Epiphyton as a Niche for Ammonia-Oxidizing Bacteria: Detailed Comparison with Benthic and Pelagic Compartments in Shallow Freshwater Lakes

Abstract

Next to the benthic and pelagic compartments, the epiphyton of submerged macrophytes may offer an additional niche for ammonia-oxidizing bacteria in shallow freshwater lakes. In this study, we explored the potential activities and community compositions of ammonia-oxidizing bacteria of the epiphytic, benthic, and pelagic compartments of seven shallow freshwater lakes which differed in their trophic status, distribution of submerged macrophytes, and restoration history. PCR-denaturing gradient gel electrophoresis analyses demonstrated that the epiphytic compartment was inhabited by species belonging to cluster 3 of the Nitrosospira lineage and to the Nitrosomonas oligotropha lineage. Both the ammonia-oxidizing bacterial community compositions and the potential activities differed significantly between compartments. Interestingly, both the ammonia-oxidizing bacterial community composition and potential activity were influenced by the restoration status of the different lakes investigated.By converting ammonia into nitrite, ammonia-oxidizing bacteria (AOB) are responsible for the first step of the nitrification process (57, 58). Comparative 16S rRNA gene sequence analyses revealed assemblages of AOB in two monophyletic groups (17, 59). The main group, containing the genera Nitrosomonas, Nitrosospira, Nitrosovibrio, and Nitrosolobus, is affiliated with the beta subclass of Proteobacteria. The second group is affiliated with the gamma subclass and includes two species of the genus Nitrosococcus, retrieved and isolated exclusively from marine environments.AOB of the beta subclass have been detected in many different environments, from aquatic habitats (20,22,35,36,47,50,51,54,56) to soils (26)(27)(28)31) and building stones (48). The distribution patterns of distinct species of AOB depend on physiological differences between distinctive representatives (23) and on environmental parameters like ammonia concentration (5, 49, 51), pH and temperature (21, 42), oxygen availability (6, 16, 43), and salinity (10, 49). Horz et al. (19) demonstrated that AOB from a grassland soil are also able to respond to multifactorial global changes. AOB are therefore considered a model group in microbial ecology studies (27). However, it remains difficult to couple results obtained from physiological experiments conducted in the laboratory with isolated strains to nitrification activities observed in the environment from which the strains were isolated (27).AOB are known to grow either free-living or attached. For example, compared with the water column of aquatic environments, solid-phase habitats, such as sediment, particulate material, and aquatic macrophytes, seemed to be differently (35,40,50) and more densely populated with nitrifying bacteria (12,33,34). This surface-attached growth has been proposed to offer resilience against environmental constraints (41). Moreover, the formation of a biofilm on surfaces provides significant benefits for AOB of the Nitrosomonas lineages that are able to produce extracellular polymeric materials...

Quantitative Assessment of Ammonia-Oxidizing Bacterial Communities in the Epiphyton of Submerged Macrophytes in Shallow Lakes

“…In a recent, qualitative study of the bacterial ammoniaoxidizing community composition that had been conducted in the same system of interconnected shallow freshwater lakes used for the present study, we demonstrated the presence of ␤-AOB on the leaves of submersed macrophytes by means of the PCR-DGGE technique based on the 16S rRNA gene. We showed that the epiphytic, benthic, and pelagic communities significantly differed from each other (12). Those data were confirmed by the findings of the present study and were completed with quantitative data on the numbers of 16S rRNA gene copies of ␤-AOB cells in the three compartments obtained by qPCR and with direct microscopic images.…”

“…The compositions of the ammonia-oxidizing bacterial communities in the benthic, pelagic, and epiphytic compartments were assessed by a nested PCR-denaturing gradient gel electrophoresis (PCR-DGGE) approach involving two primer sets specific for the amplification of DNA from ammoniaoxidizing Betaproteobacteria. The method has been described in detail by Coci et al (12).…”

“…Data related to the water retention time and the oxygen, Kjeldhal nitrogen, and phosphate concentrations in the water of the lakes were provided by the Rijkswaterstaat Directory IJsselmeergebied (RDIJ). Analytical analyses of sediment samples were performed as described by Coci et al (12).…”

“…We hypothesized that the numbers of cells would differ between the epiphytic, benthic, and pelagic compartments, as previously observed for the community composition, due to the prevailing environmental conditions (12).…”

“…The present study focused on a more quantitative estimation of the ammonia-oxidizing bacteria in the epiphyton of two different submerged macrophytes, i.e., Potamogeton pectinatus and Chara aspera, present in three shallow freshwater lakes, which form part of the series of lakes studied before (12). We hypothesized that the numbers of cells would differ between the epiphytic, benthic, and pelagic compartments, as previously observed for the community composition, due to the prevailing environmental conditions (12).…”