Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76.
Google Scholar
Stein LY, Klotz MG. The nitrogen cycle. Curr Biol. 2016;26:R94–R98.
Google Scholar
Erguder TH, Boon N, Wittebolle L, Marzorati M, Verstraete W. Environmental factors shaping the ecological niches of ammonia-oxidizing archaea. FEMS Microbiol Rev. 2009;33:855–69.
Google Scholar
Nicol GW, Leininger S, Schleper C, Prosser JI. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environ Microbiol. 2008;10:2966–78.
Google Scholar
Lehtovirta-Morley LE, Ge C, Ross J, Yao H, Nicol GW, Prosser JI. Characterisation of terrestrial acidophilic archaeal ammonia oxidisers and their inhibition and stimulation by organic compounds. FEMS Microbiol Ecol. 2014;89:542–52.
Google Scholar
Lehtovirta-Morley LE, Stoecker K, Vilcinskas A, Prosser JI, Nicol GW. Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil. Proc Natl Acad Sci USA. 2011;108:15892–7.
Google Scholar
Hayatsu M, Tago K, Uchiyama I, Toyoda A, Wang Y, Shimomura Y, et al. An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil. ISME J. 2017;11:1130–41.
Google Scholar
Prosser JI, Nicol GW. Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 2012;20:523–31.
Google Scholar
Gubry-Rangin C, Hai B, Quince C, Engel M, Thomson BC, James P, et al. Niche specialization of terrestrial archaeal ammonia oxidizers. Proc Natl Acad Sci USA. 2011;108:21206–11.
Google Scholar
Aigle A, Prosser JI, Gubry-Rangin C. The application of high-throughput sequencing technology to analysis of amoA phylogeny and environmental niche specialisation of terrestrial bacterial ammonia-oxidisers. Environ Microbiome. 2019;14:3.
Google Scholar
Antony CP, Kumaresan D, Hunger S, Drake HL, Murrell JC, Shouche YS. Microbiology of Lonar Lake and other soda lakes. ISME J. 2013;7:468–76.
Google Scholar
Montanarella L, Chude V, Yagi K, Krasilnikov P, Panah SKA, Mendonca-Santos MDL, et al. Status of the World’s Soil Resources (SWSR) – Main Report. 2015.
Vera-Gargallo B, Chowdhury TR, Brown J, Fansler SJ, Durán-Viseras A, Sánchez-Porro C, et al. Spatial distribution of prokaryotic communities in hypersaline soils. Sci Rep. 2019;9:1769.
Google Scholar
Hollister EB, Engledow AS, Hammett AJM, Provin TL, Wilkinson HH, Gentry TJ. Shifts in microbial community structure along an ecological gradient of hypersaline soils and sediments. ISME J. 2010;4:829–938.
Google Scholar
Metternicht GI, Zinck JA. Remote sensing of soil salinity: potentials and constraints. Remote Sens Environ. 2003;85:1–20.
Google Scholar
Shi YL, Liu XR, Zhang QW. Effects of combined biochar and organic fertilizer on nitrous oxide fluxes and the related nitrifier and denitrifier communities in a saline-alkali soil. Sci Total Environ. 2019;686:199–211.
Google Scholar
Konneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB, Stahl DA. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature. 2005;437:543–6.
Google Scholar
Bayer B, Vojvoda J, Offre P, Alves RJE, Elisabeth NH, Garcia JAL, et al. Physiological and genomic characterization of two novel marine thaumarchaeal strains indicates niche differentiation. ISME J. 2016;10:1051–63.
Google Scholar
Santoro AE, Dupont CL, Richter RA, Craig MT, Carini P, McIlvin MR, et al. Genomic and proteomic characterization of “Candidatus Nitrosopelagicus brevis”: An ammonia-oxidizing archaeon from the open ocean. Proc Natl Acad Sci USA. 2015;112:1173–8.
Google Scholar
Pan KL, Gao JF, Li DC, Fan XY. The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: a DNA-based stable isotope probing study. Bioresour Technol. 2019;291:8.
Google Scholar
Nejidat A. Nitrification and occurrence of salt-tolerant nitrifying bacteria in the Negev desert soils. FEMS Microbiol Ecol. 2005;52:21–29.
Google Scholar
Ward BB, O’Mullan GD. Worldwide distribution of Nitrosococcus oceani, a marine ammonia-oxidizing gamma-proteobacterium, detected by PCR and sequencing of 16S rRNA and amoA genes. Appl Environ Micro. 2002;68:4153–7.
