I know little to nothing about environmental microbiology and...

I know little to nothing about environmental microbiology and biochemistry, however, I have some general and medical knowledge in these areas. In fact, I spend a lot of my work time trying to efficiently manage bacterial infections and have noticed a few things that may (or may not) be pertinent to gold precipitation.

The number one thing I think we can focus on is BIOFILMS. Despite the body's immune system, biofilms inevitably form a coating over foreign surfaces, such as in-dwelling catheters. Antibiotic therapy is generally not effective against these biofilms. Removal of the catheter is recommended unless sepsis is suspected or proven. These films will occurs just about anywhere on a permanent wet surface in nature.

Another thing to consider, is the incredible ability of bacteria to develop resistance to substances that are bacteriostatic (inhibit growth) or bactericidal. Most (perhaps all) of today's antibiotic resistance mechanisms are thought to have been developed billions of years ago in these "primordial soup" environments.

So why would the bacteria or bacterial films precipitate gold out of hydrothermal solutions and then crystallise, over time, into nuggets? Here's my guess!

Besides Fe, which many bacteria love, most heavy metals are, in varying degrees, toxic to bacteria. Ag being a prime example. If concentrations of metals were high enough to stress or kill these bacteria living in the shallow seas, surviving organisms would have developed novel ways of surviving.

By sequestering a non toxic/inert analogue substance into the microbes' "weak spot", a defence mechanism could have been developed this way. Gold thio complexes, in solution, could have been sequestered into the bacterial structure as a defence against the sequestration of metals like Silver, Mercury and Arsenic.

The nuggets could have been grown over time, within these biofilms, in a similar way to pearls growing in oysters.

Perhaps all of this stuff has been studied to the n'th degree and my guess is complete rubbish. I like to have a punt though!
Here's a link about metal precipitation in biofilms ;

http://aem.asm.org/content/69/4/2313.full