained by studying individual organisms or defined communities is consequently extrapolated to larger communities and the environment. Both concepts have advantages and limitations (see text) and are clearly dependent on the scientific goal.