Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome

Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field. This review summarizes the current opinions in metagenomics, and provides practical guidance and advice on sample processing, sequencing technology, assembly, binning, annotation, experimental design, statistical analysis, data storage, and data sharing. As more metagenomic datasets are generated, the availability of standardized procedures and shared data storage and analysis becomes increasingly important to ensure that output of individual projects can be assessed and compared.

Background Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification. Methodology/Principal Findings Here we apply an RNA-centered meta-transcriptomic approach to simultaneously obtain information on both structure and function of a soil community. Total community RNA is random reversely transcribed into cDNA without any PCR or cloning step. Direct pyrosequencing produces large numbers of cDNA rRNA-tags; these are taxonomically profiled in a binning approach using the MEGAN software and two specifically compiled rRNA reference databases containing small and large subunit rRNA sequences. The pyrosequencing also produces mRNA-tags; these provide a sequence-based transcriptome of the community. One soil dataset of 258,411 RNA-tags of ∼98 bp length contained 193,219 rRNA-tags with valid taxonomic information, together with 21,133 mRNA-tags. Quantitative information about the relative abundance of organisms from all three domains of life and from different trophic levels was obtained in a single experiment. Less frequent taxa, such as soil Crenarchaeota, were well represented in the data set. These were identified by more than 2,000 rRNA-tags; furthermore, their activity in situ was revealed through the presence of mRNA-tags specific for enzymes involved in ammonia oxidation and CO2 fixation. Conclusions/Significance This approach could be widely applied in microbial ecology by efficiently linking community structure and function in a single experiment while avoiding biases inherent in other methods.

The potential of microalgae as a source of biofuels and as a technological solution for CO2 fixation is subject to intense academic and industrial research. In the perspective of setting up massive cultures, the management of large quantities of residual biomass and the high amounts of fertilizers must be considered. Anaerobic digestion is a key process that can solve this waste issue as well as the economical and energetic balance of such a promising technology. Indeed, the conversion of algal biomass after lipid extraction into methane is a process that can recover more energy than the energy from the cell lipids. Three main bottlenecks are identified to digest microalgae. First, the biodegradability of microalgae can be low depending on both the biochemical composition and the nature of the cell wall. Then, the high cellular protein content results in ammonia release which can lead to potential toxicity. Finally, the presence of sodium for marine species can also affect the digester performance. Physico-chemical pretreatment, co-digestion, or control of gross composition are strategies that can significantly and efficiently increase the conversion yield of the algal organic matter into methane. When the cell lipid content does not exceed 40%, anaerobic digestion of the whole biomass appears to be the optimal strategy on an energy balance basis, for the energetic recovery of cell biomass. Lastly, the ability of these CO2 consuming microalgae to purify biogas and concentrate methane is discussed.