Soil Organic Matter Degradation Research Articles

A benchmark for soil organic matter degradation under variably saturated flow conditions

Soil contains the largest terrestrial pool of organic matter, and the cycling of organic carbon in soils plays a crucial role in controlling atmospheric carbon dioxide (CO2) and global climate change. Although considerable progress has been made in previous modeling studies on the fate of soil organic matter (SOM), only a few models used a process-based approach for investigating these strongly coupled and complex soil systems, which involve SOM oxidation, transient water flow, and mass transport processes in aqueous and gaseous phases. Typically, physically based models for water flow, as well as solute and gas transport, are not coupled with state-of-the-art SOM degradation models. Reactive transport models (RTMs) provide a flexible framework for implementing different SOM degradation concepts and integrating biogeochemical processes with water flow and mass transport. Given the complex nature of carbon cycling in soils coupled with flow and mass transport, code intercomparison using well-defined benchmarks is in many cases the only practical method of model verification. The benchmark presented in this manuscript focuses on SOM oxidation under variably saturated flow conditions. The benchmark consists of three problems characterized by increasing complexity. The problems were solved using two different reactive transport codes, namely HP1 and MIN3P-THCm. The first supporting problem introduces a batch-type simulation to assess kinetic networks of SOM degradation. In the second supporting problem, transient water flow, solute transport, gas generation, and diffusive gas transport are considered. The principal problem combines the kinetic networks of SOM degradation with reactive transport under variably saturated flow conditions, including CO2 transport from soils to the atmosphere. Simulation results for the benchmark problems demonstrate an overall excellent agreement between the two codes, building confidence in the ability of RTMs to simulate complex C-cycling in dynamic environments.

Lignin chemistry of wetland soil profiles in two contrasting basins of the Louisiana Gulf coast

Recent studies indicate that loss of soil organic matter (SOM) from coastal wetlands can contribute to the hypoxia in the northern Gulf of Mexico along the Louisiana coast. In this study, coastal marsh soil profiles of two contrasting basins were investigated for lignin composition in order to assess organic matter source and degradation status under these different wetland formations. The Atchafalaya Basin is undergoing land building whereas the Barataria Basin is experiencing land loss. Lignin monomers were extracted using alkaline CuO oxidation followed by gas chromatography–mass spectrometry characterization. Marsh soil profiles from the Barataria Basin showed strong lignin storage with two-fold higher lignin contents (sum of vanillyl, syringyl, and cinnamyl phenols, Λ8) than those in the Atchafalaya Basin. Source SOM inputs in the Barataria Basin were non-woody angiosperms, whereas in the Atchafalaya Basin inputs were non-woody angiosperms and some gymnosperm inputs. Principal component analysis (PCA) showed that different soil environmental factors dominated the status of soil organic matter degradation. Soil pH was negatively related to the lignin degradation in the Atchafalaya Basin, whereas high total N contents inhibited lignin degradation in the Barataria Basin. Increasing electrical conductivity inhibited organic matter degradation in the low salinity wetlands of the Atchafalaya Basin, but positively influenced lignin decomposition in the higher salinity marsh soil profiles of Barataria Basin. Despite SOM in the Barataria Basin being more degraded than in the Atchafalaya, the nearly 10-fold greater amount of organic carbon (C) in the Barataria, coupled with net land loss, indicates that it is greater source of oxygen-consuming organic C, thus contributes more to the hypoxia in the Gulf.

Phenolic Compounds as Unambiguous Chemical Markers for the Identification of Keystone Plant Species in the Bale Mountains, Ethiopia.

Despite the fact that the vegetation pattern and history of the Bale Mountains in Ethiopia were reconstructed using pollen, little is known about the former extent of Erica species. The main objective of the present study is to identify unambiguous chemical proxies from plant-derived phenolic compounds to characterize Erica and other keystone species. Mild alkaline CuO oxidation has been used to extract sixteen phenolic compounds. After removal of undesired impurities, individual phenols were separated by gas chromatography and were detected by mass spectrometry. While conventional phenol ratios such as syringyl vs. vanillyl and cinnamyl vs. vanillyl and hierarchical cluster analysis of phenols failed for unambiguous Erica identification, the relative abundance of coumaryl phenols (>0.20) and benzoic acids (0.05—0.12) can be used as a proxy to distinguish Erica from other plant species. Moreover, a Random Forest decision tree based on syringyl phenols, benzoic acids (>0.06), coumaryl phenols (<0.21), hydroxybenzoic acids, and vanillyl phenols (>0.3) could be established for unambiguous Erica identification. In conclusion, serious caution should be given before interpreting this calibration study in paleovegetation reconstruction in respect of degradation and underground inputs of soil organic matter.

