Abstract
BackgroundMicroalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. However, these techniques are still heavily reliant upon available genomic sequence data. Chlamydomonas moewusii is a unicellular green alga capable of evolving molecular H2 under both dark and light anaerobic conditions, and has high hydrogenase activity that can be rapidly induced. However, to date, there is no systematic investigation of transcriptomic profiling during induction of H2 photoproduction in this organism.ResultsIn this work, RNA-Seq was applied to investigate transcriptomic profiles during the dark anaerobic induction of H2 photoproduction. 156 million reads generated from 7 samples were then used for de novo assembly after data trimming. BlastX results against NCBI database and Blast2GO results were used to interpret the functions of the assembled 34,136 contigs, which were then used as the reference contigs for RNA-Seq analysis. Our results indicated that more contigs were differentially expressed during the period of early and higher H2 photoproduction, and fewer contigs were differentially expressed when H2-photoproduction rates decreased. In addition, C. moewusii and C. reinhardtii share core functional pathways, and transcripts for H2 photoproduction and anaerobic metabolite production were identified in both organisms. C. moewusii also possesses similar metabolic flexibility as C. reinhardtii, and the difference between C. moewusii and C. reinhardtii on hydrogenase expression and anaerobic fermentative pathways involved in redox balancing may explain their different profiles of hydrogenase activity and secreted anaerobic metabolites.ConclusionsHerein, we have described a workflow using commercial software to analyze RNA-Seq data without reference genome sequence information, which can be applied to other unsequenced microorganisms. This study provided biological insights into the anaerobic fermentation and H2 photoproduction of C. moewusii, and the first transcriptomic RNA-Seq dataset of C. moewusii generated in this study also offer baseline data for further investigation (e.g. regulatory proteins related to fermentative pathway discussed in this study) of this organism as a H2-photoproduction strain.
Highlights
Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel
The results indicated that (i) C. moewusii strains had the most rapid H2-photoproduction activity induction, followed by faster loss of activity over longer periods of time; (ii) the SAG 24.91 strain had the highest in vitro hydrogenase activity of all strains examined, as well as faster rates of starch catabolism; (iii) SAG 24.91 had a rate of dark, fermentative H2-production activity similar to that of C. reinhardtii at earlier times, it and all other C. moewusii strains lost their dark, fermentative H2-production activity faster than C. reinhardtii over time
Three time phases with biological replicate data were used for statistical analysis to understand the transcriptomic profiling during induction of H2 photoproduction: 15 M-0427 and 15 M-0502 used as the time point for early H2 photoproduction (Phase I); 2 h-0427 and 2 h-0502 used as the time point for high H2-photoproduction rates (Phase II); and 5 h-0427and 10 h-0502 used as the time point for decreased rates of H2 photoproduction (Phase III) (Figure 1)
Summary
Microalgae can make a significant contribution towards meeting global renewable energy needs in both carbon-based and hydrogen (H2) biofuel. The development of energy-related products from algae could be accelerated with improvements in systems biology tools, and recent advances in sequencing technology provide a platform for enhanced transcriptomic analyses. These techniques are still heavily reliant upon available genomic sequence data. One approach for capture of solar energy is the exploitation of microalgae, which can photosynthetically produce H2 from water, ferment starch into H2 and organic acids, and convert CO2 into liquid biofuel, providing different renewable energy forms and concurrently contributing to solving the greenhouse gas problem [1,2,3,4]. With recent advances in next-generation sequencing (NGS) and synthetic biology technologies, more progress can be foreseen in the future for algae-based renewable energy [8]
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