Effects of temperature and fertilizer on activity and community structure of soil ammonia oxidizers

Abstract

We investigated the effect of temperature on the activity of soil ammonia oxidizers caused by changes in the availability of ammonium and in the microbial community structure. Both short (5 days) and long (6.5, 16 and 20 weeks) incubation of an agricultural soil resulted in a decrease in ammonium concentration that was more pronounced at temperatures between 10 and 25 degrees C than at either 4 degrees C or 30-37 degrees C. Consistently, potential nitrification was higher between 10 and 25 degrees C than at either 4 degrees C or 37 degrees C. However, as long as ammonium was not limiting, release rates of N2O increased monotonously between 4 and 37 degrees C after short-term temperature adaptation, with nitrification accounting for about 35-50% of the N2O production between 4 and 25 degrees C. In order to see whether temperature may also affect the community structure of ammonia oxidizers, we studied moist soil during long incubation at low and high concentrations of commercial fertilizer. The soil was also incubated in buffered (pH 7) slurry amended with urea. Communities of ammonia oxidizers were assayed by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the alpha subunit of ammonia monooxygenase. We found that a polymerase chain reaction (PCR) system using a non-degenerated reverse primer (amoAR1) gave the best results. Community shifts occurred in all soil treatments after 16 weeks of incubation. The community shifts were obviously influenced by the different fertilizer treatments, indicating that ammonium was a selective factor for different ammonia oxidizer populations. Temperature was also a selective factor, in particular as community shifts were also observed in the soil slurries, in which ammonium concentrations and pH were better controlled. Cloning and sequencing of selected DGGE bands indicated that amoA sequences belonging to Nitrosospira cluster 1 were dominant at low temperatures (4-10 degrees C), but were absent after long incubation at low fertilizer treatment. Sequences of Nitrosospira cluster 9 could only be detected at low ammonium concentrations, whereas those of Nitrosospira cluster 3 were found at most ammonium concentrations and temperatures, although individual clones of this cluster exhibited trends with temperature. Obviously, ammonia oxidizers are able to adapt to soil conditions by changes in the community structure if sufficient time (several weeks) is available.

The Biogeography of Ammonia-Oxidizing Bacterial Communities in Soil

“…Instead, we can conclude that differences in soil environmental conditions, namely differences in mean annual temperature seem to have important predictable effects on the composition of AOB communities in the soils included in this study. This result is consistent with other studies in soil and aquatic environments where a strong temperature influence on AOB community composition has also been observed [13,18,45,46].…”

“…2). Together, these results suggest that there is an important influence of temperature in shaping AOB community composition, and this pattern is evident whether we look across a range of ecosystem types (this study, [18]) or if individual soils are incubated under different temperature regimes in the laboratory [13,36,46]. The question we must then ask is: why does temperature appear to be the best predictor of AOB community composition?…”

“…Although pH, soil moisture levels, and nitrogen availability can have a strong influence on AOB activities and community composition [4,10,13], none of these factors were important determinants of differences in AOB community structure across the range of soils examined at these large inter-site spatial scales ( Table 2). Such factors may be important in individual soils, across particular gradients, or across specific experimental treatments, but they do not appear to be the environmental factors most important in regulating AOB community composition across the larger spatial scales examined here.…”

“…We do know that distinct soils often harbor distinct AOB communities. A number of environmental factors, including vegetation type [9][10][11], soil nutrient levels [12][13][14][15][16], soil microclimate [13,17,18], and management practices [19][20][21], have been found to have an important influence on the spatial variability exhibited by AOB communities. However, because most studies have compared AOB communities across a rather limited number of samples, with one notable exception being the study by Avrahami and Conrad [18], it has been difficult to ascertain which soil biotic and abiotic characteristics are related to AOB community composition across larger spatial scales.…”

Abundance and community structure of ammonia oxidizing bacteria and archaea in a Sweden boreal forest soil under 19-year fertilization and 12-year warming

“…Given that soil microorganisms are the key drivers of soil nutrient cycling (e.g., Falkowski et al 2008), their roles in mediating climate change and ecosystem functioning are not well understood (Balser et al 2001). An increasing number of reports have revealed shifts of carbon (C) substrate availability to microorganisms with temperature variations (e.g., MacDonald et al 1995;Zogg et al 1997;Flury and Gessner 2010), but there has been a lack of studies regarding effects of global warming on N cyclingassociated microbes (Avrahami et al 2003;Horz et al 2004;Tourna et al 2008).…”