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Despite the extensive diversity of bacteria and their importance to the fundamental functioning of terrestrial ecosystems, their distribution patterns are still not fully known. To fill the gap and further understand the biogeographic patterns in bacteria, we investigated the phylogeographic structure and the underlying drivers of diversification among populations of the cyanobacterium  Microcoleus  spp. The phylogenetic history was reconstructed using 16S rRNA genes and the 16S–23S internal transcribed spacer (ITS) of 495  Microcoleus  spp. isolates. Ancestral area and state reconstruction was employed to investigate the distributional and ecological patterns within  Microcoleus . Both isolation by distance and isolation by environment were tested with distance matrices analysis. The phylogenetic signal tests were conducted in order to assess the influence of the climatic preferences on the diversification of  Microcoleus  isolates. The distribution and phylogenetic diversification of  Microcoleus  are driven by both isolation by distance and environment, leading to at least 13 distinct lineages that could represent novel cyanobacterial species.  Microcoleus  spp. exhibited a distinct phylogeographic structure within the respective lineages. The ancestral area and state reconstruction revealed that  Microcoleus  most likely arose in Europe in terrestrial habitats. The phylogenetic signal showed that the phylogeny significantly affects the climatic preferences of  Microcoleus  strains. Geographic distance and contemporary climatic conditions play significant roles in shaping the distribution and diversification of  Microcoleus . The observed patterns of distribution may shift in the future due to the impact of climate change. HighlightsMicrocoleus  exhibited distinct phylogeographic structure within the respective lineages.Geographic and environmental heterogeneity affect  Microcoleus  distribution and diversification.Genetically distinct lineages coexist at the same site. Microcoleus  exhibited distinct phylogeographic structure within the respective lineages. Geographic and environmental heterogeneity affect  Microcoleus  distribution and diversification. Genetically distinct lineages coexist at the same site.

Geography and climate drive the distribution and diversification of the cosmopolitan cyanobacterium Microcoleus (Oscillatoriales, Cyanobacteria)