Generalist Strategy to Survive the Desert: Variable Nutrient Acquisition in Chloroidium, a Euryhaline Green Alga, Revealed through a Draft Genome-Scale Metabolic Network Reconstruction and Phenotype Microarray Data

Genome-scale metabolic network for green algae has been reconstructed for the model alga Chlamydomonas reinhardtii; however, despite availability of genome sequences, network for other clades of green algae have note been reported.  Here, we describe a desert green alga, Chloroidium sp. DN1 ) and its metabolism through the use of genome-scale model (GSM) reconstructions. The genome of Chloroidium sp. DN1 was sequenced using the Illumina HiSeq 2500 to yield a genome of 52.5 Mb and 10,605 predicted genes.  We created a draft metabolic network of Chloroidium sp. DN1 using the software Pathway Tools.  The metabolic network is comprised of 1,445 genes in 194 pathways. For comparison, the current working version of the C. reinhardtii model has 1,106 genes, many of overlap with Chloroidium in model pathways(~50%). Analysis of reconstructed pathways shows an abundance of sugar and amino acid assimilatory pathways that are further supported by high-throughput phenotype data.  Biolog ‘Omnilog” technology was used to discover entry-level metabolites to strengthen the model.  Chloroidium sp. DN1 was found to grow photoautotrophically and heterotrophically on 10 different carbon compounds including 2,3−Butanedione, Dihydroxy−Acetone, D−Arabitol, D−Mannitol, D-Sorbitol, D-Mannose, D-glucose, trehalose, α−Keto−Butyric Acid, D-Halose, and D-Galactose.  Overall 38 peptides/dipeptides were found to serve as nitrogen sources promoting heterotrophic growth.  Chemical resistance, including antibiotic and salt resistance, was in many cases supported by genomic evidence for responsible enzymes.  Additional network models were also created using the software tools in KBase (KBase.us) that allowed the creation of a gap-filled FBA model for FVA, knock-out, and optimization analyses.  We predicted heavy flux through several sugar biosynthesis pathways that were supported from phenotype data.  Many of these sugars have been implicated in desiccation stress resistance. The unusually broad carbon and nitrogen assimilation pathways present in this species suggests evolutionary adaptations to scarce yet diverse sources of nutrients in arid desert environments.

Key words: Alga (green) – Genomics – Phenotype microarray – Sugar assimilation