Current applications and technological advances in quantitative real-time PCR (qPCR): a versatile tool for the study of phytoplankton ecology

This chapter presents an overview of quantitative real-time PCR (qPCR), with a focus on harmful algae blooms (HABs). It includes an overview of the technology and describes the early development of qPCR assays to detect cryptic species. A review of multispecies and ecotype- or strain-level detection approaches by qPCR is provided. This is followed by examples of qPCR to investigate factors impacting phytoplankton distributions and activities. Approaches to evaluate changes in gene expression are then presented, along with a case study investigating species-specific responses to nitrogen input. Recent advancements in qPCR are discussed, with a case study demonstrating the use of portable qPCR and a comparison to lab-based instruments, followed by a description of droplet digital PCR (ddPCR), a novel advancement in technology that resolves some key issues in the use of qPCR for environmental research and monitoring. The chapter ends with a discussion of efforts to adapt qPCR for community-based science programs, with the potential to enhance our understanding of phytoplankton ecology and improve predictive capabilities for HAB events.