Effect of lake trophic status and rooted macrophytes on community composition and abundance of ammonia-oxidizing prokaryotes in freshwater sediments

Abstract

Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were compared for seven oligotrophic to mesotrophic softwater lakes and acidic heathland pools. Archaeal and bacterial ammonia monooxygenase alpha-subunit (amoA) gene diversity increased from oligotrophic to mesotrophic sites; the number of detected operational taxonomic units was positively correlated to ammonia availability and pH and negatively correlated to sediment C/N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (<0.05% of all prokaryotes) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic macrophytes with substantial release of oxygen and organic carbon into their rhizospheres, like L. uniflora and J. bulbosus, increase AOA abundance; and (iii) AOA community composition is generally determined by lake trophy, not by plant species-specific interactions.

FIG. 1.

Number of detected OTUs of AOA (closed circles) and AOB (open circles) and relative abundances of AOA (gray columns) and AOB (white columns) in unvegetated sediment and rhizosphere sediment. For definitions of the abbreviations for samples, see Table 1. Relative abundance values are the means ± the standard deviations of nine qPCR reactions with triplicate DNA extracts from three environmental replicates. Columns represent maximum estimates, where amoA gene copy numbers remained below the quantification limit of 50 copies (<) or the detection limit of 5 copies (≪) per reaction. Letters above columns indicate significant differences between samples.

FIG. 2.

Similarities of clone libraries of archaeal AmoA (A) and bacterial AmoA (B) among sites, plant species, and compartments, based on Jaccard values. The origins of sequences are indicated by closed circles (mesotrophic sites), open triangles (oligotrophic sites), and closed squares (dystrophic sites). For the definitions of abbreviations, see Table 1.

FIG. 3.

Phylogenetic affiliation of archaeal AmoA (A) and bacterial AmoA (B). Protein distance trees are displayed with bootstrap values (>50%) from parsimony analysis (1,000 replicates). Branchings not supported by both methods are drawn as multifurcations. The major lineages were also supported by maximum likelihood analysis with a reduced number of sequences. For all the OTUs obtained in this study, accession numbers and clone numbers for representative sequences from each clone library are shown in boldface type. For the definitions of abbreviations, see Table 1. The origins of sequences are indicated by closed circles (mesotrophic sites), open triangles (oligotrophic sites), and closed squares (dystrophic sites).

FIG. 3.

Phylogenetic affiliation of archaeal AmoA (A) and bacterial AmoA (B). Protein distance trees are displayed with bootstrap values (>50%) from parsimony analysis (1,000 replicates). Branchings not supported by both methods are drawn as multifurcations. The major lineages were also supported by maximum likelihood analysis with a reduced number of sequences. For all the OTUs obtained in this study, accession numbers and clone numbers for representative sequences from each clone library are shown in boldface type. For the definitions of abbreviations, see Table 1. The origins of sequences are indicated by closed circles (mesotrophic sites), open triangles (oligotrophic sites), and closed squares (dystrophic sites).