Soil organic matter decomposition as a key driver of pharmaceutical retention.

Using freshwater and greywater for irrigation introduces pharmaceuticals (PhACs) into arable lands that lack organic matter replenishment, thus altering soil composition and affecting PhACs retention throughout the vegetation period. We conducted an incubation experiment representing a simulated vegetation period using Black Soil, which covers about 21% of the world's agricultural areas. We used PhACs with diverse physicochemical properties that cover a wide range of the characteristics typical of PhACs accumulating within the rhizosphere such as carbamazepine (CBZ), 17α-ethynylestradiol (EE2), and diclofenac-sodium (DFC) and their metabolites (trans-10,11-Dihydro-10,11-dihydroxy carbamazepine (TCBZ), estrone (E1), estriol (E3), 17β-estradiol (BE2), 17α-estradiol (LE2), and 5-hydroxydiclofenac (5HODFC)). We performed separated fixed-bed experiments (15 columns) to determine the main sorption properties of PhACs at the beginning, middle and end of the simulated vegetation period. In parallel, we were monitoring the changes in soil organic matter (SOM), characterized by the indicator physicochemical parameters (e.g. soil organic carbon (SOC), the ratio of dissolved organic carbon (DOC) to SOC and the composition of soil aliphatic and aromatic compounds). We also analysed the properties of the SMC (e.g. acidic phosphatase-, dehydrogenase enzyme activity, and the composition of the communities). Chemometric modelling has allowed us to visualize how the physicochemical properties of PhACs shape the sorption processes at different decomposition stages of SOM. With these data, we estimate how parent compounds and their metabolites are retained and released by the ever-changing organic matter medium, which might be used to simulate the temporal mobility of PhACs in agricultural systems, thereby aiding in the management of soil nutrient replenishment.The enzyme activity showed that the microbial community was continuously transforming the soil organic carbon, leading to its decrease. During the incubation period, representing the early stages of the vegetation period, the hydrophobicity and van der Waals surface area of PhACs affected soil retention strength. By this period's end, the Hydrogen-bond donor/acceptor ratio shaped the sorption processes. The physicochemical property that dominates the adsorption clearly indicates the transformation of the available functional groups. We demonstrate the necessity of considering soil conditions over time rather than relying on a single observation, as it is inherently limited in its ability to represent the soil's actual state.This research was supported by OTKA K142865, NKFIH 2020–1.1.2-PIACI-KFI-2021-00309; 2021–1.2.4-TÉT-2021-00029, HUSK_2302_1.2_070 INTERREG and DKOP-23_03.

There is increasing evidence that the accessibility of soil organic matter (SOM) to microbial decomposers is more important than chemical recalcitrance for regulating SOM stability. We show that the rapid reduction in SOM decomposition following the addition of sorptive mineral phases to soils in laboratory conditions leads to decreased accessibility of SOM to microbial decomposers due to the formation of organo‐mineral complexes. We manipulated SOM accessibility in a short‐term microcosm experiment by adding different proportions of a sorptive mineral material derived from an aluminium‐rich allophanic soil to a constant mass of soil to determine the effects on SOM decomposition after 1, 4 and 8 days. The decrease in SOM decomposition with increasing proportion of added sorptive mineral phase occurred within 1 day and did not change further at 4 and 8 days. In a second experiment, we added three proportions of the sorptive mineral phases (0%, 15% and 50%) to three soils with different carbon (C) concentrations and measured rates of SOM decomposition, changes in water extractable C, the formation of organo‐mineral complexes inferred from pyrophosphate‐extractable aluminium, and the natural abundance 13C isotopic composition of CO2 derived from SOM decomposition. We confirmed that the proportional decreases in SOM decomposition with increasing organo‐mineral complexes and decreasing microbial access to SOM was the same for the three soils, suggesting that the effects are independent of soil C concentration and pH. We also showed that the short‐term reductions in SOM accessibility led to microbial decomposition of more 13C enriched substrates, suggesting preferential stabilisation of plant‐derived (13C depleted) substrates. Our study demonstrated that SOM accessibility and decomposition could be reduced rapidly and proportionally to the amount of added sorptive mineral phases resulting from increased organo‐mineral interactions irrespective of the initial soil organic carbon concentration.Highlights Addition of sorptive mineral phases reduced short‐term soil organic matter (SOM) decomposition by the same proportion for three soils. Relatively 13C depleted SOM was preferentially adsorbed onto the mineral phases. The reduction in SOM decomposition was attributed to reduced microbial access due to increased organo‐mineral interactions. The effects occurred rapidly and proportionally to the amount of added sorptive mineral phases.

