When Wet Gets Wetter: Decoupling of Moisture, Redox Biogeochemistry, and Greenhouse Gas Fluxes in a Humid Tropical Forest Soil

Upland humid tropical forest soils are often characterized by fluctuating redox dynamics that vary temporally and spatially across the landscape. An increase in the frequency and intensity of rainfall events with climate change is likely to affect soil redox reactions that control the production and emissions of greenhouse gases. We used a 24-day rainfall manipulation experiment to evaluate temporal and spatial trends of surface soil (0–20 cm) redox-active chemical species and greenhouse gas fluxes in the Luquillo Experimental Forest, Puerto Rico. Treatments consisted of a high rainfall simulation (60 mm day^?1), a fluctuating rainfall regime, and a control. Water addition generated high temporal and spatial variation in soil moisture (0.3–0.6 m³ m^?3), but had no significant effect on soil oxygen (O₂) concentrations. Extractable nitrate (NO₃ ^?) concentrations decreased with daily water additions and reduced iron (Fe(II)) concentrations increased towards the end of the experiment. Overall, redox indicators displayed a weak, non-deterministic, nonlinear relationship with soil moisture. High concentrations of Fe(II) and manganese (Mn) were present even where moisture was relatively low, and net Mn reduction occurred in all plots including controls. Mean CO₂ fluxes were best explained by soil C concentrations and a composite redox indicator, and not water addition. Several plots were CH₄ sources irrespective of water addition, whereas other plots oscillated between weak CH₄ sources and sinks. Fluxes of N₂O were highest in control plots and were consistently low in water-addition plots. Together, these data suggest (1) a relative decoupling between soil moisture and redox processes at our spatial and temporal scales of measurement, (2) the co-occurrence of aerobic and anaerobic biogeochemical processes in well-drained surface soils, and (3) an absence of threshold effects from sustained precipitation on redox reactions over the scale of weeks. Our data suggest a need to re-evaluate representations of moisture in biogeochemical models.     

Dependence of In Situ Bacterial Fe(II)-Oxidation and Fe(III)-Precipitation on Sequential Reactive Transport

A study was conducted to determine in situ rates of Fe(II) oxidation and Fe(III) precipitation along a 5.0 m reach of a ferruginous groundwater discharge zone under two distinct conditions; (i) the natural state featuring abundant flocculent mats of bacteriogenic iron oxides (BIOS) produced by Fe(II)-oxidizing bacteria, and (ii) after a manual washout of the streambed to remove the microbial mat. Examination of mat samples by differential interference contrast light microscopy revealed tangled meshworks of filamentous Leptothrix sheaths and helical Gallionella stalks intermixed with fine-grained hydrous ferric oxide (HFO) precipitates. The greatest accumulation of BIOS mat was 1.0 m downstream of the groundwater spring. Redox potential (Eh) increased sharply from 200 mV to over 300 mV over the last 2.0 m of the reach. Similarly, dissolved oxygen increased from < 10% saturation to almost 100% saturation over the last 2.0 m of the reach, whereas pH increased from 6.4 to 7.3. Pseudo-first-order rate constants determined on the basis of analytical solutions to sequential partial differential advection-dispersion-reaction equations for the linear Fe(II)→Fe(III)→HFO reaction network yielded in situ Fe(II) oxidation rate constants (k_ox) of 1.70 ± 0.20 min^?1 in natural conditions and 0.48 ± 0.14 min^?1 after washout. Corresponding Fe(III)-precipitation rates (k_p) before and after washout were 3.45 ± 0.10 min^?1 and 0.90 ± 0.01 min^?1, respectively. These values for k_ox and k_p are higher than estimates obtained from closed batch microcosm and laboratory experiments, underscoring the crucial dependence of in situ Fe(II) oxidation and Fe(III) precipitation rates on advective and dispersive mass transport. The results also highlight the influence that BIOS microbial mats exert on the reaction kinetics of the multiple heterogeneous reactions contributing not only to Fe(II)/Fe(III) redox transformations in groundwater discharge zones, but also the precipitation of HFO.     

