Giancarlo Renella

Microbial diversity and soil functions

Summary Soil is a complex and dynamic biological system, and still in 2003 it is difficult to determine the composition of microbial communities in soil. We are also limited in the determination of microbially mediated reactions because present assays for determining the overall rate of entire metabolic processes (such as respiration) or specific enzyme activities (such as urease, protease and phosphomonoesterase activity) do not allow any identification of the microbial species directly involved in the measured processes. The central problem posed by the link between microbial diversity and soil function is to understand the relations between genetic diversity and community structure and between community structure and function. A better understanding of the relations between microbial diversity and soil functions requires not only the use of more accurate assays for taxonomically and functionally characterizing DNA and RNA extracted from soil, but also high-resolution techniques with which to detect inactive and active microbial cells in the soil matrix. Soil seems to be characterized by a redundancy of functions; for example, no relationship has been shown to exist between microbial diversity and decomposition of organic matter. Generally, a reduction in any group of species has little effect on overall processes in soil because other microorganisms can take on its function. The determination of the composition of microbial communities in soil is not necessary for a better quantification of nutrient transformations. The holistic approach, based on the division of the systems in pools and the measurement of fluxes linking these pools, is the most efficient. The determination of microbial C, N, P and S contents by fumigation techniques has allowed a better quantification of nutrient dynamics in soil. However, further advances require determining new pools, such as active microbial biomass, also with molecular techniques. Recently investigators have separated 13 C- and 12 C-DNA, both extracted from soil treated with a 13 C source, by density-gradient centrifugation. This technique should allow us to calculate the active microbial C pool by multiplying the ratio between labelled and total DNA by the microbial biomass C content of soil. In addition, the taxonomic and functional characterization of 13 C-DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C-substrate added to soil.

Role of Phosphatase Enzymes in Soil

Soil phosphatases, particularly acid and alkaline phosphomonoesterases, have been extensively studied [see reviews by Ramirez-Martinez (Folia Microbiol 13:161–174, 1968); Speir and Ross (Soil phosphatase and sulphatase. Soil enzymes. Academic, London, pp 197–250, 1978); Malcom (Soil Biol Biochem 15:403–408, 1983); and Tabatabai (Soil enzymes. Methods of soil analysis. Part 2. Microbiological and biochemical properties. Soil Science Society of America, Madison, pp 775–833, 1994)] because they mineralise organic phosphorus (P) to inorganic P. The effects of agricultural and forest managements, pollutants and any environmental factor on phosphatase activities of soil cannot be adequately interpreted because the currently available enzyme assays do not discriminate between the contribution of phosphatases associated with active microbial cells and that of extracellular phosphatases stabilised by soil colloids. Despite multiple evidence indicating that phosphatases can be adsorbed by surface-reactive particles such as clay minerals or entrapped by humic materials, the visualisation of the extracellular phosphatases in the soil matrix has never been achieved because ultracytochemical tests combined with electron microscopy cannot locate enzymes in electron-dense minerals such as clays, or in soil components such as humic materials, that react with counterstainers such as OsO4.

Soil enzymology: classical and molecular approaches

It is still problematic to use enzyme activities as indicators of soil functions because: (1) enzyme assays determine potential and not real enzyme activities; (2) the meaning of measured enzyme activities is not known; (3) the assumption that a single enzyme activity is an indicator of nutrient dynamics in soil neglects that the many enzyme activities are involved in such dynamic processes; (4) spatio-temporal variations in natural environments are not always considered when measuring enzyme activities; and (5) many direct and indirect effects make difficult the interpretation of the response of the enzyme activity to perturbations, changes in the soil management, changes in the plant cover of soil, etc. This is the first review discussing the links between enzyme-encoding genes and the relative enzyme activity of soil. By combining measurements of enzyme activity in soil with expression (transcriptomics and proteomics) of genes, encoding the relative enzymes may contribute to understanding the mode and timing of microbial communities’ responses to substrate availability and persistence and stabilization of enzymes in the soil.

