Decomposition Of Labile Organic Matter Research Articles

Mechanism of Carbon Monoxide (CO) Generation and Potential Human Health Hazard during Mechanized Tunnel Driving in Organic-Rich Rocks: Field and Laboratory Study

The monitoring of carbon emissions is increasingly becoming a sustainability issue worldwide. Despite being largely unnoticed, the toxic gas carbon monoxide (CO) is ubiquitous in mechanized tunnel driving, but the individual sources, release and enrichment mechanisms are often unknown. In this study, the generation of CO from organic matter containing sedimentary rocks was investigated during mechanized tunnel driving and by reacting claystone and sandstone with 10 mM NaCl solutions for 2 months at 70 °C and 140 °C. The mineralogical and geochemical evolution of the solids and fluids was assessed by CO measurements and the XRD, DTA, TOC, IC and ICP-OES methods. The CO concentration in the atmosphere reached up to 1920 ppm (100 ppm on average) during tunnel driving, which is more than three times higher than the legal daily average dose for tunnellers, thus requiring occupational safety operations. Mineral-specific dissolution processes and the rapid decomposition of labile organic matter upon thermal alteration contributed to the liberation of CO and also carbon dioxide (CO2) from the host rocks. In mechanized tunnel driving, frictional heat and ‘cold’ combustion with temperatures reaching 50–70 °C at the drill head is an important mechanism for increased CO and CO2 generation, especially during drilling in sedimentary rocks containing significant amounts of OM and when the ventilation of the tunnel atmosphere and air mixing are limited. Under such conditions, human health damage due to CO exposure (HHDCO) can be 30 times higher compared to tunnel outlets, where CO is emitted from traffic.

Paleoenvironmental Conditions and Factors Controlling Organic Carbon Accumulation during the Jurassic–Early Cretaceous, Egypt: Organic and Inorganic Geochemical Approach

The Jurassic–Early Cretaceous was a time of variable organic carbon burial associated with fluctuations of marine primary productivity, weathering intensity, and redox conditions in the pore and bottom water at paleo-shelf areas in north Egypt. This time interval characterized the deposition of, from old to young, the Bahrein, Khatatba, Masajid, and Alam El Bueib Formations in the north Western Desert. Although several studies have been devoted to the excellent source rock units, such as the Khatatba and Alam El Bueib Formations, studies on paleoenvironmental changes in redox conditions, paleoproductivity, and continental weathering and their impact on organic carbon exports and their preservation for this interval are lacking. This study presents organic and inorganic geochemical data for the Jurassic–Lower Cretaceous sediments from the Almaz-1 well in the Shushan Basin, north Western Desert. A total of 32 cuttings samples were analyzed for their major and trace elements, carbonates, and total organic carbon (TOC) contents. Data allowed the reconstruction of paleoenvironmental conditions in the southern Tethys Ocean and assessment of the changes in paleo-redox, paleo-weathering, and marine primary productivity, and the role of sediment supply. Additionally, factors that governed the accumulation of organic matter in the sediment were interpreted. Results showed that the Khatatba Formation was deposited during a phase of enhanced marine primary productivity under prevalent anoxia, which triggered enhanced organic matter production and preservation. During the deposition of the Khatatba Formation, significant terrigenous sediment supply and continental weathering were followed by a limited contribution of coarse clastic sediment fluxes due to weak continental weathering and enhanced carbonate production. The Bahrein, Masajid, and Alam El Bueib Formations were deposited during low marine primary productivity and prevalent oxygenation conditions that led to poor organic matter production and preservation, respectively. A strong terrigenous sediment supply and continental weathering predominated during the deposition of the Bahrein Formation and the lower part of the Alam El Bueib Formation compared to the limited coarse clastic supply and continental weathering during the deposition of the carbonate Masajid Formation and the upper part of the Alam El Bueib Formation. Such conditions resulted in the enhanced dilution and decomposition of labile organic matter, and, thus, organic carbon-lean accumulation in these sediments.

