Investigation of the biodiversity and biogeography of marine microbes in Australian tropical waters

Marine microbes (including bacteria, archaea, protists, fungi and viruses) play a fundamental role in natural systems. They are not only responsible for almost half of global primary production but also process about one-half of the global biogeochemical flux of biologically important elements, such as carbon, nitrogen, phosphorus, sulphur and iron. Although they are ubiquitous and diverse in the ocean, it is difficult to characterize them due to their small size. In recent years, the development of molecular analysis and high-throughput sequencing has unveiled a large amount of novel diverse assemblages of marine microbial communities and how they are distributed over space and time. Our seawater samples were collected from Darwin to Cairns across the Arafura Sea, Torres Strait and Coral Sea during an oceanographic transect through this region in the austral spring of 2012. These basins are fully tropical and frequently hit by tropical cyclones. The Arafura Sea and Torres Strait have shallow seafloor depth, and have been identified as one of the most pristine marine environments, least impacted by human activities. This basin has been classifiedas part of the highly productive North Australian Large Marine Ecosystem. The Coral Sea is an open sea, which includes the world's largest coral reef system. The nutrient concentrations and primary production are typically very low in the euphotic zone of this basin. Although these Australian tropical basins have peculiar environmental variables and marine ecosystems, thebiodiversity and biogeography of their marine microbial communities have not been investigated systematically using molecular techniques. In this PhD thesis, we determined the abundance of autotrophic unicellular phytoplankton in the surface seawaters by flow cytometry using the fluorescence of natural photosynthetic pigments (such as chlorophyll and phycoerythrin). Generally, plastidic protist abundances were consistently lower than those of Cyanobacteria across all sampling sites. Synechococcus cell abundances ranged from 1×10⁴ to 3×10⁵ cells mL-¹ in the Arafura Sea/Torres Strait and from1×103 to 6×10⁴ cells mL-¹ in the Coral Sea. Prochlorococcus cell numbers were much higherin the Coral Sea (1-4.5×10⁵ cells mL-¹) than Synechococcus. Secondly, we reported the first investigation of marine microbial community composition at the surface of Northern Australian tropical waters using 16S and 18S rRNA gene amplicon sequencing. Throughout all of the samples, the dominant representative groups of prokaryotes included Synechococcus, Prochlorococcus and the SAR11 clade. The eukaryotic assemblages were found to be dominated by SAR supergroups (Stramenopiles, Alveolates and Rhizaria) and Archaeplastida across all sampling sites. Microbial abundances analysis showed distinct biogeographic patterns, for example, Synechococcus was the most abundant group in the Arafura Sea/Torres Strait but Prochlorococcus dominated in the Coral Sea; diatoms had a much higher abundance in the Arafura Sea/Torres Strait, whereas the Syndiniales and Cnidaria showed an opposite trend with higher abundances in the Coral Sea. Thirdly, we surveyed the diversity of marine prokaryotic and protistan community within the photic zone of the Northern Australian tropics from depths between 25 and 150 metres. The dominant groups of marine microbial community in the euphotic zone of these sampling areas have similar patterns with their structure in the surface seawaters. However, their abundances showed different vertical distribution. Generally, the phototropic plankton dominated at the upper surface layer of sampling sites and their abundance slowly decreased with depth, but the relative abundance of heterotrophic, mixotrophic or parasitic marine microbes showed an opposite trend. In addition, multivariate statistics suggested that the distribution patterns of microbial community structure in the surface waters was strongly driven by salinity, temperature and nutrient availability, with phosphate, nitrogen and silicate concentrations being particularly important. Furthermore, besides the environmental drivers, the seafloor depth in the Arafura Sea/Torres Strait (shallow basin) and the sampling depth in the Coral Sea (deep basin) were also the important factors influencing marine microbial community composition in the euphotic layer of Australian tropical waters. Overall, this study provides critical insights into patterns of local distribution of abundant microbial producers, which will provide information of great relevance to our understanding of what drives primary productivity in Australian oceans. Our research also addressed the factors that determine why different genetic groups are abundant in one location but not another. The findings help us to answer the fundamental question of how organisms adapt to a particular environmental niche. This knowledge will not only enhance our capacity to predict the resilience of ocean ecosystems and their response to climate-change, but also will help provide clarity on investment choices for a sustainable ecosystem/environment and increase healthy outcomes from activities involving human-ocean interactions such as recreation, food production, fisheries and tourism in Australian waters.