Abstract. Decomposition of soil organic matter (SOM) is limited by both the available substrate and the active decomposer community. The understanding of this colimitation strongly affects the understanding of feedbacks of soil carbon to global warming and its consequences. This study compares different formulations of soil organic matter (SOM) decomposition. We compiled formulations from literature into groups according to the representation of decomposer biomass on the SOM decomposition rate a) non-explicit (substrate only), b) linear, and c) non-linear. By varying the SOM decomposition equation in a basic simplified decomposition model, we analyzed the following questions. Is the priming effect represented? Under which conditions is SOM accumulation limited? And, how does steady state SOM stocks scale with amount of fresh organic matter (FOM) litter inputs? While formulations (a) did not represent the priming effect, with formulations (b) steady state SOM stocks were independent of amount of litter input. Further, with several formulations (c) there was an offset of SOM that was not decomposed when no fresh OM was supplied. The finding that a part of the SOM is not decomposed on exhaust of FOM supply supports the hypothesis of carbon stabilization in deep soil by the absence of energy-rich fresh organic matter. Different representations of colimitation of decomposition by substrate and decomposers in SOM decomposition models resulted in qualitatively different long-term behaviour. A collaborative effort by modellers and experimentalists is required to identify formulations that are more or less suitable to represent the most important drivers of long term carbon storage.

Planting trees on non-forested land has the potential to sequester atmospheric CO2 in biomass and soil. While afforestation on former agricultural land often results in an increased soil organic carbon sequestration, the outcomes of afforestation on pastures vary from carbon sink to source. Alpine soils are characterized by a higher proportion of labile carbon compounds compared to soils in temperate ecosystems, which makes alpine ecosystems more sensitive to environmental changes. The conversion of subalpine pasture to forests thereby might have a substantial effect on the SOC dynamics and  on soil organic matter (SOM) stabilization. In addition, the alteration in the proportion of aboveground biomass- and root-derived organic matter and the associated alterations in the soil microbial community following afforestation on subalpine pastures are not yet fully understood. In this study, the alteration in SOC stocks as well as in the SOM composition following  afforestation (0 to 130 years) with Norway spruce (Picea abies) on a subalpine pasture is investigated in the Swiss Alps. To determine the alteration of potential sources and decomposition of SOM, a multi-proxy molecular marker approach was applied. Specifically, the combination of n-fatty acids, n-alkanes, and n-alcohols was applied to identify possible sources of plant-derived SOM. For the identification of microorganism-derived SOM, a combination of phospholipid fatty acids and glycerol dialkyl glycerol tetraethers was used. Afforestation with Norway spruce on a subalpine pasture did not result in any significant change in SOC stocks (Pasture: 11.5 ± 0.5 kg m-2; 130-year-old forest 11.0 ± 0.3 kg m-2) after 130-years. The organic matter input, however, changed from grass leaves to spruce needles with increasing forest stand age. Surprisingly, root-derived organic matter seems to play a minor role in the pasture soil as well as in forest soils of all stand ages as one of the predominant sources of SOM. With increasing forest age an increased abundance of Gram+ bacteria as well as arbuscular mycorrhizal fungi was observed. In the pasture soil, a clearly higher abundance of archaea was observed compared with the forest. This shift in the soil microbial community shows its adaptation to the changes in the vegetation cover.  Furthermore, the difference in the soil microbial community structure implies a use of different carbon substrates of the microorganisms between the pasture and forests, which can have substantial effects on soil organic matter stabilization. Conclusively SOC stocks did not change after 130 years of afforestation on a subalpine pasture, but the SOM dynamics has changed due to the changes in the vegetation cover. For a better understanding of the connection between organic matter input and its decomposition, the analysis of plant polymers such as cutin and suberin polymers can help to unravel the difference in shoot- vs. root-derived organic matter and their contribution to the stable SOM pool in subalpine ecosystems.

Effects of intensities and cycles of heating on mineralization of organic matter and microbial community composition of a Mollisol under different land use types

The contribution of ericoid plants to soil nitrogen chemistry and organic matter decomposition in boreal forest soil