The active site of the [FeFe]-hydrogenase from Desulfovibrio desulfuricans. II. Redox properties, light sensitivity and CO-ligand exchange as observed by infrared spectroscopy

In [FeFe]-hydrogenases, the H cluster (hydrogen-activating cluster) contains a di-iron centre ([2Fe]_H subcluster, a (L)(CO)(CN)Fe(μ-RS₂)(μ-CO)Fe(CysS)(CO)(CN) group) covalently attached to a cubane iron-sulphur cluster ([4Fe-4S]_H subcluster). The Cys-thiol functions as the link between one iron (called Fe1) of the [2Fe]_H subcluster and one iron of the cubane subcluster. The other iron in the [2Fe]_H subcluster is called Fe2. The light sensitivity of the Desulfovibrio desulfuricans enzyme in a variety of states has been studied with infrared (IR) spectroscopy. The aerobic inactive enzyme (H_inact state) and the CO-inhibited active form (H_ox–CO state) were stable in light. Illumination of the H_ox state led to a kind of cannibalization; in some enzyme molecules the H cluster was destroyed and the released CO was captured by the H clusters in other molecules to form the light-stable H_ox–CO state. Illumination of active enzyme under ¹³CO resulted in the complete exchange of the two intrinsic COs bound to Fe2. At cryogenic temperatures, light induced the photodissociation of the extrinsic CO and the bridging CO of the enzyme in the H_ox–CO state. Electrochemical redox titrations showed that the enzyme in the H_inact state converts to the transition state (H_trans) in a reversible one-electron redox step (E _{m, pH 7}=–75 mV). IR spectra demonstrate that the added redox equivalent not only affects the [4Fe-4S]_H subcluster, but also the di-iron centre. Enzyme in the H_trans state reacts with extrinsic CO, which binds to Fe2. The H_trans state converts irreversibly into the H_ox state in a redox-dependent reaction most likely involving two electrons (E _{m, pH 7}=–261 mV). These electrons do not end up on any of the six Fe atoms of the H cluster; the possible destiny of the two redox equivalents is discussed. An additional reversible one-electron redox reaction leads to the H_red state (E _{m, pH 7}=–354 mV), where both Fe atoms of the [2Fe]_H subcluster have the same formal oxidation state. The possible oxidation states of Fe1 and Fe2 in the various enzyme states are discussed. Low redox potentials (below –500 mV) lead to destruction of the [2Fe]_H subcluster.     

Lignin decomposition is sustained under fluctuating redox conditions in humid tropical forest soils

Lignin mineralization represents a critical flux in the terrestrial carbon (C) cycle, yet little is known about mechanisms and environmental factors controlling lignin breakdown in mineral soils. Hypoxia is thought to suppress lignin decomposition, yet potential effects of oxygen (O₂) variability in surface soils have not been explored. Here, we tested the impact of redox fluctuations on lignin breakdown in humid tropical forest soils during ten‐week laboratory incubations. We used synthetic lignins labeled with ¹³C in either of two positions (aromatic methoxyl or propyl side chain C_β) to provide highly sensitive and specific measures of lignin mineralization seldom employed in soils. Four‐day redox fluctuations increased the percent contribution of methoxyl C to soil respiration relative to static aerobic conditions, and cumulative methoxyl‐C mineralization was statistically equivalent under static aerobic and fluctuating redox conditions despite lower soil respiration in the latter treatment. Contributions of the less labile lignin C_β to soil respiration were equivalent in the static aerobic and fluctuating redox treatments during periods of O₂ exposure, and tended to decline during periods of O₂ limitation, resulting in lower cumulative C_β mineralization in the fluctuating treatment relative to the static aerobic treatment. However, cumulative mineralization of both the C_β‐ and methoxyl‐labeled lignins nearly doubled in the fluctuating treatment relative to the static aerobic treatment when total lignin mineralization was normalized to total O₂ exposure. Oxygen fluctuations are thought to be suboptimal for canonical lignin‐degrading microorganisms. However, O₂ fluctuations drove substantial Fe reduction and oxidation, and reactive oxygen species generated during abiotic Fe oxidation might explain the elevated contribution of lignin to C mineralization. Iron redox cycling provides a potential mechanism for lignin depletion in soil organic matter. Couplings between soil moisture, redox fluctuations, and lignin breakdown provide a potential link between climate variability and the biochemical composition of soil organic matter.     