Google Scholar
Koops HP, Böttcher B, Möller UC, Pommerening-Röser A, Stehr G. Description of a new species of Nitrosococcus. Arch Microbiol. 1990;154:244–8.
Google Scholar
Fumasoli A, Bürgmann H, Weissbrodt DG, Wells GF, Beck K, Mohn J, et al. Growth of Nitrosococcus-related ammonia oxidizing bacteria coincides with extremely low pH values in wastewater with high ammonia content. Environ Sci Technol. 2017;51:6857–66.
Google Scholar
Olivera NL, Prieto L, Bertiller MB, Ferrero MA. Sheep grazing and soil bacterial diversity in shrublands of the Patagonian Monte, Argentina. J Arid Environ. 2016;125:16–20.
Google Scholar
Pérez-Hernandez V, Hernandez-Guzman M, Serrano-Silva N, Luna-Guido M, Navarro-Noya YE, Montes-Molina JA, et al. Diversity of amoA and pmoA genes in extremely saline alkaline soils of the former lake Texcoco. Geomicrobiol J. 2020;37:785–97.
Google Scholar
Picone N, Pol A, Mesman R, van Kessel MAHJ, Cremers G, van Gelder AH. et al. Ammonia oxidation at pH 2.5 by a new gammaproteobacterial ammonia-oxidizing bacterium. ISME J. 2020;15:1150–64.
Google Scholar
Pan H, Liu HY, Liu YW, Zhang QC, Luo Y, Liu XM, et al. Understanding the relationships between grazing intensity and the distribution of nitrifying communities in grassland soils. Sci Total Environ. 2018;634:1157–64.
Google Scholar
Santos JP, Mendes D, Monteiro M, Ribeiro H, Baptista MS, Borges MT, et al. Salinity impact on ammonia oxidizers activity and amoA expression in estuarine sediments. Estuar Coast Shelf Sci. 2018;211:177–87.
Google Scholar
Ye L, Zhang T. Ammonia-oxidizing bacteria dominates over ammonia-oxidizing archaea in a saline nitrification reactor under low DO and high nitrogen loading. Biotechnol Bioeng. 2011;108:2544–52.
Google Scholar
Luo S, Wang S, Tian L, Shi S, Xu S, Yang F, et al. Aggregate-related changes in soil microbial communities under different ameliorant applications in saline-sodic soils. Geoderma. 2018;329:108–17.
Google Scholar
Wang WJ, He HS, Zu YG, Guan Y, Liu ZG, Zhang ZH, et al. Addition of HPMA affects seed germination, plant growth and properties of heavy saline-alkali soil in northeastern China: comparison with other agents and determination of the mechanism. Plant Soil. 2011;339:177–91.
Google Scholar
Xia W, Zhang C, Zeng X, Feng Y, Jia Z. Autotrophic growth of nitrifying community in an agricultural soil. ISME J. 2011;5:1226–36.
Google Scholar
Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA. 2005;102:14683–8.
Google Scholar
Holmes AJ, Costello A, Lidstrom ME, Murrell JC. Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett. 1995;132:203–8.
Google Scholar
Fowler SJ, Palomo A, Dechesne A, Mines PD, Smets BF. Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities. Environ Microbiol. 2018;20:1002–15.
Google Scholar
Zhao ZR, Huang GH, He SS, Zhou N, Wang MY, Dang CY, et al. Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set. Sci Total Environ. 2019;691:145–55.
Google Scholar
Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat Commun. 2018;9:1517.
Google Scholar
Richter M, Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA. 2009;106:19126–31.
Google Scholar
Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J. 2017;11:2399–406.
Google Scholar
Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res. 2014;42:e73.
Google Scholar
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2020;36:1925–7.
Google Scholar
Kuroda T, Mizushima T, Tsuchiya T. Physiological roles of three Na+/H+ antiporters in the halophilic bacterium Vibrio parahaemolyticus. Microbiol Immunol. 2005;49:711–9.
Google Scholar
Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinfeder M, Schwarz J, et al. Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant. Nitrospira ISME J. 2020;14:2967–79.
Google Scholar
Padan E, Venturi M, Gerchman Y, Dover N. Na+/H+ antiporters. Biochim Biophys Acta. 2001;1505:144–57.
Google Scholar
Kraegeloh A, Amendt B, Kunte HJ. Potassium transport in a halophilic member of the bacteria domain: identification and characterization of the K+ uptake systems TrkH and TrkI from Halomonas elongata DSM 2581T. J Bacteriol. 2005;187:1036–43.
Google Scholar
Becker EA, Seitzer PM, Tritt A, Larsen D, Krusor M, Yao AI, et al. Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response. PloS Genet. 2014;10:e1004784.
