Climate change, chemistry, and community composition – can microbes save our oceans?

Some things are certain in life... like climate change! Climate change is happening and there is increasing atmospheric CO2 concentration from prior stable levels at ~280μatm pCO2(atm) to present-day levels at >400μatm and predicted to reach >750μatm mid-late century.  Dissolved CO2 decreases seawater pH; this leads to a decrease in seawater carbonate, ion concentrations, and lower saturation state for calcium carbonate minerals. But what about the microbes... 

Benthic microbial communities are directly influenced by seawater chemistry. Changes in pCO2 shall likely influence microbial community composition and their key functions in biogeochemical cycles, particularly for nitrification processes. However, microbial community compositions are so complex that sometimes, it may be difficult to accurately predict future community shifts in short-term experiments. Long-term experiments allow results to include factors of microbial acclimatization, evolutionary adaptations, complex feedbacks, and indirect effects. Natural CO2 venting systems can be used to study microbial sediment communities when exposed to pCO2 levels after a long time period.  

The study by Raulf et al. (2015) investigated microbial community composition (bacteria and archaea) in oxic sandy sediments across a natural CO2 gradient at a volcanic vent system in Papua New Guinea. Although volcanic systems are different to ‘general’ surface-sediment systems, the Authors explain how some confounding effects from nearby volcanic activity are negligible. Samples were taken from the oxic zone (<3cm surface sediment) of sandy sediments in shallow waters (1-4m water depth). Samples were analysed by the molecular fingerprinting technique ARISA using a triplicate PCR electrophoresis approach. This was combined with the MPTS technique for deeper diversity analysis and taxonomic identification of key microbial indicators.  

Results showed that as pCO2 increases, bacterial and archaeal richness increases. Additionally, as pCO2 increased, there was an increase of rare members for both bacteria and archaea. The microbial communities from sites with low/present day pCO2 concentrations were structured different than for sites with elevated pCO2. Sites with high pCO2 had communities that selected different dominant microbial types. As pCO2 increased, sequences related to bacterial nitrifying organisms like Nitrosococcus and Nitrospirales decreased. Subsequently, as pCO2 increased, there was an increase in sequences related to archaeal ammonia-oxidizing organisms like Nitrosopumilus maritimus (Phyla: Thaumarchaeota).  

So, the study predicts that as more CO2 dissolves into oceans, microbial community composition shall change; meanwhile, community richness/evenness shall increase. But why? 

Firstly, there could be direct pCO2 effects on specific cellular processes via enzyme kinetics or cell homeostasis. Additionally, increased pCO2 leads to higher nutrient availability and increased benthic cover of primary producers. So, as expected, results found an increase in biomass turnover and an increase in organic matter degrading bacterial groups like Flavobacteriaceae and Rhodobacteraceae. 

Results also found a change in the sequences related to nitrifying organisms. Nitrification is one of the biogeochemical processes most sensitive to pH change, due to decline in the availability of ammonia for nitrifying organisms. Rising oceanic pCO2 may have disadvantages for ammonia-oxidising bacteria because ammonia-oxidising archaea may be better adapted and be better competitors under acidifying conditions and limited resources. However, it’s difficult to predict how the nitrification cycle will change because biogeochemical cycles are complex, and each component has a knock-on effect to the next part of the nitrification cycle.  

Authors explain that, ecologically speaking, the observed increase in microbial diversity and larger proportion of rare microbial types at high pCO2 sites may potentially have a stabilising effect on local biological processes. A richer community of rare types might provide an increase of interchangeable biochemical functions which could replace those that may be lost or weakened... but this uncertain. So, microbial composition is sensitive to change of seawater chemistry and there shall be an impact on ecosystem functions, but maybe there’s hope in microbes! 

Referenced material: 

Raulf, F.F., Fabricius, K., Uthicke, S., de Beer, D., Abed, R.M. and Ramette, A., 2015. Changes in microbial communities in coastal sediments along natural CO2 gradients at a volcanic vent in Papua New Guinea. Environmental microbiology, 17(10), pp.3678-3691.