An assessment of iron and calcium amendments for managing phosphorus release from impacted Everglades soils

The recent implementation of agricultural best management practices (BMPs) and treatment wetlands called stormwater treatment areas (STAs) have reduced phosphorus (P) concentrations and loadings to the Everglades Protection Area (EPA) in Florida (USA). There is a concern that despite reductions in external P loadings, internal loading from the legacy P enrichment of the EPA wetland soils will continue to elevate water column P concentrations, and may impede restoration outcomes. In an effort to explore ways to reduce soil P efflux, we retrieved intact, vegetated (cattail, Typha domingensis) soil monoliths from two P-enriched areas of the EPA and deployed them at a location where they received pre-treated (low P) surface water as ex situ flow-through mesocosms for 21 months with a mid-study 7-week dry down to mimic natural hydroperiod conditions. Two treatments were tested for soils from both sites, using triplicate mesocosms for each treatment. After applying a herbicide (glyphosate) to eliminate the cattail vegetation, iron (Fe as liquid FeCl₃) amendments provided no P retention benefits in the organic soils from the two sites, and did not yield significantly (P > 0.05; n = 43) lower flux rates (6.1 and 3.5 mg Pm^?2 d^?1) than the herbicide/no soil amendment control (3.9 and 2.1 mg Pm^?2 d^?1), as was expected. A combination of low oxidation–reduction potential, heightened organic matter P mineralization, high pH, and sulfide production acted interactively to enhance Fe and P mobilization in the Fe-amended mesocosms. The herbicide/limerock (CaCO₃)-amended soils exhibited significantly lower (P ≤ 0.05; n = 43) P flux (1.3 and 1.1 mg Pm^?2 d^?1) than the herbicide/no soil amendment control soils, but it remains unknown whether the observed reduction in P efflux (ranging from 48 to 67%) would justify the expense and potential environmental impacts of applying a surficial limerock amendment to large regions of the P-enriched wetlands.     

Microbial communities acclimate to recurring changes in soil redox potential status

Rapidly fluctuating environmental conditions can significantly stress organisms, particularly when fluctuations cross thresholds of normal physiological tolerance. Redox potential fluctuations are common in humid tropical soils, and microbial community acclimation or avoidance strategies for survival will in turn shape microbial community diversity and biogeochemistry. To assess the extent to which indigenous bacterial and archaeal communities are adapted to changing in redox potential, soils were incubated under static anoxic, static oxic or fluctuating redox potential conditions, and the standing (DNA‐based) and active (RNA‐based) communities and biogeochemistry were determined. Fluctuating redox potential conditions permitted simultaneous CO₂ respiration, methanogenesis, N₂O production and iron reduction. Exposure to static anaerobic conditions significantly changed community composition, while 4‐day redox potential fluctuations did not. Using RNA : DNA ratios as a measure of activity, 285 taxa were more active under fluctuating than static conditions, compared with three taxa that were more active under static compared with fluctuating conditions. These data suggest an indigenous microbial community adapted to fluctuating redox potential.     

Iron oxidation stimulates organic matter decomposition in humid tropical forest soils

Humid tropical forests have the fastest rates of organic matter decomposition globally, which often coincide with fluctuating oxygen (O₂) availability in surface soils. Microbial iron (Fe) reduction generates reduced iron [Fe(II)] under anaerobic conditions, which oxidizes to Fe(III) under subsequent aerobic conditions. We demonstrate that Fe (II) oxidation stimulates organic matter decomposition via two mechanisms: (i) organic matter oxidation, likely driven by reactive oxygen species; and (ii) increased dissolved organic carbon (DOC) availability, likely driven by acidification. Phenol oxidative activity increased linearly with Fe(II) concentrations (P < 0.0001, pseudo R² = 0.79) in soils sampled within and among five tropical forest sites. A similar pattern occurred in the absence of soil, suggesting an abiotic driver of this reaction. No phenol oxidative activity occurred in soils under anaerobic conditions, implying the importance of oxidants such as O₂ or hydrogen peroxide (H₂O₂) in addition to Fe(II). Reactions between Fe(II) and H₂O₂ generate hydroxyl radical, a strong nonselective oxidant of organic compounds. We found increasing consumption of H₂O₂ as soil Fe(II) concentrations increased, suggesting that reactive oxygen species produced by Fe(II) oxidation explained variation in phenol oxidative activity among samples. Amending soils with Fe(II) at field concentrations stimulated short‐term C mineralization by up to 270%, likely via a second mechanism. Oxidation of Fe(II) drove a decrease in pH and a monotonic increase in DOC; a decline of two pH units doubled DOC, likely stimulating microbial respiration. We obtained similar results by manipulating soil acidity independently of Fe(II), implying that Fe(II) oxidation affected C substrate availability via pH fluctuations, in addition to producing reactive oxygen species. Iron oxidation coupled to organic matter decomposition contributes to rapid rates of C cycling across humid tropical forests in spite of periodic O₂ limitation, and may help explain the rapid turnover of complex C molecules in these soils.     

