Molecular ecology of bacterioplankton and vibrios on Singapore's reefs

Abstract

Marine microorganisms play important roles in nutrient and energy cycling in the ocean and underpin the health and stability of marine ecosystems such as coral reefs. Marine microbial communities in the water column vary seasonally and spatially, shaped by gradients in physiochemical parameters and biotic interactions. However, spatiotemporal patterns of seawater microbiomes in tropical regions were less characterized, particularly Southeast Asia. Here, I showed that the microbial community in the Singapore Strait differed among microhabitats (0.22–1 µm, 1–10 µm and 10–150 µm size fractions) and among monsoon periods. The 10–150 µm community was distinct from the 0.22–1 µm and 1–10 µm fractions and it harbored a higher microbial diversity, including potential marine pathogens, despite containing the lowest biomass. Metagenomic sequencing of these size fractionated microbiomes revealed distinct genomic functional potential between the 0.22–1 µm-enriched (free-living) genome-types and 10–150 µm-enriched (particle-enriched) genome-types, and provided genomic evidences to support the observed patterns of microspatial partitioning.

Free-living genome-types had significantly smaller estimated genome sizes with higher proportion of genes related to transport and metabolism of amino acids, nucleotides and lipids for accessing dissolved nutrients in the water column, whereas particle-enriched genome-types had larger estimated genome sizes and greater potential to utilize complex polysaccharides in particulate microenvironments. Moreover, microbial communities in all three size fractions were influenced more strongly by gradients of dissolved nutrients (inorganic nitrogen, phosphate and DOC), suggesting that microbes in the Singapore Strait are generally responsive to nutrient fluxes. Since there is tight benthic-pelagic coupling, changes in the seawater microbiome as a result of changes to the nutrient environment will inevitably affect the microbiomes of surrounding coral communities.

Nutrient enrichment is predicted as a potential emerging threat to local marine diversity, thus the responses of two local coral species (Pachyseris speciosa and Pocillopora acuta) to nutrient enrichment were investigated with artificial nutrient loading in a controlled-environment aquarium setting over 27 days. Both coral species appeared to be unaffected by low levels of nutrient input but Pocillopora acuta experienced substantial tissue lesions, discoloration and mortality after two weeks of exposure to high nutrient stress. Even so, its endosymbiont and microbial communities did not change drastically, implying some extent of microbiome resilience to environmental changes that were independent of host condition. Overall, findings of this dissertation showed that in a tropical equatorial system, dissolved nutrients were important factors that influenced the surface seawater microbial community and that long-term nutrient over-enrichment posed a significant threat to the local coral community.