Anoxic Soil Research Articles

DNA-based stable isotope probing identifies formate-metabolizing methanogenic archaea in paddy soil

Paddy methane (CH4) production is biologically dominated by methanogenic archaea that metabolize a variety of organic and/or inorganic carbon sources. Though formate is easily dissimilated into H2/CO2, formate-metabolizing methanogenic archaea are distinct from CO2-utilizing methanogen taxa. The identity of formate-metabolizing methanogenic archaea in paddy soil remains elusive. In this investigation, molecular approaches based on stable isotope probing (SIP) technique were conducted to identify the formate-metabolizing methanogenic archaea in paddy soil. CH4 emission monitor, real-time quantitative PCR (qPCR) and Denaturing Gradient Gel Electrophoresis (DGGE) analyses consistently indicated that some methanogenic archaea metabolized 13C-labeled formate in microcosm and accounted for a large portion of formate-metabolizing archaea in anoxic paddy soil. Phylogenetic identification further found that this guild was affiliated to Methanobacteriaceae. Taken together Methanobacteriaceae could be the dominant formate-metabolizing methanogenic archaea and play an important role in the CH4 production in paddy soil. These findings would extend the extant knowledge on paddy methanogenic archaea and microbial-driven paddy CH4 emission.

Nitrous oxide production and mRNA expression analysis of nitrifying and denitrifying bacterial genes under floodwater disappearance and fertilizer application.

A pulse of nitrous oxide (N2O) emission has been observed following the disappearance of floodwater by drainage. However, its mechanism is not well understood. We conducted a column study to clarify the mechanism for N2O production during floodwater disappearance by using a microsensor and determining the bacterial gene expression. An increase in N2O flux was observed following floodwater disappearance after the addition of NH4+, with a corresponding increase in the concentrations of NO3- and dissolved N2O in the oxic and anoxic soil layers, respectively. The transcription level of the bacterial amoA mRNA did not change, while that of nirK mRNA increased sharply after an hour of floodwater disappearance. An additional anoxic soil slurry experiment demonstrated that the addition of NO3- induced the expression of nirK gene and caused a concomitant increase in N2O production. These findings suggest that NO3- production in the oxic layers is important as it provides a substrate and induces the synthesis of denitrification enzymes in the anoxic layer during N2O production.

Aging and arsenite loading control arsenic mobility from ferrihydrite-arsenite coprecipitates

Iron (oxyhydr)oxides may act as a sink and source of arsenic (As) in terrestrial and aquatic systems, therefore studying the mechanisms controlling Fe (oxyhydr)oxide transformation under changing environmental conditions is essential for elucidating the fate of As, in terms of release, mobility and speciation. We provide evidence that aging and As(III) loading control the mineralogical and structural evolution of As(III)-bearing Fe (oxyhydr)oxides, and thus influence the extraction of As with compounds which frequently occur in soil solution. During a one year timeframe, partial As(III) oxidation to As(V) and accumulation on poorly crystalline Fe (oxyhydr)oxides were promoted by increasing As(III) contents, which hindered the transformation of less into more crystalline materials. The changes in crystallinity degree and surface properties resulted in the release of different proportions of As(III) and As(V) from the aged compared to the fresh coprecipitates. The extraction of both As species through mechanisms of competition, disaggregation of Fe (oxyhydr)oxides, or both was assessed by employing several anions, whose efficiency decreased in the order: inorganic phosphate> citrate> organic phosphate> chloride≥silicate. The tested extractants are key components of environments such as aquifers, waterlogged soils or the rhizosphere of paddy soils, where aqueous As(III) is mobilized from the anoxic soil layers and sequestered by Fe (oxyhydr)oxides under more oxidizing environments.