Earthworms Mitigate Pesticide Effects on Soil Microbial Activities.

Earthworms act synergistically with microorganisms in soils. They are ecosystem engineers involved in soil organic matter degradation and nutrient cycling, leading to the modulation of resource availability for all soil organisms. Using a soil microcosm approach, we aimed to assess the influence of the earthworm Aporrectodea caliginosa on the response of soil microbial activities against two fungicides, i.e., Cuprafor Micro® (copper oxychloride, a metal) and Swing® Gold (epoxiconazole and dimoxystrobin, synthetic organic compounds). The potential nitrification activity (PNA) and soil enzyme activities (glucosidase, phosphatase, arylamidase, and urease) involved in biogeochemical cycling were measured at the end of the incubation period, together with earthworm biomass. Two common indices of the soil biochemistry were used to aggregate the response of the soil microbial functioning: the geometric mean (Gmean) and the Soil Quality Index (SQI). At the end of the experiment, the earthworm biomass was not impacted by the fungicide treatments. Overall, in the earthworm-free soil microcosms, the two fungicides significantly increased several soil enzyme and nitrification activities, leading to a higher GMean index as compared to the non-treated control soils. The microbial activity responses depended on the type of activity (nitrification was the most sensitive one), on the fungicide (Swing® Gold or Cuprafor Micro®), and on the doses. The SQI indices revealed higher effects of both fungicides on the soil microbial activity in the absence of earthworms. The presence of earthworms enhanced all soil microbial activities in both the control and fungicide-contaminated soils. Moreover, the magnitude of the fungicide impact, integrated through the SQI index, was mitigated by the presence of earthworms, conferring a higher stability of microbial functional diversity. Our results highlight the importance of biotic interactions in the response of indicators of soil functioning (i.e., microbial activity) to pesticides.

The role of biochars in sustainable crop production and soil resiliency.

Biochar is a promising soil additive for use in support of sustainable crop production. However, the high level of heterogeneity in biochar properties and the variations in soil composition present significant challenges to the successful uptake of biochar technologies in diverse agricultural soils. An improved understanding of the mechanisms that contribute to biochar-soil interactions is required to address issues related to climate change and cultivation practices. This review summarizes biochar modification approaches (physical, chemical, and biochar-based organic composites) and discusses the potential role of biochar in sustainable crop production and soil resiliency, including the degradation of soil organic matter, the improvement of soil quality, and reductions in greenhouse gas emissions. Biochar design is crucial to successful soil remediation, particularly with regard to issues arising from soil structure and composition related to crop production. Given the wide variety of feedstocks for biochar production and the resultant high surface heterogeneity, greater efforts are required to optimize biochar surface functionality and porosity through appropriate modifications. The design and establishment of these approaches and methods are essential for the future utilization of biochar as an effective soil additive to promote sustainable crop production.

Long‐term Nitrogen Addition Decreases Organic Matter Decomposition and Increases Forest Soil Carbon

Core IdeasN additions alter soil microbial community composition and reduce forest soil microbial biomass and enzyme activity.Litter decomposition and soil organic matter degradation was slowed by N additions.Reduced decomposition increases soil C, but long‐term effects on forest productivity are unknown.Eastern North American forests receive anthropogenically elevated nitrogen (N) deposition that alters soil processes and forest productivity. We examined N deposition effects on soil carbon (C) and N in temperate, N‐rich forest plots fertilized annually (100 kg N ha−1y−1) since 1993. After nearly two decades, soil C in O, A, and upper 50 cm of B horizons of N‐addition plots was 17% greater (14.2 ± 0.7 kg C m−2) than control plots. Aboveground tree biomass growth and litterfall were not affected by fertilization. Fine root mass (0–1 mm) was 34% greater in N‐addition plots, but did not explain soil C increases. Rather, reduced decomposition of litter and soil organic matter drove C increases in N‐addition plots. Decomposition rates of black cherry, sugar maple, and mixed leaf litter were 43, 67, and 36%, greater, respectively, in control than N‐addition plots. Light fraction organic matter was greater in N‐addition plots than in control plots, due to either enhanced root production or decreased decomposition of soil organic matter. Soil respiration was reduced, and microbial biomass in O, A, and upper‐B horizons was lower in N‐addition plots than controls. The soil microbial community composition was also altered dramatically with N additions. Recalcitrant organic matter enzyme activity (peroxidase) was reduced in the O‐horizon by N addition. Available Ca, Mg, and K were reduced in O and A horizons by N fertilization. These results suggest that chronic elevated atmospheric N inputs can increase forest soil C storage by decreasing decomposition, however the long‐term stability of this additional C sequestration is unknown.

