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Abstract: The annual dynamics of soil bacterial community structure, including early, dose-dependent and transient modifications, was observed consecutively at different levels of copper contamination (high: 48kgCuha−1, low: 16kgCuha−1) repeated yearly over a three-year field experiment. Repeated low-level Cu contamination led to an increase in community stability to metal stress without a long-term shift in the population structure, whereas repeated high-level Cu contamination induced a novel and stable bacterial community structure. Furthermore, field experimentation highlighted that episodic climatic stress can modulate copper impact by enhancing community stability. [Copyright &y& Elsevier]

Abstract: Natamycin is commonly used to control fungal growth on agar media used for bacterial enumeration or strain isolation. However, there is no conclusive report on the possible effect of this antibiotic on bacterial growth or on the diversity of the recovered soil bacteria. Therefore, the possible effects of natamycin on the numbers of bacteria isolated at 12 °C from three different soils and soybean rhizosphere soil were investigated using natamycin concentrations ranging from 0 to 200 mg l−1. Our results demonstrate that natamycin concentrations, which inhibit the growth of fungi on the media, have a small but significant inhibitory effect on the number of bacterial colony forming units. A natamycin concentration of 50–200 mg l−1 is required for an efficient control of fungal growth on media in our experimental conditions depending on the soil type. Bacterial community structure was assessed on culturable cells (cells washed from enumeration plates: plate-wash approach) obtained at 12 °C from soybean rhizosphere soil by performing Ribosomal Intergenic Spacer Analysis (RISA) fingerprinting. We demonstrate that all natamycin concentrations used alter the structure of the recovered, culturable bacterial community, compared to control without natamycin. Using ARDRA (amplification of the 16S rDNA gene and restriction analysis) genotyping of individual isolates, some differences were observed between the bacterial isolates obtained in the presence or absence of natamycin. Bacterial isolates recovered in the presence of natamycin are more tolerant (maximal growth rate and lag phase) to this compound than those isolated without natamycin, indicating a possible selection of resistant strains. Therefore, high concentration of natamycin cannot be used for isolation of bacterial strains with the aim of studying biodiversity and could bias a selection of strains for practical applications. [Copyright &y& Elsevier]

A novel group of Se-methyltransferases is presented. The genetic determinant, named mmtA, which revealed this group was isolated from selenite and selenate-resistant freshwater bacteria. E. coli expressing mmtA and grown with a Se supplement emitted dimethyl selenide (DMSe) and dimethyl diselenide (DMDSe). Phylogenetic analysis divided MmtA-like bacterial sequences into two clusters, one grouping MmtA with S- and O-methyltransferases, and one grouping UbiE C-methyltransferases. Se methylation by some of these MmtA phyletic neighbours was investigated. [Copyright &y& Elsevier]

Abstract: Soil microbial communities play an important role in soil carbon functioning, particularly in forest ecosystems. Their variation in response to climate change may affect soil carbon processes, highlighting the importance of understanding how environmental factors affect microbial communities. This study aimed to determine to what extent an increase in the quantity of fresh litter may affect heterotrophic mineralization of organic carbon and bacterial community structure in soil and litter. A litter manipulation experiment was performed in situ in a temperate deciduous forest. Three treatments of fresh litter inputs were considered: litter exclusion, natural conditions (control) and litter addition (twice the natural rate). Microbial and functional ecological approaches were combined to consider bacterial community structure in soil and litter using a molecular fingerprinting technique, and measurement of soil respiration both in terms of efflux intensity and isotopic composition of respired CO2 (natural abundance) over one year. The quantity of fresh litter seemed to affect soil and litter bacterial community structure and to interact with soil temperature and moisture to determine the temporal variation in the bacterial community on a month to season scale. In addition, this study highlighted the large temporal variability in soil and litter bacterial community structure and that this variability may affect our ability to relate bacterial community structure to respiration processes. This highlights the need for an intensive characterisation of the bacterial community structure to relate its variations to variations in soil respiration processes. [ABSTRACT FROM AUTHOR]