Soil greenhouse gas fluxes from tropical vegetable farms, using forest as a reference

Field-based quantification of soil greenhouse gas emissions from the Philippines’ agriculture sector is missing for vegetable production systems, despite its substantial contribution to agricultural production. We quantified soil N2O emission, CH4 uptake, and CO2 efflux in vegetable farms and compared these to the secondary forest. Measurements were conducted for 13 months in 10 smallholder farms and nine forest plots on Andosol soil in Leyte, Philippines using static chambers. Soil N2O and CO2 emissions were higher, whereas CH4 uptake was lower in the vegetable farms than in the forest. Vegetable farms had annual fluxes of 12.7 ± 2.6 kg N2O-N ha−1 yr−1, −1.1 ± 0.2 kg CH4-C ha−1 yr−1, and 11.7 ± 0.7 Mg CO2-C ha−1 yr−1, whereas the forest had 0.10 ± 0.02 kg N2O-N ha ha−1 yr−1, −2.0 ± 0.2 kg CH4-C ha−1 yr−1, and 8.2 ± 0.7 Mg CO2-C ha−1 yr−1. Long-term high N fertilization rates in vegetable farms resulted in large soil mineral N levels, dominated by NO3– in the topsoil and down to 1-m depth, leading to high soil N2O emissions. Increased soil bulk density in the vegetable farms probably increased anaerobic microsites during the wet season and reduced CH4 diffusion from the atmosphere into the soil, resulting in decreased soil CH4 uptake. High soil CO2 emissions from the vegetable farms suggested decomposition of labile organic matter, possibly facilitated by plowing and large N fertilization rates. The global warming potential of these vegetable farms was 31 ± 2.7 Mg CO2-eq ha−1 yr−1 (100-year time frame).

The effect of chemical structure on hydrolysis pathways of small peptides in coastal seawater

The hydrolysis pathway of a given peptide or protein in seawater, or how it is hydrolyzed by extracellular enzymes, may depend on its chemical structure or specific amino acid composition. This knowledge is important for a better understanding of the first steps on decomposition of labile organic matter that is often dominated by proteins. The hydrolysis pathway can be estimated from the hydrolyzed fragments of small peptides through incubation experiments. Here we incubated a group of small peptides with different amino acid compositions in coastal seawater, including tetrapeptides alanine-valine-phenylalanine-alanine (AVFA) and its modifications of the N terminal A with valine (V), serine (S), arginine (R) and aspartic acid (D) (i.e., peptides VVFA, SVFA, RVFA, DVFA). Through these incubations, we evaluated the effect of chemical structure or specific amino acid composition on peptide hydrolysis pathways and the roles of different types of peptidases. Our results showed that aminopeptidases preferentially hydrolyzed tetrapeptides with N terminal A and R (29–100% of the total peptidases), followed by V (30–90%) and S (20–51%), but were ineffective with acidic amino acid D (0–14%). This pattern indicates that the N-terminal amino acid affects how a peptide is hydrolyzed in a given environment. For N-terminal amino acids with uncharged side chains, aminopeptidases preferred hydrophobic A, V to polar uncharged S, and for those with charged side chains, they preferred positively-charged R to negatively-charged D. Our results also suggest that if aminopeptidases could not access the N-terminal amino acid of a peptide, carboxypeptidases and/or endopeptidases will hydrolyze it, leading to similar peptide hydrolysis rates among different peptides although their hydrolysis pathways may differ. The effect of amino acid composition on peptide hydrolysis pathways is further demonstrated by comparing trialanine (AAA), AVF, AVFA, VFA, phenylalanine-alanine-serine-tryptophan-glycine-alanine (FASWGA) and SWGA. Overall, results from this study show that the chemical structure of a peptide affects its hydrolysis pathway in coastal seawater, and shed new lights on the early steps of organic nitrogen degradation and further nitrogen cycling in marine environments.

Influence of water discharged from a reservoir on reclaimed land into Isahaya Bay (Kyushu, Japan) on the regeneration of NH4+ in the water column

In 1997, the inner part of Isahaya Bay on the west coast of Ariake Bay, western Japan, was separated from the sea by dikes, leading to the formation of a freshwater reservoir. Since the Isahaya Reclamation Project began in the 1990s, red tides and hypoxia have become more common in the bay. Eutrophic high-turbidity water from the reservoir is frequently discharged into the bay, so NH4+ regenerated from organic matter in the discharge may be a source of nutrients for the red tides. In this work, we mixed reservoir water and seawater from the bay in experiments aimed at quantifying the NH4+ regeneration caused by the direct decomposition of labile organic matter in the high-turbidity drainage water. By comparing the results of field monitoring and mixing experiments, we estimated that the NH4+ regeneration rate under the influence of the drainage water was 192–501 μmol m−2 h−1, which was 31.5–46.8% higher than the natural NH4+ regeneration rate. This suggests that the additional NH4+ regeneration induced by the drainage water is non-negligible and that the organic matter in the drainage water may be an important source of NH4+ for red tides in the bay. This is the first study to provide data on the non-negligible amount of NH4+ regenerated upon the direct decomposition of labile organic matter in high-turbidity water drained from a reservoir on reclaimed land into the bay.

