Comments on the paper by Kemmitt et al. (2008) ‘Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass - A new perspective’ [Soil Biology & Biochemistry 40, 61-73]: The biology of the Regulatory Gate

Kemmitt et al. (Kemmitt, S.J., Lanyon, C.V., Waite, I.S., Wen, Q., Addiscott, T.M., Bird, N.R.A., O'Donnell, A.G., Brookes, P.C., 2008. Mineralization of native soil organic matter is not regulated by the size, activity or composition of the soil microbial biomass - a new perspective. Soil Biology & Biochemistry 40, 61-73) recently proposed the “Regulatory Gate” hypothesis, which states that decomposition of soil organic matter (SOM) is regulated solely by abiotic factors. Without studying the mechanisms of such regulation, Kemmitt with coauthors challenged the classical Winogradsky theory of soil microbiology and questioned the concept of autochtonous and zymogenous microbial populations. In this letter, we revive the significance of microbial activity for SOM decomposition especially for the short-term (hours to weeks) processes and show that the “Regulatory Gate” is (micro)biologically driven.We explain the results of the three experiments in Kemmitt et al. (2008) from a microbiological point of view and suggest that SOM decomposition is mainly regulated by exoenzymes. We criticize the abiotic Regulatory Gate hypothesis based on bottleneck processes and pools limiting the SOM decomposition rate, comparison of constant and changing environmental conditions, as well as the connection between community structure and functions. We explain the results of Kemmitt et al. (2008) according to the properties of soil microbial community: functional redundancy and inconsistency between the excessive (but largely inactive) pool of total microbial biomass and the real mineralization activity. Finally, we suggest that to gain new perspectives on SOM decomposition and many other biochemical processes, future studies should focus on hot spots of (micro)biological activity (i.e., the rhizosphere, drillosphere, detritosphere, biopores, etc.) rather than on the bulk soil.     

Black carbon decomposition and incorporation into soil microbial biomass estimated by C labeling

Incomplete combustion of organics such as vegetation or fossil fuel led to accumulation of charred products in the upper soil horizon. Such charred products, frequently called pyrogenic carbon or black carbon (BC), may act as an important long-term carbon (C) sink because its microbial decomposition and chemical transformation is probably very slow. Direct estimations of BC decomposition rates are absent because the BC content changes are too small for any relevant experimental period. Estimations based on CO₂ efflux are also unsuitable because the contribution of BC to CO₂ is too small compared to soil organic matter (SOM) and other sources.We produced BC by charring ¹⁴C labeled residues of perennial ryegrass (Lolium perenne). We then incubated this ¹⁴C labeled BC in Ah of a Haplic Luvisol soil originated from loess or in loess for 3.2 years. The decomposition rates of BC were estimated based on ¹⁴CO₂ sampled 44 times during the 3.2 years incubation period (1181 days). Additionally we introduced five repeated treatments with either 1) addition of glucose as an energy source for microorganisms to initiate cometabolic BC decomposition or 2) intensive mixing of the soil to check the effect of mechanical disturbance of aggregates on BC decomposition. Black carbon addition amounting to 20% of C_org of the soil or 200% of C_org of loess did not change total CO₂ efflux from the soil and slightly decreased it from the loess. This shows a very low BC contribution to recent CO₂ fluxes. The decomposition rates of BC calculated based on ¹⁴C in CO₂ were similar in soil and in loess and amounted to 1.36 10⁻⁵ d⁻¹ (=1.36 10⁻³% d⁻¹). This corresponds to a decomposition of about 0.5% BC per year under optimal conditions. Considering about 10 times slower decomposition of BC under natural conditions, the mean residence time (MRT) of BC is about 2000 years, and the half-life is about 1400 years. Considering the short duration of the incubation and the typical decreasing decomposition rates with time, we conclude that the MRT of BC in soils is in the range of millennia.The strong increase in BC decomposition rates (up to 6 times) after adding glucose and the decrease of this stimulation after 2 weeks in the soil (and after 3 months in loess) allowed us to conclude cometabolic BC decomposition. This was supported by higher stimulation of BC decomposition by glucose addition compared to mechanical disturbance as well as higher glucose effects in loess compared to the soil. The effect of mechanical disturbance was over within 2 weeks. The incorporation of BC into microorganisms (fumigation/extraction) after 624 days of incubation amounted to 2.6 and 1.5% of ¹⁴C input into soil and loess, respectively. The amount of BC in dissolved organic carbon (DOC) was below the detection limit (<0.01%) showing no BC decomposition products in water leached from the soil.We conclude that applying ¹⁴C labeled BC opens new ways for very sensitive tracing of BC transformation products in released CO₂, microbial biomass, DOC, and SOM pools with various properties.     

