See previous Successful Wine Fermentation posts: Introduction, Selecting the Right Yeast (Part I, Part II), Preparing Juice/Must for Fermentation.
Once the juice/must is properly prepared for fermentation, the winemaker needs to decide what yeast will be used. I discussed indigenous fermentation in a previous post (see Part I). Winemakers traditionally allowed their juice/must to begin fermenting naturally; yeast performing such fermentation would come from the vineyard (there are thousands of species of yeast that can be naturally present on grape skins) or from within the winery or fermenting vessel (even with all the advances in winery cleanliness, many wineries today have an "indigenous yeast" living within their facility that will kickoff fermentation if juice or must is not well protected, though this is often a vigorous commercial yeast strain). Over time, winemakers began encouraging the "best" yeast possible, and once the technology was available, began isolating these strains.
With the importance of marketing becoming increasingly important in today's industry, many winemakers want to claim that their wine is produced "naturally" or with "minimal intervention". Still, others desire the characteristics indigenous fermentation can provide; proponents of indigenous yeast fermentation claim it leads to a more harmonious finished wine that better reflects the vineyard's terrior. Indigenous yeast tend to ferment slower, and produce more textural wines when compared to their commercial counterparts.
Winemakers experimenting with indigenous yeast have had mixed results. Though some believe that commercial yeast strains are the only way to make good wine, plenty promote indigenous yeast in some form during wine production. They do so in varying levels of risk; some winemakers utilize indigenous yeast on all their juice/must, others utilize indigenous yeast on a portion of their juice/must, and others promote indigenous yeast for several days before inoculating with commercial yeast to takeover the ferment.
Most of those opposed to indigenous yeast site their disadvantages. Indigenous yeast usually have an extended lag phase, which means it can take several days to over a week for fermentation to truly begin. This leads to issues with other microorganisms (lactic acid bacteria, Brettanomyces, etc.) taking hold, which can produce undesirable compounds and inhibit yeast from beginning fermentation. Indigenous yeast are also far more susceptible to alcohol toxicity due to problems reproducing enough generations to finish ferment. They get stressed easier (may lead to volatile acid and hydrogen sulfide production) and are far more likely to get stuck towards the end of fermentation (not ferment the wine to below 2 g/L residual sugar) than their commercial counterparts.
I am a strong believer in the use of indigenous yeast and have conducted several experiments using it in production. The risks can be minimized with winemaking diligence, while wine quality can be increased greatly; ensuring the juice/must is prepared (as discussed here) is essential for successful indigenous yeast fermentation. Nevertheless, I would be hard pressed to base my entire production off indigenous yeast due to the simple fact that wines fermented with indigenous yeast often lack many qualities that commercial yeasts provide. The complexity provided when blending wines of several yeast helps make a more balanced, interesting final product.
Continue on to read about 'Successful fermentation - Inoculation'.