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Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota

Qin, Wei and Heal, Katherine R. and Ramdasi, Rasika and Kobelt, Julia N. and Martens-Habbena, Willm and Bertagnolli, Anthony D. and Amin, Shady A. and Walker, Christopher B. and Urakawa, Hidetoshi and Könneke, Martin and Devol, Allan H. and Moffett, James W. and Armbrust, E. Virginia and Jensen, Grant J. and Ingalls, Anitra E. and Stahl, David A. (2017) Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. International Journal of Systematic and Evolutionary Microbiology, 67 (12). pp. 5067-5079. ISSN 1466-5026. https://resolver.caltech.edu/CaltechAUTHORS:20171023-084958349

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Abstract

Four mesophilic, neutrophilic, and aerobic marine ammonia-oxidizing archaea, designated strains SCM1^T, HCA1^T, HCE1^T and PS0^T, were isolated from a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, and near-surface sediment in the Puget Sound estuary, respectively. Cells are straight or slightly curved small rods, 0.15–0.26 µm in diameter and 0.50–1.59 µm in length. Motility was not observed, although strain PS0^T possesses genes associated with archaeal flagella and chemotaxis, suggesting it may be motile under some conditions. Cell membranes consist of glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, with crenarchaeol as the major component. Strain SCM1^T displays a single surface layer (S-layer) with p6 symmetry, distinct from the p3-S-layer reported for the soil ammonia-oxidizing archaeon Nitrososphaera viennensis EN76^T. Respiratory quinones consist of fully saturated and monounsaturated menaquinones with 6 isoprenoid units in the side chain. Cells obtain energy from ammonia oxidation and use carbon dioxide as carbon source; addition of an α-keto acid (α-ketoglutaric acid) was necessary to sustain growth of strains HCA1^T, HCE1^T, and PS0^T. Strain PS0^T uses urea as a source of ammonia for energy production and growth. All strains synthesize vitamin B_1 (thiamine), B_2 (riboflavin), B_6 (pyridoxine), and B_(12) (cobalamin). Optimal growth occurs between 25 and 32 °C, between pH 6.8 and 7.3, and between 25 and 37 ‰ salinity. All strains have a low mol% G+C content of 33.0–34.2. Strains are related by 98 % or greater 16S rRNA gene sequence identity, sharing ~85 % 16S rRNA gene sequence identity with Nitrososphaera viennensis EN76^T. All four isolates are well separated by phenotypic and genotypic characteristics and are here assigned to distinct species within the genus Nitrosopumilus gen. nov. Isolates SCM1^T (=ATCC TSD-97^T =NCIMB 15022^T), HCA1^T (=ATCC TSD-96^T), HCE1^T(=ATCC TSD-98^T), and PS0^T (=ATCC TSD-99^T) are type strains of the species Nitrosopumilus maritimus sp. nov., Nitrosopumilus cobalaminigenessp. nov., Nitrosopumilus oxyclinae sp. nov., and Nitrosopumilus ureiphilus sp. nov., respectively. In addition, we propose the family Nitrosopumilaceae fam. nov. and the order Nitrosopumilales ord. nov. within the class Nitrososphaeria.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1099/ijsem.0.002416DOIArticle
http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.002416PublisherArticle
ORCID:
AuthorORCID
Jensen, Grant J.0000-0003-1556-4864
Additional Information:© 2017 IUMS. Published by the Microbiology Society. Received: 18/10/2016 Accepted: 03/10/2017 Cover date: 16/10/2017. We thank B. Schneider and the FHCRC EM staff for performing transmission electron microscopy, and the Captain and crew of the R/V Clifford A. Barnes for their assistance with sample collection. We thank Adam Gee, Emily Chang, Yue Zheng, Jessie Zhou, Dr Robert Morris, and Vega Shah for technical assistance and Andrea Teichgräber and Kelley Meinhardt for helpful discussions. Finally, we thank the editor, Dr Aharon Oren, for particularly helpful comments and suggestions. This work was funded by the United States National Science Foundation grants MCB-0604448 (to D. A. S.) and Dimensions of Biodiversity Program OCE-1046017 (to D. A. S., A. E. I., E. V. A., A. H. D., J. W. M.). The authors declare that there are no conflicts of interest.
Funders:
Funding AgencyGrant Number
NSFMCB-0604448
NSFOCE-1046017
Subject Keywords:Vitamin B12, nitrification, Nitrosopumilales, Nitrosopumilaceae, Nitrosopumilus, Thaumarchaeota
Issue or Number:12
Record Number:CaltechAUTHORS:20171023-084958349
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20171023-084958349
Official Citation:Qin W, Heal K, Ramdasi R, Kobelt J, Martens-Habbena W, Bertagnolli A, Amin S, Walker C, Urakawa H, Könneke M, Devol A, Moffett J, Armbrust E, Jensen G, Ingalls A, Stahl D. 16/10/2017. Int J Syst Evol Microbiol 67(12):5067-5079 doi:10.1099/ijsem.0.002416
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:82569
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:24 Oct 2017 19:59
Last Modified:03 Oct 2019 18:56

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