Differential responses of bacterial and archaeal groups at high taxonomical ranks to soil management

Little is known about abundances of the major bacterial taxa in agricultural soils and how they are affected by fertilization or other agricultural practices. Our aim was to determine the abundance and relative distribution of several bacterial phyla and one class, as well as the archaeal and crenarchaeal communities, and how they were affected by different fertilization regimes to examine whether specific responses of microorganisms could be identified at these high taxonomic ranks. We used real-time PCR with taxa specific primers to quantify the abundance of the Actinobacteria, Acidobacteria, Bacteriodetes, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Alphaproteobacteria and Crenarchaeo…

Spatial distribution of ammonia-oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

Characterization of spatial patterns of functional microbial communities could facilitate the understanding of the relationships between the ecology of microbial communities, the biogeochemical processes they perform and the corresponding ecosystem functions. Because of the important role the ammonia-oxidizing bacteria (AOB) and archaea (AOA) have in nitrogen cycling and nitrate leaching, we explored the spatial distribution of their activity, abundance and community composition across a 44-ha large farm divided into an organic and an integrated farming system. The spatial patterns were mapped by geostatistical modeling and correlations to soil properties and ecosystem functioning in terms …

Ecology of Denitrifying Prokaryotes in Agricultural Soil

Denitrification is a microbial respiratory process during which soluble nitrogen oxides are used as an alternative electron acceptor when oxygen is limiting. It results in considerable loss of nitrogen, which is the most limiting nutrient for crop production in agriculture. Denitrification is also of environmental concern, since it is the main biological process responsible for emissions of nitrous oxide, one of the six greenhouse gases considered by the Kyoto protocol. In addition to natural variations, agroecosystems are characterized by the use of numerous practices, such as fertilization and pesticide application, which can influence denitrification rates. This has been widely documente…

Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil

Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N2O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N2O emissions increased when the size of ino…

Insights into the unexplored diversity of the nitrous oxide reducing microbial community

Nitrous oxide (N2O) is a major radiative forcing and stratospheric ozone depleting gas emitted from terrestrial and aquatic ecosystems. It can be transformed to N2 by bacteria and archaea harboring the nitrous oxide reductase (N2OR), which is the only known N2O sink in the biosphere. Despite its crucial role in mitigating N2O emissions, knowledge of the N2OR in the environment remains limited. Here, we report a comprehensive phylogenetic analysis of the nosZ gene coding the N2OR in genomes retrieved from public databases. The resulting phylogeny revealed two distinct clades of nosZ, with one unaccounted for in studies investigating N2O reducing communities. Examination of N2OR structural el…

Spatial distribution of ammonia oxidizing bacteria and archaea across a 44-hectare farm related to ecosystem functioning

Unraveling biotic interactions determining soil microbial community assembly and functioning

National audience; Microbial communities are at the heart of all ecosystems and yet, a sound understanding of the ecological processes governing the assembly of these communities in the environment is missing. To address the role of biotic interactions in assembly and functioning of the soil microbiota, we used a top down manipulation approach based on the removal of various populations in a natural microbial community. Suspensions of the soil microbiota were subjected to various biocidal and filtration treatments before being inoculated into the same sterilized soil. We hypothesized that if biotic interactions are an important shaping force of the microbiota assembly, removal of microbial …

Membres du comité d’organisation scientifique

International audience; Biodiversity loss has become a global concern as increasing evidence highlights the importance of diverse species interactions as the main drivers of the ecosystem services on which society depends. This symposium focuses on the importance of above and belowground biodiversity for ecosystem functioning, multifunctionality and sustainability. Various talks will highlight the importance of biodiversity for agro-ecosystem functioning as this symposium is linked to the Biodiversa research project “Agricultural Diversification: Digging Deeper” investigating the importance of agricultural crop diversification.

Towards food, feed and energy crops mitigating climate change

Agriculture is an important source of anthropogenic emissions of the greenhouse gases (GHG), methane (CH 4 ) and nitrous oxide (N 2 O), and crops can affect the microbial processes controlling these emissions in many ways. Here, we summarize the current knowledge of plant–microbe interactions in relation to the CH 4 and N 2 O budgets and show how this is promoting new generations of crop cultivars that have the potential to mitigate GHG emissions for future agricultural use. The possibility of breeding low GHG-emitting cultivars is a paradigm shift towards sustainable agriculture that balances climate change and food and bioenergy security.

