Advances in Phytoplankton Ecology Applications of Emerging Technologies

Phytoplankton ecology has developed from an understanding of taxonomy, species dynamics and functional roles, and species interactions with the surrounding environment. New and emerging technologies enable a paradigm shift in the ways we monitor and understand phytoplankton in a range of environments. Advances in Phytoplankton Ecology: Applications of Emerging Technologies is a practical guide to these new technologies and explores their application with case studies to show how recent advances have changed our understanding of phytoplankton ecology.

Part one of this book explores how traditional taxonomy and species identification has changed, moving from morphological to molecular techniques. Part two explores the new technologies for remote and automatic monitoring and sensor technology and applications for management. Part three explores the explosion of omics techniques and their application in species identification, functional populations, trait characterization, interspecific interactions, and interaction with their environment.

This book is an invaluable guide for marine and freshwater ecology researchers to how new technologies can enhance our understanding of ecology.

Introduction: Traditional ecology into the future
Lesley A. Clementson, Ruth S. Eriksen and Anusuya Willis

Part 1: Phytoplankton taxonomy (brief review/introduction)
Ruth S. Eriksen
1.1 Cyanobacterial diversity and taxonomic uncertainty: polyphasic pathways to improved resolution
Glenn B. McGregor and Barbara C. Sendall
1.2. Uses of molecular taxonomy in identifying phytoplankton communities from the Continuous Plankton Recorder Survey
Rowena Stern, Declan Schroeder, Andrea Highfield, Manal Al-Kandari, Luigi Vezzulli and Anthony Richardson
1.3. Impact of molecular approaches on dinoflagellate taxonomy and systematics -
Christopher J S.. Bolch
1.4. From molecules to ecosystem functioning: insight into new approaches to taxonomy to monitor harmful algae diversity in Chile.
Jorge I. Mardones, Bernd Krock, Lara Marcus, Catharina Alves-de-Souza, Satoshi Nagai, Kyoko Yarimizu, Alejandro Clément, Nicole Correa, Sebastian Silva, Javier Paredes, and Peter Von Dassow

Part 2: Monitoring and sensing systems (brief review/introduction)
Lesley A. Clementson
2.1. Integrating Imaging and Molecular Approaches to Assess Phytoplankton Diversity
Lisa Campbell, Chetan Gaonkar and Darren W. Henrichs
2.2. Advances in in situ systems for phytoplankton research and monitoring
Matthew C. Smith, Levente Bodrossy and Pascal Craw
2.3. Applications of satellite remote sensing technology to analysis of phytoplankton community structure on large scales
Astrid Bracher, Robert J. W. Brewin, Áurea M. Ciotti, and Lesley A. Clementson, Takafumi Hirata, Tihomir Kostadinov, Colleen B. Mouw and Emanuele Organelli
2.4. Modelling phytoplankton processes in multiple functional types
Mark Baird, Stephanie Dutkiewicz, Anna Hickman, Mathieu Mongin, Monika Soja-Wozniak, Jennifer Skerratt, Karen Wild-Allen
2.5 Managing the societal uses of phytoplankton: Technology applications and needs
Andrew D.L. Steven

Part 3 Omics in aquatic ecology (brief review/introduction)
Anusuya Willis
3.1. Current applications and technological advances in quantitative real time PCR (qPCR): A versatile tool for the study of phytoplankton ecology
Kathryn J. Coyne, Yanfei Wang, Susanna A. Wood, Peter D. Countway and Sydney M. Greenlee
3.2. Phytoplankton diversity and ecology through the lens of high throughput sequencing technologies
Adriana Lopes dos Santos, Catherine Gerikas Ribeiro, Denise Ong, Laurence Garczarek, Xiao Li Shi, Scott D. Nodder, Daniel Vaulot and Andres Guitierrez Rodrigues
3.3 Comparative genomics for understanding intraspecific diversity
Anusuya Willis, Jason N. Woodhouse, Brett A. Neilan and Michele A. Burford
3.4. Transcriptomic and metatranscriptomic approaches in phytoplankton: insights and advances
Bethany C. Kolody , Matthew J. Harke, Sharon E. Hook and Andrew E. Allen
3.5. From Genes to Ecosystems: using molecular information from diatoms to understand ecological processes
John A. Berges, Erica B. Young, Kimberlee Thamatrakon and Alison R. Taylor
3.6 Global marine phytoplankton revealed by the Tara Oceans expedition
Flora Vincent, Federico M. Ibarbalz and Chris Bowler

Lesley completed a MSc (Melbourne University) and began her career as a biological oceanographer, but in the early 1990s expanded to marine bio-optics and ocean color validation in preparation for the launch of the first routine ocean color satellite sensor – SeaWiFS. She has established the leading bio-optical laboratory in the Southern Hemisphere and one of the leading bio-optical laboratories globally. Through participation in the NASA sponsored SeaHARRE experiments, Lesley’s method for pigment analysis in marine samples was assessed as world class for over 10 years. Lesley works on numerous projects both nationally and internationally on a broad range of topics relating to phytoplankton ecology. She was awarded the Australian Marine Science Association’s National Technical Award in 2016 and was inducted to the Tasmanian Honour Roll for Women for contributions to science in 2017. Lesley, a Principal Research Scientist in CSIRO Oceans and Atmosphere, has been a Research Group Leader of the Coasts program and a team leader of the Algal Ecology and Resources team.
Ruth completed a PhD (University of Tasmania) in ecotoxicology, integrating the role of trace metal speciation on copper toxicity in marine and estuarine species. Through this project, she discovered the microscopic world of phytoplankton, which has subsequently become a passion and major area of research. Ruth established Tasmania's first NATA accredited phytoplankton testing facility and helped develop monitoring and detection programs for the salmonid and shellfish industries, focusing on HAB species. In her role in CSIRO Oceans and Atmosphere as a Research Biologist, she has completed several Antarctic voyages, focusing on lower trophic level interactions, biodiversity and biogeography. Major projects are on the IMOS National Reference Stations (NRS), the Australian Continuous Plankton Recorder (AusCPR) Survey, and the Southern Ocean Time Series (SOTS). Ruth currently holds an adjunct position with