Influence of iron redox cycling on organo-mineral associations in Arctic tundra soil

Arctic tundra stores large quantities of soil organic matter under varying redox conditions. As the climate warms, these carbon reservoirs are susceptible to increased rates of decomposition and release to the atmosphere as the greenhouse gases carbon dioxide (CO2) and methane (CH4). Geochemical interactions between soil organic matter and minerals influence decomposition in many environments but remain poorly understood in Arctic tundra systems and are not considered in decomposition models. The accumulation of iron (Fe) oxyhydroxides and organo-iron precipitates at redox interfaces may be particularly important for carbon cycling given that ferric iron [Fe(III)] species can enhance decomposition by serving as terminal electron acceptors in anoxic soils or inhibit microbial decomposition by binding organic molecules. Here, we examine chemical properties of solid-phase Fe and organic matter in organic and mineral horizons within the seasonally thawed active layer of Arctic tundra on the North Slope of Alaska. Spectroscopic techniques, including micro-X-ray fluorescence (μXRF) mapping, micro-X-ray absorption near-edge structure (μXANES) spectroscopy, and Fourier transform infrared spectroscopy (FTIR), were coupled with chemical sequential extractions and physical density fractionations to evaluate the spatial distribution and speciation of Fe-bearing phases and associated organic matter in soils.Organic horizons were enriched in poorly crystalline and crystalline iron oxides, and approximately 60% of total Fe stored in organic horizons was calculated to derive from upward translocation from anoxic mineral horizons. Ferrihydrite and goethite were present as coatings on mineral grains and plant debris, and in aggregates with clays and particulate organic matter. Minor amounts of ferrous iron [Fe(II)] were present in iron sulfides (i.e., pyrite and greigite) in mineral horizon soils and iron phosphates (vivianite) in organic horizons. Concentrations of organic carbon in the organic horizons (28±5wt.% C) were approximately twice the concentrations in the mineral horizons (14±2wt.% C), and organic matter was dominated by base-extractable and insoluble organics enriched in aromatic and aliphatic moieties. Conversely, water-soluble organic molecules and organics solubilized through acid-dissolution of iron oxides comprised <2% of soil organic C and were consistent with a mixture of alcohols, sugars, and small molecular weight organic acids and aromatics released through decomposition of larger molecules. Integrated over the entire depth of the active layer, soils contained 11±4kgm−2 low-density, particulate organic C and 19±6kgm−2 high-density, mineral-associated organic C, indicating that 63±19% of organic C in the active layer was associated with the mineral fraction.We conclude that organic horizons were enriched in poorly crystalline and crystalline iron oxide phases derived from upward translocation of dissolved Fe(II) and Fe(III) from mineral horizons. Precipitation of iron oxides at the redox interface has the potential to contribute to mineral protection of organic matter and increase the residence time of organic carbon in arctic soils. Our results suggest that iron oxides may inhibit organic carbon degradation by binding low-molecular-weight organic compounds, stabilizing soil aggregates, and forming thick coatings around particulate organic matter. Organic matter released through acid-dissolution of iron oxides could represent a small pool of readily-degradable organic molecules temporarily stabilized by sorption to iron oxyhydroxide surfaces. The distribution of iron in organic complexes and inorganic phases throughout the soil column constrains Fe(III) availability to anaerobic iron-reducing microorganisms that oxidize organic matter to produce CO2 and CH4 in these anoxic environments. Future predictions of carbon storage and respiration in the arctic tundra should consider such influences of mineral stabilization under changing redox conditions.

Changes and relations of photosynthesis and iron cycling in anoxic paddy soil amended with high concentrations of sulfate.

Sulfate contamination is an increasingly serious environmental problem related to microbial reduction processes in anoxic paddy soil. This study revealed the changes and interrelations of ferric iron [Fe(III)] reduction, ferrous iron [Fe(II)] oxidation, and oxygenic photosynthesis in an anoxic paddy soil (Fe-accumuli-Stagnic Anthrosols) amended with a range of high sulfate concentrations. Soil slurries mixed with 0 (control), 50, 100, 200, and 400mmolkg-1 Na2SO4 were incubated anaerobically under dark and light conditions. The changes in chlorophyll a (Chl a), Fe(II), pH levels, and the chlorophyll absorption spectrum were determined over a 42-day period. Fe(II) concentrations increased with the addition of sulfate under dark conditions, while Fe(III) reduction potential was enhanced by increasing sulfate addition. The effect of light on Fe(II) concentration was observed after 16days of incubation, when Fe(II) started to decrease markedly in the control. The decrease in Fe(II) slowed with increasing sulfate addition. The concentrations of Chl a increased in all treatments after 16days of incubation under light conditions. There was a reduction in Chl a accumulation with increasing sulfate at the same incubation time. The absorption peaks of chlorophyll remained shorter than the 700-nm wavelength throughout the incubation period. The pH of all treatments decreased in the first week and then increased thereafter. The pH increased with sulfate addition and light conditions. In conclusion, contamination with high concentrations of sulfate could accelerate Fe(III) reduction while inhibiting oxygenic photosynthesis, which correspondingly slows chemical Fe(II) oxidation in an anoxic paddy soil.