Importance of denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil

Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N2O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N2O emissions increased when the size of ino…

Molecular analyses of soil denitrifying bacteria

Effects of nitrogen fertilization on soil N2O reducing bacteria and their importance for mitigating N2O emissions

EABIOmECT3; Arable soils are a major source of nitrous oxide (N2O). The only known sink in Earth’s biosphere is the reduction of N2O to N2 via the N2O reductase encoded by the nosZ gene, identified as nosZ clade I and II. The nosZI gene is mainly found among denitrifying bacteria, whereas >50% of microorganisms with nosZII lack other denitrification genes. The abundance and phylogenetic diversity of nosZII was previously shown to correlate with a soils N2O sink capacity. To provide a proof of principle, we manipulated 11 indigenous soil microbial communities by increasing the abundance of a non-denitrifying N2O-reducing strain capable of growth with N2O as the only electron acceptor. Conseq…

Relationship between N-cycling communities and ecosystem functioning in a 50-year-old fertilization experiment.

The relative importance of size and composition of microbial communities in ecosystem functioning is poorly understood. Here, we investigated how community composition and size of selected functional guilds in the nitrogen cycle correlated with agroecosystem functioning, which was defined as microbial process rates, total crop yield and nitrogen content in the crop. Soil was sampled from a 50-year fertilizer trial and the treatments comprised unfertilized bare fallow, unfertilized with crop, and plots with crop fertilized with calcium nitrate, ammonium sulfate, solid cattle manure or sewage sludge. The size of the functional guilds and the total bacterial community were greatly affected by …

Inter-laboratory evaluation of the ISO standard 11063 "Soil quality - Method to directly extract DNA from soil samples"

International audience; Extracting DNA directly from micro-organisms living in soil is a crucial step for the molecular analysis of soil microbial communities. However, the use of a plethora of different soil DNA extraction protocols, each with its own bias, makes accurate data comparison difficult. To overcome this problem, a method for soil DNA extraction was proposed to the International Organization for Standardization (ISO) in 2006. This method was evaluated by 13 independent European laboratories actively participating in national and international ring tests. The reproducibility of the standardized method for molecular analyses was evaluated by comparing the amount of DNA extracted, …

Spatial patterns of bacterial taxa in nature reflect ecological traits of deep branches of the 16S rRNA bacterial tree

International audience; Whether bacteria display spatial patterns of distribution and at which level of taxonomic organization such patterns can be observed are central questions in microbial ecology. Here we investigated how the total and relative abundances of eight bacterial taxa at the phylum or class level were spatially distributed in a pasture by using quantitative PCR and geostatistical modelling. The distributions of the relative abundance of most taxa varied by a factor of 2.5–6.5 and displayed strong spatial patterns at the field scale. These spatial patterns were taxon-specific and correlated to soil properties, which indicates that members of a bacterial clade defined at high t…

Soil carbon quality and nitrogen fertilization structure bacterial communities with predictable responses of major bacterial phyla

Abstract Agricultural practices affect the soil ecosystem in multiple ways and the soil microbial communities represent an integrated and dynamic measure of soil status. Our aim was to test whether the soil bacterial community and the relative abundance of major bacterial phyla responded predictably to long-term organic amendments representing different carbon qualities (peat and straw) in combination with nitrogen fertilization levels and if certain bacterial groups were indicative of specific treatments. We hypothesized that the long-term treatments had created distinctly different ecological niches for soil bacteria, suitable for either fast-growing copiotrophic bacteria, or slow-growing…

Impact of land use, pesticide application and agricultural management practices on the phosphorus foraging capacity of mycorrhizal fungi in 217 european agricultural soils

More than 80% of vascular plants form symbiotic associations with arbuscular mycorrhizal fungi (AMF). Several studies have shown the potential of AMF to provide plants with phosphorus (P) via their hyphal network. Most of these studies have been performed in the greenhouse under controlled conditions using standardized soil mixtures. However, few studies have investigated hyphal P transfer in natural soils, severely limiting our understanding of the main drivers of P transfer by AMF in real agricultural soils. As a consequence, the potential of using AMF as a tool to increase crop yield remains a mystery. Using agricultural soils from a large field observation study in Europe, we aimed at a…

Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community

The recent development and application of numerous methods mainly based on 16S rDNA analyses have brought insights into the questions of which and how many bacterial populations can be found in a given ecosystem. A new and challenging question for microbial ecologists has emerged from the exploration of this diversity: what is its significance for ecosystem functioning? We propose the denitrifying bacteria as a model microbial community for understanding the relationship between community structure and activity, and have summarized the recent progress in studies of this functional community.

Microbial diversity in relation to soil functional operating range