Effect of simulated ocean acidification on the composition of microbial assemblages in New Zealand’s coastal sediment and their potential for ammonia oxidation

The ocean’s pH has decreased by 0.1 units in the last two centuries due to anthropogenic CO2 emissions and it is predicted will continue to decrease by 0.3 units during the next century. One key ecosystem process that may be altered by such a decrease is the microbial oxidation of ammonia, the first step of nitrification. At low pH, the equilibrium concentration shifts towards ammonium rather than ammonia and therefore ammonia oxidation by microorganisms can be inhibited. Previous studies have demonstrated an inhibitory effect of a low seawater pH on ammonia oxidation in the seawater column. Such effect on ammonia oxidation in coastal sediment, however, is not well understood. The relevance of studying the potential effect of acidified seawater on the oxidation of ammonia in coastal sediment is that nitrate, the end product of nitrification, is the second most preferred electron acceptor used by microorganisms to decompose organic matter. Nitrate is also an essential source of nitrogen for primary producers. I established a facility of recirculating seawater to study the effect of an experimental pH decrease of 0.3 units on the oxidation of ammonia in two contrasting types of coastal sediment, sandy and muddy sediment. My objectives were to investigate (1) the assemblage structure of ammonia-oxidising archaea and bacteria; and (2) the gene expression of amoA, the gene for the enzyme that catalyses ammonia oxidation. I also investigated the effect of the seawater pH decrease on the pH of the muddy sediment pore water. Overall, my study was inconclusive. I was able, however, to demonstrate that the seawater pH decrease altered the pore water pH in muddy sediment. I found enhanced pore water pH diel variations at the upper oxic zone, which were attributed to intensified respiration and photosynthesis of diatoms stimulated by the supply of CO2. This suggested that the diatom’s CO2-growth stimulation might play an important role in the effect of the future acidified ocean on the sediment’s biogeochemistry. I also demonstrated a shift in the pore water pH at the suboxic zone towards lower pH, suggesting that the seawater pH decrease exceeded the buffering capacity of the sediment. In terms of sandy coastal sediment, I was able to determine that the experimentally lowered seawater pH did not have a significant effect on the structure of the overall microbial assemblage (not only ammonia-oxidising microorganisms, which were scarce). The reason for this study to be inconclusive was low statistical power. Such low statistical power resulted mainly from the excessive depth of sediment sampled for analyses, the low amounts of nucleic acids extracted from the sediments and the presence of inhibitors in these extractions, which prevented the nucleic acids from being amplified or detected by the technique used. Informing the sampling with a preliminary pore water pH profile, improving the nucleic acids extraction technique and trying alternative methods to overcome inhibition would improve the outcome of future studies.

Del Río Hernández C. E., 2016. Effect of simulated ocean acidification on the composition of microbial assemblages in New Zealand’s coastal sediment and their potential for ammonia oxidation. MSc thesis, Auckland University of Technology, 124 p. Thesis.


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