Redox Fluctuations Frame Microbial Community Impacts on N-cycling Rates in a Humid Tropical Forest Soil

Fluctuating soil redox regimes may facilitate the co-occurrence of microbial nitrogen transformations with significantly different sensitivities to soil oxygen availability. In an upland humid tropical forest, we explored the impact of fluctuating redox regimes on gross nitrogen cycling rates and microbial community composition. Our results suggest that the rapidly fluctuating redox conditions that characterize these upland soils allow anoxic and oxic N processing to co-occur. Gross nitrogen mineralization was insensitive to soil redox fluctuations. In contrast, nitrifiers in this soil were directly affected by low redox periods, yet retained some activity even after 3–6 weeks of anoxia. Dissimilatory nitrate reduction to ammonium (DNRA) was less sensitive to oxygen exposure than expected, indicating that the organisms mediating this reductive process were also tolerant of unfavorable (oxic) conditions. Denitrification was a stronger sink for NO₃⁻ in consistently anoxic soils than in variable redox soils. Microbial biomass and community composition were maintained with redox fluctuation, but biomass decreased and composition changed under static oxic and anoxic soil regimes. Bacterial community structure was significantly correlated with rates of nitrification, denitrification and DNRA, suggesting that redox-control of soil microbial community structure was an important determinant of soil N-cycling rates. Specific nitrogen cycling functional groups in this environment (such as nitrifiers, DNRA organisms, and denitrifiers) appear to have adapted to nutrient resources that are spatially and temporally variable. In soils where oxygen is frequently depleted and re-supplied, characteristics of microbial tolerance and resilience can frame N cycling patterns.     

Does the environment around the H-cluster allow coordination of the pendant amine to the catalytic iron center in [FeFe] hydrogenases? Answers from theory

[FeFe] hydrogenases are H₂-evolving enzymes that feature a diiron cluster in their active site (the [2Fe]_H cluster). One of the iron atoms has a vacant coordination site that directly interacts with H₂, thus favoring its splitting in cooperation with the secondary amine group of a neighboring, flexible azadithiolate ligand. The vacant site is also the primary target of the inhibitor O₂. The [2Fe]_H cluster can span various redox states. The active-ready form (H_ox) attains the Fe^IIFe^I state. States more oxidized than H_ox were shown to be inactive and/or resistant to O₂. In this work, we used density functional theory to evaluate whether azadithiolate-to-iron coordination is involved in oxidative inhibition and protection against O₂, a hypothesis supported by recent results on biomimetic compounds. Our study shows that Fe–N(azadithiolate) bond formation is favored for an Fe^IIFe^II active-site model which disregards explicit treatment of the surrounding protein matrix, in line with the case of the corresponding Fe^IIFe^II synthetic system. However, the study of density functional theory models with explicit inclusion of the amino acid environment around the [2Fe]_H cluster indicates that the protein matrix prevents the formation of such a bond. Our results suggest that mechanisms other than the binding of the azadithiolate nitrogen protect the active site from oxygen in the so-called H _ox ^inact state.     

