The chemical and functional characterization of soil N and its biotic components

The aim of this review is to describe and discuss the concepts that have been employed to interpret N mineralization–immobilization in soil, and how N turnover is related to the characteristics of organic N and the biota conducting the transformations. A brief survey of the period before the arrival of electronic searches became available provides access to the classical literature that can help interpret today’s challenges. Classical (acid hydrolysis) and modern spectrometry and spectroscopy techniques indicate that protein N is the prevalent component of organic N in soil. The presence of heterocyclic N can indicate its abiotic, partial synthesis as in fire-affected soils. Clays and pedogenic oxides can protect organic N against microbial degradation. The evidence for such protection is mostly based on in vitro studies involving pure clays, and proteins and their relevance to field conditions requires further work. The proteomic approach, with extraction and characterization of proteins stabilised by soil colloids (structural proteomics) might give further insights into this area. Functional proteomics can improve our understanding of the degradation of organic pollutants and organic debris as well as identifying the molecular colloquia between microorganisms and between soil biota and plant roots. Subdivision of organic N into sub-pools has helped to interpret mechanistic studies and modelling of N dynamics. Uncomplexed organic matter, obtained by physical fractionation procedures, is considered a labile pool. The interpretation of N mineralization measurements is affected by immobilization during microbial attack especially in high-C environments. Transfer of materials among particle size fractions and changes in microbiological properties of aggregates also can occur during fractionation procedures. Classical mineralization–immobilization turnover (MIT) does not always occur since microorganisms (and plants) can take up amino acid N with intracellular deamination. Protozoa, due to their grazing activities, can influence not only N mineralization but also the composition of rhizosphere–plant growth stimulating communities. Differences between N-poor and N-rich microsites, occurring in the same soil, can markedly affect the competition for N between plants and microorganisms especially the nitrifiers. The use of molecular techniques has allowed the identification of unculturable microorganisms and functional genes in the N cycle. Archeae are probably capable of oxidising NH4 to NO3 and anerobic ammonia oxidation (Ammonox) bacteria have been identified in biofilms and probably also occur in soils. The use of nitrate as an electron acceptor is encoded by specific gene clusters but nitrate reduction also occurs in dissimilatory nitrate reduction.