Nitrogen fixation in Pampinifervens, a new species-rich genus of Aquificaceae that inhabits a wide pH range in terrestrial hot springs

Abstract

Members of the Aquificota play important roles in hydrogen, sulfur, and carbon cycles in geothermal systems as ubiquitous and abundant chemolithoautotrophs; however, their roles in the nitrogen cycle are poorly defined. Here, we show that Aquificaceae isolate T-2^T from Tengchong, China, fixes nitrogen based on growth with dinitrogen as the sole nitrogen source and incorporation of ¹⁵N atoms when grown with ¹⁵N₂. We further show evidence that suggests its nitrogen fixation (nif) genes are transcribed in situ in a nearby spring. We propose the name Pampinifervens diazotrophicum gen. et sp. nov., with strain T-2^T (= JCM 35475^T = DSM 116324^T) as the nomenclatural type. Its close relative designated Pampinifervens florentissimum sp. nov. T-8^T (= CGMC 1.5214^T = JCM 33569^T) does not fix nitrogen but respires nitrate. Analysis of 104 metagenome-assembled genomes from 84 metagenomes allowed us to circumscribe the genus Pampinifervens and identify at least 16 sympatric Pampinifervens species that dominate the Aquificaceae populations in diverse hot springs in southwest China, with distinct species globally. Analysis of these Pampinifervens genomes revealed variable presence of nif and denitrification genes and frequent gene loss and horizontal transfer. Genes for pH homeostasis were also present in Pampinifervens genomes, with a proliferation in species from Tengchong, consistent with the wide pH growth range of both Pampinifervens isolates and the prevalence of Pampinifervens in both alkaline and acidic springs. The dynamic evolution of nif and denitrification genes, along with pH homeostasis genes, may facilitate the diversification of Pampinifervens into diverse springs with different nitrogen availability.