Ocean Biogeochemistry and Climate Change white paper: Microbial Processes

Heres the text I compiled for the  National Marine Science Plan white paper. This one pager is not referenced so contact me for those if you want them. The text will be part discussed at

National Marine Science Symposium
Shine Dome & QT,  Canberra
25 – 26 November 2014
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Ocean Biogeochemistry and Climate Change white paper: Microbial Processes

 Microbially mediated transformations drive much of the biogeochemical cycling in the ocean, including that of the major elements C, N, S, Si, P, Fe as well as trace metals and micronutrients. The powerful combination of biogeochemical analysis and ‘omics methods (including genomics, transcriptomics and proteomics) continues to identify novel taxa, genes, pathways, proteins and regulatory elements that comprise critical components of specific biogeochemical cycles, and that can be mechanistically linked to rate measures.

For example, a highly diverse but phylogenetically discrete clade of marine cyanobacteria, comprising the genera Prochlorococcus and Synechococcus, are responsible for the majority of carbon fixation, with different ecotypes performing this function under different nutrient and light regimes. Other microbes capture energy from light by undertaking anoxygenic photosynthesis, or use energy generation from proteorhopdopsin as light-dependent adaptive strategy to starvation survival.

Similarly, diverse chemoheterotrophic taxa have been linked to specialized roles in carbon, sulfur and nitrogen cycle in both the surface and the deep ocean. For example, in the nitrogen cycle different microbes are responsible for nitrogen fixation, nitrification, denitrification, and anaerobic ammonium oxidation, and these can act as bioindicators for these processes.

Moreover, fundamental biological links between major biogeochemical cycles are being identified, that will prove critical to understanding and predicting the response of biogeochemical cycles to change. For example, the versatility in trace metal usage by cyanobacterial metal-binding catalytic proteins involved in phosphorous cycling may lead to differential co-limitation of P with either Zn or Fe. Hence, the relative availability of Zn or Fe in low P environments may drive biological selection between phototrophic (carbon fixing) organisms with different metal binding capabilities, while maintaining the functionality of the phosphorous cycle.

 The source and fate of the organic carbon pool is regulated by marine bacterioplankton. Primary productivity delivers ~60 gigatonnes of organic carbon to the ocean per year. The fate of this carbon is strongly influenced by microbial activity that results in fractionation of carbon into different reactivity classes. The biological carbon pump results in the downward flux of particulate organic matter and the sequestration of ~300 million tonnes p.a. into the deep ocean or the ocean floor. The absolute quantity of carbon sequestered is largely determined by the amount that is metabolized by heterotrophic microbial consumers on its downward journey. Indeed, most new organic carbon is bioavailable or labile and is rapidly returned to the atmosphere as CO2 on the order of hours to days. Where there is tight coupling between production and consumption, such as in the oligotrophic ocean, concentrations of labile DOC may be below detection. The largest pool of organic matter in the ocean is refractory DOC (RDOC) suspended in the pelagia. This constitutes ~700 billion tonnes of DOC, more than all biomass on land and nearly as much carbon as all the CO2 in the atmosphere. This RDOC may remain effectively sequestered for up to 6000 years. While RDOC can be produced by mechanisms such as photodegradation, input from oil seeps and spills etc, much RDOC is produced via the microbially mediated conversion of bioavailable organic carbon into the refractory DOC, termed the microbial carbon pump. This microbial method provides an important conceptual framework for the origin of RDOC, as no chemical equilibrium would limit the conversion of bioavailable DOC to RDOC, and there is no concomitant acidification effect from increased carbon storage.

In addition to the controls on oceanic carbon flux, marine microbes also produce and recycle other climatically important gases, including dimethyl sulfide (DMS). Interactions between marine phytoplankton and bacterial populations influence the amount of DMS that is released to the atmosphere, which has direct climatic relevance because DMS is a precursor for substances that act as cloud condensation nuclei in the atmosphere. However, while marine microorganisms are the key determinant of ocean to atmosphere DMS release, our understanding of the ecological processes that control the amounts and rates of DMS production is rudimentary.

Effects of a changing seascape

Enhanced water column stratification is one predicted outcome of warming waters in Australia. We can posit the impacts this would have on microbial processes have from our current knowledge. For instance, by increasing regions of warm, nutrient poor waters, stratification could increase the prevalence and importance of nitrogen fixation, or, by reducing nutrient input from deep convection, lead to an increase in microbial respiration, which favours the microbial carbon pump and production of RDOC. However, our incomplete understanding of microbial impacts on ocean biogeochemistry is highlighted by recent findings that challenge our understanding of fundamental marine processes

For instance, novel and highly active nitrogen fixing organisms have been identified inhabiting cool, temperate waters where N2 would not be considered a growth-limiting nutrient, reshaping our understanding of the amount and mode of atmospheric N2 input to the ocean from microbial sources. Similarly we have identified novel microbial sinks of fixed N that may limit primary productivity, such as the globally important, microbial mediated, anaerobic ammonium oxidation. This process may be responsible for 30-50% of the dinitrogen gas produced in the oceans. Hence, a grand challenge is to mechanistically link the variability in quantity and quality of marine DOC, iron and nutrients over space and time with the microbial phylogenetic and functional diversity that produces and / or modulates it. To accomplish this we require a much greater knowledge of baseline communities and how they change over seasons and in response to basin scale climatic forcing such as the ENSO.


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