Shear stress and sediment resuspension in relation to submersed macrophyte biomass

We examined the impacts of macrophyte beds dominated by a canopy-forming (Myriophyllum sibiricum) and a meadow-forming (Chara canescens) species on bottom shear stress (τ) and resuspension in shallow Lake Christina, Minnesota (U.S.A.). Studies were conducted in late summer, 1998, when macrophyte biomass levels exceeded 200 g m^?2, and in early summer, 2000, when biomass was greatly reduced (<20 g m^?2) in both plant beds. The critical shear stress (τ_c) of sediments, measured experimentally in the laboratory, was low (1.4 dynes cm^?2) indicating potential for resuspension in the absence of macrophytes. During 1998, turbidity was low at the M. sibiricum and Chara station, rarely increasing when calculated bottom τ (calculated from wave theory assuming no biomass obstruction) exceeded τsub c sub, indicating that both beds reduced sediment resuspension at high biomass levels. In situτ (estimated τ), measured via gypsum sphere dissolution, did not exceed τ_c above the sediment interface in either bed during 1998. In contrast, sediment resuspension occurred in both beds during similar high winds in 2000. However, estimated τ was lower than calculated bottom τ, suggesting that at low biomass, macrophytes were having some impact on τ.     

Prediction of reducible soil iron content from iron extraction data

Soils contain various iron compounds that differ in solubility, reducibility and extractability. Moreover, the contribution of the various iron compounds to total iron (Fe) and total Fe concentrations differs highly among soils. As a result, the total reducible Fe content can also differ among soils, and so does the dynamics of iron reduction. These factors complicate the prediction of reducible Fe based on Fe extraction data and hamper the application of process-based models for reduced or waterlogged soils where redox processes play a key-role. This paper presents a theoretical analysis relating reducible to extractable Fe reported in the literature. Predictions made from this theoretical analysis were evaluated in soil incubations using 18 rice paddy soils from all over the world. The incubation studies and the literature study both show that reducible Fe can be related to Fe from some selected, but not all, iron extractions. The combination of measurements for labile Fe(III)oxides (derived from oxalate-extractable Fe) and stabile Fe(III)oxides (derived from dithionite-citrate-extractable Fe) shows highly significant correlations with reducible Fe with high coefficients of determination (r² = 0.92–0.95 depending on the definition of stabile Fe(III)oxides). Given the high diversity in rice soils used for the incubations, these regression equations will have general applicability. Application of these regression equations in combination with soil database information may improve the predictive ability of process-based models where soil redox processes are important, such as CH₄ emission models derived for rice paddies or wetlands.     

Neutrophilic, nitrate-dependent, Fe(II) oxidation by a Dechloromonas species

A species of Dechloromonas, strain UWNR4, was isolated from a nitrate-reducing, enrichment culture obtained from Wisconsin River (USA) sediments. This strain was characterized for anaerobic oxidation of both aqueous and chelated Fe(II) coupled to nitrate reduction at circumneutral pH. Dechloromonas sp. UWNR4 was incubated in anoxic batch reactors in a defined medium containing 4.5–5 mM NO₃ ^?, 6 mM Fe²⁺ and 1–1.8 mM acetate. Strain UWNR4 efficiently oxidized Fe²⁺ with 90 % oxidation of Fe²⁺ after 3 days of incubation. However, oxidation of Fe²⁺ resulted in Fe(III)-hydroxide-encrusted cells and loss of metabolic activity, suggested by inability of the cells to utilize further additions of acetate. In similar experiments with chelated iron (Fe(II)-EDTA), encrusted cells were not produced and further additions of acetate and Fe(II)-EDTA could be oxidized. Although members of the genus Dechloromonas are primarily known as perchlorate and nitrate reducers, our findings suggest that some species could be members of microbial communities influencing iron redox cycling in anoxic, freshwater sediments. Our work using Fe(II)-EDTA also demonstrates that Fe(II) oxidation was microbially catalyzed rather than a result of abiotic oxidation by biogenic NO₂ ^?.     

Oxygen Dependency of Neutrophilic Fe(II) Oxidation by Leptothrix Differs from Abiotic Reaction

