Phytoplankton blooms on the South African west coast and programmed cell death in microbial communities

Abstract

Phytoplankton blooms on the west coast of South Africa within the southern Benguela upwelling system are increasing in incidence and severity. The roles of physical oceanographic and meteorological conditions in initiating these blooms have been largely resolved. What remains unresolved are questions about the biology and ecology of bloom organisms and how to untangle these from abiotic factors. Furthermore, the blooms last for several weeks and then collapse. The demise of these blooms raises questions about mechanisms of phytoplankton mortality. A variety of abiotic and biotic stress conditions induce a genetically controlled and active type of cell death called programmed cell death (PCD) in phytoplankton. Therefore, algal blooms have emerged as an ideal environment for studying PCD. In this thesis, I investigated phytoplankton bloom events on the west coast of South Africa. Using molecular phylogeny (18S and 28 rRNA) and electron microscopy (SEM and TEM) the causative organism of a major harmful algal bloom (HAB) event in 2015 was identified. The community composition dynamics of these algal blooms can be investigated using massively parallel sequencing (MPS) through the 18S rRNA gene. A computational pipeline for in silico assessing primers called Piscator (https://github.com/PiscatorX/piscator-pipeline) was developed to identify the best performing primers for studying algal blooms. Combining MPS of the 18S gene and metatranscriptomics analysis, I investigated the dynamics of community composition and gene expression patterns of a diatom-dominated bloom in March 2018. Evidence of gene expression of proteolytic proteases called metacaspases involved in the PCD pathway was documented. The community-level effects of PCD were evaluated in light of the Black Queen Hypothesis (BQH). Using existing studies and theoretical frameworks, I found that PCD may function as a BQ in microbial communities. Furthermore, I also provided arguments for using more structured frameworks such as the multilevel selection theory to understand the selection of PCD in phytoplankton. This thesis contributes to the existing literature by providing new empirical findings on the causative organisms, community composition dynamics, gene expression patterns and metacaspase expression in algal blooms on the South African west coast. In addition, anew theoretical framework for the role of PCD in microbial communities is provided