In this corpus the Wood–Ljungdahl (WL) pathway is a genomic marker. It was tested, alongside [NiFe]-hydrogenase and sulfate reduction, for enrichment in isolates from deep clay-confined subsurface settings 1,2.
Aliases: WL; WL_complete, the completeness flag used in the clay-subsurface comparison tables 1.
Cohort-level enrichment
At cohort level, a complete Wood–Ljungdahl pathway was scored in 5 of 9 deep-cohort genomes versus 15 of 140 soil-baseline genomes. The odds ratio was 10.4, with a Benjamini–Hochberg-adjusted p (p_BH, a false-discovery-rate-corrected p-value) of 0.004 1. This enrichment did not survive within-phylum control, described below, so it should not be read as evidence of a habitat-specific signal 1.
Phylogenetic confound (Bacillota_B)
The bacillota-b phylum includes desulfosporosinus, BRH-c4a and BRH-c8a, the lineages that dominate the deep anchor cohort and the cultured clay isolates. It carries Wood–Ljungdahl and group 1 nife-hydrogenase at high background rates even in soil samples. Its soil-baseline mean toolkit score, a per-genome count of the marker toolkit as defined in the report, was 1.65 1,2. This caveat refines the cohort-level result above: a lineage effect confounds the enrichment 1,2.
Within Bacillota_B, deep-clay isolates were not enriched for Wood–Ljungdahl beyond their phylum congeners (5/5 vs 15/19, p=0.54). The same null held for NiFe-hydrogenase (5/5 vs 14/19, p=0.54) 1,2. These markers therefore track the Bacillota_B lineage rather than deep-clay habitat per se 1. Only dissimilatory-sulfate-reduction survived the phylogenetic control (5/5 vs 4/19, p_BH=0.04), where p_BH is the Benjamini–Hochberg-adjusted p-value 2. This null rests on a small within-phylum sample of 5 deep-clay isolates. It means no enrichment was detectable at this resolution, not that any effect is ruled out 1,2.
Literature context
The clay report attributes to Bagnoud a minimalistic Opalinus clay food web in which Desulfobulbaceae c16a expressed the complete Wood–Ljungdahl pathway, group 1 [NiFe]-hydrogenase and Sat–AprAB–DsrAB. In that work, three MAGs (metagenome-assembled genomes, reconstructed from community sequencing) recurred across seven independent boreholes 1. This is a cited literature result, not a measurement made by the project 1.