Abstract: The effect of copper on the abundance, diversity and resistance of viable heterotrophic and copper resistant bacterial populations (CuR) was evaluated in soils differing only by their amount and type of organic matter. These soils have been obtained using a vineyard soil that had been subjected to three different organic matter managements (Not Amended (NA) or amended with Straw (S) or Conifer Compost (CC)) in a long term field experiment. Soil microcosms were artificially contaminated with copper (250 mg Cu kg−1 of soil) and incubated for 35 days. Throughout the incubation, a differential copper impact on viable heterotrophic and CuR bacterial enumeration was demonstrated according to the soil organic status with a magnitude which followed the order: NA > CC ≥ S. Diversity of CuR bacteria revealed no significant difference between the uncontaminated soils, as determined by 16S rRNA sequencing. However, copper spiking induced an enrichment of particular populations depending on soil, with Methylobacterium, Ralstonia and Staphylococcus like species becoming dominant in NA, S and CC soils, respectively. Evaluation of the copA gene distribution and diversity, through PCR detection and sequencing, revealed that few CuR bacteria (from 7 to 13%) possessed this genetic determinant before the addition of metal. Copper contamination induced an increase in the dissemination of homologous copA genes only in Ralstonia like species indigenous to S soils. From a functional point of view, copper minimum inhibitory concentration for each CuR strain was measured. It did not highlight variable copper resistance efficiency between strains belonging to different taxonomic groups, harboring or not the copA gene, and originating from different soils contaminated or not by copper. [Copyright &y& Elsevier]

Abstract: Extracting and purifying a representative fraction of bacteria from soil is necessary for the application of many techniques of microbial ecology. Here the influence of different soil types on the quantitative and qualitative recovery of bacteria by soil grinding and Nycodenz density gradient centrifugation was investigated. Three soils presenting contrasted physicochemical characteristics were used for this study. For each soil, the total (AODC: acridine orange direct count) and culturable (cfu: colony-forming units) bacterial densities were measured in three distinct fractions: (i) the primary soil, (ii) the soil pellet (soil remaining after centrifugation), and (iii) the extracted cells. The automated–ribosomal intergenic spacer analysis (A-RISA) was used to characterize the community structure directly from the DNA extracted from each fraction. The physicochemical characteristics of soils were found to influence both the efficiency of bacterial cell recovery and the representativeness of the extracted cells in term of community structures between the different fractions. Surprisingly, the most representative extracted cells were obtained from the soil exhibiting the lowest efficiency of cell recovery. Our results demonstrated that quantitative and qualitative cell recovery using Nycodenz density gradient centrifugation are not necessarily related and could be differentially biased according to soil type. [Copyright &y& Elsevier]

Crop-livestock systems are complex farming systems in which many agricultural practices are combined. Sustainable management of soils in these farming systems requires comprehensive assessment of soil quality and consideration of soil properties and functions in an integrated way. This study evaluated soil quality in a 12-km² watershed that contains intensive crop-livestock farming systems typical of western France and characterized by high animal density and the co-existence of annual crops (cereals and forages, sometimes in rotation with temporary grasslands) and permanent grasslands. Physical (bulk density, aggregate stability), chemical (pH, copper, organic carbon, nitrogen, available phosphorus, C:N) and biological properties (bacterial and fungal abundance and diversity) of the soil were measured in the upper 15 cm of soil at 164 sampling points. Cropping systems at each point were described in detail from farm surveys, which collected data on crop rotations, manure and crop-residue management, fertilizer application and tillage. The variability in soil properties and the impact of cropping systems were quantified at the watershed scale. The percentage of variance of soil properties explained by the cropping system ranged from 6 to 47%, reaching 47%, 36% and 29% for aggregate stability after a fast wetting test, total nitrogen and organic carbon, respectively. Soil biological properties were explained less, but significantly so, by the cropping system as well. Soil properties were combined into a soil quality index. Among variables, crop rotation influenced soil quality the most, much more than manure application. Permanent grasslands and crop rotations with temporary grasslands had significantly higher soil quality indices than annual crops. This approach requires further development to analyze trade-offs among soil properties in crop-livestock systems. [ABSTRACT FROM AUTHOR]