Nutrient input influences fungal community composition and size and can stimulate manganese (II) oxidation in caves.

Little is known about the fungal role in biogeochemical cycling in oligotrophic ecosystems. This study compared fungal communities and assessed the role of exogenous carbon on microbial community structure and function in two southern Appalachian caves: an anthropogenically impacted cave and a near-pristine cave. Due to carbon input from shallow soils, the anthropogenically impacted cave had an order of magnitude greater fungal and bacterial quantitative-polymerase chain reaction (qPCR) gene copy numbers, had significantly greater community diversity, and was dominated by ascomycotal phylotypes common in early phase, labile organic matter decomposition. Fungal assemblages in the near-pristine cave samples were dominated by Basidiomycota typically found in deeper soils (and/or in late phase, recalcitrant organic matter decomposition), suggesting more oligotrophic conditions. In situ carbon and manganese (II) [Mn(II)] addition over 10 weeks resulted in growth of fungal mycelia followed by increased Mn(II) oxidation. A before/after comparison of the fungal communities indicated that this enrichment increased the quantity of fungal and bacterial cells, yet decreased overall fungal diversity. Anthropogenic carbon sources can therefore dramatically influence the diversity and quantity of fungi, impact microbial community function, and stimulate Mn(II) oxidation, resulting in a cascade of changes that can strongly influence nutrient and trace element biogeochemical cycles in karst aquifers.

Plant species richness leaves a legacy of enhanced root litter-induced decomposition in soil

Increasing plant species richness generally enhances plant biomass production, which may enhance accumulation of carbon (C) in soil. However, the net change in soil C also depends on the effect of plant diversity on C loss through decomposition of organic matter. Plant diversity can affect organic matter decomposition via changes in litter species diversity and composition, and via alteration of abiotic and/or biotic attributes of the soil (soil legacy effect). Previous studies examined the two effects on decomposition rates separately, and do therefore not elucidate the relative importance of the two effects, and their potential interaction. Here we separated the effects of litter mixing and litter identity from the soil legacy effect by conducting a factorial laboratory experiment where two fresh single root litters and their mixture were mixed with soils previously cultivated with single plant species or mixtures of two or four species. We found no evidence for litter-mixing effects. In contrast, root litter-induced CO2 production was greater in soils from high diversity plots than in soils from monocultures, regardless of the type of root litter added. Soil microbial PLFA biomass and composition at the onset of the experiment was unaffected by plant species richness, whereas soil potential nitrogen (N) mineralization rate increased with plant species richness. Our results indicate that the soil legacy effect may be explained by changes in soil N availability. There was no effect of plant species richness on decomposition of a recalcitrant substrate (compost). This suggests that the soil legacy effect predominantly acted on the decomposition of labile organic matter. We thus demonstrated that plant species richness enhances root litter-induced soil respiration via a soil legacy effect but not via a litter-mixing effect. This implies that the positive impacts of species richness on soil C sequestration may be weakened by accelerated organic matter decomposition.

Profiling Rhizosphere Chemistry: Evidence from Carbon and Nitrogen K‐Edge XANES and Pyrolysis‐FIMS

The rhizosphere is a region of complex interactions among plants, soil, and microbiota and by its very nature, it presents many technical challenges to the analyst. Whereas previous studies have generally focused on root exudation in artificial systems, we compared whole‐soil samples from bulk and rhizosphere soils developed under field pea (Pisum sativa L.). Synchrotron‐based C and N K‐edge x‐ray absorption near‐edge structure (XANES) spectroscopy and pyrolysis field‐ionization mass‐spectrometry (Py‐FIMS) were used to investigate plant effects on the organic chemistry of the rhizosphere in a growth chamber experiment. Soil type appeared to play a significant role in the development of the rhizosphere. Indeed, the C and N K‐edge XANES analyses revealed patterns of rhizosphere development that were strongly influenced by soil type. Relative to the bulk soil, pea rhizospheres developed on a clay soil showed increases in heterocyclic N compounds, proteins, and carboxylates. Pea rhizospheres developed on a sandy clay loam soil showed increased nitroaromatic compounds and reduced aromatics, while proteins, carbohydrates, and carboxylic compounds remained unchanged relative to the bulk soils. Pyrolysis mass spectrometry results showed that rhizosphere processes promote selective enrichment of lipid compounds (alkanes, alkenes, alkylamides, alkylaromatics, and alkyl, benzoic, and phthalic esters) with a concomitant depletion of carbohydrates, proteins, phenols, and lignins. These results suggest enhanced decomposition of labile organic matter at a molecular level in the rhizosphere, presumably as a result of enhanced microbial activity. The presence of nitroaromatic and alkylamide compounds in the rhizosphere indicates a unique cycling of N in this region. Synchrotron‐based analysis of whole soils offers useful, corroborating information regarding the organic chemistry of the rhizosphere when compared with established pyrolytic techniques.