Plant-borne flavonoids released into the rhizosphere: impact on soil bio-activities related to plant nutrition. A review

Plants produce and release in the surrounding soil, the so-called rhizosphere, a vast variety of secondary metabolites. Among them, flavonoids are the most studied, mainly for their role in the establishment of rhizobium–legume symbiosis; on the other hand, some studies highlight that they are also important in the plant strategies to acquire nutrients from the soil, for example, by acting on its chemistry. The scope of this review is to give a quick overview on the types and amounts of plant-released flavonoids in order to focus on their effects on soil activities that in turn can influence nutrient availability and so plant mineral nutrition; emphasis is given to the different nutrient cycles, soil enzyme, and soil bacteria activities, and their influence on soil macrofauna and roots of other plants. Finally, the possible outcome of the climate change on these processes is discussed.

Influence of cadmium on the metabolic quotient, l - : d -glutamic acid respiration ratio and enzyme activity : microbial biomass ratio under laboratory conditions

Abstract This study was carried out to investigate the effect of very high cadmium concentrations (50 and 500 μg Cd g–1 soil) on some biochemical and microbiological measurements under laboratory conditions involving daily soil samplings. The data for both DTPA- and water-soluble Cd showed two distinctive patterns during soil incubation; from 0 to 4 days, values were about 50–500 and 1–100 μg g–1 dry weight soil, whereas they decreased markedly after 7 days. Both daily respiration and the ATP content but not the microbial biomass C determined by the fumigation–extraction method were lowered by high DTPA- and water-soluble Cd concentrations. Dehydrogenase and phosphatase activities as well as both enzyme activity : microbial biomass ratios were decreased by the high DTPA- and water-soluble Cd concentrations. In the first 2 days of incubation, the metabolic quotient (qCO2) was also decreased by the highest values of available Cd. The early (after 6 h) mineralization of l- but not d-glutamic acid to CO2 was inhibited during the 0–4 day incubation period by the highest Cd concentration. Possibly the l-enantiomer was used by a larger fraction of soil microorganisms than the d-enantiomer or, if they were used by the same fraction of soil microorganisms, the d-enantiomer was mineralized at a lower rate. The l- : d-glutamic acid respiration ratio was decreased by the high available Cd content because under polluted conditions soil microorganisms probably discriminated less between the two stereoisomers of glutamic acid.

Additive effects of copper and zinc on cadmium toxicity on phosphatase activities and ATP content of soil as estimated by the ecological dose (ED50)

The ecological dose (ED50) of Cd on alkaline and acid phosphatase activity and the ATP content of three contrasting forest soils was measured with or without Cu and Zn to assess the additive toxic effects of these two metals. Soils polluted with Cu and/or Zn were treated with increasing Cd concentrations to give the following metal combinations: Cd, Cd+Cu, Cd+Zn and Cd+Cu+Zn. Alkaline and acid phosphatase activities and ATP content of the three soils were analysed 4 h, 7 and 28 days after the metal additions. The ED50 values were obtained by interpolating the enzyme activities or ATP data with a kinetic model and the goodness of fit was satisfactory. Generally, the ED50 values of both acid and alkaline phosphatase activities for Cd were lower (higher toxicity) with than without Cu and Zn and the effect of Cu and Zn was particularly adverse when these two metals were both added to soils. The alkaline phosphatase was more sensitive in the acid and neutral soil whereas the acid phosphatase was more sensitive in the alkaline soil. Both phosphatase activities and the ATP content were more sensitive in the sandy than in the finer textured soils. The ATP content was less sensitive to the additive effects. Increasing toxicity was observed during the incubation. Analysis of 1 M NH4NO3-extractable Cd, Cu and Zn revealed that Cd competed with Zn for the adsorption sites but not with Cu. However, the lower ED50 values for Cd of the two phosphatase activities and of the ATP content in the presence of heavy metal combinations could be not explained by the heavy metal solubility data. It is concluded that the ED50 may be a sensitive tool for assessing additve toxic effects to soil biochemical parameters.

