Salinity‐driven ecology and diversity changes of heterocytous cyanobacteria in Australian freshwater and coastal‐marine microbial mats

N(2)‐fixing heterocytous cyanobacteria are considered to play a minor role in sustaining coastal microbial mat communities developing under normal marine to hypersaline conditions. Here, we investigated microbial mats growing under different salinities from freshwater mats of Giblin River (Tasmania) to metahaline and hypersaline mats of Shark Bay (Western Australia). Analyses of genetic (rRNA and mRNA) and biological markers (heterocyte glycolipids) revealed an unexpectedly large diversity of heterocytous cyanobacteria in all the studied microbial mat communities. It was observed that the taxonomic distribution as well as abundance of cyanobacteria is strongly affected by salinity. Low salinity favoured the presence of heterocytous cyanobacteria in freshwater mats, while mats thriving in higher salinities mainly supported the growth unicellular and filamentous non‐heterocytous genera. However, even though mRNA transcripts derived from heterocytous cyanobacteria were lower in Shark Bay (<6%) microbial mats, functional analyses revealed that these diazotrophs were transcribing a substantial proportion of the genes involved in biofilm formation and nitrogen fixation. Overall, our data reveal an unexpectedly high diversity of heterocytous cyanobacteria (e.g. Calothrix, Scytonema, Nodularia, Gloeotrichia, Stigonema, Fischerella and Chlorogloeopsis) that had yet to be described in metahaline and hypersaline microbial mats from Shark Bay and that they play a vital role in sustaining the ecosystem functioning of coastal‐marine microbial mat systems.