Millennial-scale carbon accumulation and molecular transformation in a permafrost core from Interior Alaska

Abstract Organic carbon stored in high-latitude permafrost represents a potential positive feedback to climate warming as well as a valuable store of paleoenvironmental information. The below-freezing conditions have effectively removed permafrost organic material from the modern carbon cycle and preserved its pre-freezing bulk and molecular states. The conditions that lead to efficient burial of organic carbon (OC) within permafrost were investigated by measuring OC stocks, past accumulation rates, and biogeochemical composition of a permafrost core taken from Interior Alaska dating back to 40 ka. The post-glacial Marine Isotope Stage 1 is represented by the top 1.2 m of the core and contains 64.7 kg OC/m2 with an accumulation rate of 4.3 g OC/m2/yr. The sediments that accumulated around the Last Glacial Maximum contain 9.9 kg OC/m2 with an accumulation rate of 0.5 g OC/m2/yr. Carbon storage (144.7 kg OC/m2) and accumulation (26.1 g OC/m2/yr) are both observed to be greatest between 35 and 40 ka, late during the Marine Isotope Stage 3 global interstadial. The extent of OC degradation was assessed using lignin and amino acid biomarkers with both approaches indicating well-preserved contemporary active layer and interstadial OC, whereas stadial OC was highly degraded. Lignin compositional indices throughout the core appear altered by sorptive processes that confounded some expected trends in the overall organic matter composition, while amino acids provided a more integrated pattern of change. Significant correlations between carbon-normalized hydroxyproline and total lignin concentrations further support the usefulness of hydroxyproline as an indicator for the abundance of plant organic matter. A novel amino acid plant-microbial index of the ratio of microbial-specific muramic acid and diaminopimelic acid biomarkers to the plant-specific hydroxyproline biomarker, indicate a transition from plant-dominated organic matter in fresh organic soils (index values of 0.01–0.20) to more microbial-dominated organic matter in degraded mineral soils (index values of 0.50–2.50). The branched glycerol dialkyl glycerol tetraether composition is complex and is not immediately compatible with existing temperature transfer functions. Residence time within the active layer is interpreted to integrate key factors such as primary productivity, inorganic sediment delivery, and other climate factors that control soil organic matter degradation. The Marine Isotope Stage 3, mid-Wisconsin interstadial period at this locality was forest-dominated and suggests the currently prevailing tundra ecotone is sensitive to environmental change. The majority of buried permafrost OC is high in degradability and if thawed, would be expected to be highly vulnerable to microbial decomposition.

Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere.

Stable isotope probing of microbial nucleic acids applied in the rhizosphere enables (a) the identification of the active microbial community involved in root exudate assimilation and those involved in soil organic matter degradation, and (b) the study of the impact of plants via root exudates on the in situ expression of microbial functions. By incubating plants under 13CO2, fresh carbon exuded by the plant will be labeled and hence the microbial community assimilating 13C-root exudates will incorporate 13C into their cellular macromolecules. Labeled DNA, RNA, and proteins can be used to identify microorganisms that assimilated the root exudates. We provide a step-by-step protocol on how to apply stable isotope probing of DNA and RNA in the plant rhizosphere to identify the active microbial communities and analyze their gene expression.

Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation.

Plant strategies for soil nutrient uptake have the potential to strongly influence plant–microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.

