Ecosystems are highly complex webs of species that mix in space and time, creating intricate relationships and feedbacks that are difficult to study, regardless of changes in acidification. Shell-forming species seem to be highly sensitive to changes in pH, in fact some species have been directly and negatively impacted by acidification – there is a vast and growing body of literature on this including responses like metabolic changes in fish and subsequent behavioral or generational impacts. On the other hand, photosynthesizing plants in the ocean (algae and seagrasses) use CO2, so they stand to benefit. In the case of algae, it is possible that elevated CO2 will help boost growth. In fact, as more and more research is done on the effects of elevated CO2 and decreased pH on marine organisms, the results can differ depending on what species is being studied and how the studies are done.
Understanding the influence of acidification on entire ecosystems is difficult due to both the complexity of the chemistry and the complexity of marine ecosystems themselves. Very specific and technical experiments must be performed to recreate the acidified carbonate chemistry conditions of the Mid-Atlantic ocean. The problem is exacerbated by the interactions of changes in pH with changes in other environmental characteristics such as temperature, eutrophication and increases in UV radiation. These interactions, or multiple stressors, can sometimes exacerbate the impacts of changes in pH; or in other cases buffer against those impacts or even reverse them. Careful and extensive experiments are necessary to tease these apart.
And finally, many of the experiments to date have been performed with only a single species in isolation. Ecosystems are a complex network of species that interact via food webs, symbioses and a myriad of other mechanisms. It is possible that species might interact with one another in a way that exacerbates impacts of acidification or helps to mitigate the impacts. For example, faster growth by seagrasses due to elevated CO2 might theoretically help to locally increase pH and make local habitats fully saturated with calcium carbonate and in this way prevent shell deformations in shelled species that would be seen in the absence of the seagrasses. It is also possible that negative impacts to phytoplankton, a critical food source for other species at the bottom of the food web, can negatively impact species that feed on phytoplankton to survive.
Ultimately, experiments performed on ecologically relevant scales and with suites of interacting species would be the most pertinent, but because of the complexity of adding CO2 to the ocean on ecological scales, they are nearly impossible. Ecosystems in the coastal ocean or estuaries worsen this problem. The coastal ocean is characterized by large fluctuations in pH on timescales ranging from hours to years. These pH "weather" events that can be caused by precipitation, nutrient runoff, seasonal cycles of respiration or oceanic events like upwelling, can exert a large influence on the ecology of the coastal system, and make it difficult to assess longer term trends in coastal pH ‘climate’ and corresponding impacts on the ecology.
Waldbusser, GG, and Salisbury, JE. 2014. Ocean acidification in the coastal zone from an organism's perspective: multiple system parameters, frequency domains, and habitats. Annual Review of Marine Science, 6: 221-247.