Preservation and sustainable use of soil biological communities represent major challenges in the current agroecological context. However, to identify the agricultural practices/systems that match with these challenges, innovative tools have to be developed to establish a diagnosis of the biological status of the soil. Here, we have developed a statistical polynomial model to predict the molecular biomass of the soil microbial community according to the soil physicochemical properties. For this, we used a dataset of soil molecular microbial biomass estimates and pedoclimatic properties derived from analyses of samples collected in the context of the “French monitoring soil quality network = Réseau de Mesures de la qualité des Sols” (RMQS). This sampling network has provided 2115 soil samples covering the range of variability of soil type and land use at the scale of France. The best model obtained from the data showed that soil organic carbon content, clay content, altitude, and pH were the best explanatory variables of soil microbial biomass while other variables such as longitude, latitude and annual temperature were negligeable. Based on these variables, the multilinear model developed allowed very accurate prediction of the soil microbial biomass, with an excellent adjusted coefficient of determination R adj 2 of 0.6772 ( P < 10 −3 ). In addition to R adj 2 , the model was further validated by results from cross validation and sensitivity analyses. The model provides a reference value for microbial biomass for a given pedoclimatic condition, which can then be compared with the corresponding measured data to provide for the first time a robust diagnosis of soil quality. Application of the model to a set of soil samples obtained at the scale of an agricultural landscape is presented and discussed, showing the suitability of the model to diagnose of the impact of particular agricultural practices such as tillage and catch crops in field conditions, at least over the French nation. [ABSTRACT FROM AUTHOR]

Land use practices alter the biomass and structure of soil microbial communities. However, the impact of land management intensity on soil microbial diversity ( i.e . richness and evenness) and consequences for functioning is still poorly understood. Here, we addressed this question by coupling molecular characterization of microbial diversity with measurements of carbon (C) mineralization in soils obtained from three locations across Europe, each representing a gradient of land management intensity under different soil and environmental conditions. Bacterial and fungal diversity were characterized by high throughput sequencing of ribosomal genes. Carbon cycling activities ( i.e ., mineralization of autochthonous soil organic matter, mineralization of allochthonous plant residues) were measured by quantifying 12 C- and 13 C-CO 2 release after soils had been amended, or not, with 13 C-labelled wheat residues. Variation partitioning analysis was used to rank biological and physicochemical soil parameters according to their relative contribution to these activities. Across all three locations, microbial diversity was greatest at intermediate levels of land use intensity, indicating that optimal management of soil microbial diversity might not be achieved under the least intensive agriculture. Microbial richness was the best predictor of the C-cycling activities, with bacterial and fungal richness explaining 32.2 and 17% of the intensity of autochthonous soil organic matter mineralization; and fungal richness explaining 77% of the intensity of wheat residues mineralization. Altogether, our results provide evidence that there is scope for improvement in soil management to enhance microbial biodiversity and optimize C transformations mediated by microbial communities in soil. [ABSTRACT FROM AUTHOR]

Intensive land use practices necessary for providing food and raw materials are known to have a deleterious effect on soil. However, the effects that such practices have on soil microbes are less well understood. To investigate the effects of land use intensification on soil microbial communities we used a combined T-RFLP and pyrosequencing approach to study bacteria, archaea and fungi in spring and autumn at five long term observatories (LTOs) in Europe; each with a particular land use type and contrasting levels of intensification (low and high). Generally, due to large gradients in soil variables, both molecular methods revealed that soil microbial communities were structured according to differences in soil conditions between the LTOs, more so than land use intensity. Moreover, variance partitioning analysis also showed that soil properties better explained the differences in microbial communities than land use intensity effects. Predictable responses in dominant bacterial, archaeal and fungal taxa to edaphic conditions (e.g. soil pH and resource availability) were apparent between the LTOs. Some effects of land use intensification at individual field sites were observed. However, these effects were manifest when land use change affected soil conditions. Uniquely, this study details the responses of different microbial groups to soil type and land use intensification, and their relative importance across a range of European field sites. These findings reinforce our understanding of drivers impacting soil microbial community structure at both field and larger geographic scales. [ABSTRACT FROM AUTHOR]