The effect of traditional slash‐and‐burn agriculture on soil organic matter, nutrient content, and microbiota in tropical ecosystems of Papua New Guinea

AbstractSlash‐and‐burn agriculture followed by tillage and western style agriculture often lead to loss of soil organic matter and soil degradation. Traditional slash‐and‐burn agriculture affects large areas of land across the tropical zone. However, there are few detailed studies about this practice. To evaluate the effect of traditional slash‐and‐burn agriculture on soil properties (total C, N, P, and C fractions of soil and available P, Ca, Mg, K, NO3, pH, and microbial community biomass and composition), we studied a chronosequence represented by active gardens, abandoned gardens (5–10 years old), secondary forest in abandoned garden sites (20–40 years old), and primary forest with no evidence of cultivation for at least 60 years. No significant differences between individual succession stages were found in total C, N, and P and in C fractions, pH, conductivity, and microbial biomass. In addition, stocks of C, N, and P in the soil did not differ between succession stages. By contrast, the concentration of available P, Ca, Mg, K, and NO3 was highest in active gardens. Litter was absent in active gardens, and the highest amount of litter on the soil surface was found in primary forest. Our results show that traditional slash‐and‐burn agriculture had a strong effect on nutrient availability but no effect on the total CNP stocks and soil C fractions.

Molecular-level changes in soil organic matter composition after 10 years of litter, root and nitrogen manipulation in a temperate forest

With climate change, forests are expected to receive increased inputs of carbon (C) and nitrogen (N) but it is unclear how this will modify forest C cycling and storage at the molecular-level. To investigate the response of forest soil organic matter (SOM) to changes in soil inputs, a study area was established in a Michigan hardwood forest as part of the Detrital Input and Removal Treatments (DIRT) network. Experimental treatments were comprised of both exclusions of detrital inputs (No Litter, No Roots, No Inputs) and additions of C and N (Double Litter, N-Addition, Double Litter + N, Wood). After 10 years of treatment, the soils were characterized using elemental analysis, molecular biomarker techniques, nuclear magnetic resonance spectroscopy, and microbial biomass C measurements. Although manipulation of detrital inputs did not significantly change the soil C and N content after 10 years, alterations in the cycling and distribution of SOM components were observed. Root exclusion enhanced SOM degradation, while doubling litter favoured the degradation of more labile forms of soil C such as unsaturated n-alkanoic acids and simple sugars. N-Addition and Double Litter + N increased the concentrations of extractable biomarkers, including aliphatic and cyclic lipids and compounds derived from cutin, suberin, and lignin. Microbial biomass C also varied with experimental litter input manipulations and N addition, and these data were consistent with the observed changes in SOM composition. Overall, the observed shifts in SOM chemistry after 10 years of manipulating ecosystem inputs highlight the sensitivity of natural systems to changes in amounts of C and N inputs from roots and litter, and N inputs from external sources.

Plant host habitat and root exudates shape fungal diversity.

The rhizospheric microbiome is clearly affected by plant species and certain of their functional traits. These functional traits allow plants to adapt to their environmental conditions by acquiring or conserving nutrients, thus defining different ecological resource-use plant strategies. In the present study, we investigated whether plants with one of the two nutrient-use strategies (conservative versus exploitative) could influence fungal communities involved in soil organic matter degradation and root exudate assimilation, as well as those colonizing root tissues. We applied a DNA-based, stable-isotope probing (DNA-SIP) approach to four grass species distributed along a gradient of plant nutrient resource strategies, ranging from conservative to exploitative species, and analyzed their associated mycobiota composition using a fungal internal transcribed spacer (ITS) and Glomeromycotina 18S rRNA gene metabarcoding approach. Our results demonstrated that fungal taxa associated with exploitative and conservative plants could be separated into two general categories according to their location: generalists, which are broadly distributed among plants from each strategy and represent the core mycobiota of soil organic matter degraders, root exudate consumers in the root-adhering soil, and root colonizers; and specialists, which are locally abundant in one species and more specifically involved in soil organic matter degradation or root exudate assimilation on the root-adhering soil and the root tissues. Interestingly, for arbuscular mycorrhizal fungi analysis, all plant roots were mainly colonized by Glomus species, whereas an increased diversity of Glomeromycotina genera was observed for the exploitative plant species Dactylis glomerata.

Effects of precipitation reduction on the composition and stability of soil organic matter in a young Cunninghamia lanceolata plantation.

