Fluctuations in Ammonia Oxidizing Communities Across Agricultural Soils are Driven by Soil Structure and pH

The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators) of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR) of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively), and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 μgN h−1 gdw−1 and 1.68 ± 0.11 μgN h−1 gdw−1, being higher in soils with higher clay content (1.09 ± 0.12 μgN h−1 gdw−1) and lower in soils with lower clay percentages (0.27 ± 0.04 μgN h−1 gdw−1). Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10%) the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%). Similar trends were observed for the sizes of these communities. The present work represents a first step toward defining a NOR for soil nitrification. The sensitivity of the process and organisms to impacts from the milieu support their use as proxies in the NOR of agricultural soils. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil type-specific manner

Responses of soil nitrite-oxidizers to global environmental changes

Background/Question/Methods
There is increasing evidence that global change can alter the structure of plant
communities with large impacts on the functioning of terrestrial ecosystems. However, little is known about the impact of global change on soil microbial communities. In particular, the response of soil nitrite-oxidizers microorganisms that mediate the second step of nitrification, a key process of the nitrogen cycle, has never been investigated.
Here, we examined the effects of four main global environmental changes on the activity, the abundance and the diversity of soil nitrite-oxidizers in an annual grassland ecosystem as part of the Jasper Ridge Global Change Experiment (CA, USA). This experiment includes four treatments - CO2, temperature, precipitation and nitrogen - with two levels per treatment (ambient and elevated, with elevated treatment based on prediction for the end of the century), and all of their factorial combinations. We measured potential nitrite oxidation, the abundance of soil Nitrobacter- and Nitrospiralike nitrite-oxidizers (using quantitative PCR targeting nxrA and 16S rRNA gene, respectively) and the diversity of soil Nitrobacter-like nitrite-oxidizers (using cloning sequencing targeting the nxrA gene) in each treatment combination at the end of the 7th and 8th growing seasons under treatments. Furthermore, we analyzed to what extent changes in the activity of the soil nitrite-oxidizers result from changes in their abundance or diversity.

Results/Conclusions
Simulated global environmental changes significantly altered the activity, as well as the abundance and the diversity of soil nitrite-oxidizers. Potential nitrite oxidation decreased with increased precipitation and increased with elevated CO2 when combined with added nitrogen or precipitation. The abundance of soil Nitrobacter-like nitrite-oxidizers also decreased with increased precipitation and increased with elevated levels of CO2 and nitrogen. In contrast, the abundance of soil Nitrospira-like nitrite-oxidizers increased with enhanced precipitation and decreased with elevated levels of CO2 and temperature. Finally, the structure of the soil Nitrobacter-like nitrite-oxidizers was significantly altered by the treatments. Consistent with results reported by Attard et al. (2010) for agroecosystems, we found that changes in potential rates of nitrite oxidation in response to treatments were partly explained by changes in the abundance of soil Nitrobacter-like nitrite-oxidizers, but not by changes in the abundance of soil Nitrospiralike nitrite-oxidizers, suggesting that Nitrobacter-like nitrite-oxidizers were the main functional players of the soil nitrite-oxidizing microbial community.
Our study provides evidence that global change could alter the abundance and diversity of soil nitrite-oxidizers, with potential impacts for soil nitrogen cycling.

*The audio track for talks in this symposium may be obtained at the following web address:*

*https://sites.google.com/site/esa2010symposium13audiocontent/esa2010-symposium13-audio-content

Niche construction by the invasive Asian knotweeds (species complex Fallopia): impact on activity, abundance and community structure of denitrifiers and nitrifiers

info:eu-repo/semantics/publishe

Spatial heterogeneity of NO soil emissions at the Hombori Mali AMMA site: link with microbial activities