Carbohydrate and amino acid composition of dissolved organic matter leached from soil

Low molecular weight organic substances (LMWOS) in soil and soil solution include mainly amino acids, carboxylic acids, and carbohydrates. Due to their high bioavailability they play a crucial role in the cycles of C and nutrients in soils. The variety of soil processes that involve LMWOS requires identifying their composition to elucidate reactions and transformations. In most studies, LMWOS are extracted under artificial conditions, e.g. batch experiments, which may overestimate the actual concentrations. This study measures the composition of carbohydrates and amino acids in solution of a Haplic Luvisol leached in a column experiment. A combined system for simultaneous leaching and blowout of CO₂ was used to estimate LMWOS decomposition. ¹⁴C-labeled glucose was added as a highly sensitive tracer to control the efficiency of the LMWOS extraction by leaching and to estimate LMWOS decomposition during leaching. High performance liquid chromatography (HPLC), optimized for soil extracts, was used to analyze LMWOS composition. For HPLC optimization, different preparations of leached solutions (filtration vs. centrifugation, and drying vs. no-drying) were compared. For sugar determination, drying had no influence on the solution concentrations. In contrast, amino acid concentrations significantly decreased by drying LMWOS eluted substances. Combining the HPLC identification of eluted substances with ¹⁴C tracer application revealed that about 5% of the glucose could be leached unchanged within 786 min (13.1 h), whereas about 84% remained in the soil, 9% were decomposed to CO₂, and 2% were transformed to other LMWOS and recovered in the soil solution. The total amino acid concentration (TAC) in soil solution was about 8.2 μmol l⁻¹, dominated by alanine (14.4% of TAC), glycine (13.4%), glutamic acid (9.9%), serine (9.4%), and leucine (9.3%). The total carbohydrate concentration was about 2.4 μM, dominated by glucose (29.9%), glucuronic acid (26.8%), and galacturonic acid (17.3%). Ratios of hexoses to pentoses, amino sugars glucosamine to galactosamine, and neutral sugars to uronic acids were determined. All three parameters pointed to the dominant influence of plants as the source of LMWOS in the leached soil solution. Within the small contribution of microorganisms, bacteria dominated over fungi. These used biomarker ratios as well as LMWOS concentrations differed widely from the ones obtained with conventional batch extraction. More research is necessary to evaluate the application of these biomarkers to soil solutions.     

Rice rhizodeposition and its utilization by microbial groups depends on N fertilization

Rhizodeposits have received considerable attention, as they play an important role in the regulation of soil carbon (C) sequestration and global C cycling and represent an important C and energy source for soil microorganisms. However, the utilization of rhizodeposits by microbial groups, their role in the turnover of soil organic matter (SOM) pools in rice paddies, and the effects of nitrogen (N) fertilization on rhizodeposition are nearly unknown. Rice (Oryza sativa L.) plants were grown in soil at five N fertilization rates (0, 10, 20, 40, or 60 mg N kg^?1 soil) and continuously labeled in a ¹³CO₂ atmosphere for 18 days during tillering. The utilization of root-derived C by microbial groups was assessed by ¹³C incorporation into phospholipid fatty acids. Rice shoot and root biomass strongly increased with N fertilization. Rhizodeposition increased with N fertilization, whereas the total ¹³C incorporation into microorganisms, as indicated by the percentage of ¹³C recovered in microbial biomass, decreased. The contribution of root-derived ¹³C to SOM formation increased with root biomass. The ratio of ¹³C in soil pools (SOM and microbial biomass) to ¹³C in roots decreased with N fertilization showing less incorporation and faster turnover with N. The ¹³C incorporation into fungi (18:2ω6,9c and 18:1ω9c), arbuscular mycorrhizal fungi (16:1ω5c), and actinomycetes (10Me 16:0 and 10Me 18:0) increased with N fertilization, whereas the ¹³C incorporation into gram-positive (i14:0, i15:0, a15:0, i16:0, i17:0, and a17:0) and gram-negative (16:1ω7c, 18:1ω7c, cy17:0, and cy19:0) bacteria decreased with N fertilization. Thus, the uptake and microbial processing of root-derived C was affected by N availability in soil. Compared with the unfertilized soil, the contribution of rhizodeposits to SOM and microorganisms increased at low to intermediate N fertilization rates but decreased at the maximum N input. We conclude that belowground C allocation and rhizodeposition by rice, microbial utilization of rhizodeposited C, and its stabilization within SOM pools are strongly affected by N availability: N fertilization adequate to the plant demand increases C incorporation in all these polls, but excessive N fertilization has negative effects not only on environmental pollution but also on C sequestration in soil.     

