Microbial oceanography of the Southern Ocean water masses

Microorganisms from all three domains of life - Bacteria, Archaea and Eukarya are the base of the marine food web and the key engines sustaining the marine nutrient budget via both primary production and nutrient remineralization. Microbial biogeography and ecology are closely tied to hydrography and the physical oceanographic processes related to the global ocean circulation. Within the Southern Ocean, understanding of the microbial biogeography is still at its infancy, particularly within the pelagic dark ocean which is a large reservoir of both microbes and organic matter available for microbial activity. The Southern Ocean is a region with pivotal influence on the global nutrient circulation and climate but is also a hotspot for the impacts of climate change. As microbial biogeography links both the causes and consequences of microbial interactions with their environment, there is an urgent need to better understand the biogeographic distribution of the Southern Ocean microbial community, the key players within this ecosystem. This thesis explores the microbial community composition within the full water column along several transects of the Southern ocean. High-throughput tag sequencing of microbial marker genes (16S and 18S rRNA genes) and bioinformatics analysis were used to examine the relationship of the community with environmental and geographical variables. The initial study considered the bacterial community from the Pacific and Indian sectors of the Southern Ocean. This work investigated if the bacterial community composition was strictly delineated by the hydrography of distinct water masses despite being geographically distant and tested the hypothesis if uniform environments of the abyssopelagic water masses promote a more homogenous microbiota. Extending previous findings, bacterial biogeography was explained in part by water mass hydrography, but also exhibited community composition variations at the family taxonomic level between sectors. Deeper water masses harbored a remarkably high bacterial beta-diversity across sites and was only weakly explained by water mass hydrography. Depth and bacterial lifestyle were major considerations in the influence of environmental factors on the Southern Ocean bacterial community composition. Subsequent work involved an expanded scope to include a high resolution (0.5-1 latitudinal degree interval) microbial sampling and analysis from surface to depth of a latitudinal transect within the South Pacific Ocean. Bacterial, archaeal and eukaryotic taxonomic profiles were constructed for each of the 1045 samples. All the microbial domains showed strong depth stratification but displayed varying patterns and intensities of delineation by water mass hydrography. These samples were used to focus in on the diversity of Phaeocystis, a ubiquitously distributed keystone phytoplankton with fundamental contributions to the marine carbon and sulfur cycles. Previous Phaeocystis studies have been centered primarily on its colonial forms, including massive blooms of Phaeocystis during the austral spring-summer. Through analysis of 18S rRNA gene sequences, this study showed that Phaeocystis was an abundant phytoplankton in high latitude waters even in the late autumn, contributing up to 12% of the eukaryotic sequences detected. Stable oceanographic fronts within surface waters were shown to structure the Phaeocystis community which also exhibited patterns of low diversity in a thriving community. P. globosa, a species commonly reported only within the northern hemisphere, was detected within the Subantarctic to Subtropical as well as equatorial upwelling regions. Overall, this thesis has provided the first high vertical and spatial resolution genomics survey of the Southern Ocean, filling in critical knowledge gaps of Southern Ocean microbial oceanography, and represents an important first step towards a microbial atlas of the Southern Ocean.