Abstract
ABSTRACTNiche 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.
Highlights
Nitrifiers are chemolithoautotrophs, which are defined by their ability to use reduced inorganic nitrogen compounds as an energy source and inorganic carbon to fulfill the carbon need
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
The Calvin-Benson-Bassham (CBB) cycle is present in different genera of nitrite-oxidizing bacteria (NOB) including Nitrobacter, Nitrococcus, Nitrotoga and Nitrolancea (Daims, Lucker and Wagner 2016) and generally found in AOB belonging to Proteobacteria (Badger and Bek 2008)
Summary
Nitrifiers are chemolithoautotrophs, which are defined by their ability to use reduced inorganic nitrogen compounds as an energy source and inorganic carbon to fulfill the carbon need. As the study of Alfreider et al (2017) was mostly based on sequence analysis from selected samples, the abundance, distribution and the ecological niche preferences of different guilds of nitrifiers remained unexplored.
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