Elemental affinity for siderite found in a Japanese paddy subsoil

ABSTRACTSiderite (FeCO3), a type of carbonate mineral, is very occasionally recognized as a nodule in anoxic soils and sediments. During siderite formation, elements are expected to be accumulated or excluded between siderite and bulk soil. Therefore, we verified the affinity of 40 elements for siderite found in the gley horizon of a smectite-rich paddy field in northeastern Japan from the elemental concentration of the soil and the siderite dissolved in 2.88 mol L−1 hydrochloric acid (10% HCl). The concentration ratio of the target element of the soil to the siderite was expressed by the product of the dimensionless R0 value and ratio of titanium (Ti) concentration of the soil to the siderite (Csiderite /Csoil) = R0 (Tisiderite /Tisoil). The affinity of each element for the siderite was analyzed by comparing the R0 values. In comparison with Ti used as the reference element, P, Cr, Co and Mo were accumulated (R0 > 1.0), and alkali metals, such as Li, Na and K, and chalcophile elements, such as Cu, Zn, Cd and Pb, tended to be equal or excluded from the siderite (R0 ≦1.0). Of the group 2 elements, Ca, Sr and Ba were accumulated, while Mg was excluded. The affinity of Mn for siderite exceeded that of Fe as the main component of the siderite, which reflects the fact that siderite was formed in a fresh water condition. The siderite size did not influence the elemental affinity. Observation of micromorphology using a scanning electron microscope showed that the siderite nodules were aggregations of siderite particles and clays, suggesting that the siderite grew by taking in clay around it. The rare earth element (REE) distribution pattern showed a tendency not to increase linearly but to increase with forming a concave curve at the intervals of the four elements with the increase of atomic number (i.e. tetrad effects). Although these findings are from the lower horizons of anoxic soils, the elemental affinity for siderite of this study is useful in order to elucidate the complex elemental dynamics in the anoxic environment.

Thailand’s catastrophic flood: Bangkok tree mortality as a function of taxa, habitat, and tree size

Urban areas have unique environments such as high air temperature, soil compaction and disturbance, and air and water pollution often impose plant stresses. Natural disasters can impose even greater stresses on plants in such areas. In 2011 Bangkok, Thailand experienced its worst flooding in over two decades, inundated up to a meter for a month. Here we report on tree tolerance to submerged, anoxic soils based on mortality. We identified over 6500 trees by taxa: 395 species in 219 genera within 60 families, which were categorized into three groups: susceptible (>50% mortality), tolerant (<50% mortality), and highly tolerant (no mortality). Among all the species, 18% were categorized as flood susceptible, 75% as tolerant, and 7% as highly tolerant. The floods resulted in decreased overall species richness by 18%, particularly in the Magnoliaceae and Lauraceae families, for which the mortality was 100% and 66%, respectively. Flood susceptible species were mostly from high rainfall habitats such as the hill evergreen forest. As expected, highly flood tolerant species were from the mangrove forests, beach/strand forests, and swamp plant communities, where the root zones are persistently saturated with lower quality water. Unexpectedly, many species native to higher temperature, drier, often deciduous lowland habitats were found to be flood tolerant, and were from the cultivated fruit and ornamental species. The results also indicated that smaller and younger trees suffered more mortality than larger and more mature trees. Therefore, during the tree selection process for planting in urban environments that may be at risk of frequent flooding, species from a wide spectrum of ecological habitats should be considered; particularly those characterized by one or more environmental stresses, such as drought, salt, heat, or saturated soils.

Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis

Purpose Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (13C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011).

Plants, microorganisms, and soil temperatures contribute to a decrease in methane fluxes on a drained Arctic floodplain.

