Bioturbation and Benthic Ammonia-oxidizing Micro-organisms in Relation to Ocean Acidification

The current rate of CO₂ dissolving into the ocean will cause the pH of the surface water to decrease as far as 0.3-0.5 units (worst case scenario). This process is known as Ocean Acidification (OA). There are few studies that indicate what impact this will cause to marine microbial processes, especially the biogeochemical cycles, such as the nitrogen cycle, that will suffer detrimental consequences. Ammonia oxidation rates have been shown to drop by 3-44% with decreasing pH values. Ammonia-oxidation is a limiting step of the nitrification process, detailed below:

Ammonium (NH₄⁺) à Nitrite (NO₂^-) à Nitrate (NO₃^-)

The oxidation of ammonium is often used to indicate overall nitrification rates. Sediments are a particularly important site of nitrification (as much as 10—10000 fold more than over-lying water colum) where organic matter degradation and nutrient regeneration are linked. Previous work by this group have shown that overlying pH has no effect on surface sediment oxidation rates, however this may be due to the carbonate minerals within the sediment acting as a buffer against OA, or that the changing pH simply favours other sediment microbes able to cope with the drop. However, Blackford & Gilbert suggest considering the effects of OA on benthic macrofauna in relation to microbial sediment communities. This study uses a 14-week mesocosm experiment to determine the effect of OA on Thalassinidean shrimps and how this may affect the ammonium-oxidation rates of the microbial communities found within the shrimps’ burrows. Past work by this group has shown that shrimp burrows contain a more diverse microbial community than surrounding sediment surfaces and that the bioturbidation activity of these shrimp is known to increase the nitrification/denitrification rates within sediment. In the wild these shrimp are found in densities of up to 50/m².

Four different pH treatments were analysed. These were 7.9, 7.7, 7.3 and 6.8. 8.1 was also used as a control, ambient pH. Sand/mud sediment was collecte from Jennycliff Bay and was defaunated of large macrofauna by hand. All Upogebia deltaura recovered were kept aside. The sediment was distributed between 10 tanks and settled overnight. A population of 14/m² of shrimp was added to each tank. All were monitored and allowed to establish burrows before the experiment was carried out. Water flowed between the tanks for nine weeks prior to the changes in pH. This is believed to have allowed the microbial communities to re-establish. CP grade 99.95% CO₂ gas was then used to treat the tanks until the desired pH was reached, this remained the same for 14 weeks. At the end of the exposure periodammonia-oxidation rates were made from the overlying water and within the surface sediments. Shrimp burrows were broken apart and ammonia-oxidation rates were taken from the burrow walls. The ammonia-oxidation rates were determined using a colormetric assay. Phenol-chloroform treatment was used in conjunction with bead-beating to extract DNA. Q-PCR assays were performed to quantify bacterial and archaeal 16S rRNA and amoA genes. Carbonate system parameters such as dissolved organic carbon (DIC), pCO₂ and calcite/aragonite saturation states were calculated. Shrimp haemolymph pH was also extracted for those individuals large enough.

Ammonia-oxidation rates were found to decrease in the overlying water-column with decreasing pH by as much as 23% when comparing the pre-exposure pH (8.06) and the year-2100 worst case scenario (7.67). There was also a significant difference between ammonia-oxidation rates on the surface sediment and the burrow walls. Additionally, there was no effect of pH on ammonia-oxidation within sediments although it did decrease by 80% within burrow walls when comparing pH 8.10-7.9. At pH 7.7 burrow wall oxidation rates were lower than in surface sediments. There were also recorded differences in the carbonate systems, as would be expected. pCO₂ levels were significantly different between treatments. DIC also increased significantly throughout the exposure period by an averaged 9%. At pH 7.35 and 6.8 the DIC increased by 32% and 65% respectively. Inorganic carbon was also seen to lower in reduced pH systems; this was greatest in the surface sediments. Surprisingly, bacterial and archaeal 16S rRNA gene abundances were seen to significantly  increase with a reduced pH. This change was also seen in amoA genes, however there was only a significant difference in archaeal genes, not bacterial genes. No distinct trend was seen between bacterial : archaeal genes with pH. Also there was no significant correlation between bacterial/archaeal amoA gene numbers and rates of ammonia-oxidation. Out of the totalled 20 shrimp in the experiment, 4 did not survive the full exposure period. Three shrimp were from pH 6.8 and one from pH 7.35. Shrimp haemolymph pH was found to be significantly lower at pH 6.8.

It was found that a drop in pH within the overlying water-column caused both a significant reduction of ammonia-oxidation within the burrow wall sediments and a notable decreased in inorganic carbon within surface sediments. The OA also caused shrimp mortality below pH 7.7 and extracellular acidosis. The sediment microbial communities are already known to survive in lower pH than those in the water column. This study indicates that metabolic microbial derived CO₂ reduces the carbonate saturation state of the sediment, driving dissolution of carbonate minerals; reducing the inorganic carbon content in sediments. This dissolution helps to buffer the pH explaining why there was little effect upon ammonia-oxidation rates on surface sediments. However, this is in opposition to other work involving Heart Urchins. Further work has also indicated that increased CO₂ conditions will cause an over-production of carbon in primary producers, increasing sedimentation of organic matter. This could lead to greater microbial production rates in surface sediments. However, this study shows that under a lower pH both bacterial and archaeal 16S rRNA genes increased and that some microbes responded positively to the change. Other work has indicated that high pCO₂ conditions led to increased growth rates, increased bacterial protein production and possible enhanced heterotrophy. This study indicates that pH does not simply inhibit ammonia-oxidation as at the ambient pH of 8.1, oxidation rates in the burrow walls were on average fivetimes higher than surface sediment oxidation rates. However, at 7.9 oxidation rates were lower than surface sediments. Evidently, in areas with high U. deltaura populations there could be a significant impact upon exchange of nutrients. This in turn could affect denitrification rates and ecosystem function.

This study is significant as it highlight the limitations of using a singular organisms to study the effects of OA on microbial ocean processes.

Laverock B, Kitidis V, Tait K, Gilbert J.A, Osborn A.M & Widdicombe S. 2013. Bioturbidation determines the response of benthic ammonia-oxidizing microorganisms to ocean acidification, Phil. Trans. R Soc. B. 368: 20120441.