Agronomic Practices for Improving Gentle Remediation of Trace Element-Contaminated Soils

The last few decades have seen the rise of Gentle soil Remediation Options (GRO), which notably include in situ contaminant stabilization (“inactivation”) and plant-based (generally termed “phytoremediation”) options. For trace element (TE)-contaminated sites, GRO aim to either decrease their labile pool and/or total content in the soil, thereby reducing related pollutant linkages. Much research has been dedicated to the screening and selection of TE-tolerant plant species and genotypes for application in GRO. However, the number of field trials demonstrating successful GRO remains well below the number of studies carried out at a greenhouse level. The move from greenhouse to field conditions requires incorporating agronomical knowledge into the remediation process and the ecological restoration of ecosystem services. This review summarizes agronomic practices against their demonstrated or potential positive effect on GRO performance, including plant selection, soil management practices, crop rotation, short rotation coppice, intercropping/row cropping, planting methods and plant densities, harvest and fertilization management, pest and weed control and irrigation management. Potentially negative effects of GRO, e.g., the introduction of potentially invasive species, are also discussed. Lessons learnt from long-term European field case sites are given for aiding the choice of appropriate management practices and plant species.

Microbial biomass, respiration and enzyme activities after in situ aided phytostabilization of a Pb- and Cu-contaminated soil.

We conducted a pilot-scale experiment to study the effects of an aided phytostabilisation on soil microbial and biological endpoints in an ore dust-contaminated soil. Soil was amended with alkaline fly ashes plus peat to reduce mobility of trace elements and vegetated with a proprietary grass/herb mixture. Results indicated that the proposed aided phytostabilization approach of Cu-Pb contaminaed soil significantly increased microbial biomass and respiration, reduced microbial stress and increased key soil enzyme activities. Further research is needed to unambiguously determine whether the soil biochemical endpoints that were studied responded more to decreased metal mobility or to general soil amelioration.

Effects of Root Exudates in Microbial Diversity and Activity in Rhizosphere Soils

The rhizosphere is the soil volume at the root-soil interface that is under the influence of the plant roots and the term was introduced by Hiltner in 1904 (Brimecombe et al. 2001). Microbial population in the rhizosphere has continuous access to a flow of low and high molecular weight organic substrates derived from roots. This continuous flow of organic compounds may affect together with specific physiochemical and biological conditions microbial activity and community structure of the rhizosphere soil (Sorensen 1997; Brimecombe et al. 2001). Current techniques still lack the adequate sensitivity and resolution for data collection at the micro-scale, and the question ‘How important are various soil processes acting at different scales for ecological function?’ is therefore challenging to answer. The nano-scale secondary ion mass spectrometer (NanoSIMS) represents the latest generation of ion microprobes, which link high-resolution microscopy with isotopic analysis. Recently Herrmann et al. (2007) have described the principles of NanoSIMS and discusses the potential of this tool to contribute to the field of biogeochemistry and soil ecology. Both microbial activity and microbial diversity of the rhizosphere have been extensively studied as testimonies by numerous chapters and books (Keister and Creagen 1991; Lynch 1990a; Pinton et al. 2001, 2007; Waisel et al. 1991). This interest depends on the important effects that microorganisms inhabiting the rhizosphere have on plant activity. Both beneficial and detrimental interactions occur between microorganisms and plants (Lynch 1990b); among the former symbiotic dinitrogen fixation, association with mycorrhizae, biocontrol against pathogens and production of plant growth promoting compounds by beneficial rhizobacteria have

Effects of Cd- and Zn-enriched sewage sludge on soil bacterial and fungal communities

The effects of sewage sludge selectively enriched with Cd and Zn, both singly and in combination, on the bacterial, fungal, Alphaproteobacteria and Actinobacteria communities of a soil under arable or grassland management were studied with a PCR-DGGE approach. The effects of Cd and Zn were evaluated after a short time (7 d) when the Cd and Zn solubility were low and the C availability was high, and again after 180 d when the labile sludge C was mineralized and the effects of heavy metals predominated. In the arable soil all treatments induced significant short-term changes in the studied microbial groups, and long-term changes were observed in Actinobacteria and fungal communities. In the grassland soil, all treatments induced significant short-term changes in the studied microbial groups except for Alphaproteobacteria and fungi, and long-term effects on the actinobacteria and fungal communities. It was concluded that incorporation of Cd- and Zn-rich sludge into soils may have both short- and long-term effects on various bacterial phylogenetic groups whereas the metals may be better tolerated by the dominant soil fungi. In this study the impact was greater in arable than in grassland soil.