Sponsor
Funding for this project was provided by the U.S. National Science Foundation (DEB 1557042, OISE-0968421), and NASA (80NNSC17KO548). The work (proposal: https://doi.org/10.4693 6/10.25585/60000691 and https://doi.org/10.46936/10.25585 /60007554) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. This research was also supported by National Science Foundation grant and the National Natural Science Foundation of China grants (40972211, 92251302, 91951205, 32370011, 32200007, 32200010, and 32170014), and National Science Foundation DEB-1134877.
Published In
Systematic and Applied Microbiology
Document Type
Article
Publication Date
7-29-2025
Subjects
Nitrogen -- Environmental aspects, Nitrogen -- Analysis
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 from Tengchong, China, fixes nitrogen based on growth with dinitrogen as the sole nitrogen source and incorporation of N atoms when grown with N. 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 (= JCM 35475 = DSM 116324) as the nomenclatural type. Its close relative designated Pampinifervens florentissimum sp. nov. T-8 (= CGMC 1.5214 = JCM 33569) 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.
Rights
Copyright © 2025 The Authors. Published by Elsevier GmbH.. All rights reserved.
Locate the Document
DOI
10.1016/j.syapm.2025.126644
Persistent Identifier
https://archives.pdx.edu/ds/psu/44000
Publisher
Elsevier BV
Citation Details
Palmer, M., Nou, N. O., Turello, L. A., Power, C. E., Ong, J. C., Covington, J. K., Lai, D., Mayali, X., Reysenbach, A.-L., Qi, Y.-L., Dodsworth, J. A., Jiao, J.-Y., Liu, L., Lian, Z.-H., Li, M.-M., Liu, Y., Murali, R., Briggs, B. R., Zuo, H., … Hedlund, B. P. (2025). Nitrogen fixation in Pampinifervens, a new species-rich genus of Aquificaceae that inhabits a wide pH range in terrestrial hot springs. Systematic and Applied Microbiology, 48(5), 126644.