Crop protection in industrial algae farming: detecting weedy algae and characterizing bacterial communities

Abstract

Microalgae are a promising source of feedstock for biofuel and bioproducts. Algae have higher rates of biomass production than terrestrial crops, and therefore can use less land for producing equivalent energy compared to other biofuels. Elite algae strains are chosen based on traits such as fast and robust growth, and rapid production of desired biochemical products, including fatty acids and other high-energy compounds. Monocultures of elite strains are grown in large algae production systems. A major challenge algae growers face is consistently growing robust cultures of elite algae. This is due to unwanted organisms invading cultures such as weedy algae that contain less desirable biochemical products, and bacteria that can detract from algae growth, thereby reducing overall system productivity. Historically, algae have not been grown at scales required for biofuels and bioproducts, and thus there is a lack of fundamental pest management knowledge and developed tools. In this work, we developed three polymerase chain reaction (PCR)-based tools for detecting and quantifying weedy and elite algae. We developed a simple and inexpensive CAPS (cleaved amplified polymorphic sequence) assay that can determine the presence of dominant algae species in cultures. Also, we developed and validated qPCR primers were able to detect one weedy algae cell in 108 cells in a culture. Compared to flow cytometry, the qPCR primers were 104 times more sensitive for detecting weedy algae. We validated tools by monitoring industrial algae systems, and exhibited their utility for assisting in culture management decisions. Bacteria are also prevalent in industrial algae cultures yet little is understood about their dynamics or role in the ecosystem of elite algae cultures. We sampled small, medium and large cultures from an industrial algae system growing elite algae Nannochloropsis salina, and sequenced the 16S rDNA gene and used QIIME bioinformatics program to analyze data. In this study, we characterized bacterial communities diversity, richness, and composition in industrial algae bioreactors during the scale-up process, through time and during various algae growth rates. We demonstrate that bacterial diversity richness increases as the size of the algae production system increases in the scale-up process. Therefore, larger cultures are comprised of more complex communities than smaller cultures, thus increasing the probability of detrimental algae-bacteria interactions. We identified a single core bacterium Saprospiraceae that was present in 100% of samples, and was on average the most abundant bacterium in all systems. Further, we identified a Deltaproteobacterium that was detected at abnormally high relative abundances in poorly growing algae cultures. Identifying pest bacteria that can detract from elite algae growth is an important step in developing crop protection strategies. We isolated bacteria from a poorly performing algae system and determined their influence on algae growth. We identified a single isolate, S7 as a growth inhibiting bacteria that was capable of completely inhibiting Nannochloropsis gaditana and N. salina growth. The bacterium was characterized as Bacillus pumilus. Additionally, we identified nutrients and cell concentrations required for inhibition of N. gaditana and N. salina. B. pumilus inhibition effect is species-specific as it did not inhibit weedy algae, Chlorella vulgaris and Tetraselmis striata. Due to this, B. pumilus is capable of manipulating algae population composition and reducing productivity. Contaminating organisms such as bacteria will often be prevalent in algae systems and understanding their influence on culture productivity is essential for successful large-scale cultivation of algae. In summary, we 1) developed molecular tools to monitor weedy algae that can be used by growers, 2) characterized bacterial communities in industrial algae system cultures, and 3) identified a novel pest for elite algae, N. gaditana and N. salina.