Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.

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Alkaliphilic cyanobacteria have gained significant interest due to their robustness, high productivity, and ability to convert CO2 into bioenergy and other high value products. Effective nutrient management, such as re-use of spent medium, will be essential to realize sustainable applications with minimal environmental impacts. In this study, we determined the solubility and uptake of nutrients by an alkaliphilic cyanobacterial consortium grown at high pH and alkalinity. Except for Mg, Ca, Co, and Fe, all nutrients are in fully soluble form. The cyanobacterial consortium grew well without any inhibition and an overall productivity of 0.15 g L−1 d−1 (AFDW) was achieved. Quantification of nutrient uptake during growth resulted in the empirical formula CH1.81N0.17O0.20P0.013S0.009 for the consortium biomass. We showed that spent medium can be reused for at least five growth/harvest cycles. After an adaptation period, the cyanobacterial consortium fully acclimatized to the spent medium, resulting in complete restoration of biomass productivity.

Phycocyanin is a natural blue pigment produced by cyanobacteria and is a valuable compound for food and cosmetic industries. At present, phycocyanin is manufactured with expensive and resource-heavy biotechnology, impeding its widespread use as a blue dye substitute. Here we show that cells of an alkaliphilic cyanobacterium lyse spontaneously in dark incubations mimicking natural soda lake environments, releasing concentrated phycocyanin. Proteogenomics showed that lysis likely resulted from a programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. This response explains the high turnover rates of cyanobacterial cells observed in soda lakes. Cells of Arthrospira platensis (Spirulina), currently used worldwide for phycocyanin production, lyse and release their pigments in the same manner. We propose this natural form of programmed cell death could reduce the costs and resources needed to produce phycocyanin, enabling displacement of current artificial blue colourants associated with adverse health effects.