According to the lanthanide methylotrophy atlas report, lanmodulin can bind rare-earth elements (REEs) 1. That report found lanmodulin, validated by bakta annotation, in 62 genomes, all in three α-Proteobacterial methylotroph families 1. These are genome-annotation counts from one report. They are not measurements of protein expression or REE binding 1.
The report detected Bakta-validated product = 'Lanmodulin' in 62 genomes from 10 species. All of them (62 / 62 = 100 %) fall within Beijerinckiaceae, Acetobacteraceae or Hyphomicrobiaceae, the three α-Proteobacterial methylotroph families pre-specified in hypothesis H3. A one-sided binomial test against the 80 % threshold gave p = 9.8 × 10⁻⁷, and the report rated H3a as strongly supported 1.
The dominant lanmodulin carrier is methylobacterium-extorquens, with 22 genomes and 1 lanmodulin copy each, so paralogs do not explain the pattern. The other contributors are an uncharacterised Acetobacteraceae genus (g__BOG-930, 12 genomes), M. thiocyanatum (6), M. rhodesianum (6), M. aminovorans (4), Hyphomicrobium_B (2) and Methylocella (2) 1.
Among Methylobacterium genomes, the report found xoxf in 102/209 and lanmodulin in 46/209. In this genus, the lanthanide-dependent methanol dehydrogenase gene therefore appears more often than the chelator. The report describes these counts as consistent with an existing model and as broader population-genomic context for it 1. This supports the page’s central claim that chelator carriage is narrower than dehydrogenase carriage, and it connects to lanthanide-dependent-methanol-dehydrogenase-predominance 1.
Dehydrogenase Presence Does Not Imply Chelator Presence
xoxF, from any annotation source, co-occurred in 49 / 62 = 79.0 % of lanmodulin-bearing genomes. This is just under the pre-registered 80 % threshold (one-sided binomial p = 0.65), so H3b was not formally supported. The report gives two possible explanations for the 13/62 lanmodulin-without-xoxF genomes. One is incomplete annotation. The other is a genuine alternative lanthanide-handling pathway, because lanmodulin can bind REEs without being co-located with a lanthanide-MDH operon. The report does not decide between them 1. This null result refines the narrow-distribution claim: lanmodulin is restricted to methylotroph families, but the threshold miss does not by itself show that lanmodulin is weakly coupled to xoxF. Biological decoupling remains a hypothesis alongside annotation incompleteness 1.
Taken together, these counts suggest the hypothesis that the two genes do not mark each other reliably in either direction. Many Methylobacterium genomes carry xoxF without lanmodulin, and some lanmodulin genomes lack annotated xoxF. If this holds, it matters for environmental surveys that rely on dehydrogenase markers, such as those discussed in environmental-distribution-of-lanthanide-methylotrophy. The inference rests on annotation-based counts from a single project 1.
Open Directions
- Re-annotate the 13/62 lanmodulin-without-xoxF genomes with a profile-HMM or homology search for xoxF and other lanthanide-MDH genes. This would test whether the shortfall below the 80 % threshold reflects annotation incompleteness or a genuine alternative lanthanide-handling pathway 1.
- Map xoxF carriage (102/209 Methylobacterium genomes) and lanmodulin carriage (46/209) onto a Methylobacterium phylogeny. This would show whether lanmodulin gain or loss is clade-structured and whether the chelator-dehydrogenase mismatch has a phylogenetic basis 1.
- Screen the uncharacterised Acetobacteraceae genus
g__BOG-930(12 lanmodulin genomes) for methylotrophy genes and environmental origin. This would test whether lanmodulin carriage outside Methylobacterium also tracks a methylotrophic lifestyle 1.