Graded degradation of nucleotide second-messenger signaling and selective retention of structural metalloproteins in the Kryptonia phylum

The Kryptonia are a candidate bacterial phylum of extreme thermophiles from terrestrial hot springs with reduced genomes and obligate fermentative metabolism. How microbes adapt to oligotrophic extremes through selective gene loss remains a central evolutionary question. We address this through comparative genomics of 51 Kryptonia genomes (49 hot-spring isolates, 2 non-hot-spring European MAGs; §4.1) spanning all five candidate genera, plus a community metagenome. We report a phylum-wide graded degradation of nucleotide second-messenger signaling. The c-di-GMP pathway shows asymmetric loss: 44 of 45 GGDEF domains (97.8%) are catalytically inactive (EDNLIG, DDDLIG, EDNLFA, DENLIG, SAHSFG) with non-Gly substitutions at both catalytic glycine positions; one genome retains a single active GGEEF, consistent with secondary acquisition. No EAL phosphodiesterases exist (0/51), yet HD-domain phosphohydrolases are universally retained (PF01966, 51/51), with canonical HD-GYP[DE] enzymes in 46/51 (90%)—consistent with degradation of environmental c-di-GMP of community origin (Black Queen Hypothesis). AlphaFold3 predictions of six representative GGDEF domains corroborate a molecular-fossil model: all inactive domains retain the canonical (β/α)8 TIM-barrel fold (Cα-RMSD 5.0–6.1 Å vs. active GGEEF), and the allosteric I-site (RxxD) is fully degenerated in all 44 inactive domains. Codon-based selection analysis shows housekeeping-grade purifying selection on retained HD-GYP (M0 ω = 0.008) and near-neutral drift confined to acidic surface patches of the inactivated GGDEF scaffold (ω ≈ 0.85). Structural metalloproteins—[4Fe-4S] clusters, zinc ribbons and multi-heme cytochromes—are stably retained (3,021 non-redundant proteins, 2.83% of the proteome), contrasting with degraded signaling metalloproteins. Community analysis identifies Fervidibacter sacchari as the sole c-di-GMP helper in this metagenome, with Kryptonia as a cheater. We propose an energy-economics model in which costly, shareable steps are lost while low-cost, resource-recovering steps are retained, extending the Black Queen Hypothesis to intracellular signaling.