NO emissions from soil would be of comparable intensity as fossil fuel combustion at the global scale. Emissions in West Africa are of special interest since frequent convective episodes are observed in this region, with subsequent impact on the upper tropospheric chemistry. We report here results of a two-week campaign performed in the region of Hombori, Mali, at the beginning of the wet season. NO emissions from soil were measured using dynamic chamber and an ozone-chemiluminescence analyser. All classical meteorological parameters, and particularly, soil temperature and moisture, were recorded for the whole period. A set of 186 individual measurements of NO fluxes is available for analysis. These measurements are representative of eight different sites representative of the region, each site encompassing a range of locations with the landscape. Spatial heterogeneity of the fluxes was investigated from the flux database. We also tested to what extent flux heterogeneity could be explained by the spatial heterogeneity of soil characteristics and two key soil microbial activities, namely nitrification and denitrification, as measured in the laboratory on a set of 58 soil samples. We will analyse the relationship between in situ and laboratory measurements, and will identify the main processes driving NO emission for soils at the experimental sites. [no pdf

Spatial heterogeneity of NO soil emissions at the Hombori Mali AMMA site: link with microbial activities

NO emissions from soil would be of comparable intensity as fossil fuel combustion at the global scale. Emissions in West Africa are of special interest since frequent convective episodes are observed in this region, with subsequent impact on the upper tropospheric chemistry. We report here results of a two-week campaign performed in the region of Hombori, Mali, at the beginning of the wet season. NO emissions from soil were measured using dynamic chamber and an ozone-chemiluminescence analyser. All classical meteorological parameters, and particularly, soil temperature and moisture, were recorded for the whole period. A set of 186 individual measurements of NO fluxes is available for analysis. These measurements are representative of eight different sites representative of the region, each site encompassing a range of locations with the landscape. Spatial heterogeneity of the fluxes was investigated from the flux database. We also tested to what extent flux heterogeneity could be explained by the spatial heterogeneity of soil characteristics and two key soil microbial activities, namely nitrification and denitrification, as measured in the laboratory on a set of 58 soil samples. We will analyse the relationship between in situ and laboratory measurements, and will identify the main processes driving NO emission for soils at the experimental sites. [no pdf

Four years of experimental climate change modifies the microbial drivers of N2O fluxes in an upland grassland ecosystem

International audienceEmissions of the trace gas nitrous oxide (N2O) play an important role for the greenhouse effect and stratospheric ozone depletion, but the impacts of climate change on N2O fluxes and the underlying microbial drivers remain unclear. The aim of this study was to determine the effects of sustained climate change on field N2O fluxes and associated microbial enzymatic activities, microbial population abundance and community diversity in an extensively managed, upland grassland. We recorded N2O fluxes, nitrification and denitrification, microbial population size involved in these processes and community structure of nitrite reducers (nirK) in a grassland exposed for 4 years to elevated atmospheric CO2 (+200 ppm), elevated temperature (+3.5 °C) and reduction of summer precipitations (−20%) as part of a long-term, multifactor climate change experiment. Our results showed that both warming and simultaneous application of warming, summer drought and elevated CO2 had a positive effect on N2O fluxes, nitrification, N2O release by denitrification and the population size of N2O reducers and NH4 oxidizers. In situN2O fluxes showed a stronger correlation with microbial population size under warmed conditions compared with the control site. Specific lineages of nirK denitrifier communities responded significantly to temperature. In addition, nirK community composition showed significant changes in response to drought. Path analysis explained more than 85% of in situN2O fluxes variance by soil temperature, denitrification activity and specific denitrifying lineages. Overall, our study underlines that climate-induced changes in grassland N2O emissions reflect climate-induced changes in microbial community structure, which in turn modify microbial processe

A microcosm approach to evaluate the mesotrione effects on microbial communities of an agricultural soil

International audienc

Variations in snow depth modify N-related soil microbial abundances and functioning during winter in subalpine grassland