It is hard to predict the response of soil organic matter (SOM) to global climate change due to its heterogenous chemical structure. With the development of molecular techniques to identify the structure, sources and stages of SOM degradation, long-standing questions regarding the composition and stability of SOM might be resolved. To investigate the effects of changes in precipitation patterns on the stability of SOM, we analyzed the specific compositions and extent of degradation of SOM using biomarkers, in a young Cunninghamia lanceolata plantation after reducing 50% of precipitation (P) for two years. The results showed that precipitation reduction (P-treatment) significantly reduced the levels of free lipids. Relative to control (CT), P-treatment decreased short-chain n-alkanoic acids (C16-18) and terpenoids and steroids by 62.8% and 19.1%, respectively. However, P-treatment did not significantly change the concentrations of other aliphatic compounds. Although there was no observable difference in the total lignin content between treatments, P-treatment significantly reduced the acid to aldehyde ratios for syringyl [(Ad/Al)s] and vanillyl [(Ad/Al)v]. Thus, the labile compositions of SOM were accelerated to decomposition under rainfall pattern change. Although the recalcitrant compositions (lignin) were relatively stable, their long-term stability should be further monitored.

The detrital input and removal treatment (DIRT) network: Insights into soil carbon stabilization

Ecological research networks functioning across climatic and edaphic gradients are critical for improving predictive understanding of biogeochemical cycles at local through global scales. One international network, the Detrital Input and Removal Treatment (DIRT) Project, was established to assess how rates and sources of plant litter inputs influence accumulations or losses of organic matter in forest soils. DIRT employs chronic additions and exclusions of aboveground litter inputs and exclusion of root ingrowth to permanent plots at eight forested and two shrub/grass sites to investigate how soil organic matter (SOM) dynamics are influenced by plant detrital inputs across ecosystem and soil types.Across the DIRT network described here, SOM pools responded only slightly, or not at all, to chronic doubling of aboveground litter inputs. Explanations for the slow or even negative response of SOM to litter additions include increased decomposition of new inputs and priming of old SOM. Evidence of priming includes increased soil respiration in litter addition plots, decreased dissolved organic carbon (DOC) output from increased microbial activity, and biochemical markers in soil indicating enhanced SOM degradation. SOM pools decreased in response to chronic exclusion of aboveground litter, which had a greater effect on soil C than did excluding roots, providing evidence that root-derived C is not more critical than aboveground litter C to soil C sequestration. Partitioning of belowground contributions to total soil respiration were predictable based on site-level soil C and N as estimates of site fertility; contributions to soil respiration from root respiration were negatively related to soil fertility and inversely, contributions from decomposing aboveground litter in soil were positively related to site fertility. The commonality of approaches and manipulations across the DIRT network has provided greater insights into soil C cycling than could have been revealed at a single site.

The impacts of four potential bioenergy crops on soil carbon dynamics as shown by biomarker analyses and DRIFT spectroscopy

AbstractPerennial bioenergy crops accumulate carbon (C) in soils through minimally disturbing management practices and large root inputs, but the mechanisms of microbial control over C dynamics under bioenergy crops have not been clarified. Root‐derived C inputs affect both soil microbial contribution to and degradation of soil organic matter resulting in differing soil organic carbon (SOC) concentrations, storage, and stabilities under different vegetation regimes. Here, we measured biomarker amino sugars and neutral sugars and used diffuse reflectance mid‐infrared Fourier transform spectroscopy (DRIFTS) to explore microbial C contributions, degradation ability, and SOC stability, respectively, under four potential bioenergy crops, M.×giganteus (Miscanthus × giganteus), switchgrass (Panicum virgatum L.), a mixed prairie, and a maize (Zea mays L.)–maize–soybean (Glycine max(L.) Merr.) (MMS) rotation over six growing seasons. Our results showed that SOC concentration (g/kg) increased by 10.6% in mixed prairie over the duration of this experiment and SOC storage (Mg/ha) increased by 17.0% and 15.6% in switchgrass and mixed prairie, respectively. Conversion of row crops to perennial grasses maintained SOC stability and increased bacterial residue contribution to SOC in M.×giganteus and switchgrass by 20.0% and 15.0%, respectively, after 6 years. Degradation of microbe‐derived labile SOC was increased in M.×giganteus, and degradation of both labile and stable SOC increased in MMS rotation. These results demonstrate that microbial communities under perennial grasses maintained SOC quality, while SOC quantity increased under switchgrass and mixed prairie. Annual MMS rotation displayed decreases in aspects of SOC quality without changes in SOC quantity. These findings have implications for understanding microbial control over soil C quantity and quality under land‐use shift from annual to perennial bioenergy cropping systems.