Soil organic matter (SOM) is of global importance as it represents a greater carbon pool than atmosphere or terrestrial vegetation and it strongly regulates primary productivity. SOM is thus integral to global climate change mitigation and food security. Recent advances reveal a pivotal role of soil microbes in both SOM formation and decomposition, placing them at the nexus of global biogeochemical cycles. However, the soil microbial traits that best promote SOM formation and persistence, and the environmental conditions that best promote such traits, remain poorly characterised – particularly in the tropics. In this thesis, I evaluated the interplay between microbial function and composition, vegetation, and SOM dynamics in tropical soils. My experimentation spanned laboratory and field study scales in two continents: (i) soil carbon cycling was examined following manipulations of soil microbial composition and function under controlled laboratory conditions in microcosms, (ii) the responses of soil microbes and SOM were compared in decadalold high diversity rainforest restoration plantings and reference soils under pasture and old-growth rainforest in tropical northeast Australia, and (iii) tropical tree monoculture and mixed species plantings in the Philippines were assessed for restoration of soil microbial traits and SOM. Several insights were gained that advance knowledge on SOM dynamics in the tropical context. Soil microbial substrate use efficiency, an indicator of SOM formation potential, changed significantly with microbial composition, increasing with greater fungal dominance. Stable SOM under Australian rainforest restoration plantings was unchanged circa two decades after plantation establishment, with no sign of recovery towards reference old- growth rainforest levels, which coincided with similarly stagnant microbial recovery. Soil microbial composition explained most of the variation in SOM across land uses in the Philippines, where SOM was also slow to recover, and microbial composition in turn correlated strongly with aboveground plant composition. The results thus indicate that (i) microbial composition can have a direct influence on efficiency of formation of SOM precursor material (microbial residues), and (ii) slow microbial recovery with reforestation coincides with slow SOM recovery. In combination with previous research suggesting that microbial traits are major determinants of SOM formation and persistence, the results prompt me to speculate that reliable restoration of stable SOM through tropical reforestation may often be constrained by limited restoration of the soil microbial community. This in turn may require more comprehensive restoration of aboveground plant community composition, or, potentially, upon active manipulation of soil microbial communities to circumvent long lag times that may prevent effective restoration of soil function. Future developments in forest restoration and climate mitigation efforts may require a shift towards integrating the soil microbial community. A deliberate and nuanced examination of soil microbial communities is needed to clarify their role in soil recovery, with a focus on designing and testing more effective interventions to overcome barriers to the recovery of degraded land.

AggModel: A soil organic matter model with measurable pools for use in incubation studies

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.

Soil organic matter (SOM) dynamics under long-term warming are critical to understanding how climate change may impact carbon cycling. This study investigates the effects of century scale soil warming on SOM dynamics and microbial communities in a subarctic deciduous forest near the Takhini Hot Springs in Yukon Territory, Canada. Utilizing a natural geothermal gradient, we examine changes in soil microbial community composition and functional potential as carbon use efficiency. Initial findings indicate that warming increases microbial decomposition of litter and native SOM, with significant substrate preference of plant-derived particulate organic matter to microbially-derived compounds, particularly in deeper soil layers. We hypothesize that warming enhances microbial activity, leading to increased decomposition and altered SOM composition. As a result, microbial communities adapt to relatively oligotrophic conditions, observable as an increase in traits associated with a high carbon use efficiency (CUE), like higher codon use bias, as it enhances translational efficiency and reduces metabolic costs.    Our methodology incorporates the 18O-CUE method to measure microbial CUE by tracking microbial growth using 18O-labeled water under steady-state conditions. Incubation experiments will quantify CUE across different temperatures, testing the mechanisms of temperature adaptation in the soil microbial communities. Additionally, exoenzyme analysis, of enzymes involved in SOM decomposition, e.g. N-acetyl glucosaminidase, β-glucosidase, along the same temperature gradients will be performed to connect changes in soil properties to soil functions. To decouple the immediate effects of temperature on enzyme activity from the sustained impacts of long-term warming, we will use Arrhenius plots as a framework.    This research will enhance our understanding of the link between SOM dynamics under climate change and microbial adaptation, providing a framework for predicting long-term ecological responses in subarctic ecosystems. The outcomes will inform broader ecological models and potential mitigation strategies for climate change impacts on soil health and carbon cycling.

Elevated temperatures drive abiotic and biotic degradation of organic matter in a peat bog under oxic conditions

Both temperature and nutrient availability have essential roles in regulating the decomposition of soil carbon (C) and nitrogen (N), the main controls on organic matter accumulation in forest ecosystems. However, there is a lack of information about how N deposition and phosphorus (P) additions might impact soil C and N decomposition rates in subtropical forests under climate warming. We measured soil organic C and N mineralisation rates and corresponding exoenzyme activities in a subtropical forest soil that had received N and/or P additions for six years in experimental conditions at a range of temperatures between 10 and 40°C. Our results showed that soil organic C and N decomposition rates were positively correlated with the activities of their corresponding enzymes, which suggests that the extracellular enzyme activities could be the main influence on soil organic matter (SOM) decomposition rates. N additions had a significant positive effect on soil organic C mineralisation and enhanced oxidase and hydrolase activities. P additions had little effect on soil organic C and N decomposition rates. These results challenge the assumptions that soil microorganisms are N‐rich and P availability restricts organic matter decomposition, and provides additional evidence that N, not P, regulates organic matter decomposition in subtropical forests. While N additions significantly influenced the soil C and N decomposition rates, they had little effect on their sensitivity to temperature. In contrast, P additions had a significant effect on the temperature sensitivities of SOM decomposition and the βG and NAG Vmax. Overall, our results show that SOM decomposition is vulnerable to both N and P additions, and both should be considered when predicting how SOM decomposition and C cycling might change under warming.Highlights The effect of N and/or P additions on the temperature sensitivity of SOM decomposition was explored. N stimulated soil organic C decomposition rates and corresponding enzyme activities. P promoted the sensitivity of SOM decomposition to temperature changes. N and P additions could affect the stability of SOM in subtropical forests in the future.

