Priming effects: Interactions between living and dead organic matter

In this re-evaluation of our 10-year old paper on priming effects, I have considered the latest studies and tried to identify the most important needs for future research. Recent publications have shown that the increase or decrease in soil organic matter mineralization (measured as changes of CO₂ efflux and N mineralization) actually results from interactions between living (microbial biomass) and dead organic matter. The priming effect (PE) is not an artifact of incubation studies, as sometimes supposed, but is a natural process sequence in the rhizosphere and detritusphere that is induced by pulses or continuous inputs of fresh organics. The intensity of turnover processes in such hotspots is at least one order of magnitude higher than in the bulk soil. Various prerequisites for high-quality, informative PE studies are outlined: calculating the budget of labeled and total C; investigating the dynamics of released CO₂ and its sources; linking C and N dynamics with microbial biomass changes and enzyme activities; evaluating apparent and real PEs; and assessing PE sources as related to soil organic matter stabilization mechanisms. Different approaches for identifying priming, based on the assessment of more than two C sources in CO₂ and microbial biomass, are proposed and methodological and statistical uncertainties in PE estimation and approaches to eliminating them are discussed. Future studies should evaluate directions and magnitude of PEs according to expected climate and land-use changes and the increased rhizodeposition under elevated CO₂ as well as clarifying the ecological significance of PEs in natural and agricultural ecosystems. The conclusion is that PEs - the interactions between living and dead organic matter - should be incorporated in models of C and N dynamics, and that microbial biomass should regarded not only as a C pool but also as an active driver of C and N turnover.     

Carbon mineralisation in soil adjacent to plant residues of contrasting biochemical quality

A fraction of the C of residues incorporated into soil diffuses into the adjacent soil where it is eventually mineralised by microorganisms. Our aim was to quantify the contribution of this adjacent soil to the overall mineralisation of residue-C. For this, we incorporated two different residues labelled with ¹³C, with contrasting biochemical characteristics, namely mature wheat straw and young rye leaves, in soil cores. When 15% mineralisation of residue-C was measured for both residues, we separated a particulate fraction (the residues), the adjacent soil (4-5 mm thick) and a distant soil fraction, and incubated them separately for 5 h. We found that 76% of the mineralised wheat straw-C came from the particulate fraction and 23% from the soil adjacent to the residues. For rye leaves, 67% of the evolved CO₂ came from the particulate fraction and 33% from the adjacent soil. It showed that the adjacent soil had a significant role in the mineralisation of carbon from the residues, even if the main source of residue-derived CO₂ was the particulate fraction itself. The functional importance of the soil adjacent to the residues increased with the amount of soluble organic compounds that had been leached from the residue into the adjacent soil, suggesting a strong interaction between the initial quality of the crop residue and the resulting spatial heterogeneity of the decomposing microorganisms and C within the soil.     

A microcosm experiment to evaluate the influence of location and quality of plant residues on residue decomposition and genetic structure of soil microbial communities

The effects of location (soil surface vs. incorporated in soil) and nature of plant residues on degradation processes and indigenous microbial communities were studied by means of soil microcosms incubation in which the different soil zones influenced by decomposition i.e. residues, soil adjacent to residues (detritusphere) and distant soil unaffected by decomposition (bulk soil) were considered. Plant material decomposition, organic carbon assimilation by the soil microbial biomass and soil inorganic N dynamics were studied with ¹³C labelled wheat straw and young rye. The genetic structure of the community in each soil zone were compared between residue locations and type by applying B- and F-ARISA (for bacterial- and fungal-automated ribosomal intergenic spacer analysis) directly to DNA extracts from these different zones at 50% decomposition of each residue. Both location and biochemical quality affected residue decomposition in soil: 21% of incorporated ¹³C wheat straw and 23% left at the soil surface remained undecomposed at the end of incubation, the corresponding values for ¹³C rye being 1% and 8%. Residue decomposition induced a gradient of microbial activity with more labelled C incorporated into the microbial biomass of the detritusphere. The sphere of influence of the decomposing residues on the dynamics of soluble organic C and inorganic N in the different soil zones showed particular patterns which were influenced by both residue location and quality. Residue degradation stimulated particular genetic structure of microbial community with a gradient from residue to bulk soil, and more pronounced spatial heterogeneity for fungal than for bacterial communities. The initial residue quality strongly affected the resulting spatial heterogeneity of bacteria, with a significance between-zone discrimination for rye but weak discrimination between the detritusphere and bulk soil, for wheat straw. Comparison of the different detrituspheres and residue zones (corresponding to different residue type and location), indicated that the genetic structure of the bacterial and fungal communities were specific to a residue type for detritusphere and to its location for residue, leading to conclude that the detritusphere and residue corresponded to distinct trophic and functional niches for microorganisms.     

Impact of wheat straw decomposition on successional patterns of soil microbial community structure

The dynamics of indigenous bacterial and fungal soil communities were followed throughout the decomposition of wheat straw residue. More precisely, such dynamics were investigated in the different soil zones under the influence of decomposing wheat straw residue (i.e. residues, soil adjacent to residue = detritusphere, and bulk soil). The genetic structures of bacterial and fungal communities were compared throughout the decomposition process long by applying B- and F-ARISA (for bacterial and fungal-automated ribosomal intergenic spacer analysis) to DNA extracts from these different zones. Residue decomposition induced significant changes in bacterial and fungal community dynamics with a magnitude of changes between the different soil zones ordered as followed: residue > detritusphere > bulk soil, confirming the spatial structuration of the sphere of residue influence to the 4-6 mm soil zone in contact with residue. Furthermore, significant differences in the structure of bacterial and fungal communities were apparent between the early (14 and 28 days) and late (from 56 to 168 days) stages of decomposition. These could be related to ecological attributes such as the succession of r- (copiotrophs) and K- (oligotrophs) strategists. Microbial diversity at the early (28 days) and late (168 days) stages of degradation was further analysed by a molecular inventory of 16S and 18S rDNA in DNA extracts from the residue zone. This confirmed the succession of different populations during residue decomposition. Fluorescent Pseudomonas spp. and Neurospora sp. were dominant in the early stage with subsequent stimulation of Actinobacteria and Deltaproteobacteria taxa, as well as Basidiomycota fungal taxa and Madurella spp. According to the ecological attributes of these populations, microbial succession on fresh organic residue incorporated in soil would be dominated by copiotrophs and r-strategists in the early stages, with oligotrophs (K-strategists) increasing in relative abundance as substrate quantity and/or quality declines over time.     

Regulation of bacterial and fungal MCPA degradation at the soil-litter interface

Much is known about mechanisms and regulation of phenoxy acid herbicide degradation at the organism level, whereas the effects of environmental factors on the performance of the phenoxy acid degrading communities in soils are much less clear. In a microcosm experiment we investigated the small-scale effect of litter addition on the functioning of the MCPA degrading communities. ¹⁴C labelled MCPA was applied and the functional genes tfdA and tfdAα were quantified to characterise bacterial MCPA degradation. We identify the transport of litter compounds as an important process that probably regulates the activity of the MCPA degrading community at the soil-litter interface. Two possible mechanisms can explain the increased tfdA abundance and MCPA degradation below the litter layer: 1) transport of α-ketoglutarate or its metabolic precursors reduces the costs for regenerating this co-substrate and thereby improves growth conditions for the MCPA degrading community; 2) external supply of energy and nutrients changes the internal resource allocation towards enzyme production and/or improves the activity of bacterial consortia involved in MCPA degradation. In addition, the presence of litter compounds might have induced fungal production of litter-decaying enzymes that are able to degrade MCPA as well.