Neutrophilic Fe(II) oxidizing microorganisms are found in many natural environments. It has been hypothesized that, at low oxygen concentrations, microbial iron oxidation is favored over abiotic oxidation. Here, we compare the kinetics of abiotic Fe(II) oxidation to oxidation in the presence of the bacterium Leptothrix cholodnii Appels isolated from a wetland sediment. Rates of Fe(II) oxidation were determined in batch experiments at 20°C, pH 7 and oxygen concentrations between 3 and 120 μmol/l. The reaction progress in experiments with and without cells exhibited two distinct phases. During the initial phase, the oxygen dependency of microbial Fe(II) oxidation followed a Michaelis-Menten rate expression (K_M = 24.5 ± 10 μmol O₂/l, v_max = 1.8 ± 0.2 μmol Fe(II)/(l min) for 10⁸ cells/ml). In contrast, abiotic rates increased linearly with increasing oxygen concentrations. At similar oxygen concentrations, initial Fe(II) oxidation rates were faster in the experiments with bacteria. During the second phase, the accumulated iron oxides catalyzed further oxidative iron precipitation in both abiotic and microbial reaction systems. That is, abiotic oxidation also dominated the reaction progress in the presence of bacteria. In fact, in some experiments with bacteria, iron oxidation during the second phase proceeded slower than in the absence of bacteria, possibly due to an inhibitory effect of extracellular polymeric substances on the growth of Fe(III) oxides. Thus, our results suggest that the competitive advantage of microbial iron oxidation in low oxygen environments may be limited by the autocatalytic nature of abiotic Fe(III) oxide precipitation, unless the accumulation of Fe(III) oxides is prevented, for example, through a close coupling of Fe(II) oxidation and Fe(III) reduction.     

Nature of iron deposits on the cardiac walls in β-thalassemia by Mössbauer spectroscopy

An identification of the nature and an estimation of the particle size distribution of the iron deposits on thalassemic heart tissue is carried out by variable temperature Mössbauer spectroscopy. Comparison of Mössbauer spectra obtained for the thalassemic heart tissue (I) with those of normal heart tissue (II) and of horse spleen ferritin (III) identifies the iron deposits to be small, superparamagnetic particles of ferritin and/or hemosiderin, two closely related iron storage proteins containing an iron core of (FeOOH)₈(FeO · OPO₃H₂). The dependence of the superparamagnetic relaxation time, τ₂, of magnetically ordered fine particles on their volume V via the magnetic anisotropy constant K of the material and the condition τ > τ_L, the Larmor precession time of the nuclear magnetic moment of ⁵⁷Fe about an effective magnetic field, for observation of hyperfine structure are used in analyzing the Mössbauer data to yield the particle size distribution. Particle diameters are estimated to be $\text{74 ± 12}\text{A}\text{?}$.     

Lignin content and chemical characteristics in maize and wheat vary between plant organs and growth stages: consequences for assessing lignin dynamics in soil

In forest ecosystems, the silicon (Si) mass-balance at the watershed scale can be strongly influenced by readily soluble Si components, such as dissolved Si, adsorbed Si, amorphous silica (biogenic and pedogenic opal) and short-range ordered aluminosilicates. The aim of the present study is to (a) identify the components of the readily soluble Si pool in the Cambisol found below three tree species, under homogeneous soil and climate conditions, and (b) study the impact of Si recycling by tree species on the Si pools. We therefore measured the concentrations of Si extracted by Na₂CO₃ (Si_alk), oxalate (Si_ox) and CaCl₂. The Si_alk concentration decreased from the humus layer to 15 cm depth and then slightly increased until a depth of 75 cm. In the humus layer, the Si_alk concentration consisted mainly of phytoliths and differed significantly between tree species (expressed as mg SiO₂ g^-1): Douglas fir (14.5?±?0.65) > European beech (11.8?±?0.30) > Black pine (5.4?±?0.31). Below 7.5 cm, the Si_alk content did not differ significantly between tree species, and the Si_ox content, increasing significantly, was mainly comprised of Si adsorbed onto amorphous Fe oxides. These results suggest that (a) tree species can impact the readily soluble Si content in the topsoil, through different rates of Si uptake and phytolith restitution by the vegetation, and (b) the soil’s readily soluble Si pool is mainly comprised of phytoliths and adsorbed Si. Here, the readily soluble Si pool is thus controlled by both the iron dynamics and Si biocycling.     

