Techniques for Quantifying Phytoplankton Biodiversity

Abstract

The biodiversity of phytoplankton is a core measurement of the state and activity of marine ecosystems. In the context of historical approaches, we review recent major advances in the technologies that have enabled deeper characterization of the biodiversity of phytoplankton. In particular, highthroughput sequencing of single loci/genes, genomes, and communities (metagenomics) has revealed exceptional phylogenetic and genomic diversity whose breadth is not fully constrained. Other molecular tools-such as fingerprinting, quantitative polymerase chain reaction, and fluorescence in situ hybridization-have provided additional insight into the dynamics of this diversity in the context of environmental variability. Techniques for characterizing the functional diversity of community structure through targeted or untargeted approaches based on RNA or protein have also greatly advanced. A wide range of techniques is now available for characterizing phytoplankton communities, and these tools will continue to advance through ongoing improvements in both technology and data interpretation.

Antarctic phytoplankton community composition and size structure: importance of ice type and temperature as regulatory factors

“…FCM, however, provides fundamental information (for the ≤ 20 µm size fraction) on the abundances of the various populations while enhancing the ability to differentiate important physicochemical correlations with phytoplankton community structure and thus provides a vital tool for studying phytoplankton dynamics. The addition of large cell flow cytometry and high through-put sequencing of sorted phytoplankton populations (Eiler et al 2013;Johnson and Martiny 2015;Massana et al 2015;Visco et al 2015), would enhance analysis of the phytoplankton community.…”

Dimensions of marine phytoplankton diversity

“…Additional data are derived from separate measurement of size and growth: these are shown as light lines centred at the mean and arms covering range. These are for the pico-prokaryotes (green) Prochlorococcus and Synechococcus (Morel et al, 1993;Johnson et al, 2006;Christaki et al, 1999;Moore et al, 1998;Agawin and Agustí, 1997) and the diazotrophs (light blue) Crocosphaera and Trichodesmium (Garcia and Hutchins, 2014;Webb et al, 2009;Wilson et al, 2017;Bergman et al, 2013;Boatman et al, 2017;Breitbarth et al, 2008;Hutchins et al, 2007;Kranz et al, 2010;Shi et al, 2012). of group-specific accessory pigments) and scattering of light. The absorption spectra are flatter with larger sizes following Finkel and Irwin (2000) to account for self-shading, and scattering spectra are also influenced by size following Stramski et al (2001) (see Text S1.3, Fig.…”

Niche partitioning and biogeography of high light adapted Prochlorococcus across taxonomic ranks in the North Pacific

“…These broad ecogenomic patterns appear even more complex, in light of recent studies that show Prochlorococcus clades can be composed of hundreds of sub-populations that apparently diverged a few million years ago and possibly represent ancient niche partitioning (Kashtan et al, 2014;Johnson and Martiny, 2015). This 'micro-diversity' is a dominant feature of broader bacterial communities (Acinas et al, 2004), but how micro-diversity maps onto a hierarchical genomic diversification framework or its impact on microbial community structure and function remain unclear (Koeppel et al, 2008) in spite of some evidence of its importance for ecological specialization (Hunt et al, 2008;Yung et al, 2014).…”