As surface temperatures are expected to rise in the future, ice-rich permafrost may thaw, altering soil topography and hydrology and creating a mosaic of wet and dry soil surfaces in the Arctic. Arctic wetlands are large sources of CH4 , and investigating effects of soil hydrology on CH4 fluxes is of great importance for predicting ecosystem feedback in response to climate change. In this study, we investigate how a decade-long drying manipulation on an Arctic floodplain influences CH4 -associated microorganisms, soil thermal regimes, and plant communities. Moreover, we examine how these drainage-induced changes may then modify CH4 fluxes in the growing and nongrowing seasons. This study shows that drainage substantially lowered the abundance of methanogens along with methanotrophic bacteria, which may have reduced CH4 cycling. Soil temperatures of the drained areas were lower in deep, anoxic soil layers (below 30cm), but higher in oxic topsoil layers (0-15cm) compared to the control wet areas. This pattern of soil temperatures may have reduced the rates of methanogenesis while elevating those of CH4 oxidation, thereby decreasing net CH4 fluxes. The abundance of Eriophorum angustifolium, an aerenchymatous plant species, diminished significantly in the drained areas. Due to this decrease, a higher fraction of CH4 was alternatively emitted to the atmosphere by diffusion, possibly increasing the potential for CH4 oxidation and leading to a decrease in net CH4 fluxes compared to a control site. Drainage lowered CH4 fluxes by a factor of 20 during the growing season, with postdrainage changes in microbial communities, soil temperatures, and plant communities also contributing to this reduction. In contrast, we observed CH4 emissions increased by 10% in the drained areas during the nongrowing season, although this difference was insignificant given the small magnitudes of fluxes. This study showed that long-term drainage considerably reduced CH4 fluxes through modified ecosystem properties.

Are global mangrove carbon stocks driven by rainfall?

AbstractMangrove forests produce significant amounts of organic carbon and maintain large carbon stocks in tidally inundated, anoxic soils. This work analyzes new and published data from 17 regions spanning a latitudinal gradient from 22°N to 38°S to assess some of the global drivers (temperature, tidal range, latitude, and rainfall) of mangrove carbon stocks. Mangrove forests from the tropics have larger carbon stocks (895 ± 90 t C ha−1) than the subtropics and temperate regions (547 ± 66 t C ha−1). A multiple regression model showed that 86% of the observed variability is associated with annual rainfall, which is the best predictor of mangrove ecosystem carbon stocks. Therefore, a predicted increase in rainfall along the tropical Indo‐Pacific may increase mangrove forest carbon stocks. However, there are other potentially important factors that may regulate organic matter diagenesis, such as nutrient availability and pore water salinity. Our predictive model shows that if mangrove deforestation is halted, global mangrove forest carbon stocks could increase by almost 10% by 2115 as a result of increased rainfall in the tropics.

Interactions Between Fe(III)-oxides and Fe(III)-phyllosilicates During Microbial Reduction 2: Natural Subsurface Sediments

ABSTRACTDissimilatory microbial reduction of solid-phase Fe(III)-oxides and Fe(III)-bearing phyllosilicates (Fe(III)-phyllosilicates) is an important process in anoxic soils, sediments and subsurface materials. Although various studies have documented the relative extent of microbial reduction of single-phase Fe(III)-oxides and Fe(III)-phyllosilicates, detailed information is not available on interaction between these two processes in situations where both phases are available for microbial reduction. The goal of this research was to use the model dissimilatory iron-reducing bacterium (DIRB) Geobacter sulfurreducens to study Fe(III)-oxide vs. Fe(III)-phyllosilicate reduction in a range of subsurface materials and Fe(III)-oxide stripped versions of the materials. Low-temperature (12 K) Mossbauer spectroscopy was used to infer changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) (Fe(II) phyllosilicate). A Fe partitioning model was employed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicates. The results showed that in most cases Fe(III)-oxide utilization dominated (70–100%) bulk Fe(III) reduction activity, and that electron transfer from oxide-derived Fe(II) played only a minor role (ca. 10–20%) in Fe partitioning. In addition, the extent of Fe(III)-oxide reduction was positively correlated to surface area-normalized cation exchange capacity and the Fe(III)-phyllosilicate/total Fe(III) ratio. This finding suggests that the phyllosilicates in the natural sediments promoted Fe(III)-oxide reduction by binding of oxide-derived Fe(II), thereby enhancing Fe(III)-oxide reduction by reducing or delaying the inhibitory effect that Fe(II) accumulation on oxide and DIRB cell surfaces has on Fe(III)-oxide reduction. In general our results suggest that although Fe(III)-oxide reduction is likely to dominate bulk Fe(III) reduction in most subsurface sediments, Fe(II) binding by phyllosilicates is likely to play a key role in controlling the long-term kinetics of Fe(III) oxide reduction

