First exploration of Nitrobacter diversity in soils by a PCR cloning-sequencing approach targeting functional gene nxrA

Nitrite oxidoreductase (NXR) is the key enzyme responsible for the oxidation of NO2 to NO3 in nitrite-oxidizing bacteria. For the first time a molecular approach for targeting the nxrA gene was developed, encoding the catalytic subunit of the NXR, to study diversity of Nitrobacter-like organisms based on the phylogeny of nxrA gene sequences in soils. NxrA sequences of the Nitrobacter strains analysed (Nitrobacter hamburgensis, Nitrobacter vulgaris, Nitrobacter winogradskyi, Nitrobacter alkalicus) by PCR, cloning and sequencing revealed the occurrence of multiple copies of nxrA genes in these strains. The copy number and similarity varied among strains. The diversity of Nitrobacter-like nxrA sequences was explored in three soils (a French permanent pasture soil, a French fallow soil, and an African savannah soil) using a cloning and sequencing approach. Most nxrA sequences found in these soils (84%) differed from nxrA sequences obtained from Nitrobacter strains. Moreover, the phylogenetic distribution and richness of nxrAlike sequences was extremely variable depending on soil type. This nxrA tool extends the panel of functional genes available for studying bacteria involved in the nitrogen cycle

Relations biodiversite-fonctionnement chez les micro-organismes.

National audienceThe role of microorganisms as key components in the functioning of ecosystems and biodiversity is discussed. The latest methodologies developed to study microbial diversity and functioning of ecosystems are considered, as DNA extraction and isotope labeling, fluorescent in situ hybridization and microautoradiography, and tracking of a substrate labeled with a stable isotope. Investigations related to correlations between microbial diversity and functioning in situ are considered. An example is illustrated of a correlation of erosion of microbial diversity of natural microbial community in prairie soil and erosion of species diversity in an ecosystem

Grass populations control nitrification in savanna soils

1. Nitrification plays a key role in the functioning of many natural ecosystems. It is directly involved in plant nitrogen nutrition and soil N losses through leaching and denitrification. The control of this process by plants is poorly understood, although modifications of nitrification would allow plants to manipulate competition for N and induce changes in ecosystem N balance. In a wet tropical savanna ecosystem (Lamto, Côte d'Ivoire), the soil N cycle is characterized by distinct high- and low-nitrification sites. Previous publications showed that nitrification was positively or negatively correlated with root densities of the dominant grass covering these sites. These contrasting sites were chosen to investigate the extent to which vegetation controls long-term nitrification. 2. In situ experimental plots were created where grass individuals originating from high- or low-nitrifying soils were transplanted into both soils. Nitrifying enzyme activity (NEA) was measured up to 24 months after transplanting. Grasses from both sites significantly modified NEA up to rates similar to those at their respective control sites. 3. The level of individual plant control (inhibition and stimulation) was correlated with grass biomass. The potential mechanisms of this control is discussed, along with its consequences for ecosystem N cycling (such as N losses), as the denitrifying enzyme activity (DEA) is much higher in the high-nitrification site. Such results suggest that plant species can have important consequences for N cycling at the population level

