Aliases: NiFe-hydrogenase, NiFe hydrogenase. The corpus evidence concerns group 1 [NiFe]-hydrogenase, a subgroup of this enzyme class, and does not cover the class as a whole. The cohort comparison table in the clay analysis uses the label NiFe_complete for its [NiFe]-hydrogenase completeness call. That label is an analysis marker, not another name for the enzyme. The deep-clay subsurface analysis scored [NiFe]-hydrogenase markers as part of an anaerobic “toolkit” in confined-clay genomes, together with the wood-ljungdahl-pathway and dissimilatory-sulfate-reduction 1,2.
Prevalence in deep-clay genomes
Among the 9 deep-clay anchor genomes in the KBase Data Lakehouse, 7 carry group 1 [NiFe]-hydrogenase markers and 5 carry the dissimilatory sulfate reduction module (Sat, AprAB, DsrAB). These include direct hits on the BRH-c8a lineage, which Bagnoud’s nomenclature calls Peptococcaceae c8a, and on the desulfosporosinus lineage 1.
At cohort level, the [NiFe]-hydrogenase completeness marker (NiFe_complete) occurred in 7 of 9 deep anchor genomes versus 35 of 140 soil-baseline genomes. The odds ratio was 10.5 with an adjusted p of 0.004. As the next section shows, this apparent enrichment does not survive within-phylum control 1.
The report cites Bagnoud’s finding of a minimalistic Opalinus clay food web. In that food web, Desulfobulbaceae c16a expressed the complete Wood–Ljungdahl pathway, group 1 [NiFe]-hydrogenase and Sat–AprAB–DsrAB, and three metagenome-assembled genomes (MAGs, genomes reconstructed from metagenomic reads) recurred across seven independent boreholes. This is literature context reported by the project, not a measurement made in the corpus 1.
Phylogenetic confound (Bacillota_B)
Caveat: the bacillota-b phylum contains Desulfosporosinus, BRH-c4a and BRH-c8a, which are the lineages that dominate the deep anchor cohort and cultured clay isolates. This phylum carries Wood–Ljungdahl and group 1 [NiFe]-hydrogenase at high background rates even in soil samples, with a Bacillota_B baseline mean toolkit score of 1.65. Cohort-level enrichment of these markers is therefore confounded by phylogeny 1,2.
Null result: within Bacillota_B, [NiFe]-hydrogenase is not enriched in deep-clay isolates relative to phylum congeners (5/5 vs 14/19, p=0.54), and neither is Wood–Ljungdahl (5/5 vs 15/19, p=0.54). These markers track the Bacillota_B lineage, not deep-clay habitat per se. Only sulfate reduction survives the phylogenetic control (5/5 vs 4/19, p_BH=0.04) 1,2.