Components of the microbial community are instrumental in several processes of the marine food web and global chemical cycles.
Photosynthesis: Phytoplankton absorb CO2 and harness the energy of sunlight to manufacture sugars and other cell components, releasing oxygen. The sunlight is absorbed by chlorophylls and carotenoids, which can be used to identify the various groups of phytoplankton in the water.
Respiration: All organisms (from microbes to whales) oxidize intracellular carbon reserves to produce the energy necessary for cell function (growth, movement, chemical metabolism). This process of respiration releases to the atmosphere much of the CO2 taken up by phytoplankton.
Feeding: The ocean has been likened to a vast very dilute jelly, containing a continuum of matter ranging from small molecules to large aggregates (see Aggregation below). Microbes are able to consume matter throughout this size range, changing the kind and size of these compounds. This alters the availability of these food sources to other organisms. Bacteria release enzymes that convert complex matter to simple molecules that can be absorbed across their cell membrane. Protozoa have various means of consuming cells and can graze on a large range of particles from molecules to cells larger than themselves (see video image Agents of death). All protists are grazed by crustaceans and other zooplankton.
Microbial loop: The processes discussed above operate simultaneously in a microbial community, whose collective metabolism is called the microbial loop. Most of the carbon in the marine ecosystem is cycled through this loop, strongly influencing the quality, quantity and size distribution of food available to higher organisms.
Aggregation: There are several processes by which particles can aggregate. Particulate and dissolved organic matter can spontaneously aggregate in seawater, a process aided by mixing. Grazing protozoa and higher organisms repackage matter into faecal pellets. Mucilage produced by algae provides a substrate that can be colonized by other cells. Aggregates support a rich and diverse microbial community within which the close proximity of organisms enhances recycling of matter via the microbial loop. Such aggregates are often called marine snow.
Sedimentation: There is a continuous 'rain' of particles from the sunlit upper waters to the ocean depths where there is insufficient light for photosynthesis and hence respiration rules. Much of the matter is recycled en route. Sedimentation to the deep ocean is the principal global process by which CO2 is biologically removed from the atmosphere for geological time scales.
Succession: The composition and abundance of marine microbes varies greatly due to physical and environmental factors including, light, temperature, salinity, depth, nutrient concentrations, the nature, extent and persistence of sea ice, the depth and speed of vertical mixing of the water column, and grazing pressure.
Large areas of the Southern Ocean are unproductive. This is thought to be due to both strong vertical mixing that carries cells out of the sunlit portion of the water column and low concentrations of micronutrients (especially iron) that limit phytoplankton growth. Most microbial production occurs close to the Antarctic continent. Here they bloom in or on the bottom of the sea ice during spring, or occur as brief, spectacular water column blooms near the margin of the sea ice as it retreats southward during spring and summer.
In spring, as sunlight returns to Antarctic waters, phytoplankton concentrations begin to increase. Phaeocystis antarctica, a flagellate around 6 µm diameter that forms gelatinous colonies up to 2 cm in diameter, is often the first species to bloom in ice-edge waters. Subsequent blooms are often comprised of large (>20µm) diatoms, which are superimposed upon a background of nanoplanktonic (2–20µm) flagellates and diatoms. Towards the end of the season, phytoplankton abundance declines and protozoan and bacterial concentrations increase to consume the remainder of the summer's production. However, at many sites around the Antarctic coastline there is little interannual consistency in the timing, abundance or successional sequence of marine microbes.
Production by phytoplankton over the entire Southern Ocean can vary 25% between years and, at a single location, can vary by a factor of 5–10 between years. Small-scale variation in the physical and biological environment causes significant differences in the composition and abundances of protists (phytoplankton and protozoan) communities over distances of meters. The composition of and abundance viruses and bacterial communities can vary over distances of centimetres. Thus, while patterns are apparent in the overall community structure and function, the Antarctic marine microbial community constantly changes in response to an ever-changing environment.