Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

Anne Daebeler,Mads Albertsen,Michaela Steinfeder,Katharina Kitzinger,Thomas Zechmeister,Jasmin Schwarz,Per H Nielsen,Hanna Koch,Holger Daims,Craig W Herbold,Michael Wagner,Søren M Karst

doi:10.1038/s41396-020-0724-1

Abstract

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospira distribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3–12.8 g salt/l), highly alkaline (pH 8.9–10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members from Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, “Candidatus Nitrospira alkalitolerans”, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. “Ca. Nitrospira alkalitolerans” also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

Highlights

Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players of the nitrogen cycle in virtually all oxic habitats including soil, freshwater and marine ecosystems, engineered environments, and geothermal springs [1,2,3,4,5,6,7,8,9]
We discovered and investigated unusually alkalitolerant Nitrospira in saline-alkaline lakes of the national park “Neusiedler See-Seewinkel”, Burgenland, Austria using targeted amplicon profiling of the 16S rRNA gene and nxrB, of which the latter encodes the beta-subunit of nitrite oxidoreductase
This study shows that diverse Nitrospira phylotypes are able to colonize saline-alkaline lakes, and that members of these lineages can carry out chemolithoautotrophic nitrite oxidation under strongly alkaline conditions up to pH 10.5

Summary

Introduction

Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players of the nitrogen cycle in virtually all oxic habitats including soil, freshwater and marine ecosystems, engineered environments, and geothermal springs [1,2,3,4,5,6,7,8,9]. In most terrestrial and engineered environments, the predominant known NOB are uncultured members of the genus Nitrospira [1, 10,11,12,13]. Within this highly diverse genus, six phylogenetic lineages (named lineage I to VI) have been described, some of which seem to colonize distinct habitat types [1, 4, 8, 14, 15]. Dashed circles enclose lakes with similar Nitrospira communities (see Fig. 3)

Methods

Results

Conclusion