Oxygen input controls the spatial and temporal dynamics of arsenic at the surface of a flooded paddy soil and in the rhizosphere of lowland rice (Oryza sativa L.): a microcosm study

The impact of oxygen (O₂) input at the soil surface and in the rhizosphere of rice (Oryza sativa L.) on the spatial and temporal dynamics of arsenic (As) was investigated in a flooded paddy soil. A soil microcosm and root-mat technique were designed to mimic submerged conditions of paddy fields. Water-filled containers with (planted) or without (unplanted) 27-day-old rice seedlings were fitted for 20 days on top of microcosms containing an As-affected soil (Bangladesh). After the initial establishment of strongly reduced conditions (?230 mV) in both planted and unplanted soils, the redox potential gradually increased until the day 8 to reach?+?50 mV at 2 mm from the surface of unplanted soils only. This oxidation was associated with an accumulation of NH₄-oxalate extractable As (25.7 mg kg^?1) in the 0.5-mm top layer, i.e. at levels above the initial total content of As in the soil (14 mg kg^?1) and a subsequent depletion of As in soil solution at 2 mm from soil surface. Root O₂-leakage induced the formation of an iron (Fe) plaque in root apoplast, with no evidence of outer rhizosphere oxidation. Arsenic content reached 173 mg kg^?1 in the Fe plaque. This accumulation induced a depletion of As in soil solution over several millimetres in the rhizosphere. Arsenic contents in root symplast and shoots (112 and 2.3 mg kg^?1, respectively) were significantly lower than in Fe plaque. Despite a large As concentration in soil solution, Fe plaque appeared highly efficient to sequester As and to restrict As acquisition by rice. The oxidation-mediated accumulation of As in the Fe plaque and in the oxidised layer at the top of the soil mobilised 21 and 3% of the initial amount of As in the planted and unplanted soils, respectively. Soil solution As concentration steadily decreased during the last 16 days of the soil stage, likely indicating a decrease in the ability of the soil to re-supply As from the solid-phase to the solution. The driving force of As dynamic in soil was therefore attributed to the As diffusion from reduced to oxidised soil layers. These results suggest a large mobility of As in the soil during the flooded period, controlled by the setting of oxic/anoxic interfaces at the surface of soil in contact with flooding water and in the rhizosphere of rice.     

Wildfire Effects on Soil Gross Nitrogen Transformation Rates in Coniferous Forests of Central Idaho, USA

Forest fires often result in a series of biogeochemical processes that increase soil nitrate (NO₃ ^?) concentrations for several years; however, the dynamic nature of inorganic nitrogen (N) cycling in the plant–microbe–soil complex makes it challenging to determine the direct causes of increased soil NO₃ ^?. We measured gross inorganic N transformation rates in mineral soils 2 years after wildfires in three central Idaho coniferous forests to determine the causes of the elevated soil NO₃ ^?. We also measured key factors that could affect the soil N processes, including temperature during soil incubation in situ, soil water content, pH and carbon (C) availability. We found no significant differences (P = 0.461) in gross nitrification rates between burned and control soils. However, microbial NO₃ ^? uptake rates were significantly lower (P = 0.078) in burned than control soils. The reduced consumption of NO₃ ^? caused slightly elevated NO₃ ^? concentrations in the burned soils. C availability was positively correlated with microbial NO₃ ^? uptake rates. Despite reduced microbial NO₃ ^? uptake capacity in the burned soils, soil microbes were a strong enough N sink to maintain low soil NO₃ ^? concentrations 2 years post fire. Soil NH₄ ⁺ concentrations between the treatments were not significantly different (P = 0.673). However, gross NH₄ ⁺ production and microbial uptake rates in burned soils were significantly lower (P = 0.028 and 0.035, respectively) than in the controls, and these rates were positively correlated with C availability. Our results imply that C availability is an important factor regulating soil N cycling of coniferous forests in the region.     

HdrC2 from Acidithiobacillus ferrooxidans Owns Two Iron–Sulfur Binding Motifs But Binds Only One Variable Cluster Between [4Fe–4S] and [3Fe–4S]

