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In some particular cases, CDS mapped with transcripts were not assigned to any function by GenDB. In this case, the 10 most active CDS according to their RPKM value were blasted against the protein RefSeq database (April 2015) and the top hit was assigned as the CDS function. For comparison between different bins, the RPKM values were normalized to the assembly depth (sequencing coverage) of each bin. Detection of genes and transcripts specific for methanogenesis All DNA sequences assigned to the three different methanogenic pathways (modules M00567, M00356, and M00357) were downloaded from the KEGG database (Kanehisa and Goto, 2000) in April 2015 and blasted (blastn; cutoff e-value 3e-03) against the CDS sequences obtained with GenDB from the methanogen super-contig and against all unbinned contigs. RPKM value of the mapped mRNA transcripts was used to evaluate the activity of the identified enzymes. Metagenomic and metatranscriptomic reads and assembled contigs are accessible via NCBI under the Bioproject PRJNA281982. The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers ""type"":""entrez-nucleotide"",""attrs"":""text"":""LCWY00000000"",""term_id"":""829682660"",""term_text"":""LCWY00000000""LCWY00000000 and ""type"":""entrez-nucleotide"",""attrs"":""text"":""LCWZ00000000"",""term_id"":""829949050"",""term_text"":""LCWZ00000000""LCWZ00000000. The versions described in this paper are versions ""type"":""entrez-nucleotide"",""attrs"":""text"":""LCWY01000000"",""term_id"":""829682660"",""term_text"":""gbLCWY01000000 and ""type"":""entrez-nucleotide"",""attrs"":LCWZ01000000""LCWZ01000000. The sequenced reads were submitted to the Sequence Read Archive with sample accession numbers SRS923957 for the metagenomic reads and SRS923955 for the metatranscriptomic reads. The 17 16S rRNA sequences used for the generation of the phylogenetic trees were submitted to GenBank under the sample number SAMN03565345, with accession numbers KR476494 to KR476510. Results In this work, the anaerobic digestion of the microalgae Spirulina at alkaline conditions, pH ~ 10, 2.0 M Na+, 60�C95 g CaCO3 L?1, was studied in combination with the analysis of the metagenome and metatranscriptome of the anaerobic haloalkaline microbial community. Biogas rich in methane The anaerobic digestion at alkaline conditions produced, as expected, biogas rich in methane throughout the different experiments. In the Alk-HRT reactor, the composition of the biogas was not constant and varied with the changes in the HRT. The mean see more percentage of methane throughout the experiment was 83% while the carbon dioxide content was 12% (Figure ?(Figure1A).1A).