Problems posed by natural environments for monitoring microorganisms

Microorganisms in natural environments have evolved to withstand fluctuations in physical and chemical conditions. This means that they often manifest very different biochemical and morphological features compared with those seen during laboratory culture. A major limitation in natural ecosystems is nutrient limitation under which microorganisms are exposed to starvation conditions and grow slowly or not at all. This review identifies the role of inimical processes on microbial properties such as the responses to starvation that may result in the adoption of viable but nonculturable (VBNC) states, discusses the problems that altered physiological states pose for detection and identification and highlights novel methods that have been developed to circumvent these difficulties. These factors dictate that to survive and respond to environmental stimuli, a cell must have evolved sophisticated programs of gene expression. These include the sigma factor rpoS that directs RNA polymerase to transcribe genes whose expression aids survival during severe nutrient limitation or cell-cell communication systems that promote a concerted population response termed quorum sensing.