Google Scholar
Cardoso FS, Castro RF, Borges N, Santos H. Biochemical and genetic characterization of the pathways for trehalose metabolism in Propionibacterium freudenreichii, and their role in stress response. Microbiology. 2007;153:270–80.
Google Scholar
Sadeghi A, Soltani BM, Nekouei MK, Jouzani GS, Mirzaei HH, Sadeghizadeh M. Diversity of the ectoines biosynthesis genes in the salt tolerant Streptomyces and evidence for inductive effect of ectoines on their accumulation. Microbiol Res. 2014;169:699–708.
Google Scholar
Ngugi DK, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, et al. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. ISME J. 2015;9:396–411.
Google Scholar
Spang A, Poehlein A, Offre P, Zumbragel S, Haider S, Rychlik N, et al. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol. 2012;14:3122–45.
Google Scholar
Glover HE. The relationship between inorganic nitrogen oxidation and organic carbon production in batch and chemostat cultures of marine nitrifying bacteria. Arch Microbiol. 1985;142:45–50.
Google Scholar
Lehtovirta-Morley LE, Ross J, Hink L, Weber EB, Gubry-Rangin C, Thion C, et al. Isolation of ‘Candidatus Nitrosocosmicus franklandus’, a novel ureolytic soil archaeal ammonia oxidiser with tolerance to high ammonia concentration. FEMS Microbiol Ecol. 2016;92:fiw057.
Google Scholar
Kits KD, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature. 2017;549:269–72.
Google Scholar
Hink L, Gubry-Rangin C, Nicol GW, Prosser JI. The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions. ISME J. 2018;12:1084–93.
Google Scholar
Shen JP, Zhang LM, Zhu YG, Zhang JB, He JZ. Abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea communities of an alkaline sandy loam. Environ Microbiol. 2008;10:1601–11.
Google Scholar
Jia Z, Conrad R. Bacteria rather than archaea dominate microbial ammonia oxidation in an agricultural soil. Environ Microbiol. 2009;11:1658–71.
Google Scholar
Millero FJ, Feistel R, Wright DG, McDougall TJ. The composition of Standard Seawater and the definition of the Reference-Composition Salinity Scale. Deep-Sea Res Part I-Oceanogr Res Pap. 2008;55:50–72.
Google Scholar
Mosier AC, Allen EE, Kim M, Ferriera S, Francis CA. Genome sequence of “Candidatus Nitrosopumilus salaria” BD31, an ammonia-oxidizing archaeon from the San Francisco bay estuary. J Bacteriol. 2012;194:2121–2.
Google Scholar
Matsutani N, Nakagawa T, Nakamura K, Takahashi R, Yoshihara K, Tokuyama T. Enrichment of a novel marine ammonia-oxidizing archaeon obtained from sand of an eelgrass zone. Microbes Environ. 2011;26:23–29.
Google Scholar
Park BJ, Park SJ, Yoon DN, Schouten S, Damste JSS, Rhee SK. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria. Appl Environ Micro. 2010;76:7575–87.
Google Scholar
Parada AE, Fuhrman JA. Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor. ISME J. 2017;11:2510–25.
Google Scholar
Wu YJ, Whang LM, Fukushima T, Chang SH. Responses of ammonia-oxidizing archaeal and betaproteobacterial populations to wastewater salinity in a full-scale municipal wastewater treatment plant. J Biosci Bioeng. 2013;115:424–32.
Google Scholar
Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota dominate subsurface ammonia-oxidizing communities in semi-arid floodplains in the western United States. Micro Ecol. 2020;80:778–92.
Google Scholar
Wang HT, Gilbert JA, Zhu YG, Yang XR. Salinity is a key factor driving the nitrogen cycling in the mangrove sediment. Sci Total Environ. 2018;631-2:1342–9.
Google Scholar
Oren A. Thermodynamic limits to microbial life at high salt concentrations. Environ Microbiol. 2011;13:1908–23.
Google Scholar
Ito M, Guffanti AA, Oudega B, Krulwich TA. mrp, a multigene, multifunctional locus in Bacillus subtilis with roles in resistance to cholate and to Na+ and in pH homeostasis. J Bacteriol. 1999;181:2394–402.
Google Scholar
Krulwich TA, Sachs G, Padan E. Molecular aspects of bacterial pH sensing and homeostasis. Nat Rev Microbiol. 2011;9:330–43.
Google Scholar
Swartz TH, Ikewada S, Ishikawa O, Ito M, Krulwich TA. The Mrp system: a giant among monovalent cation/proton antiporters? Extremophiles. 2005;9:345–54.