Abstract: The phytostimulatory PGPR Azospirillum lipoferum CRT1 was inoculated to maize seeds and the impact on the genetic structure of the rhizobacterial community in the field was determined during maize growth by Automated Ribosomal Intergenic Spacer Analysis (ARISA) of rhizosphere DNA extracts. ARISA fingerprints could differ from one plant to the next as well as from one sampling to the next. Inoculation with strain CRT1 enhanced plant-to-plant variability of the ARISA fingerprints and caused a statistically significant shift in the composition of the indigenous rhizobacterial community at the first two samplings. This is the first study on the ecological impact of Azospirillum inoculation on resident bacteria done in the field and showing that this impact can last at least one month. [Copyright &y& Elsevier]

Abstract: The dynamics of indigenous bacterial and fungal soil communities were followed throughout the decomposition of wheat straw residue. More precisely, such dynamics were investigated in the different soil zones under the influence of decomposing wheat straw residue (i.e. residues, soil adjacent to residue=detritusphere, and bulk soil). The genetic structures of bacterial and fungal communities were compared throughout the decomposition process long by applying B- and F-ARISA (for bacterial and fungal-automated ribosomal intergenic spacer analysis) to DNA extracts from these different zones. Residue decomposition induced significant changes in bacterial and fungal community dynamics with a magnitude of changes between the different soil zones ordered as followed: residue>detritusphere>bulk soil, confirming the spatial structuration of the sphere of residue influence to the 4–6mm soil zone in contact with residue. Furthermore, significant differences in the structure of bacterial and fungal communities were apparent between the early (14 and 28 days) and late (from 56 to 168 days) stages of decomposition. These could be related to ecological attributes such as the succession of r- (copiotrophs) and K- (oligotrophs) strategists. Microbial diversity at the early (28 days) and late (168 days) stages of degradation was further analysed by a molecular inventory of 16S and 18S rDNA in DNA extracts from the residue zone. This confirmed the succession of different populations during residue decomposition. Fluorescent Pseudomonas spp. and Neurospora sp. were dominant in the early stage with subsequent stimulation of Actinobacteria and Deltaproteobacteria taxa, as well as Basidiomycota fungal taxa and Madurella spp. According to the ecological attributes of these populations, microbial succession on fresh organic residue incorporated in soil would be dominated by copiotrophs and r-strategists in the early stages, with oligotrophs (K-strategists) increasing in relative abundance as substrate quantity and/or quality declines over time. [Copyright &y& Elsevier]

Abstract: The functional and genetic structures of a soil bacterial community were characterized after inoculation into three different sterile soils using a protein and DNA fingerprinting method, respectively. Principal component analysis (PCA) of profiles revealed that, depending on soil characteristics, bacterial communities with similar genetic structures harbored different functional structures and thus could potentially be of differing ecological significance for soil functioning. Co-inertia analysis between protein fingerprinting data and the corresponding sets of soil physicochemical characteristics demonstrated the correlation between the functional structure of the bacterial community and soil parameters, with pH, clay and CaCO3 contents being the most discriminating factors. [Copyright &y& Elsevier]

Abstract: The effects of location (soil surface vs. incorporated in soil) and nature of plant residues on degradation processes and indigenous microbial communities were studied by means of soil microcosms incubation in which the different soil zones influenced by decomposition i.e. residues, soil adjacent to residues (detritusphere) and distant soil unaffected by decomposition (bulk soil) were considered. Plant material decomposition, organic carbon assimilation by the soil microbial biomass and soil inorganic N dynamics were studied with 13C labelled wheat straw and young rye. The genetic structure of the community in each soil zone were compared between residue locations and type by applying B- and F-ARISA (for bacterial- and fungal-automated ribosomal intergenic spacer analysis) directly to DNA extracts from these different zones at 50% decomposition of each residue. Both location and biochemical quality affected residue decomposition in soil: 21% of incorporated 13C wheat straw and 23% left at the soil surface remained undecomposed at the end of incubation, the corresponding values for 13C rye being 1% and 8%. Residue decomposition induced a gradient of microbial activity with more labelled C incorporated into the microbial biomass of the detritusphere. The sphere of influence of the decomposing residues on the dynamics of soluble organic C and inorganic N in the different soil zones showed particular patterns which were influenced by both residue location and quality. Residue degradation stimulated particular genetic structure of microbial community with a gradient from residue to bulk soil, and more pronounced spatial heterogeneity for fungal than for bacterial communities. The initial residue quality strongly affected the resulting spatial heterogeneity of bacteria, with a significance between-zone discrimination for rye but weak discrimination between the detritusphere and bulk soil, for wheat straw. Comparison of the different detrituspheres and residue zones (corresponding to different residue type and location), indicated that the genetic structure of the bacterial and fungal communities were specific to a residue type for detritusphere and to its location for residue, leading to conclude that the detritusphere and residue corresponded to distinct trophic and functional niches for microorganisms. [Copyright &y& Elsevier]

