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 13C‐ and 12C‐DNA, both extracted from soil treated with a 13C 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 13C‐DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C‐substrate added to soil.

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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 rhizobiumlegume 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.

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 13C‐ and 12C‐DNA, both extracted from soil treated with a 13C 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 13C‐DNA allows us to understand more precisely the changes in the composition of microbial communities affected by the C‐substrate added to soil.

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In New Caledonia, one third of the Island is composed of ultramafic rocks, and lateritic soils enriched in Fe, Ni and Cr. Open-cast mining occurs all around the Island, and processes of erosion and sedimentation, which occur naturally along the coastline, are strongly amplified by mining activities. Due to their position, at the interface between land and sea, mangroves receive extensive amounts of particles emanating from rivers through estuaries. The purpose of this study is to understand the distribution and partitioning of some transitional metals (Fe, Mn, Ni, Cr) in sediments and pore-waters in a mangrove swamp, which is situated downstream of a catchment characterized by lateritic soils that were exploited a century ago. Quantitative analyses on bulk and after selective extraction, were carried out on cores collected along a transect within the intertidal zone, i.e. beneath a Rhizophora stylosa stand, an Avicennia marina stand, and within a salt flat. Mean metal concentrations were (μmol g − 1): Fe (1997) > Ni (44.2) > Cr (31.9) > Mn (8.8). Thus, Ni, Cr and Fe concentrations in this study are substantially higher than mangrove world average. In addition, Ni concentrations are 10 to 100 times higher than in other New Caledonian mangrove developing downstream of a catchment not composed of ultramafic rocks. The studied mangrove is characterized by gradients of water and organic contents with depth and along the intertidal zone, which induced different redox conditions, and thus different metals partitioning. Transitional metals are deposited in the mangrove mainly as oxides and/or oxy-hydroxides, that are subsequently dissolved by bacteria for the decomposition of organic matter, and which leads to a strong increase of metals in the dissolved phase. Then, dissolved metals were precipitated with organic and sulfide compounds. To conclude, organic diagenesis in mangrove sediments leads to the transfer of transitional metals from oxide form to organic and sulfide forms.

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