Formation of the Azodication (ABTS2+) from ABTS [2,2′-Azinobis-(3-ethylbenzothiazoline-6-sulphonate)] in Sterile Plant Cultures: Root–Exuded Oxidoreductases Contribute to Rhizosphere Priming

Rhizosphere priming by terrestrial plants comprises increased or repressed efflux of CO2 and N from soil organic matter (SOM), decaying under the impact of temperature, moisture, and the composition of rhizodeposits. Contemporarily, increases in water solubility vs. losses in molecular size, aromaticity, and the content in phenolic OH groups denote the degradation of SOM in planted soil. Root peroxidases (POs) and ‘polyphenoloxidases’ are surmised to contribute to these effects, however, final evidence for this is lacking. Therefore, seedlings of white mustard, alfalfa, and oilseed rape with wide spans in PO release were grown in hydroponic cultures at variable levels of Cu/Fe/Mn as Fenton metals, but also under P and Fe starvation to stimulate the release of carboxylic acids that form catalytic Mn3+ chelants from Mn2+ and MnO2. The shortage in active oxygen as a cosubstrate of POs delayed the immediate oxidation of 2,2′-azinobis-(3-ethylbenzothiazoline-6-sulphonate) (ABTS) supplements to the green ABTS•+ by PO/H2O2, the possible formation of Mn3+ via PO catalyzed aryloxy radicals from root–released phenolics, and of HO• by metal cations in H2O2 dependent Fenton–like reactions. Enhanced by exuded and external malate, O2 independent MnO2 supplements in some treatments formed ABTS•+ spontaneously. The culture fluids then turned red in all treatments within 24–60 h by the formation of azodication (ABTS2+) derivatives in a second plant initiated oxidation step that is known to be catalyzed by substrate radicals. It is concluded that plants initiate oxidative activities that contribute to rhizosphere priming in an environment of oxidoreductase and carboxylate exudates, the indicated presence of mediating substrate radicals, and the cations and (hydr)oxides of transition metals. Pathways of H2O2 production upon the degradation of carboxylates and by the POs themselves are indicated.

Impact of irrigation management on paddy soil N supply and depth distribution of abiotic drivers

In rice production, water-saving irrigation management is expanding and likely alters depth profiles of soil moisture, redox potential (Eh) and microbial activity. It is, however, unclear how such conditions then impact net soil N-release and availability to the rice crop, because we do not know well enough how water-saving irrigation management shapes depth-distribution of Eh and reductive processes, and microbial activity. A field experiment with rice was laid out on a typical young floodplain paddy soil of Bangladesh with three irrigation schemes, viz. continuous flooding (CF), safe alternate wetting and drying (AWD) and direct seeded rice (DSR), with 120 kg N ha−1 (N120) or without (N0) urea application. We evaluated changes in soil mineral N and plant N uptake, CH4 and CO2 emissions and soil pH, and at multiple depths soil Eh and temperature, dissolved C, Fe and Mn throughout 2015 dry (Boro) season (Jan–Apr). Eh stayed at or above ∼+300 mV except for sudden drops to ∼−200 mV with irrigation events in DSR. Eh quickly dropped to methanogenic conditions, under both AWD and CF; rises to ∼+200 mV were observed during AWD-drainage events but were restricted to upper 5.5 or 12.5 cm depths. Throughout the growing season there was a pronounced increase in reductive dissolution of Fe and Mn (hydro-) oxides, buildup of dissolved C, and CH4 effluxes under AWD and CF but not DSR, likely at least partially driven by the gradual soil warming from ∼20 °C till 28 °C. Predominant aerobic conditions under DSR lead to a nearly doubled C-emissions (CO2 + CH4) compared to AWD and CF, suggesting more soil organic matter (OM) degradation in the former case, while soil mineral N plus plant N build-up rate followed an opposite order. Urea application did not raise soil exchangeable N levels, even prior to significant plant uptake from 28 DAT (days after transplanting), and we forward temporal abiotic NH4+-fixation and N-removal processes as explanations. We conclude that regardless of some distinctions in temporal evolutions of puddle layer Eh, solution C, Fe and Mn, and CH4-emission, soil N-supply was quite comparable under AWD and CF, as was rice yield. In the context of N availability, AWD could be safely adopted for rice growth in the Bangladeshi Boro season. The eventual fertilizer N recovery efficiency was higher for CF (42%) than for AWD (32%), but AWD saved 12% irrigation water. While DSR saved 45% water there was a large yield penalty, likely due to drought stress but also by poor germination caused by cold night temperatures in mid-January, while seedling transplantation in CF and AWD plots was only later on 28 January. Further research should be conducted to investigate the fast and pronounced removal of exchangeable inorganic N after initial N buildup by soil OM mineralization, especially in CF and AWD. At this moment most likely candidate processes appear clay-NH4+ fixation and anaerobic NH4+-oxidation.