Effects of grazing on microbial functional groups involved in soil N dynamics

International audienceEnhancement of soil nitrogen (N) cycling by grazing has been observed in many grassland ecosystems. However, whether grazing affects the activity only of the key microbial functional groups driving soil N dynamics or also affects the size (cell number) and/or composition of these groups remains largely unknown. We studied the enzyme activity, size, and composition of five soil microbial communities (total microbial and total bacterial communities, and three functional groups driving N dynamics: nitrifiers, denitrifiers, and free N-2 fixers) in grassland sites experiencing contrasting sheep grazing regimes (one light grazing [LG] site and one intensive grazing [IG] site) at two topographical locations. Enzyme activity was determined by potential carbon mineralization, nitrification, denitrification, and N-2 fixation assays. The size of each community (except N-2 fixers) was measured by the most-probable-number technique. The composition of the total soil microbial community was characterized by phospholipid fatty acid analysis (PLFA), and the genetic structure of the total bacterial community was assessed by ribosomal intergenic spacer analysis. The genetic structures of the ammonia-oxidizing, nitrate-reducing, and N-2- fixing communities were characterized by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) or by polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) targeting group-specific genes. Greater enzyme activities, particularly for nitrification, were observed in IG than in LG sites at both topographical locations. The numbers of heterotrophs, nitrifiers, and denitrifiers were higher in IG than in LG sites at both topographical locations. The amplitude of changes in community size was higher than that of community enzyme activity. Phospholipid and nucleic acid analyses showed that the composition/structure of all the communities, except nitrate reducers, differed between IG and LG sites at both locations. For each community, changes in activity were correlated with changes in the occurrence of a few individual PLFAs or DNA fragments. Our results thus indicate that grazing enhances the activity of soil microbial communities but also concurrently induces changes in the size and composition/structure of these communities on the sites studied. Although the generality of our conclusions should be tested in other systems, these results are of major importance for predicting the effects of future disturbances or changed grazing regimes on the functioning of grazed ecosystems

Effects of management regine and plant species on the enzyme activity and genetic structure of N-fixing, denitrifying and nitrifying bacterial communities in grassland soils

Management by combined grazing and mowing events is commonly used in grasslands, which influences the activity and composition of soil bacterial communities. Whether observed effects are mediated by management-induced disturbances, or indirectly by changes in the identity of major plant species, is still unknown. To address this issue, we quantified substrate-induced respiration (SIR), and the nitrification, denitrification and free-living N2-fixation enzyme activities below grass tufts of three major plant species (Holcus lanatus, Arrhenatherum elatius and Dactylis glomerata) in extensively or intensively managed grasslands. The genetic structures of eubacterial, ammonia oxidizing, nitrate reducing, and free-living N2-fixing communities were also characterized by ribosomal intergenic spacer analysis, and denaturing gradient gel electrophoresis (DGGE) or restriction fragment length polymorphism (RFLP) targeting group-specific genes. SIR was not influenced by management and plant species, whereas DEA was influenced only by plant species, and management x plant species interactions were observed for fixation and nitrification enzyme activities. Changes in nitrification enzyme activity were likely largely explained by the observed changes in ammonium concentration, whereas N availability was not a major factor explaining changes in denitrification and fixation enzyme activities. The structures of eubacterial and free-living N2-fixing communities were essentially controlled by management, whereas the diversity of nitrate reducers and ammonia oxidizers depended on both management and plant species. For each functional group, changes in enzyme activity were not correlated or were weakly correlated to overall changes in genetic structure, but around 60% of activity variance was correlated to changes in 5 RFLP or DGGE bands. Although our conclusions should be tested for other ecosystems and seasons, these results show that predicting microbial changes induced by management in grasslands requires consideration of management x plant species interactions

Sécheresses et incendies répétés accroissent mutuellement leur impact sur l'écosystème

International audienceIn a recent research project performed in South-Eastern France on the impact of repeated fires on many components of forest environment (vegetation, fauna, microbiology, soil physics, chemical properties, organic matter, nutrients) we showed a strong interaction between repeated droughts and repeated fires. Each disturbance significantly increases the impact of the other one. Repeated droughts can stop and even reverse the recovery process after fire, and delay this recovery when they occurred before fire. Repeated fires lessen the resistance and resilience of the ecosystem to drought. Forest regeneration processes are threatened even in usually fire-prone environments usually resilient. Soil biological activity is severely affected, and particularly some key groups as earthworms and bacteria contributing to nitrogen cycle. Soil physics and chemical properties appear to be degraded as a habitat, and indirectly the reduction of biological activity limits their recovery, including a negative carbon balance. Four successive years appear to be the critical threshold for drought and four times in 50 years the critical threshold for fires. As climate change may lead to higher drought frequency and fire occurrence is tied to drought, the drought/fire interaction may degrade forest ecosystems more rapidly than expected from separate assessment of drought and fire impacts