Water management impacts rice methylmercury and the soil microbiome

Rice farmers are pressured to grow rice using less water. The impacts of water-saving rice cultivation methods on rice methylmercury concentrations are uncertain. Rice (Oryza sativa L. cv. Nipponbare) was cultivated in fields using four water management treatments, including flooded (no dry-downs), alternating wetting and drying (AWD) (with one or three dry-downs), and furrow-irrigated fields (nine dry-downs) (n=16 fields). Anoxic bulk soil was collected from rice roots during the rice maturation phase, and rice grain was harvested after fields were dried. Total mercury and methylmercury concentrations were determined in soil and polished rice samples, and the soil microbiome was analyzed using 16S (v4) rRNA gene profiling. Soil total mercury did not differ between fields. However, compared to continuously flooded fields, soil and rice methylmercury concentrations averaged 51% and 38% lower in the AWD fields, respectively, and 95% and 96% lower in the furrow-irrigated fields, respectively. Compared to flooded fields, grain yield was reduced on average by <1% in the AWD fields and 34% in the furrow-irrigated fields. Additionally, using 16S (v4) rRNA gene profiling, the relative abundance of genera (i.e., highest resolution via this method) known to contain mercury methylators averaged 2.9-fold higher in flooded and AWD fields compared to furrow-irrigated fields. These results reinforce the benefits of AWD in reducing rice methylmercury concentrations with minimal changes in rice production yields. In the furrow-irrigated fields, a lower relative abundance of genera known to contain mercury methylators suggests an association between lower concentrations of soil and rice methylmercury and specific soil microbiomes.

Solid-solution partitioning and thionation of diphenylarsinic acid in a flooded soil under the impact of sulfate and iron reduction

Diphenylarsinic acid (DPAA) is a major organic arsenic (As) compound derived from abandoned chemical weapons. The solid-solution partitioning and transformation of DPAA in flooded soils are poorly understood but are of great concern. The identification of the mechanisms responsible for the mobilization and transformation of DPAA may help to develop effective remediation strategies. Here, soil and Fe mineral incubation experiments were carried out to elucidate the partitioning and transformation of DPAA in anoxic (without addition of sulfate or sodium lactate) and sulfide (with the addition of sulfate and sodium lactate) soil and to examine the impact of sulfate and Fe(III) reduction on these processes. Results show that DPAA was more effectively mobilized and thionated in sulfide soil than in anoxic soil. At the initial incubation stages (0–4weeks), 6.7–74.5% of the total DPAA in sulfide soil was mobilized likely by sorption competition with sodium lactate. At later incubation stage (4–8weeks), DPAA was almost completely released into the solution likely due to the near-complete Fe(III) reduction. Scanning transmission X-ray microscopy (STXM) results provide further direct evidence of elevated DPAA release coupled with Fe(III) reduction in sulfide environments. The total DPAA fraction decreased significantly to 24.5% after two weeks and reached 3.4% after eight weeks in sulfide soil, whereas no obvious elimination of DPAA occurred in anoxic soil at the initial two weeks and the total DPAA fraction decreased to 10.9% after eight weeks. This can be explained in part by the enhanced mobilization of DPAA and sulfate reduction in sulfide soil compared with anoxic soil. These results suggest that under flooded soil conditions, Fe(III) and sulfate reduction significantly promote DPAA mobilization and thionation, respectively, and we suggest that it is essential to consider both sulfate and Fe(III) reduction to further our understanding of the environmental fate of DPAA.

