Long-Term Effects of Soil Remediation with Willow Short Rotation Coppice on Biogeographic Pattern of Microbial Functional Genes

Short rotation coppice (SRC) is increasingly being adopted for bioenergy production, pollution remediation and land restoration. However, its long-term effects on soil microbial communities are poorly characterized. Here, we studied soil microbial functional genes and their biogeographic pattern under SRC with willow trees as compared to those under permanent grassland (C). GeoChip analysis showed a lower functional gene diversity in SRC than in C soil, whereas microbial ATP and respiration did not change. The SRC soil had lower relative abundances of microbial genes encoding for metal(-oid) resistance, antibiotic resistance and stress-related proteins. This indicates a more benign habitat under SRC for microbial communities after relieving heavy metal stress, consistent with the lower phytoavailability of some metals (i.e., As, Cd, Ni and Zn) and higher total organic carbon, NO3--N and P concentrations. The microbial taxa-area relationship was valid in both soils, but the space turnover rate was higher under SRC within 0.125 m(2), which was possibly linked to a more benign environment under SRC, whereas similar values were reached beyond thisarea. Overall, we concluded that SRC management can be considered as a phytotechnology that ameliorates the habitat for soil microorganisms, owing to TOC and nutrient enrichment on the long-term

Metaproteomics of soil microbial communities

Chapter 16 - Metaproteomics of Soil Microbial Communitie

Environmental proteomics: A long march in the pedosphere

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

Past, Present and Future in Soil Enzymology

The bibliography on soil enzymes is extensive as showed by books and many review chapters devoted to the subject. The assays of soil enzymes are generally simple, accurate, sensitive and relatively rapid and for this reasons they have been extensively used to determine the effects of contaminants, changes in management practices and effects of environmental factors and plant cover on soil metabolism. However, the present enzyme assays determine potential rather than real enzyme activities due to the optimal conditions of the assays and they do not discriminate the contribution of extracellular stabilised enzymes from that of intracellular enzyme activities. The determination of the latter is important to evaluate the answer of soil microorganisms to any effect on soil. Methods based on fumigation of soil with chloroform or with the physiological response of soil microorganisms to glucose addition to soil present drawbacks. Presently, enzyme activities are still used to evaluate the response of soil metabolism to any effect not only in arable soils but also in forest soils. However, not always the past bibliography and the limits of the present enzyme assays are considered. A few innovative studies have been carried out. Measurements of enzyme activities have been combined with those on microbial diversity evaluated by molecular techniques. Both synthesis and persistence of phosphomonoesterases have been quantified in studies based on the stimulation of microbial growth by adding easily degradable organic compounds to soil. Metcalfe et al. (Metcalfe AC, Krsek M, Gooday GW, Prosseer JI, Wellington EM (2002) Appl Environ Microbiol 68:5042–5050) covered all events from gene presence, through gene expression and up to the detection of target enzyme in soil. The addition of sludge to a pasture soil increased chitinase activity and the number of actinobacteria but selected actinobacterium-like chitinase sequences. Enzyme assays distinguishing the contribution of extracellular stabilised enzymes from that of intracellular enzyme activities are needed. Future research should increase the number of enzyme activities which can be determined in soil. For example, an accurate assay for determining nuclease activity in soil is not available. It is important to set up accurate methods for extracting intracellular and stabilised extracellular proteins, which are largely prevailing, so as to be able to carry out the proteomic approach in soil. The understanding of microbial synthesis of proteins (functional proteomic) as affected by different environmental conditions can increase our knowledge on the synthesis of enzymes in soil whereas the characterization of proteins protected against microbial degradation by their interactions with surface-reactive particles or their inclusion within humic component (structural proteomic) can give insights on the stabilization of organic N, including enzymes, in soil. The set up of suitable techniques is needed to visualise the location of stabilised enzymes in soil sections by both scanning electron microscopy and transmission electron microscopy. Acid phosphatase activity has been detected in small (7 × 20 nm) fragments of microbial membranes, roots, mycorrhizae, etc. of soil but not in naturally-electron dense soil components (minerals) and in soil components reacting with OsO4 (humus) and this does not permit to localize extracellular enzymes or proteins stabilized by clay minerals or humic materials (Ladd JN, Butler JHA (1966) Aust J Soil Res 4:41–54)

Soil Proteomics

Proteomics is a post-genomic approach with the potential to interrogate natural complex systems such as soils. However, the great potentials of soil proteomics are currently limited by either the complexity of the soil matrix which is reactive, structured, teeming with microbial communities which are at the same time extremely diverse, in heterogeneous physiological state and normally poorly characterized. Taken together, these soil features pose problems of protein sampling, extraction and purification. This chapter, though not exhaustive, aims to illustrate the main approaches and achievements in soil proteomics and indicate some future directions for further developments soil proteomics