Google Scholar
Oren A. Bioenergetic aspects of halophilism. Microbiol Mol Biol R. 1999;63:334–48.
Google Scholar
Mackay MA, Norton RS, Borowitzka LJ. Organic osmoregulatory solutes in Cyanobacteria. J Gen Microbiol. 1984;130:2177–91.
Google Scholar
Sadler M, McAninch M, Alico R, Hochstein LI. The intracellular Na+ and K+ composition of the moderately halophilic bacterium, Paracoccus halodenitrificans. Can J Microbiol. 1980;26:496–502.
Google Scholar
Brown AD. Compatible solutes and extreme water stress in eukaryotic micro-organisms. Adv Micro Physiol. 1978;17:181–243.
Google Scholar
Reed RH, Warr SRC, Richardson DL, Moore DJ, Stewart WDP. Multiphasic osmotic adjustment in a euryhaline cyanobacterium. FEMS Microbiol Lett. 1985;28:225–9.
Google Scholar
Welsh DT, Herbert RA. Osmoadaptation of Thiocapsa roseopersicina OP-1 in batch and continuous culture: Accumulation of K+ and sucrose in response to osmotic stress. FEMS Microbiol Ecol. 1993;13:151–7.
Google Scholar
Sauvage D, Hamelin J, Larher F. Glycine betaine and other structurally related compounds improve the salt tolerance of Rhizobium meliloti. Plant Sci Lett. 1983;31:291–302.
Google Scholar
Campbell MA, Chain PSG, Dang H, Sheikh EI, Norton AF, Ward JM, et al. MG. Nitrosococcus watsonii sp. nov., a new species of marine obligate ammonia-oxidizing bacteria that is not omnipresent in the world’s oceans: calls tovalidate the names’Nitrosococcus halophilus’ and ‘Nitrosomonas mobilis’. FEMS Microbiol Ecol. 2011;76:39–48.
Google Scholar
Arguelles JC. Physiological roles of trehalose in bacteria and yeasts: a comparative analysis. Arch Microbiol. 2000;174:217–24.
Google Scholar
Widderich N, Czech L, Elling FJ, Könneke M, Stöveken N, Pittelkow M, et al. Strangers in the archaeal world: osmostress-responsive biosynthesis of ectoine and hydroxyectoine by the marine thaumarchaeon Nitrosopumilus maritimus. Environ Microbiol. 2016;18:1227–48.
Google Scholar
Bursy J, Pierik AJ, Pica N, Bremer E. Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase. J Biol Chem. 2007;282:31147–55.
Google Scholar
Kol S, Merlo ME, Scheltema RA, de Vries M, Vonk RJ, Kikkert NA, et al. Metabolomic characterization of the salt stress response in Streptomyces coelicolor. Appl Environ Micro. 2010;76:2574–81.
Google Scholar
Csonka LN. Physiological and genetic responses of bacteria to osmotic stress. Microbiol Rev. 1989;53:121–47.
Google Scholar
Saum SH, Sydow JF, Palm P, Pfeiffer F, Oesterhelt D, Muller V. Biochemical and molecular characterization of the biosynthesis of glutamine and glutamate, two major compatible solutes in the moderately halophilic bacterium Halobacillus halophilus. J Bacteriol. 2006;188:6808–15.
Google Scholar
Ventosa A, Nieto JJ, Oren A. Biology of moderately halophilic aerobic bacteria. Microbiol Mol Biol R. 1998;62:504–44.
Google Scholar
Mahan MJ, Csonka LN. Genetic analysis of the proBA genes of Salmonella typhimurium: physical and genetic analysis of the cloned proB+A+ genes of Escherichia coli and of a mutant allele that confers proline overproduction and enhanced osmotolerance. J Bacteriol. 1983;156:1249–62.
Google Scholar
Empadinhas N, Pereira PJB, Albuquerque L, Costa J, Sa-Moura B, Marques AT, et al. Functional and structural characterization of a novel mannosyl-3-phosphoglycerate synthase from Rubrobacter xylanophilus reveals its dual substrate specificity. Mol Microbiol. 2011;79:76–93.
Google Scholar
Santos H, da Costa MS. Compatible solutes of organisms that live in hot saline environments. Environ Microbiol. 2002;4:501–9.
Google Scholar
Koops HP, Purkhold U, Pommerening-Röser A, Timmermann G, Wagner M. The Lithoautotrophic Ammonia-Oxidizing Bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds). The Prokaryotes: a Handbook on the Biology of Bacteria, 3rd edn. New York, USA: Springer Science+Business Media; 2006, pp 778–811.
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