Soil organic matter balance as a practical tool for environmental impact assessment and management support in arable farming

Selenium (Se) is an essential micronutrient for animals and humans. In the food chain, the intake of Se by animals and humans depends largely on Se content in plants, whereas the major source of Se in plants lies in the soil. Therefore, understanding Se bioavailability in soils for plant uptake and its controlling factors and mechanisms is important. The objective of this thesis is to study the amount, speciation, bioavailability, plant uptake and fertilization of Se in agricultural soils in the Netherlands and underlying controlling factors and mechanisms, to provide guidance for soil testing and fertilization recommendation for efficient Se management in agriculture. The majority of agricultural soils (grassland and arable land) in the Netherlands contains low total Se (i.e. in the range of Se deficient), which is predominantly present as organic Se. Only a small fraction of total Se is present as inorganic Se (mainly as selenite) and residual Se. In this thesis, the evidences of association between Se and soil organic matter in these low Se soils have been shown. The associations include: (1) the total Se content is positively correlated to soil organic matter content; (2) the solubility and extractability of Se in soils follow the solubility and extractability of soil organic C; (3) the majority of Se present in soils is in organic form, both in the soil solution and solid phase; (4) the distributions of Se and organic C in the different fractions of solid organic matter (i.e. humic acids, hydrophobic organic neutral, hydrophilic acids) and dissolved organic matter (i.e. hydrophilic acids and fulvic acids) are comparable; and (5) the Se richness in solid and dissolved organic matter are related to properties of soil organic matter from different land uses. The relatively high soil organic matter content in these low Se soils is likely responsible for these associations. In general, Se content in crops (e.g. grass and wheat) grown on grassland soils and arable land soils, respectively in the Netherlands is low due to low amount of bioavailable Se in the soils. Different soil parameters determine Se plant uptake in these low Se soils with predominantly organic Se, depending on the properties of Se-containing soil organic matter. The intensity parameter of Se-rich dissolved organic matter (DOM) in soil solution (i.e. Se to DOC ratio in 0.01 M CaCl2 extraction) determines Se plant uptake in soils containing Se-rich organic matter (e.g. potato arable land soils), whereas the buffer capacity of labile organic Se to supply Se-rich DOM in soil solution limits Se plant uptake in soils containing Se-poor organic matter (e.g. grassland soils). Further research is needed to confirm the generality of the conclusion above, because the two experiments were carried out under different conditions (pot experiment and field experiment), using different plant species (wheat and grass) and covering different soil types from different land uses (potato fields and grassland). Site-specific properties in the field in addition to soil parameters included in the current study may largely (> 50%) determine Se content in grass under field conditions, which is in contrast with the results of the pot experiment in which the soil parameter explains 88% of Se content in wheat shoots. In general, the content of Se-rich DOM in soils increases with the increase of soil pH (with the decrease of soil C:N ratio), and the amount of labile organic matter in soils that can resupply Se-rich DOM is determined by the amount of clay (and Fe-(hydr)oxide). NPK fertilization, as one of the external factors, can reduce Se plant uptake, especially in organic-rich soils. Selenium (as selenate) fertilization on grassland with N plus cattle slurry or NPK application shows a positive effect to increase Se content in grass grown on different soil types with a large range of total Se, pH, clay content and organic matter content. Selenium content in grass grown on different soil types upon Se fertilization becomes more similar than before the fertilization. The results indicate that the effectiveness of Se fertilization is only weakly modified by soil properties, probably due to the high solubility of selenate in the soils. Nevertheless, the Se fertilization tends to be slightly more effective on sandy soils than on clay and organic rich soils. This thesis has shown that the content and quality of soil organic matter play an important role in determining the amount, speciation and bioavailability of Se in low Se soils with predominantly organic Se. The results in this thesis can be used as guidance to develop soil testing and fertilization recommendation for efficient Se management, especially in low Se soils with predominantly organic Se, such as in Dutch agricultural soils.

Soil organic matter decomposition and carbon sequestration in temperate coniferous forest soils affected by soluble and insoluble spruce needle fractions