Abstract: Temporal airborne bacterial genetic community structure and meteorological factors were analysed above an urban area in the northwest of France from December 2003 to April 2004 with a sampling strategy considering different time intervals (from an hour to a month). Principal component analysis (PCA) of B-ARISA (Bacterial-Automated Ribosomal Intergenic Spacer Analysis) profiles revealed a hierarchy in the temporal variability of bacterial community: daily

Abstract: The density, genetic structure and diversity of airborne bacterial communities were assessed in the outdoor atmosphere. Two air samples were collected on the same location (north of France) at two dates (March 2003 (sample1) and May 2003 (sample 2)). Molecular culture-independent methods were used to characterise airborne bacterial communities regardless of the cell culturability. The automated-ribosomal intergenic spacer analysis (A-RISA) was performed to characterise the community structure in each sample. For both sampling dates, complex A-RISA patterns were observed suggesting a highly diverse community structure, comparable to those found in soil, water or sediment environments. Furthermore, differences in the genetic structure of airborne bacterial communities were observed between samples 1 and 2 suggesting an important variability in time. A clone library of 16S rDNA directly amplified from air DNA of sample 1 was constructed and sequenced to analyse the community composition and diversity. The Proteobacteria group had the greatest representation (60%), with bacteria belonging to the different subdivisions - (19%), -(21%), -(12%) and -(8%). Firmicute and Actinobacteria were also well represented with 14% and 12%, respectively. Most of the identified bacteria are known to be commonly associated with soil or plant environments suggesting that the atmosphere is mainly colonised transiently by microorganisms from local sources, depending on air fluxes. [Copyright &y& Elsevier]

• Frequent land-use changes stimulate priming effect hampering carbon storage targets. • Temporary grassland rotations modify SOM quality and shape microbial communities. • Variance partition models identified predictors of priming effect at landscape scale. • Fluorescence analyses of water soluble SOM identified markers of priming effect. • Rotations including grassland for 40–60% of time were the less prone to priming effect. Soils can act as a carbon sink, and the chemical and biological transformation of vegetal litter into soil organic matter (SOM) is widely influenced by land-use and other biogeochemical parameters. However, the increase of new carbon inputs to soil has the potential to trigger the mineralization of stabilized SOM, a process called priming effect. The objective of this manuscript is to investigate, at a landscape scale (5 km²), the factors influencing the susceptibility of SOM to priming effect. To achieve this objective, physical, chemical, and metagenomics analyses were conducted on 88 soil samples and successively combined with agronomical data and soil incubation for the quantification of carbon fluxes. Variance partitioning models highlighted that priming effect is controlled by complex interactions of biotic and abiotic factors, which include soil chemistry, quality of SOM, shape and abundance of microbial communities. Fluorescence properties of the dissolved organic matter has been found as a strong descriptor for priming effect. Depending on the time of crop rotation devoted to grassland, two different components leading to priming effect were identified. The introduction of grassland for 40–60% of the time of rotation achieved the lowest susceptibility to priming effect, and higher indexes of microbial diversity, whereas higher or lower proportions of time of the rotation devoted to grassland resulted in an increase of priming effect and a decrease of bacterial evenness. [ABSTRACT FROM AUTHOR]