Interactions Between Fe(III)-Oxides and Fe(III)-Phyllosilicates During Microbial Reduction 1: Synthetic Sediments

ABSTRACTFe(III)-oxides and Fe(III)-bearing phyllosilicates are the two major iron sources utilized as electron acceptors by dissimilatory iron-reducing bacteria (DIRB) in anoxic soils and sediments. Although there have been many studies on microbial Fe(III)-oxide and Fe(III)-phyllosilicate reduction with both natural and specimen materials, no controlled experimental information is available on the interaction between these two phases when both are available for microbial reduction. In this study, the model DIRB Geobacter sulfurreducens was used to examine the pathways of Fe(III) reduction in Fe(III)-oxide stripped subsurface sediment that was coated with different amounts of synthetic high surface area (HSA) goethite. Cryogenic (12K) 57Fe Mössbauer spectroscopy was used to determine changes in the relative abundances of Fe(III)-oxide, Fe(III)-phyllosilicate, and phyllosilicate-associated Fe(II) [Fe(II)-phyllosilicate] in bioreduced samples. Analogous Mössbauer analyses were performed on samples from abiotic Fe(II) sorption experiments in which sediments were exposed to a quantity of exogenous soluble Fe(II) (FeCl2⋅2H2O) comparable to the amount of Fe(II) produced during microbial reduction. A Fe partitioning model was developed to analyze the fate of Fe(II) and assess the potential for abiotic Fe(II)-catalyzed reduction of Fe(III)-phyllosilicates. The microbial reduction experiments indicated that although reduction of Fe(III)-oxide accounted for virtually all of the observed bulk Fe(III) reduction activity, there was no significant abiotic electron transfer between oxide-derived Fe(II) and Fe(III)-phyllosilicatesilicates, with 26–87% of biogenic Fe(II) appearing as sorbed Fe(II) in the Fe(II)-phyllosilicate pool. In contrast, the abiotic Fe(II) sorption experiments showed that 41 and 24% of the added Fe(II) engaged in electron transfer to Fe(III)-phyllosilicate surfaces in synthetic goethite-coated and uncoated sediment. Differences in the rate of Fe(II) addition and system redox potential may account for the microbial and abiotic reaction systems. Our experiments provide new insight into pathways for Fe(III) reduction in mixed Fe(III)-oxide/Fe(III)-phyllosilicate assemblages, and provide key mechanistic insight for interpreting microbial reduction experiments and field data from complex natural soils and sediments.

Bacterial Community Structure and Functional arrA Gene Diversity Associated with Arsenic Reduction and Release in an Industrially Contaminated Soil

ABSTRACTThis study aimed at evaluating potential arsenic (As) mobility in an industrially contaminated soil (64 mg/kg of As) of the Meuse River basin, and at identifying key bacterial groups that drive soil As dynamics. Both speciation and release of As from this soil was followed under anaerobic conditions using a laboratory batch experiment. In the presence of exogenous carbon sources, AsV initially present in the soil matrix and/or adsorbed on synthetic hydrous ferric oxides were solubilized and mainly reduced to AsIII by indigenous soil microflora. After a 1-month incubation period in these biotic conditions, AsIII accounted for 80–85% of the total dissolved As and more than 60% of the solid-phase As. Bacterial community structure (i.e., 16S rDNA-based capillary electrophoresis single-strand conformation polymorphism profiles) changed with incubation time and As amendment. The detection of distantly related arsenate respiratory reductase genes (arrA), as functional markers of AsV respirers, indicates that novel dissimilatory AsV-reducing bacteria may be involved in As biotransformation and mobility in anoxic soils. Since As and iron were concomitantly released, a crucial role of indirect As-mobilizing bacteria on As behavior was also revealed. Our results show that the majority of As within the soil matrix was bioavailable and bioaccessible for heterotrophic AsV reduction to AsIII, which may increase As toxicity and mobility in the contaminated soils.