Characterization of solid and aqueous phases of a peat bog profile using molecular fluorescence spectroscopy, ESR and FT-IR, and comparison with physical properties

A peat core (10×10×100 cm) was removed from Etang de la Gruère, an ombrotrophic peat bog in the Jura Mountains of Switzerland. The core was sliced into 3 cm sections and the samples characterized with respect to ash content, bulk density, moisture content, and concentrations of C and H. Solid peat residues were freeze-dried, milled very finely and analyzed using Fourier transform infrared (FT-IR) and electron spin resonance (ESR) spectroscopy. Pore waters expressed from the peat slices were collected, filtered (0.2 μm membrane filters) and analyzed using fluorescence emission, excitation and synchronous-scan spectroscopy, in addition to pH. Taken together, the physical properties of the core and the ESR measurements of solid peats appear to record the variation in humification of refractory organic matter (peat). The fluorescence and FT-IR data, on the other hand, appear to characterize the extent of recent decomposition of labile organic matter. In fact, these data indicate the presence of two distinct zones in the bog: (i) the acrotelm, or zone of active decay, which may be oxygenated, depending on the season and the depth to the water table, and (ii) the catotelm which is always anoxic, and where organic matter decomposition rates are negligible.

A simulation model of organic matter and nutrient accumulation in mangrove wetland soils

The distribution and accumulation of organic matter, nitrogen (N) and phosphorus (P) in mangrove soils at four sites along the Shark River estuary of south Florida were investigated with empirical measures and a process-based model. The mangrove nutrient model (NUMAN) was developed from the SEMIDEC marsh organic matter model and parameterized with data from mangrove wetlands. The soil characteristics in the four mangrove sites varied greatly in both concentrations and profiles of soil carbon, N and P. Organic matter decreased from 82% in the upstream locations to 30% in the marine sites. Comparisons of simulated and observed results demonstrated that landscape gradients of soil characteristics along the estuary can be adequately modeled by accounting for plant production, litter decomposition and export, and allochthonous input of mineral sediments. Model sensitivity analyses suggest that root production has a more significant effect on soil composition than litter fall. Model simulations showed that the greatest change in organic matter, N, and P occurred from the soil surface to 5 cm depth. The rapid decomposition of labile organic matter was responsible for this decrease in organic matter. Simulated N mineralization rates decreased quickly with depth, which corresponded with the decrease of labile organic matter. The increase in organic matter content and decrease in soil bulk density from mangrove sites at downstream locations compared to those at upstream locations was controlled mainly by variation in allochthonous inputs of mineral matter at the mouth of the estuary, along with gradients in mangrove root production. Research on allochthonouns sediment input and in situ root production of mangroves is limited compared to their significance to understanding nutrient biogeochemistry of these wetlands. More accurate simulations of temporal patterns of nutrient characteristics with depth will depend on including the effects of disturbance such as hurricanes on sediment redistribution and biomass production.

The influence of humic substances on the geochemistry of iodine in nearshore and hemipelagic marine sediments

Iodine is characteristically enriched at the surface of hemipelagic and nearshore sediments deposited under oxygenated conditions. In such sediments, bulk I/C org ratios usually decrease with depth to values which are characteristic of anoxic sediments, reflecting a preferential release of I during early diagenesis. There is some debate as to whether sedimentary I is associated with the iron oxyhydroxide phase or with the organic fraction, and whether the decrease in I/C org with depth is due to the dissolution of the iron oxyhydroxides or the decomposition of labile organic matter. It is shown that in a surficial hemipelagic sediment sample and in a nearshore sediment core I is mainly associated with the organic fraction and, moreover, that humic substances are involved in the surficial iodine enrichment. Laboratory experiments on the uptake and release of I by and from sedimentary humic substances also suggest a mechanism whereby humic materials reduce iodate at the sediment/water interface to an electrophilic I species which further reacts with the organic matter to produce iodinated organic molecules. During burial, this excess I could be displaced from the organic matrix by nucleophiles such as sulphide ions or thiosulphate, thus providing a possible explanation for the decrease in I/C org ratio with depth observed in many nearshore and hemipelagic sediments.