Autotrophic carbon fixation strategies used by nitrifying prokaryotes in freshwater lakes

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.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

“…We recovered two Nitrospira genomes with amoABC and nxrAB suggesting comammox ability for the first time in a freshwater lake water column (to our knowledge), although previous studies have hinted at their existence 33 . These genomes belong to the previously described lineage II Clade A, consistent with known Nitrospira comammox lineages (Figure 5A).…”

Comparison of the microbiomes of two drinking water distribution systems—with and without residual chloramine disinfection

“…Nitrospira -like OTUs were also abundant in the no-residual DWDS and may have included comammox Nitrospira , as they are efficient at utilizing ammonia in nutrient-poor environments and have been previously observed in drinking water systems [72, 73]. The prominence of AOA concurrent to Nitrospira has been seen in deep, oligotrophic freshwater lakes—similar to the water supply source of the no-residual DWDS—and may be related to the carbon fixation strategies of these organisms [74]. Overall, the apparent diversity of nitrifiers in the no-residual DWDS (i.e., AOA, AOB, and NOB) was in contrast to the Nitrosomonas -dominated biofilms in the chloraminated DWDS and mirrored the broader observations of richness and evenness in the two systems.…”

Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

“…Pathways that were more prevalent specifically at the dLB were also observed. The alternative C fixation pathway (rTCA) was detected in higher numbers, probably due to the abundance of Nitrospirae which behave as nitrite-oxidizing chemoautotrophs by using it (Lücker et al 2010) and have been correlated well with the presence of Thaumarchaeota in other lakes (Alfreider et al 2018). However, Wood-Ljungdhal or DC4HB pathways that have been described from microbes inhabiting marine systems (Hügler and Sievert 2010) were not found at high ratios in dLB.…”