Formation of mineral N (NH4+, NO3—) during mineralization of organic matter from coal refuse material and municipal sludge

In 1994, the 14 hectare plateau of a coal refuse bank in Landsweiler‐Reden (Southwest‐Germany) was covered with a mixture consisting of 80% (v/v) refuse materials, 10% (v/v) composted wood and 10% (v/v) of sewage sludge as part of a reclamation project. The amount of sludge dry matter applied was approximately 450 Mg ha⁻¹ to a depth of 2 m. The approximate amount of nitrogen (N) applied with the substrate was 20 Mg ha⁻¹ (total N). From April 1996 until November 1997, contents of mineral nitrogen and nitrogen mineralization were monitored down to a depth of 2 m. Nitrogen mineralization was monitored by means of a modified buried bag procedure using a retrievable cylindrical receptacle. The contents of NH₄⁺‐ and NO₃⁻‐N were largest at the beginning of the observation period, reaching a peak value of 650 kg ha⁻¹ in May 1996. Then, mineral N stabilized in 1997 at a level of 200 kg N ha⁻¹, with the soil profile below 150 cm contributing about 75% to this amount. Net nitrogen mineralization was characterized by the same depth distribution. Other than in surface horizons, mineralization activity at the bottom of the profile continued into 1997 with the same intensity as in 1996. Variability among replicate buried bag incubations was high (CV > 100% on several occasions). Nitrogen loss through leaching was estimated at 630 kg N ha⁻¹ over the observation period, averaging at 360 kg N ha⁻¹ a⁻¹. The reclamation procedure used in this study may have the potential to contaminate ground water in hydrologically sensitive areas.     

Review: Factors affecting rhizosphere priming effects

Living plants change the local environment in the rhizosphere and consequently affect the rate of soil organic matter (SOM) decomposition. The rate may increase for 3‐ to 5‐folds, or decrease by 10 % to 30 % by plant cultivation. Such short‐term changes of rate (intensity) of SOM decomposition are due to the priming effect. In the presence of plants, a priming effect occurs in the direct vicinity of the living roots, and it is called rhizosphere priming effect (RPE). Plant‐mediated and environmental factors, such as, plant species, development stage, soil organic matter content, photosynthesis intensity, and N fertilization which affect RPE are reviewed and discussed in this paper. It was concluded that root growth dynamics and photosynthesis intensity are the most important plant‐mediated factors affecting RPE. Environmental factors such as amount of decomposable C in soil and N_min content are responsible for the switch between following mechanisms of RPE: concurrence for N_min between roots and microorganisms, microbial activation or preferential substrate utilization. Succession of mechanisms of RPE along the growing root in accordance with the rhizodeposition types is suggested. Different hypotheses for mechanisms of filling up the C amount loss by RPE are suggested. The ecosystematic relevance of priming effects by rhizodeposition relates to the connection between exudation of organic substances by roots, the increase of microbial activity in the rhizosphere through utilization of additional easily available C sources, and the subsequent intensive microbial mobilization of nutrients from the soil organic matter.     

Oxidation of methane and dehydrogenase activity in a Mollic Gleysol

It was found that during a 4-day incubation of a Mollic Gleysol with 352 μl 1^?1 methane in the headspace, the rate of methane consumption declined exponentially from an initial value of 9.13 μmol kg^?1 hour^?1 (about 5% of total CO₂ evolved) according to first-order kinetics. The increase of dehydrogenase activity due to methane amendment did not exceed 15% of the control value and reached the maximum after two days of incubation.     

Qualitative assessment of rhizodeposits in non‐sterile soil by analytical pyrolysis

Estimation of the amount of root exudates and simultaneous identification of their composition in non‐sterile soil is a challenging objective in rhizosphere research. We coupled 3 methods: (1) labeling of corn in ¹⁴CO₂ atmosphere to separate root‐derived and soil‐derived organic substances in the rhizosphere, (2) a previously developed leaching method to collect rhizodeposits, and (3) pyrolysis field ionization mass spectrometry (Py‐FIMS) to investigate the molecular‐chemical composition of rhizodeposits. Eluted rhizodeposits accounted for 2.8 % (Loam) and 0.97 % (nutrient solution in quartz sand) of recovered ¹⁴C and showed clear differences in composition between the growth substrates. The ¹⁴CO₂ evolved mostly by root respiration accounted for 3.5–4.0 % without significant differences according to growth substrate or diurnal dynamics. Principal component analysis of the Py‐FI mass spectra of leachates showed a clear diurnal dynamics of the amount and the composition of corn rhizodeposits collected during day‐time and night‐time. Differences originated mostly from signals assigned to carbohydrates, sterols, and peptides. This approach is recommended for forthcoming studies of rhizodeposition in different soil substrates, crops grown, and time‐series of exudate sampling.