The third-quarter conference call represents perhaps the most important conversation between investors and management at Solazyme (TVIA) in the company's history. Shareholders will learn the details of construction progress at the company's first two commercial scale facilities in Moema, Brazil, and Clinton, Iowa. Moema should have been completed by now, so commissioning and start-up should be right around the corner. As if production updates weren't important enough, there are several more burning questions on the minds of investors. Here are three things to look for when Solazyme reports earnings on Tuesday.

1. What's up with the Roquette dispute and possible lawsuit?
When Solazyme and Roquette dissolved their joint venture dedicated to developing nutritional products from naturally occurring microalgae strains, all of Solazyme's intellectual property thrown into the venture came back to the company. Management was buzzing with hopes of accelerating the commercialization of key products and is even in the process of rededicating its demonstration facility in Peoria to focus on the high margin products. Unfortunately, those expectations may not be so realistic. It appears that Solazyme and Roquette are still in dispute over key technologies and may even be entangled in a lawsuit. Eesh.

Solazyme may have had its technology returned, but Roquette has its own competing microalgae platform for producing nutritional products. Was that what led to the conclusion of the joint venture in the first place? Investors may not want to hear it, but Roquette is a much larger company, with many more resources, and the manufacturing facility that was formerly part of the joint venture. If there is a lawsuit ongoing and the company wanted to fight Solazyme to the bitter end, it could draw upon more capital than the development industrial biotech.

The dispute could put a halt to Solazyme's commercialization plans for its nutritional portfolio. Since the company hasn't talked about it much, perhaps it's not a big issue after all. Keep your eyes open to see if management provides an update on the situation.

2. How will the sugarcane inter-harvest period in early 2014 affect Moema production?
At the beginning of each year, sugarcane stockpiles dwindle to annual lows in what is called the inter-harvest period. Some large ethanol facilities draw down their inventory during this time, but for the most part, production reaches its lowest point of the year as well. Unless Solazyme and Bunge (BG -3.49%) have set aside adequate stockpiles for inter-harvest, it seems unlikely that the two will be able to maintain operations for at least a couple of weeks.

Many facilities schedule downtime to repair and upgrade equipment, which is exactly what fellow industrial biotech Amyris will do at its biorefinery in Brotas. Since Moema will have only been operating for several months when inter-harvest arrives, it could probably plan to shut down to fix early kinks in its process, too. The point is there is a high chance ramp-up -- and therefore product sales -- will be impeded by a lack of sugar. Is that the case or did management make the necessary arrangements ahead of time?

3. When will SBR consolidate results? What specifically needs to be achieved?
The Solazyme Bunge Renewable Oils joint venture, or SBR, is setup so that Solazyme can consolidate the financial results on its balance sheet. However, the venture is unconsolidated during construction of Moema -- a necessary component to landing the loan from the Brazil Development Bank -- and investors are still in the dark about when consolidation occurs. Will it happen at commissioning? Start up? Once Moema hits some other production milestone?

Bunge is selling sugar to the joint venture, so it isn't exactly a one-way street financially, but it doesn't make much sense to consolidate early in the ramp-up process. The company is already rumored to be looking into selling its sugar business due to low margins; why would it want to forgo splitting revenue on product sales in the beginning (unconsolidated) just to split losses on operations with Solazyme (consolidated)? Large companies look at things on a much longer time horizon, so it is quite possible Bunge will opt to consolidate SBR immediately. If that doesn't occur (and, likely, even if it does), Solazyme will not be able to meet 2014 revenue guidance. Let's see if management provides more clearance on the matter.

Foolish bottom line
The third-quarter conference call will be incredibly important for investors. Then again, the importance will heighten with each subsequent quarter as investors and analysts patiently wait for production updates. Even if management sails through its conference call on Tuesday, there will be plenty of time for mistakes to disrupt Solazyme's plans for 2014 and beyond. Hopefully that doesn't occur, especially given the dismal attitude toward the industrial biotech sector, but only time will tell.