The environmental conditions created in the Southwestern deserts of the United States are conducive to the production of green microalgae biomass, for use as a feedstock intended for conversion to carbon neutral liquid biodiesel. One promising heat-tolerant, rapidly-growing, high lipid content species is the chlorophyte, Chlorella sorokiniana (Shihira and Krauss, 1965) (isolate DOE 1412), which has been selected for pilot-scale production as part of a larger algal biofuels project to assess its potential for long-term productivity in open, outdoor monoculture production systems. Molecular analysis exposed the presence of the pathogenic bacterium, Vampirovibrio chlorellavorus (Gromov & Mamkaeva, 1972) causing infection and death of DOE 1412, which occurred most rapidly at air temperatures exceeding 34 °C. This Gram-negative bacterium has been reported to attach to and utilize the cellular contents of several Chlorella species, leading to yellowing and flocculation of algal cells, and death of the host. A quantitative PCR assay was developed to monitor pathogen accumulation using the 16S ribosomal RNA gene, in addition to the algal 18S ribosomal RNA gene for normalization. The assay is highly sensitive, with limits of quantification for the 16S and 18S gene targets calculated to be 19 and 131 copies, respectively. The qPCR assay was used to monitor several outdoor reactors inoculated with the DOE1412, throughout the warm season growth-to-harvest cycle to understand the disease cycle and inform disease management decisions. Further, the bacterium was monitored in paddlewheel DOE 1412 cultures treated with benzalkonium chloride (BAC), a biocide tested for the ability V. chlorellavorus attack of DOE 1412. The treatment resulted in a reduced growth rate for DOE 1412, but prolonged the duration of the production cycle resulting in increased total harvestable yield, compared to untreated control cultures.

A multi-wavelength laser diode based optical sensor was designed, developed and evaluated for monitoring and control microalgae growth in real-time. The sensor measures optical density of microalgae suspension at three wavelengths: 650 nm, 685 nm and 780 nm, which are commonly used for estimating microalgae biomass concentration and chlorophyll content. The sensor showed capability of measuring cell concentration up to 1.05 g L⁻¹ without sample dilution or preparation. The performance of the sensor was evaluated using both indoor photobioreactors and outdoor paddle wheel reactors. It was shown that the sensor was capable of monitoring the dynamics of the microalgae culture in real-time with high accuracy and durability. Specific growth rate (μ) and ratios of optical densities (OD ratios) at different wavelengths were calculated and were used as good indicators of the health of microalgae culture. A series of experiments was conducted to evaluate the sensor's capability of detecting environmental disturbances in microalgae systems, for instance, induced by dust or Vampirovibrio chlorellavorus, a bacteria found to cause crash of microalgae culture. Optical densities measured from the sensor were insensitive to the amount of dust that consisted of 59.7% of dry weight of microalgae in the system. However, the sensor was able to detect multiple events of introduction of dust timely by μ and OD ratios. The sensor was also capable of detecting subtle changes of culture in color that leads to a total crash of the culture before it can be differentiated by naked eye. The sensor was further integrated into an existing outdoor raceway to demonstrate the sensor's potential of being a core component to control microalgae production system. A real-time monitoring and control program along with a graphical user interface (GUI) was developed for a central control station aiming at improving resource use efficiency for biomass production.