Combined imaging and molecular techniques for evaluating microbial function and composition: A review

Abstract

In most cases, microbial function will determine the direction and onset of specific metabolic pathways as defined by their favorable thermodynamic outcome. Thus, the degree of chemical alteration in contact with minerals and bacteria can be directly proportional to the biological activity. This activity can influence redox conditions both from a localized perspective and global scale. Under these conditions, microscale mechanisms become important, impacting both molecular diffusion and the distribution of substrates and products. Visualizing microorganisms in their natural environments is no simple task and requires analytical tools that can measure cell function and chemical speciation at the sub‐micrometer level. In the last decade, the scientific community has observed a rapid increase in development of advanced imaging methods (eg, high‐resolution secondary mass spectrometry [NanoSIMS]) and synchrotron‐based approaches such as scanning transmission X‐ray microscopy (STXM). Coupled to culture‐independent techniques (eg, next generation sequencing technologies), these combined approaches excel at exploring microbial/mineral and sediment dynamics leading to valuable insight into both structure and function of single cells and diverse microbial communities in engineered and natural environments. This review focuses on recent advances in high‐resolution imaging and molecular‐based tools used to characterize microbial communities and function within natural systems. Copyright © 2017 John Wiley & Sons, Ltd.