A new mechanistic framework to predict OCS fluxes from soils

Abstract. Estimates of photosynthetic and respiratory fluxes at large scales are needed to improve our predictions of the current and future global CO2 cycle. Carbonyl sulfide (OCS) is the most abundant sulfur gas in the atmosphere and has been proposed as a new tracer of photosynthetic gross primary productivity (GPP), as the uptake of OCS from the atmosphere is dominated by the activity of carbonic anhydrase (CA), an enzyme abundant in leaves that also catalyses CO2 hydration during photosynthesis. However soils also exchange OCS with the atmosphere, which complicates the retrieval of GPP from atmospheric budgets. Indeed soils can take up large amounts of OCS from the atmosphere as soil microorganisms also contain CA, and OCS emissions from soils have been reported in agricultural fields or anoxic soils. To date no mechanistic framework exists to describe this exchange of OCS between soils and the atmosphere, but empirical results, once upscaled to the global scale, indicate that OCS consumption by soils dominates OCS emission and its contribution to the atmospheric budget is large, at about one third of the OCS uptake by vegetation, also with a large uncertainty. Here, we propose a new mechanistic model of the exchange of OCS between soils and the atmosphere that builds on our knowledge of soil CA activity from CO2 oxygen isotopes. In this model the OCS soil budget is described by a first-order reaction–diffusion–production equation, assuming that the hydrolysis of OCS by CA is total and irreversible. Using this model we are able to explain the observed presence of an optimum temperature for soil OCS uptake and show how this optimum can shift to cooler temperatures in the presence of soil OCS emission. Our model can also explain the observed optimum with soil moisture content previously described in the literature as a result of diffusional constraints on OCS hydrolysis. These diffusional constraints are also responsible for the response of OCS uptake to soil weight and depth observed previously. In order to simulate the exact OCS uptake rates and patterns observed on several soils collected from a range of biomes, different CA activities had to be invoked in each soil type, coherent with expected physiological levels of CA in soil microbes and with CA activities derived from CO2 isotope exchange measurements, given the differences in affinity of CA for both trace gases. Our model can be used to help upscale laboratory measurements to the plot or the region. Several suggestions are given for future experiments in order to test the model further and allow a better constraint on the large-scale OCS fluxes from both oxic and anoxic soils.

Influence of sample matrix on the alkaline extraction of Cr(VI) in soils and industrial materials

An accurate and efficient determination of the highly toxic Cr(VI) in solid materials is important to determine the total Cr(VI) inventory of contaminated sites and the Cr(VI) release potential from such sites into the environment. Most commonly, total Cr(VI) is extracted from solid materials following a hot alkaline extraction procedure (US EPA method 3060A) where a complete release of water-extractable and sparingly soluble Cr(VI) phase is achieved. This work presents an evaluation of matrix effects that may occur during the hot alkaline extraction and in the determination of the total Cr(VI) inventory of variably composed contaminated soils and industrial materials (cement, fly ash) and is compared to water-extractable Cr(VI) results. Method validation including multiple extractions and matrix spiking along with chemical and mineralogical characterization showed satisfying results for total Cr(VI) contents for most of the tested materials. However, unreliable results were obtained by applying method 3060A to anoxic soils due to the degradation of organic material and/or reactions with Fe2+-bearing mineral phases. In addition, in certain samples discrepant spike recoveries have to be also attributed to sample heterogeneity. Separation of possible extracted Cr(III) by applying cation-exchange cartridges prior to solution analysis further shows that under the hot alkaline extraction conditions only Cr(VI) is present in solution in measurable amounts, whereas Cr(III) gets precipitated as amorphous Cr(OH)3(am). It is concluded that prior to routine application of method 3060A to a new material type, spiking tests are recommended for the identification of matrix effects. In addition, the mass of extracted solid material should to be well adjusted to the heterogeneity of the Cr(VI) distribution in the material in question.

