Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes. Issue 10 (18th August 2018)

• Record Type: Journal Article
• Authors: Alfreider, Albin; Grimus, Victoria; Luger, Martin; Ekblad, Anja; Salcher, Michaela M; Summerer, Monika
• Is Part Of: FEMS microbiology ecology. Volume 94:Issue 10(2018:Oct.)
• Publication Date: 2018-08-18
• Subjects: chemoautotrophs -- nitrifiers -- lakes -- CO2 fixation pathways; Microbial ecology -- Periodicals; Microbiology -- Periodicals; 579.17
• DOI: 10.1093/femsec/fiy163
• Languages: English
• ISSNs: 0168-6496

Abstract

ABSTRACT: Niche specialization of nitrifying prokaryotes is usually studied with tools targeting molecules involved in the oxidation of ammonia and nitrite. The ecological significance of diverse CO2 fixation strategies used by nitrifiers is, however, mostly unexplored. By analyzing autotrophy-related genes in combination with amoA marker genes based on droplet digitial PCR and CARD-FISH counts targeting rRNA, we quantified the distribution of nitrifiers in eight stratified lakes. Ammonia oxidizing (AO) Thaumarchaeota using the 3-hydroxypropionate/4-hydroxybutyrate pathway dominated deep and oligotrophic lakes, whereas Nitrosomonas -related taxa employing the Calvin cycle were important AO bacteria in smaller lakes. The occurrence of nitrite oxidizing Nitrospira, assimilating CO2 with the reductive TCA cycle, was strongly correlated with the distribution of Thaumarchaeota . Recently discovered complete ammonia-oxidizing bacteria (comammox) belonging to Nitrospira accounted only for a very small fraction of ammonia oxidizers (AOs) present at the study sites. Altogether, this study gives a first insight on how physicochemical characteristics in lakes are associated to the distribution of nitrifying prokaryotes with different CO2 fixation strategies. Our investigations also evaluate the suitability of functional genes associated with individual CO2 assimilation pathways to study niche preferences of different guilds of nitrifying microorganisms based on an autotrophic perspective. Abstract : CO2 fixation strategies used by nitrifiers were investigated in lakes, suggesting that Thaumarchaeota using the 3-hydroxypropionate/4-hydroxybutyrate pathway were dominant in deep and oligotrophic lakes, whereas bacteria employing the Calvin cycle were important in samples with an elevated nutrient status.