Study on the diversity and ecological functions of bacterial communities in the Southern Ocean

Abstract

The prokaryotes play significant roles in the biogeochemical cycles and remineralization of organic materials in the marine ecosystem. The Southern Ocean (SO) is of global significance because of its role against global warming through the absorption of carbon dioxide and formation of cold Antarctic bottom water. Since ecological functions of microorganisms including carbon fixation and nutrient cycling in SO are directly linked to the global ecosystem, understanding or prediction of the microbial functions in SO is important. However, few studies regarding diversity and ecological functions of bacteria in SO have been performed until now mainly due to the difficulties in access to this area. In addition, most studies on the bacterial diversity were performed by traditional molecular approaches such as fingerprinting and clonal sequencing of 16S rRNA gene and it led to limited understanding of the full extent of diversity. In this study, to expand the knowledge on the bacterial diversity of seawater and sediments in the SO, high-throughput sequencing of 16S rRNA gene was applied. Moreover, since the patterns of bacterial diversity are largely determined by physicochemical parameters, the relationship between the bacterial diversity and environmental factors was explored to provide insights into the change pattern of each bacterial group. In addition, as a basis of physiological studies, bacterial culture from marine sediments was performed and the physiological characteristics of culturable bacteria were investigated. Finally, to understand the metabolic potential and ecological functions of JS1 lineage of Atribacteria, a predominant but uncultivated bacterial group in anoxic marine sediment, single cell genomics was applied to analyze the genomic features. Bacterial diversity of seawaters and the sediments was analyzed according to regional and local scale. On the regional scale study, bacterial community structure of the surface seawaters across 1600 to 3000 km in SO according to the frontal systems was investigated. On the local scale study, the vertical and horizontal variability of bacterial communities in the seawater and sediments of the Ross Sea was performed. Characterization of the bacterial communities at different water depths was performed at greater resolution covering various regions over the Terra Nova Bay (TNB) of the Ross Sea. In addition, the dynamics of the bacterial community in surface waters was carried out to investigate whether the surface water bacterial community is affected by the local conditions such as distance from glacier front or land. The benthic bacterial diversity, along with the spatial variability in the Ross Sea including sediments from Australian-Antarctic Ridge was analyzed. The regional study revealed that three bacterial groups, Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria dominated in seawaters in the SO. Regardless of the dominance of these three groups, relative abundance of Cyanobacteria and Actinobacteria diminished or disappeared in the south of Subantarctic Front and Verrucomicrobia and SAR406 was not recovered in south of Polar Front indicating the distribution of specific group is influenced differently by fronts. The clear biogeographic pattern in the bacterial communities according to the frontal systems was revealed implying the different and distinct metabolic traits and functions exist in each frontal zone. In addition, bacterial communities were clearly divided by the Subantarctic Front and Southern Boundary, the northernmost and southernmost boundaries of the Antarctic Circumpolar Current (ACC), respectively, showing significant correlations with environmental variables. Among the physicochemical variables with strong correlation each other, temperature best determined the community separation. The local scale study on the bacterial diversity in the seawater of the Ross Sea revealed highly diverse bacterial lineages which were not recovered using traditional molecular approaches in this region. The bacterial community composition in the seawater of the Ross Sea according to the vertical and horizontal variability showed the clear vertical stratification of bacterial diversity along the depth and less differentiation according to the horizontal distance. Three bacterial groups, Bacteroidetes, Alphaproteobacteria, and Gammaproteobacteria, dominated throughout the whole water column. Along the depth increase, Deltaproteobacteria, SAR406, Verrucomicrobia, Planctomycetes, Lentisphaerae, Chloroflexi, Gemmatimonadetes, Planctomycetes, and Firmicutes which were rarely recovered in surface waters, increased and the bacterial diversity also increased. Horizontal distribution of bacterial composition revealed the high portion of Bacteroidetes near the land indicating the association of this group with algal bloom. The vertical and horizontal variability of bacterial communities indicated that the steep gradient in the environments along the depth than the horizontal distance is closely related with bacterial assemblage variability. Among the physicochemical parameters, oxygen level and concentration of nitrite and nitrate explained well about this variability. The spatial comparison in the bacterial communities of marine sediment revealed diverse bacterial populations compared to previous studies in this region and the presence of the high portion of uncultivated groups. Distinct bacterial communities between aerobic and anaerobic sediments outcompeting the geological location were revealed. In the aerobic surface sediments, Gammaproteobacteria, Deltaproteobacteria, Bacteroidetes, and Planctomycetes dominated while Ca. Atribacteria, Chloroflexi, and Actinobacteria were found in higher abundance in the anoxic sediment horizon. Also the portion of candidate phyla was higher in anoxic sediments than surface samples. This indicated the redox state in the sediments plays significant roles for shaping the bacterial community structures. To further examine the ecological functions of bacteria, marine sediments with a large portion of uncultivated groups were cultivated in oligotrophic medium at low temperature. In spite of the limited coverage of cultivated bacterial diversity, many candidate novel species with less than 98.65% 16S rRNA gene similarity to known species were recovered. Forty-six and 25% of bacterial isolates showed extracellular protease and/or lipase activities indicating that the isolated strains contribute to the hydrolysis of major organic constituents and are therefore involved in carbon and nitrogen cycling at the low temperature of sediments of Ross Sea. The ecological function of JS1 lineage of candidate phylum Atribacteria, which was known to be predominant in the anoxic sediments, has been poorly understood due to the lack of cultivated bacterial strains until now. Since the high portion of Ca. Atribacteria JS1 lineage in the anoxic sediments of the Ross Sea was revealed through the bacterial community investigation, single cell sorting and amplification of genomic DNA as complements for cultivation method were applied to elucidate the metabolism and function of this group. Eighteen single cell amplified genomes of JS1 species have been obtained and co-assembled. The highest coverage JS1 genome revealed how this species is dominant in anaerobic environments of the Ross Sea. The metabolic versatility of this species as an acetate producer and syntrophic acetate oxidizer seemed to show increased survivability in nature through syntrophic interactions with partner methanogens or using various heterotrophic substrates to outcompete other primary and secondary fermenters. This versatile growth mode seemed to explain the dominance of Ca. Atribacteria JS1 within anoxic sediments of the Ross Sea. Thus, the genomic insights from this study shed light on the ecological function of Ca. Atribacteria JS1 in methane-related carbon cycling.