International audienceIn alpine and arctic ecosystems, the snowpack has been shown to insulate soils from the winter climatic harshness. Ongoing climate change modifies snowpack quantity and quality, but the consequences of these changes on the soil functioning remain largely unknown. We benefited from a subalpine landscape of the French Alps where, 700 years ago, agricultural practices led to the formation of terraces. Subsequently , on each terrace, snow thickness patterns significantly differed between the bank and the front areas inducing strong divergence in their soil microclimatic conditions. Using this framework, we measured abundances and activities of nitrifiers and denitrifiers, together with a set of environmental variables, on three grassland terraces between December and May to test the following hypotheses: (i) soil N-related microbial abundances and activities are sensitive to soil microclimatic variations and differ along the terrace snow depth gradient during winter, (ii) a thicker snowpack favors higher abundances and activities, and (iii) the driving forces for nitrification and denitrification abundances and activities vary along the snow depth gradient. Our results showed significantly and changing N-related microbial activities and abundances during winter despite partly frozen soils, and suggested the selection and/or adaptation of psychrophilic microbial communities. Moreover, activities as well as abundances of ni-trifiers and denitrifiers were significantly higher under a weak or absent snowpack during winter, and mostly related to soil water content and soil surface temperature according to our models. We suggest that strongly variable soil abiotic conditions at the front stations enabled the release of nutrients from soil organic and inorganic compounds favoring psychrophilic bacterial abundances and activities. Contrastingly , a thicker and permanent snowpack maintained circum-zero soil temperatures during winter which limited the microbial community's turnover and release of organic and inorganic N. This created N-limited conditions and N-competition between microbial populations resulting in lower abundances and activities. Overall, changes in the snowpack depth strongly affect the soil microbial functioning of subalpine grasslands with potential consequences on nutrient dynamic and other trophic levels

Denitrifying bacterial communities display different temporal fluctuation patterns across Dutch agricultural soils

Considering the great agronomic and environmental importance of denitrification, the aim of the present study was to study the temporal and spatial factors controlling the abundance and activity of denitrifying bacterial communities in a range of eight agricultural soils over 2 years. Abundance was quantified by qPCR of the nirS, nirK and nosZ genes, and the potential denitrification enzyme activity (DEA) was estimated. Our data showed a significant temporal variation considerably high for the abundance of nirK-harboring communities, followed by nosZ and nirS communities. Regarding soil parameters, the abundances of nosZ, nirS and nirK were mostly influenced by organic material, pH, and slightly by NO3 (-), respectively. Soil texture was the most important factor regulating DEA, which could not be explained by the abundance of denitrifiers. Analyses of general patterns across lands to understand the soil functioning is not an easy task because the multiple factors influencing processes such as denitrification can skew the data. Careful analysis of atypical sites are necessary to classify the soils according to trait similarity and in this way reach a better predictability of the denitrifiers dynamics

Successional patterns of key genes and processes involved in the microbial nitrogen cycle in a salt marsh chronosequence

Here, we investigated the patterns of microbial nitrogen cycling communities along a chronosequence of soil development in a salt marsh. The focus was on the abundance and structure of genes involved in N fixation (nifH), bacterial and archaeal ammonium oxidation (amoA; AOB and AOA), and the abundances of genes involved in denitrification (nirS, nirK, nosZ). Potential nitrification and denitrification activities were also measured, and increases in nitrification were found in soils towards the end of succession, whereas denitrification became maximal in soils at the intermediate stages. The nifH, nirK and nirS gene markers revealed increases in the sizes of the respective functional groups towards the intermediate stage (35 years), remaining either constant (for nifH) or slightly declining towards the latest stage of succession (for nirK and nirS). Moreover, whereas the AOB abundance peaked in soils at the intermediate stage, that of AOA increased linearly along the chronosequence. The abundance of nosZ was roughly constant, with no significant regression. The drivers of changes in abundance and structure were identified using path analysis; whereas the ammonia oxidizers (AOA and AOB) showed patterns that followed mainly N availability, those of the nitrogen fixers followed plant diversity and soil structure. The patterns of denitrifiers were group-dependent, following the patterns of plant diversity (nirK and nirS) and belowground shifts (nosZ). The variation observed for the microbial groups associated with the same function highlights their differential contribution at different stages of soil development, revealing an interplay of changes in terms of niche complementarity and adaptation to the local environment