Macroevolution of micro-organisms
Prokaryotes dominate the Tree of Life, but our understanding of the macroevolutionary processes generating this diversity is still limited. Habitat transitions are thought to be a key driver of prokaryote diversity, but relatively little is still known about how prokaryotes successfully transition and persist across environments, and how these processes might vary between biomes and lineages. Here, we investigate biome transitions and specialisation in natural populations of a focal bacterial phylum, the Myxococcota, sampled across a range of replicated soils and freshwater and marine sediments in Cornwall (UK). By targeted deep sequencing of the protein-coding gene rpoB, we found >2000 unique Myxococcota lineages, with the majority (77%) being biome specialists and with only <5% of lineages distributed across the salt barrier. Discrete character evolution models revealed that biome specialists very rarely evolved into lineages specialised to another biome. Instead, generalists mediated transitions between biome specialists. State dependent diversification models found variation in speciation rate across the tree, but this variation was independent of biome association or specialisation. These results were robust to phylogenetic uncertainty, assumed amounts of missing phylogenetic information, and different levels of species delineation. Overall, our results are consistent with a “jack-of-all-trades” trade-off where generalists suffer a cost in any individual environment, resulting in rapid evolution of niche specialists and shed light on how bacteria could  transition between biomes.