Distribution of microbial communities in a forest soil profile investigated by microbial biomass, soil respiration and DGGE of total and extracellular DNA

Abstract We studied the distribution of the indigenous bacterial and fungal communities in a forest soil profile. The composition of bacterial and fungal communities was assessed by denaturing gradient gel electrophoresis (DGGE) of total and extracellular DNA extracted from all the soil horizons. Microbial biomass C and basal respiration were also measured to assess changes in both microbial biomass and activity throughout the soil profile. The 16S rDNA-DGGE revealed composite banding patterns reflecting the high bacterial diversity as expected for a forest soil, whereas 18S rDNA-DGGE analysis showed a certain stability and a lower diversity in the fungal communities. The banding patterns of the different horizons reflected changes in the microbial community structure with increasing depth. In particular, the DGGE analysis evidenced complex banding patterns for the upper A1 and A2 horizons, and a less diverse microflora in the deeper horizons. The low diversity and the presence of specific microbial communities in the B horizons, and in particular in the deeper ones, can be attributed to the selective environment represented by this portion of the soil profile. The eubacterial profiles obtained from the extracellular DNA revealed the presence of some bands not present in the total DNA patterns. This could be interpreted as the remainders of bacteria not any more present in the soil because of changes of edaphic conditions and consequent shifting in the microbial composition. These characteristic bands, present in all the horizons with the exception of the A1, should support the concept that the extracellular DNA is able to persist within the soil. Furthermore, the comparison between the total and extracellular 16S rDNA-DGGE profiles suggested a downwards movement of the extracellular DNA

Microbial community structure and proteolytic activity in the rhizosphere of maize plants differing in nitrogen use efficiency

The rhizosphere, the thin soil layer influenced by the presence of plant roots has different physico-chemical properties from the bulk soil because of the active or passive rhizodepositions, which sustain larger and more active microbial populations in the rhizosphere than in bulk soil, and this plays a key role in soil organic matter decomposition and nutrient solubilization. The rhizosphere is chemically complex and dynamic microenvironment and this makes it difficult to study. Progresses in the study of the rhizosphere can be achieved by using rhizoboxes allowing the plant growth and precise sampling of rhizosphere. Plants select microbial bacterial and fungal populations in the rhizosphere during the plant growth, and while plant mechanisms involved in increased N uptake efficiency have been clarified, the importance of the rhizosphere microbial communities in nutrient availability to plants are still poorly understood. Nitrogen is the main nutrient limiting the plant growth and the crop yields and today, the nitrogen use efficiency (NUE) of crops at field scale is still relatively low, with detrimental effects on groundwater quality and atmosphere due to NO3- leaching and NH3 and nitrous oxide emissions caused be excessive fertilization, and large efforts have been carried out to increase the NUE to enhance the crop production and reduce the environmental impact of agriculture, especially through plant breeding and preparation of fertilizers with slow N release. We evaluated the changes in the biochemical activity and microbial community structure induced by the inbred maize (Zea mais L.) lines Lo5 and T250 characterized by high and low NUE using rhizobox experiments. The adopted experimental approach allowed to describe the relative plant induced changes on the different rhizosphere chemical and microbiological components and provide information to improve the crop NUE. In this work we studied the changes in the biochemical activity and microbial community structure in the rhizosphere of the inbred maize (Zea mais L.) lines Lo5 and T250 characterized by high and low NUE, repectively, using rhizobox experiments. Because of the importance of the proteolytic activity in soil N mineralization, the proteolytic activity in the rhizosphere of the two maize lines was also studied by the assessment of the diversity and abundance of the apr and npr genes coding for coding for alkaline protease and neutral metalloprotease, respectively, and determination of the protease activity. The results showed that the Lo5 plant, having the higher NUE, induced the greater modification in the rhizosphere chemical properties, induced significantly faster depletion of inorganic N, higher bacteria diversity, proteolytic populations and protease activity. The importance of the plant activity in modifying microbial community structure, protease functions and rhizosphere biochemical activity will be presented

Hydrolase activity, microbial biomass and community structure in long-term Cd-contaminated soils

Long-term effects of high Cd concentrations on enzyme activities, microbial biomass and respiration and bacterial community structure of soils were assessed in sandy soils where Cd was added between 1988 and 1990 as Cd(NO3)(2) to reach concentrations ranging from 0 to 0.36 mmol Cd kg(-1) dry weight soil. Soils were mantained under maize and grass cultivation, or 'set-aside' regimes, for 1 year. Solubility of Cd and its bioavailability were measured by chemical extractions or by the BIOMET bacterial biosensor system. Cadmium solubility was very low, and Cd bioavailability was barely detectable even in soils polluted with 0.36 mmol Cd kg(-1). Soil microbial biomass carbon (BC) was slightly decreased and respiration was increased significantly even at the lower Cd concentration and as a consequence the metabolic quotient (qCO(2)) was increased, indicating a stressful condition for soil microflora. However, Cd-contaminated soils also had a lower total organic C (TOC) content and thus the microbial biomass C-to-TOC ratio was unaffected by Cd. Alkaline phosphomonoesterase, arylsulphatase and protease activities were significantly reduced in all Cd-contaminated soils whereas acid phosphomonoesterase, beta-glucosidase and urease activites were unaffected by Cd. Neither changes in physiological groups of bacteria, nor of Cd resistant bacteria could be detected in numbers of the culturable bacterial community. Denaturing gradient gel electrophoresis analysis of the bacterial community showed slight changes in maize cropped soils containing 0.18 and 0.36 mmol Cd kg(-1) soil as compared to the control. It was concluded that high Cd concentrations induced mainly physiological adaptations rather than selection for metal-resistant culturable, soil microflora, regardless of Cd concentration, and that some biochemical parameters were more sensitive to stress than other

Is microbial species richness increased by aided phytostabilization of trace element contaminated soils?

Godkänd; 2007; 20081015 (juku