Seasonal Changes of Freshwater Ammonia-Oxidizing Archaeal Assemblages and Nitrogen Species in Oligotrophic Alpine Lakes

Abstract

The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% ؎ 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.For almost 30 years, the ubiquity of nitrification, particularly in the most oligotrophic environments, had constituted an enigma for ecologists (28,52). First, because of very low natural abundances of ammonia-oxidizing bacteria (AOB), the a priori unique microorganisms with the potential to catalyze the first step of nitrification had been reported (e.g., 0.1% of total bacterial assemblage in oceanic habitats) (9, 38), and second, because field measurements indicated that the oxidation of ammonia (NH 4 ϩ ) to nitrate was feasible in situ even in the most oligotrophic habitats, where NH 4 ϩ concentrations were below the affinity threshold for AOB (8). Five years ago, metagenomics provided an answer to the enigma and radically changed the general perception of the nitrification process (65, 67). The presence of putative ammonia monooxygenase subunits (amoA, amoB, and amoC) within the genomes of widespread and abundant microorganisms of the domain Archaea (65, 67), as well as the chemolithoautotrophic growth using ammonia as an energy source observed in the recently isolated Crenarchaeota Nitrosopumilus maritimus (37), has fuelled...

Vertical segregation and phylogenetic characterization of ammonia-oxidizing Archaea in a deep oligotrophic lake

“…S1). Most of the sequences matched the soil/fresh-1 group (cluster A, in Auguet et al, 2011). In turn, OTU À 12 (very abundant at the bottom of the lake in winter-spring, and responsible for splitting this sample from the remaining April samples, Figure 6a) fell into the fresh/low-salinity group (cluster C), which has 95% identity with the amoA sequence of N. limnia.…”

“…Spatio-temporal changes in the distribution of planktonic freshwater AOA are, however, poorly documented (Pouliot et al, 2009;Llirós et al, 2010;Auguet et al, 2011) in contrast to what is known in the marine realm. The characteristic AOA abundance peak observed in the oxygen-minimum zone and dimly lit oceanic waters are often associated to maxima in nitrite concentrations, suggesting active ammonia oxidation in these areas.…”

“…We initially used denaturing gradient gel fingerprinting (DGGE) on the whole samples set for a rapid screening on the vertical shifts in archaeal 16S rRNA gene diversity (see Auguet et al, 2011 for specific PCR and DGGE conditions). Next, according to the shifts observed in the fingerprints, we selected six samples to describe the phylogenetic composition and vertical changes by PCR cloning of both the 16S rRNA (general archaeal primer set 21f-958r, 937 bp fragment length) and the archaeal amoA (primer set Arch-amoAF -Arch-amoAR, 635 bp fragment length) genes following previously reported conditions and see also the original references for the primers therein).…”

“…LlorensMarès et al, 2012). This lake is completely different from Lake Redó AT located in the Aigü es Tortes National Park, a shallow (12 m depth) well-mixed lake with a very low water-residence time (see more details in Auguet and Casamayor, 2008;Auguet et al, 2011). Local precipitation is the sole source of water for Lake Redon, as there are no permanent rivers in the basin, and the lake has a small catchment area of c. 1.5 km 2 .…”

Some Mixotrophic Flagellate Species Selectively Graze on Archaea

“…In the last decade, several studies have shown the broad distribution and abundance of Archaea in aquatic ecosystems (50)(51)(52) and their potential relevance in the sulfur, nitrogen, and carbon cycles (33,(53)(54)(55). However, their specific ecological interactions within the microbial communities remain largely unknown.…”