Abstract
The ocean is the largest biome on Earth and hosts an immense diversity of marine microorganisms. These include prokaryotes (bacteria and archaea), protists, fungi, viruses and microzooplankton. They form the base of marine food webs and sustain higher trophic levels through their critical role in the ocean carbon cycle and many other biogeochemical processes. Microorganisms are found across a large variety of ecosystems and show both global and local biogeographical distribution patterns. Different types of microbial organisation, e.g. free-living and surface-attached, led to a multifarious lifestyle. Over time, the specialized nature of both environmental lifestyles resulted in the development of unique communities with different capabilities. In this thesis both lifestyles were studied, and a further distinction between biotic and abiotic surface associated communities was made.
Climate change related stressors in the ocean have been linked to multiple changes that threaten the marine environment, such as increased sea surface temperature, ocean acidification, and deoxygenation. These changes have already impacted the structure, composition, and function of microorganism communities in several marine habitats. However, due to the large diversity that exists within the prokaryotic and eukaryotic groups, a lot is still unknown. In order to detect and quantify short-term and long-term responses to environmental change, baseline studies are needed that show the natural spatial and temporal variability within and between communities. This was the main objective in this thesis, to characterize microbial communities in different unique ecosystems by applying 16S and 18S amplicon sequencing and thereby providing a framework for future studies on climate change and future work on interspecies and interkingdom interactions.
In Chapter 2 free-living protist communities were studied along the Munida transect, off the east coast of the South Island, New Zealand. The transect is defined by Neritic Water, Subtropical Water, the Southland Front and sub-Antarctic Surface Water. The five-year study of protist communities along the transect employed amplicon sequencing of the 18S rRNA gene and optical methods (flow cytometry and FlowCam) to reveal spatiotemporal patterns and size distributions of the protist assemblages. The Southland Front was found to be a diversity hotspot with strong temporal structuring. The different water masses were primarily dominated by pico- and nanophytoplankton throughout the year, but only supported distinct protist communities amongst all four water masses in spring. The strongest differentiation in protist communities was found between the subtropical and sub-Antarctic water mass and was not only limited to spring but consistent all-year round. In addition, samples were taken during a marine heatwave (MHW) and allowed for the characterisation of potential heatwave induced community shifts. During the MHW, protist diversity was highly reduced across the Southland Front and the communities were dominated by a dinoflagellate parasitoid species (Syndiniales). A substantial increase was also found in the small green algae Chloropicophyceae. These results demonstrate direct evidence of the importance of long-term studies and the provision of baseline data to detect environmental changes.
In a temperate Macrocystis pyrifera dominated kelp forest (Karitane, New Zealand), biofilm community composition and development was characterised over a small spatial scale (~200 m) using settlement plates (Chapter 3). Biofilm community succession was compared between the interior and exterior kelp bed, for prokaryotic (16S rRNA) and eukaryotic (18S rRNA) communities. At high taxonomic level the prokaryotic communities did not reveal any patterns, while eukaryotes showed obvious successional shifts and structural differences across the kelp bed. Overall, a delay in succession was observed at the exterior kelp bed for both kingdoms, likely due to wave disruption. For prokaryotic communities, the delayed development caught up with the interior biofilms after 20 days, while eukaryotic communities remained completely distinct between the two locations for the duration of the study (32 days). Overall, this study suggests that during early biofilm development prokaryotic communities are more strongly structured by inter-species interactions rather than the environment. The opposite trend was observed for the eukaryotic communities.
The biofilm taxonomic compositions of both prokaryotic and eukaryotic communities were additionally used in Chapter 4 for a comparison with M. pyrifera blade-associated microbial assemblages. Kelp are increasingly being threatened by direct and indirect anthropogenic stressors and therefore characterising the diversity and composition of the kelp microbiome will aid in understanding how and to what extent the microbiome contributes to kelp health. Distinct communities were observed between the kelp blades, the settlement plates and seawater. However, some generalist colonising species were present on both the kelp surface and the settlement plates (e.g. Microtrichaceae, E. siliculosus, and Trochilia sp.), while others were considered to be kelp-specific (e.g. Blastopirellula, Persicirhabdus, Granulosicoccus, and U. leptochaeta). Epi-endophytic prokaryotic and eukaryotic communities developing on young (meristem) and old (apex) kelp blade tissue, proved to be distinct from one another, from seawater communities, and from biofilms on the settlement plates. The spatial structuring along the kelp blade was also associated with a higher diversity of microorganisms on the blade apex. Further, a higher similarity was found for the eukaryotic biofilms between the kelp blade meristem and the young biofilms on the settlement plates than for the prokaryotic assemblages between those sample types. Overall, the kelp exerted a higher selection pressure on the prokaryotic communities compared to the eukaryotic epi-endobionts.
To look at the possible responses of tropical biofilm communities to future ocean acidification, settlement plates were deployed near a CO2 vent system in Dominica, Lesser Antilles (Chapter 5). Unique biofilm communities were found at the high pCO2 site (~575 µatm) with species replacement being the driving force for the change in biofilm composition compared to the control site. Successional shifts during biofilm development were observed sooner at the acidified site suggesting a faster biofilm development. A higher phytoplankton biomass was present at the high pCO2 site which was indicated by elevated chlorophyll-a concentrations. Additionally, microeukaryotic diversity increased under elevated pCO2 levels, which included an increase in relative abundance of the toxin producing dinoflagellate Alexandrium and a small shift towards chain-forming diatom species.
Overall, this thesis established an important baseline of protist community composition, diversity and seasonality, and of biofilm composition and development. Thereby providing a framework for future studies looking at changes in free-living protist communities in the western South Pacific, and biofilm community dynamics in coastal ecosystems, including M. pyrifera associated microbiome interactions. This thesis also provided clear evidence of changes in microbial community composition and diversity in response to a marine heatwave event and ocean acidification. These findings have a wider application as they can be used to predict microbial responses to future environmental interruptions. However, more research is needed to identify the nature of these changes and the impact they have on the whole ecosystem.