Nitrification and denitrification are key steps in nitrogen (N) cycling. The coupling of these processes, which affects the flow of N in ecosystems, requires close interaction of nitrifying and denitrifying microorganisms, both spatially and temporally. The diversity, temporal and spatial variations in the microbial communities affecting these processes was examined, in relation to N cycling, across 12 sites in the Fitzroy river estuary, which is a turbid subtropical estuary in central Queensland. The estuary is a major source of nutrients discharged to the Great Barrier Reef near-shore zone. Measurement of nitrogen fluxes showed an active denitrifying community during all sampling months. Archaeal ammonia monooxygenase (amoA of AOA, functional marker for nitrification) was significantly more abundant than Betaproteobacterial (β-AOB) amoA. Nitrite reductase genes, functional markers for denitrification, were dominated by nirS and not nirK types at all sites during the year. AOA communities were dominated by the soil/sediment cluster of Crenarchaeota, with sequences found in estuarine sediment, marine and terrestrial environments, whereas nirS sequences were significantly more diverse (where operational taxonomic units were defined at both the threshold of 5% and 15% sequence similarity) and were closely related to sequences originating from estuarine sediments. Terminal-restriction fragment length polymorphism (T-RFLP) analysis revealed that AOA population compositions varied spatially along the estuary, whereas nirS populations changed temporally. Statistical analysis of individual T-RF dominance suggested that salinity and C:N were associated with the community succession of AOA, whereas the nirS-type denitrifier communities were related to salinity and chlorophyll-α in the Fitzroy river estuary.

Beneficial effects of CO₂on photosynthetic organisms will be a key driver of ecosystem change under ocean acidification. Predicting the responses of macroalgal species to ocean acidification is complex, but we demonstrate that the response of assemblages to elevated CO₂are correlated with inorganic carbon physiology. We assessed abundance patterns and a proxy for CO₂:HCO₃⁻use (δ¹³C values) of macroalgae along a gradient of CO₂at a volcanic seep, and examined how shifts in species abundance at other Mediterranean seeps are related to macroalgal inorganic carbon physiology. Five macroalgal species capable of using both HCO₃⁻and CO₂had greater CO₂use as concentrations increased. These species (and one unable to use HCO₃⁻) increased in abundance with elevated CO₂whereas obligate calcifying species, and non-calcareous macroalgae whose CO₂use did not increase consistently with concentration, declined in abundance. Physiological groupings provide a mechanistic understanding that will aid us in determining which species will benefit from ocean acidification and why.

Ocean acidification (OA) is the reduction in seawater pH due to the absorption of human-released CO₂ by the world’s oceans. The average surface oceanic pH is predicted to decline by 0.4 units by 2100. However, kelp metabolically modifies seawater pH via photosynthesis and respiration in some temperate coastal systems, resulting in daily pH fluctuations of up to ±0.45 units. It is unknown how these fluctuations in pH influence the growth and physiology of the kelp, or how this might change with OA. In laboratory experiments that mimicked the most extreme pH fluctuations measured within beds of the canopy-forming kelp Ecklonia radiata in Tasmania, the growth and photosynthetic rates of juvenile E. radiata were greater under fluctuating pH (8.4 in the day, 7.8 at night) than in static pH treatments (8.4, 8.1, 7.8). However, pH fluctuations had no effect on growth rates and a negative effect on photosynthesis when the mean pH of each treatment was reduced by 0.3 units. Currently, pH fluctuations have a positive effect on E. radiata but this effect could be reversed in the future under OA, which is likely to impact the future ecological dynamics and productivity of habitats dominated by E. radiata.