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Trace elements (TEs) availability, biochemical activity and functional gene diversity was studied in a Cu-contaminated soil, revegetated for six years with a mixed stand of willow, black poplar, and false indigo-bush, and amended or not with compost plus dolomitic limestone (OMDL). The OMDL amendment significantly reduced Cu and As availability and soil toxicity, and increased the biochemical activity and microbial functional diversity assessed with the GEOCHIP technique, as compared to the unamended soil (Unt). The OMDL soil showed significantly higher abundance of 25 functional genes involved in decomposition organic compounds, and 11, 3 and 11 functional genes involved in the N, P and S biogeochemical cycles. Functional gene abundance was positively correlated with nutrient contents but negatively correlated with Cu availability and soil toxicity. The abundance of microbial functional genes encoding for resistance to various TEs also increased, possibly due to the microbial proliferation and lower Cu exposure in the presence of high total soil Cu concentration. Genes encoding for antibiotic resistance due to the co-occurrence of TEs and antibiotic resistant genes on genetic mobile elements. Overall, phytomanagement confirmed its potential to restore the biological fertility and diversity of a severely Cu-contaminated soil, but the increase of TEs and antibiotic resistant gene abundances deserve attention in future studies.

Environmental proteomics, the study of the expression profile of proteins extracted directly from living organisms and some stabilized extracellular proteins present in environmental samples, is a developing branch of soil science since the seminal papers appeared twenty years ago. Soil microbial communities hold the key to understanding terrestrial biodiversity; they are extremely complex and their physiological responses to dynamic environmental parameters are under-characterized. Therefore, the slow development of environment-related proteomic databases, and the high chemical reactivity of environmental matrices hamper the extraction, quantification, and characterization of proteins; and soil proteomics remains still in its infancy. We underscore the main achievements of environmental proteomics focusing on soil ecosystems, and we identify technical gaps that need to be bridged in the context of relevant ecological concepts that have received little attention in the development of proteomics methods. This analysis offers a new framework of research of soil proteomics toward improved understanding of the causal linkages between the structure and function of the soil microbiome, and a broader grasp of the sensitivity of terrestrial ecosystems to environmental change.

Phytomanagement of heavy metal polluted soils with woody plants is considered a sustainable management option for restoring polluted sites while preserving the soil resource. Like any plant, woody plants establish complex interactions with soil microbiome by shaping the microbial community composition through rhizodepositions, which select microbial physiological groups which increase the nutrients available in the rhizosphere. Beside the fundamental role in nutrient cycling, the rhizosphere microbiome improves water and nutrient uptake, produces plant promoting factors such as phytohormones, and protects plants from pathogens. Plant microbe interactions in the rhizosphere of woody plants are more complex than those of herbaceous plants because they create a more complex phytosphere effect, due to their longer life cycles, deeper rooting, and by creating a persistent canopy conditioned micro-environment. While woody plant-microbe interactions in the rhizosphere have been studied in forest ecosystems or their effects on forest productions, interactions during phytomanagement interventions are less known. [ABSTRACT FROM AUTHOR]