Effect of aqueous Fe(II) on Sb(V) sorption on soil and goethite

The effects of Fe(II) on the sorption and precipitation of Sb(V) on soils and goethite were investigated using batch experiments and X-ray photoelectron spectroscopy (XPS) in this study. The sorption capacity of Sb(V) were much higher in anoxic soil than oxic soil. Typically, dissolved Fe(II) concentration in anoxic soils decreased significantly with increasing Sb(V), which may be suggestive of Fe-Sb precipitation. The elevated concentrations of Fe(II) (1 mM) enhanced the sorption capacity of Sb(V) on goethite significantly. However, synchrotron radiation X-ray diffraction showed no new characteristic peak, indicating that this Fe-Sb precipitate might be poor crystallinity or amorphous. Moreover, Sb(III) was detected in anoxic soil, and the reduction of Sb(V) to Sb (III) improved the sorption capacity of Sb in anoxic soil because of the low solubility and migration of Sb(III). Nevertheless, Fe-Sb co-precipitation and Sb(V) reduction to Sb(III) might contribute simultaneously to the increased sorption capacity of Sb(V) on anoxic soils. This research could improve our current understanding of soil Sb chemistry in paddy and wetland soils.

Changes in the composition and diversity of microbial communities during anaerobic nitrate reduction and Fe(II) oxidation at circumneutral pH in paddy soil

Kinetics of nitrate (NO3−) reduction and ferrous iron (Fe(II)) oxidation in paddy soil were investigated under anoxic conditions at circumneutral pH using three different treatments (i.e., Lactate + Fe(II), Lactate + NO3−, and Lactate + NO3− + Fe(II)). The results revealed that NO3− could be rapidly reduced to nitrite (NO2−) within two days in treatments of Lactate + NO3− and Lactate + NO3− + Fe(II), and the presence of Fe(II) facilitated the NO2− reduction. Whereas no obvious Fe(II) oxidation was observed in treatment of Lactate + Fe(II), Fe(II) oxidation took place only when NO3− was added. Illumina high-throughput sequencing used to profile the diversity and abundance of microbial communities showed that the phyla of Proteobacteria and Firmicutes had a dominant presence in all three treatments with lactate. Acidaminobacter, Proteiniclasticum, Alkaliphilus, and Natronincola_Anaerovirgula were found to be the dominant genera during NO3− reduction without Fe(II) after addition of lactate, and all were seldom reported to be associated with NO3− reduction. Azospira, Zoogloea, and Dechloromonas dominated during NO3− reduction in the presence of Fe(II), and all are betaproteobacterial NO3−-reducing bacteria that do not produce ammonium as end products of NO3− reduction. Whereas Azospira, Zoogloea, and Dechloromonas have been isolated or identified from NO3−-reducing Fe(II) oxidation culture previously, the NO2− produced by these NO3− reducing bacteria can also oxidize Fe(II) abiotically, resulting in facilitated NO2− disappearance in the treatment of Lactate + NO3− + Fe(II). These findings increase our understanding of the processes of NO3− reduction in the absence and presence of Fe(II) in anoxic paddy soil at circumneutral pH and extend our knowledge of the microbial communities involved in these processes.

Geochemical drivers of organic matter decomposition in arctic tundra soils

Climate change is warming tundra ecosystems in the Arctic, resulting in the decomposition of previously-frozen soil organic matter (SOM) and release of carbon (C) to the atmosphere; however, the processes that control SOM decomposition and C emissions remain highly uncertain. In this study, we evaluate geochemical factors that influence microbial production of carbon dioxide (CO2) and methane (CH4) in the seasonally-thawed active layer of interstitial polygonal tundra near Barrow, Alaska. We report spatial and seasonal patterns of dissolved gases in relation to the geochemical properties of Fe and organic C in soil and soil solution, as determined using spectroscopic and chromatographic techniques. The chemical composition of soil water collected during the annual thaw season varied significantly with depth. Soil water in the middle of the active layer contained abundant Fe(III), and aromatic-C and low-molecular-weight organic acids derived from SOM decomposition. At these depths, CH4 was positively correlated with the ratio of Fe(III) to total Fe in waterlogged transitional and low-centered polygons but negatively correlated in the drier flat- and high-centered polygons. These observations contradict the expectation that CH4 would be uniformly low where Fe(III) was high due to inhibition of methanogenesis by Fe(III)-reduction reactions. Our results suggest that vertically-stratified Fe redox reactions influence respiration/fermentation of SOM and production of substrates (e.g., low-molecular-weight organic acids) for methanogenesis, but that these effects vary with soil moisture. We infer that geochemical differences induced by water saturation dictate microbial products of SOM decomposition, and Fe geochemistry is an important factor regulating methanogenesis in anoxic tundra soils.