Succession of bacteria and archaea involved in the nitrogen cycle of a seasonally stratified lake

Abstract

Human-driven changes affect nutrient inputs, oxygen solubility, and the hydrodynamics of lakes, which affect biogeochemical cycles mediated by microbial communities. However, information on the succession of microbes involved in nitrogen cycling in seasonally stratified lakes is still incomplete. Here, we investigated the succession of nitrogen-transforming microorganisms in Lake Vechten over a period of 19 months, combining 16S rRNA gene amplicon sequencing and quantification of functional genes. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) and anammox bacteria were abundant in the sediment during winter, accompanied by nitrate in the water column. Nitrogen-fixing bacteria and denitrifying bacteria emerged in the water column in spring when nitrate was gradually depleted. Denitrifying bacteria containing nirS genes were exclusively present in the anoxic hypolimnion. During summer stratification, abundances of AOA, AOB, and anammox bacteria decreased sharply in the sediment, and ammonium accumulated in hypolimnion. After lake mixing during fall turnover, abundances of AOA, AOB, and anammox bacteria increased and ammonium was oxidized to nitrate. Hence, nitrogen-transforming microorganisms in Lake Vechten displayed a pronounced seasonal succession, which was strongly determined by the seasonal stratification pattern. These results imply that changes in stratification and vertical mixing induced by global warming are likely to alter the nitrogen cycle of seasonally stratified lakes.

Keywords: ammonia-oxidizing archaea; ammonia-oxidizing bacteria; anaerobic ammonium oxidation; denitrification; nitrogen fixation; stratified lake.

Figure 1.

Spatio-temporal dynamics of environmental parameters in Lake Vechten over a period of 19 months. (A) Temperature, (B) dissolved oxygen (DO), (C) nitrate, and (D) ammonium. Environmental parameters were measured for 244 water samples indicated by black dots.

Figure 2.

Dynamics of functional genes in the sediment of Lake Vechten. (A) Archaeal amoA genes (AOA), bacterial amoA genes (AOB), hzsA genes (anammox bacteria), (B)nirS genes (DNB), nirK genes (DNB), and nifH genes (NFB). Values show the mean ± standard deviation (SD) of three technical replicates (qPCR measurements) per sample.

Figure 3.

Spatio-temporal dynamics of (A)nirS genes (DNB), (B)nirK genes (DNB), and (C)nifH genes (NFB) in the water column of Lake Vechten. Functional genes were quantified for 125 water samples indicated by black dots.

Figure 4.

Heatmap of z-score transformed relative abundances of putative nitrogen-transforming bacterial genera in the water column and sediments of Lake Vechten. The colors of bacterial genus names indicate different functional groups: green, AOB; blue, NOB; red, NFB; purple, bacterial genera performing both nitrogen fixation and denitrification; and black, DNB. Only genera representing >0.02% of the total bacterial community are shown in the figure.

Figure 5.

RDA of the influence of environmental variables in the water column (explanatory variables, blue arrows) on the abundance of nirS, nirK, and nifH genes (response variables, red arrows). Symbols represent sampling points (yellow, spring; orange, summer; cyan, fall; green, winter). All explanatory variables in the triplot are significant (see Table S5). Total variation explained by the RDA model was 29.4%.

Figure 6.

Conceptual model of the seasonal succession of nitrogen-transforming microorganisms and seasonal transition of inorganic nitrogen (NO₃⁻, NH₄⁺) in the sediment and the water column of Lake Vechten over one year. AOA, ammonia-oxidizing archaea; AOB, ammonia-oxidizing bacteria; Anammox, anaerobic ammonium oxidizing bacteria; NFB, nitrogen-fixing bacteria; nirK DNB, denitrifying bacteria with the nirK gene; and nirS DNB, denitrifying bacteria with the nirS gene. (1) aerobic ammonium oxidation; (2) aerobic nitrite oxidation; (3) anaerobic ammonium oxidation; (4) denitrification; (5) nitrogen fixation; and (6) mineralization.