Genome streamlining, proteorhodopsin, and organic nitrogen metabolism in freshwater nitrifiers

Abstract

Microbial nitrification is a critical process governing nitrogen availability in aquatic systems and provides energy for aphotic carbon fixation. Nitrifiers are phylogenetically and physiologically diverse, but the factors controlling this diversity, and its biogeochemical implications, are poorly understood, particularly in freshwater systems. Here, we characterized the taxonomic, genomic, and metabolic diversity of free-living nitrifiers across Earth’s largest freshwater system, the Laurentian Great Lakes. Surprisingly, ammonia oxidizing Bacteria (AOB) related to Nitrosospira dominated over ammonia oxidizing Archaea (AOA) at most stations, even in oligotrophic lakes with extremely low substrate concentrations. Nitrite oxidizing Bacteria (NOB) Ca. Nitrotoga and Nitrospira each dominated a subset of stations, even switching within a lake. Among four ecotypes of Nitrosospira we identified, one encodes proteorhodopsin, which could enhance survival of this AOB in transparent, low nutrient lakes. Genome reconstructions for free-living AOA, AOB, and NOB indicate small genomes across all taxa and diverse adaptations to sunlight and oxidative stress. Our findings expand the known functional diversity of nitrifiers and provide the first integrated picture of freshwater nitrifier genomics and ecology. As lakes worldwide undergo rapid environmental change, understanding the relationship between microbial biodiversity and nitrogen cycling is essential for predicting future ecosystem health and services.

Some like it cold: the cellular organization and physiological limits of cold‐tolerant nitrite‐oxidizing Nitrotoga

“…Namely, Nitrotoga might be able to oxidize hydrogen and lactate. Notably, these putative additional pathways of energy conservation were lacking in very streamlined Nitrotoga MAGs from the Great Lakes (Podowski et al ., 2021). Some Nitrotoga spp.…”

“…(2021), Podowski et al . (2021) and Singleton et al . (2021) (Supplementary Table S5) and two Gallionellaceae RefSeq assemblies (GCF_000974685.2 and GCF_000145255.1) as outgroup (Na et al ., 2018).…”

“…The UBCG pipeline was used to extract and align 92 single-copy core genes from 23 Nitrotoga genomes that were published by Boddicker and Mosier (2018), Kitzinger et al (2018), Ishii et al (2020), Nayfach et al (2020), Buck et al (2021), Podowski et al (2021) and Singleton et al (2021) (Supplementary Table S5) and two Gallionellaceae RefSeq assemblies (GCF_000974685.2 and GCF_000145255.1) as outgroup (Na et al, 2018). Based on the concatenated alignment comprising 88 344 columns, a maximum-likelihood phylogenomic tree was calculated using IQ-TREE 1.6.12 (Nguyen et al, 2015) via W-IQ-TREE (Trifinopoulos et al, 2016) with 1000 bootstrap replications and the integrated Modelfinder (Kalyaanamoorthy et al, 2017), which identified GTR + F + I + G4 as best-fitting substitution model.…”

Gallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms

“…The Gallionellaceae also includes a recently identified genus, Candidatus Nitrotoga, which are chemolithotrophic nitrite-oxidizing bacteria (NOB). Like the iron-oxidizing Gallionellaceae, they are widespread in freshwater and engineered environments, including permafrost (39), coastal sediments (40), freshwater (41), freshwater sediments (42), and the activated sludge of wastewater treatment facilities (43, 44). There are only two isolates, Ca .…”