Molecular Insights into Arctic Soil Organic Matter Degradation under Warming.

Molecular composition of the Arctic soil organic carbon (SOC) and its susceptibility to microbial degradation are uncertain due to heterogeneity and unknown SOC compositions. Using ultrahigh-resolution mass spectrometry, we determined the susceptibility and compositional changes of extractable dissolved organic matter (EDOM) in an anoxic warming incubation experiment (up to 122 days) with a tundra soil from Alaska (United States). EDOM was extracted with 10 mM NH4HCO3 from both the organic- and mineral-layer soils during incubation at both -2 and 8 °C. Based on their O:C and H:C ratios, EDOM molecular formulas were qualitatively grouped into nine biochemical classes of compounds, among which lignin-like compounds dominated both the organic and the mineral soils and were the most stable, whereas amino sugars, peptides, and carbohydrate-like compounds were the most biologically labile. These results corresponded with shifts in EDOM elemental composition in which the ratios of O:C and N:C decreased, while the average C content in EDOM, molecular mass, and aromaticity increased after 122 days of incubation. This research demonstrates that certain EDOM components, such as amino sugars, peptides, and carbohydrate-like compounds, are disproportionately more susceptible to microbial degradation than others in the soil, and these results should be considered in SOC degradation models to improve predictions of Arctic climate feedbacks.

Change of the pathway of methane production with progressing anoxic incubation of paddy soil

Rates and pathways of methane production in rice fields were found to change with season. However, field conditions are complex and thus, it is still unclear which of the many environmental factors cause these changes. One possible factor is the availability of degradable organic carbon. Therefore, we investigated the change in rate and pathway of CH4 production under controlled laboratory conditions by progressing incubation of Italian paddy soil under anaerobic conditions. We studied the functional (pathway, rate) and structural (abundance, taxonomic composition) responses of methanogenic archaeal communities without and with addition of rice straw. Initially, rice straw significantly enhanced CH4 production rates and acetate accumulation. Later on, the values strongly decreased with the progress of degradation. A high contribution of acetoclastic methanogenesis (62–75%) was initially observed, while hydrogentrophic methanogenesis became dominant in the late degradation phase, both in soil without and with amendment of rice straw. The percentage contribution of the hydrogenotrophic pathway scaled with the percentage of the organic carbon mineralized to CH4 plus CO2 during the incubation time, irrespectively whether or not the soil was amended with rice straw. It was low (<33%), when >60% of the carbon was still available, but increased to >50% when available carbon had decreased to <30%. The methanogenic archaeal communities also exhibited changes over the subsequent degradation phases, but especially when the soil was amended with rice straw. Thus, rice straw amendment initially favored acetoclastic Methanosarcina and hydrogentrophic Methanocella, which subsequently decreased, while acetoclastic Methanothrix (‘Methanosaeta’) was favored and increased in the late degradation phases. The results demonstrate strong functional and structural responses of methanogenic archaeal communities to progressing degradation of rice straw and/or soil organic matter, but indicate that the hydrogenotrophic methanogenic pathway was in particular controlled by the availability of degradable organic carbon.

Soil-borne fungi challenge the concept of long-term biochemical recalcitrance of pyrochar

Pyrogenic organic matter (PyOM) is assumed to be biochemically recalcitrant, but recent studies indicated a quick decrease of PyOM in post-fire soils. Regardless erosion and abiotic degradation, microbial decomposition has been the explanation for this response, but no direct proof has been provided up to now. In the present study, we were able to demonstrate for the first time that the soil-borne fungus Fusarium oxysporum is not only colonizing the pore system of pyrochar (PyC) but is also involved in the degradation of its aromatic network. We showed that PyC not only stimulates microbial degradation of soil organic matter (SOM), but is also attacked and decomposed by microorganisms. Our observations are based on the chemical and morphological alterations of a sewage-sludge derived PyC produced at 600 °C after its amendment to a Calcic Cambisol by solid-state 13C nuclear magnetic resonance spectroscopy, analytical pyrolysis, elemental analysis, field emission scanning electron microscopy and DNA-based analysis of the isolated fungi. We showed that biofilms detected in the PyC play an essential role in the degradation process. These results are indispensable for a reliable assessment of the carbon sequestration potential of PyC in soils but also for improving global C cycling models.