This article is reposted from the old Wordpress incarnation of Not Exactly Rocket Science.

Look into the oceans past the sharks, seals and fish and you will find the tiny phytoplankton. These small organisms form the basis of life in the seas but if their populations get to big, they can also choke the life from it by forming large and suffocating algal blooms.

The waters of San Francisco Bay have never had big problems with these blooms and if anything, scientists worried that the waters didn't have enough phytoplankton. All that changed in 1999, when the phytoplankton population started growing. It has doubled in size since.

Now, scientists from the United States Geological Survey (USGS) have found that the blooms are the result of a long chain of ecological changes in the area. The plankton are just players in a large ensemble drama involves clams, mussels, fish, crabs and a cold snap.

Just as smoke indicates fire, blooms of phytoplankton are usually signs of water pollution. The plankton grow in number when they dine on nutrients cast into the water by industrial waste water and agricultural run-offs loaded with fertiliser. In large numbers, the algal blooms smother large reaches of water, soak up oxygen and suffocate local food chains. They have been responsible for turning areas like Chesapeake Bay on the Eastern seaboard into a marine dead zone.

But that's not the case in San Francisco Bay. Until recently, the area has proven to be incredibly resilient to harmful phytoplankton blooms despite receiving as much nitrogen and phosphorus as Chesapeake Bay did.

The wind and tides help by churning the water up and prevent the nutrients from collecting in certain patches. The water is also more turbid, which prevents growing phytoplankton from receiving enough light. And nutrient discharges into the estuary have actually fallen by 10% a year of late, thanks to improved treatment plants. So despite having less food, the phytoplankton were growing more quickly.

James Cloern from the United States Geological Survey (USGS) began to suspect that he was looking at the problem from the wrong end. instead of changing food levels, some higher-level barrier had lifted to give the phytoplankton free reign to multiply. Fortunately, the USGS had been monitoring the condition of the bay for some time and in this ream of data, Cloern found the clues that would solve the mystery.

Phytoplankton are eaten by bivalve shellfish like mussels and clams that filter them from the water. In the past, these plankton-predators brought balance to the phytoplankton population and stopped them from getting a foothold despite an abundance of nutrients.

Cloern found that the shellfish started to disappear after 1998, with numbers falling to just 5% of their original levels. This population crash was the result of the shellfish-eating predators including common shrimps, Dungeness crabs and English soles, whose populations tripled in the same time frame.

These predators typically make their home in colder waters further north, but after 1998, the surface temperatures of the San Francisco Bay fell slightly. Weather patterns in the preceding years transported large volumes of cold water from the Arctic north down the coast of the eastern Pacific Ocean and Cloern thinks that this was enough to drive the cold-water predators further south.

All in all, Cloern has pieced together a chain of ecological changes that dominoed through the San Francisco Bay area. Weather conditions that cooled the waters kicked things off, drawing large populations of fish and crustaceans that ate up large numbers of shellfish. This lifted a predatory barrier from phytoplankton, which were then able to make full use of nutrient-rich water to create large blooms.

In this case, humans it seems were not to blame. This particular chain reaction wasn't caused by us introducing new species, over-fishing existing ones or polluting the water. But that doesn't mean that we can't draw lessons from it.

In Chesapeake Bay, the over-harvesting of oysters contributed to the degradation of the habitat by removing a population check on the numbers of phytoplankton - a very similar situation to the one Cloern found in San Francisco. And I have previously blogged on how shark-hunting in the eastern seaboard caused the collapse of scallop stocks by freeing medium-sized shellfish eaters like skates and rays from predatory control.

All these cases serve to show just how interconnected and delicate the ocean environment is. Predators, in particular, sit at the top of a sensitive set of checks and balances. Push them out of play and the whole system could become unrecognisably changed.

Reference: Cloern, J., Jassby, A., Thompson, J., Hieb , K., , . (2007). A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay. . Proceedings of the National Academy of Sciences, 104(47), 18561-18565.