Ammonium Availability Affects the Ratio of Ammonia-Oxidizing Bacteria to Ammonia-Oxidizing Archaea in Simulated Creek Ecosystems

Abstract

The ammonia-oxidizing microbial community colonizing clay tiles in flow channels changed in favor of ammonia-oxidizing bacteria during a 12-week incubation period even at originally high ratios of ammoniaoxidizing archaea to ammonia-oxidizing bacteria (AOB). AOB predominance was established more rapidly in flow channels incubated at 350 M NH 4 ؉ than in those incubated at 50 or 20 M NH 4 ؉ . Biofilm-associated potential nitrification activity was first detected after 28 days and was positively correlated with bacterial but not archaeal amoA gene copy numbers.Nitrogen transformation processes in small-river ecosystems are primarily associated with the sediment or epilithic biofilms (4,5,18). Here, nitrification as the first step in coupled nitrification-denitrification is a key step in the removal of the allochthonous nitrogen load, preventing the eutrophication of downstream ecosystems (1,5,29,39). The activity and community composition of biofilm-associated nitrifying microorganisms have been investigated extensively in wastewater treatment systems (27,36), in drinking water distribution systems (17, 41), and in lakes, large rivers, and estuaries (7,19,21,39) but only rarely in small-creek ecosystems. The first and ratelimiting step in nitrification, oxidation of ammonia, is carried out by ammonia-oxidizing archaea (AOA) (14) and ammoniaoxidizing bacteria (AOB) (16). Molecular surveys targeting the amoA gene, which encodes catalytic subunit A of ammonia monooxygenase, the key enzyme of ammonia oxidation (33), as well as cultivation-based studies, indicated that pH (26), salinity (25, 34), and especially ammonium availability (6, 22) could play important roles in the ecological niche differentiation of AOA and AOB. However, only little is known about archaeal versus bacterial ammonia oxidizers in creek or river ecosystems or about the association of AOA with biofilms (37,43). In this study, we used flow channels (FC) as simulated creek ecosystems to investigate the influence of ammonium availability (i) on the establishment of biofilm-associated nitrification activity, (ii) on the community composition of biofilm-associated AOA and AOB, and (iii) on temporal patterns of the abundance of AOA and AOB during a 12-week incubation period.FC experiment. Water for FC was obtained from three shell limestone creeks (Ammerbach, Leutra South, and Leutra North) located near the city of Jena (Thuringia, Germany). The creeks differed in their nutrient concentrations, with the highest nutrient load at Ammerbach resulting from diffuse wastewater inputs (Table 1). Flow velocities ranged from 0.105 Ϯ 0.092 to 0.230 Ϯ 0.224 m s Ϫ1 . Plexiglas FC measuring 160 by 10 by 18 cm (see Fig. S1 in the supplemental material) were set up in triplicate for each creek. Concentrations of NH 4 ϩ in the water phase of the FC were adjusted to 350 mol liter Ϫ1 (Ammerbach; FC 1 to 3), 50 mol liter Ϫ1 (Leutra South, FC 4 to 6), and 20 mol liter Ϫ1 (Leutra North, FC 7 to 9) to run the experiment at three distinct levels of NH 4 ϩ . pHs and concentrat...

Active Autotrophic Ammonia-Oxidizing Bacteria in Biofilm Enrichments from Simulated Creek Ecosystems at Two Ammonium Concentrations Respond to Temperature Manipulation

“…Furthermore, community analysis of ammonia-oxidizing prokaryotes in freshwater sediments and soils indicated a numerical predominance of AOA at low ammonium concentrations (18,29) and a positive effect of ammonium availability on the population size of AOB (53). Similar effects have been observed in natural and simulated small creek ecosystems with different ammonium concentrations (30). However, it is uncertain how temperature will affect the AOB dominance observed at relatively high ammonium availability, as well as the AOB and AOA community structures.…”

“…Metagenomic studies have shown that members of the kingdom Crenarchaeota (or Thaumarchaeota, as recently proposed [13,63]) within the domain Archaea also contain the amo genes (69,70), and subsequent studies have demonstrated the existence of ammonia-oxidizing archaea (AOA) (58). The numerical dominance of amoA-containing Archaea in soils (43) and in aquatic environments (30,47), their distribution worldwide (24), and the capacity of enrichments of Archaea and isolates to oxidize ammonia (17,28,34) raise questions regarding their relevance to ammonia oxidation in freshwater environments and, specifically, within epilithic stream biofilms.…”

Stream Biofilm Responses to Flow Intermittency: From Cells to Ecosystems

“…Studies addressing the effect of flow intermittency on archaeal communities are scarce compared to those with bacteria, and this can be taken as an indication that Archaea constitute a minor component of streambed microbial communities. Even in permanent rivers and streams Bacteria outnumber Archaea in all streambed compartments (Battin et al, 2001;Herrmann et al, 2011;Merbt et al, 2011Merbt et al, , 2015Buriánková et al, 2013), but is also true that Archaea occur in arid soils, microbial mats and freshwater sediments exposed to desiccation (Rothrock and (Rothrock and Garcia-Pichel, 2005;Soule et al, 2009;Timonen and Bomberg, 2009;Conrad et al, 2014). Despite this information, no conclusive data on the ecological function of the Archaea in streambeds are available.…”

Diversity, abundance and expression of nitrite reductase (nirK)-like genes in marine thaumarchaea

“…Finally, nitrite reductase has been proposed to be involved in detoxification of nitrite in AOB cultures (Beaumont et al, 2002;Cantera and Stein, 2007a). Nitrite detoxification has yet to be examined in AOA cultures, but AOA are generally more competitive in low-ammonia environments (Martens-Habbena et al, 2009;Di et al, 2010;Herrmann et al, 2011) where nitrite concentrations are unlikely to reach toxic levels.…”