The heterodisulfide reductase complex HdrABC from Acidithiobacillus ferrooxidans was suggested to own novel features that act in reverse to convert the sulfane sulfur of GS _n H species (n > 1) into sulfite in sulfur oxidation. The HdrC subunit is potentially encoded by two different highly upregulated genes sharing only 29 % identity in A. ferrooxidans grown in sulfur-containing medium, which were named as HdrC1 and HdrC2, respectively and had been confirmed to contain iron–sulfur cluster by expression and characterization, especially the HdrC1 which had been showed to bind only one [4Fe–4S] cluster by mutations. However, the mutations of the HdrC2 remain to be done and the detailed binding information of it is still unclear. Here, we report the expression, mutations, and molecular modeling of the HdrC2 from A. ferrooxidans. This HdrC2 had two identical motifs (Cx₂Cx₂Cx₃C) containing total of eight cysteine residues potentially for iron–sulfur cluster binding. This purified HdrC2 was exhibited to contain one variable cluster converted between [4Fe–4S] and [3Fe–4S] according to different conditions by the UV-scanning and EPR spectra. The site-directed mutagenesis results of these eight residues further confirmed that the HdrC2 in reduction with Fe²⁺ condition loaded only one [4Fe–4S]⁺ with spin S = 1/2 ligated by the residues of Cys73, Cys109, Cys112, and Cys115; the HdrC2 in natural aeration condition lost the Fe atom ligated by the residue of Cys73 and loaded only one [3Fe–4S]⁰ with spin S = 0; the HdrC2 in oxidation condition loaded only one [3Fe–4S]⁺ with spin S = 1/2. Molecular modeling results were also in line with the experiment results.     

Accelerated microbial organic matter mineralization following salt-water intrusion into tidal freshwater marsh soils

The impact of salt-water intrusion on microbial organic carbon (C) mineralization in tidal freshwater marsh (TFM) soils was investigated in a year-long laboratory experiment in which intact soils were exposed to a simulated tidal cycle of freshwater or dilute salt-water. Gas fluxes [carbon dioxide (CO₂) and methane (CH₄)], rates of microbial processes (sulfate reduction and methanogenesis), and porewater and solid phase biogeochemistry were measured throughout the experiment. Flux rates of CO₂ and, surprisingly, CH₄ increased significantly following salt-water intrusion, and remained elevated relative to freshwater cores for 6 and 5 months, respectively. Following salt-water intrusion, rates of sulfate reduction increased significantly and remained higher than rates in the freshwater controls throughout the experiment. Rates of acetoclastic methanogenesis were higher than rates of hydrogenotrophic methanogenesis, but the rates did not differ by salinity treatment. Soil organic C content decreased significantly in soils experiencing salt-water intrusion. Estimates of total organic C mineralized in freshwater and salt-water amended soils over the 1-year experiment using gas flux measurements (18.2 and 24.9 mol C m^?2, respectively) were similar to estimates obtained from microbial rates (37.8 and 56.2 mol C m^?2, respectively), and to losses in soil organic C content (0 and 44.1 mol C m^?2, respectively). These findings indicate that salt-water intrusion stimulates microbial decomposition, accelerates the loss of organic C from TFM soils, and may put TFMs at risk of permanent inundation.     

Does radial oxygen loss and iron plaque formation on roots alter Cd and Pb uptake and distribution in rice plant tissues?

Background and Aims

Metal (e.g. Cd and Pb) pollution in agricultural soils and crops have aroused considerable attention in recent years. This study aimed to evaluate the effects of ROL and Fe plaque on Cd and Pb accumulation and distribution in the rice plant.

Methods

A rhizobag experiment was employed to investigate the correlations among radial oxygen loss (ROL), Fe plaque formation and uptake and distribution of Cd and Pb in 25 rice cultivars.

Results

Large differences between the cultivars were found in rates of ROL (1.55 to 6.88 mmol O₂ kg^?1 root d.w. h^?1), Fe plaque formation (Fe: 6,117–48,167 mg kg^?1; Mn: 127–1,089 mg kg^?1), heavy metals in shoot (Cd: 0.13–0.35 mg kg^?1; Pb: 4.8–8.1 mg kg^?1) and root tissues (Cd: 1.1–3.5 mg kg^?1; Pb: 45–199 mg kg^?1), and in Fe plaque (Cd: 0.54–2.6 mg kg^?1; Pb: 102–708 mg kg^?1). Rates of ROL were positively correlated with Fe plaque formation and metal deposition on root surfaces, but negatively correlated with metal transfer factors of root/plaque and distributions in shoot and root tissues.

Conclusions

ROL-induced Fe plaque promotes metal deposition on to root surfaces, leading to a limitation of Cd and Pb transfer and distribution in rice plant tissues.