Anoxic Soil Research Articles

Use of high-resolution ground conductivity measurements for denitrifying conservation practice placement.

Accurate field-scale maps of soil properties including features such as texture, soil organic matter (SOM) content, and hydraulic conductivity are essential for proper placement of conservation practices that utilize anoxic soil environments for denitrification. However, in many cases, soil maps inaccurately represent subsoil properties and can mislead managers about where to install new practices. Non-invasive methods of subsoil property analysis including electromagnetic induction techniques are a potentially efficient method for improving existing field-scale soil maps. In this study, we quantified the accuracy of existing soil maps in an agricultural field in north-central Iowa. Of 60 soil cores collected and reclassified, 19 were identified as taxadjunct at the soil series level primarily due to hydrologic indicators and soil particle size. We assessed the correlation among physical and chemical soil properties measured in-lab and geophysical responses measured in-field. We identified significant correlation of SOM and sand to electrical conductivity for individual core and mean soil series data. From this analysis, we developed a conservation practice suitability map and evaluated the potential for field-scale geophysical investigations to serve as a new tool for agricultural conservation planning and placement of site-specific denitrifying conservation practices. Study results suggest that incorporating a geophysical conductivity investigation into conservation planning may improve understanding of critical soil properties beyond those ascertained with limited soil borings.

Can As concentration in crop be controlled by Se fertilization? A meta-analysis and outline of As sequestration mechanisms.

Arsenic (As) is a pollutant with a strong toxic effect on animals, plants and human beings. Exogenous selenium (Se) has been suggested to reduce the accumulation of As in crops, but contradictory results were found in the published literature. In order to clarify the possible processes, we collected the literature that reports on the effects of Se application on As uptake and accumulation in crops, analyzed the data by meta-analysis, and tested the effects of different factors on As accumulation by meta-regression model and subgroup analysis. The results highlighted a significant dose-dependent reduction of As content in crops after Se addition. Exogenous Se can significantly reduce As concentrations in grains by 18.76%. The reduction was dose-dependent for rice grains under aerobic soil conditions but not for rice grains under anoxic soil conditions. Se-enriched soils (greater than 0.5 mg kg-1) significantly reduced As concentrations in grains. Selenium significantly decreased the transfer factor of As from root to shoot. Moreover, selenite had a stronger inhibiting effect on the transport of As from root to shoot than selenate. The inhibition of selenium fertilization on As concentrations seems to take place in root and soil, while physiological processes in rice may be involved in restricting uptake and transport from root to shoot. These findings provide new ideas for effectively alleviating the transfer of As to the human body through the food chain.

Spartina alterniflora has the highest methane emissions in a St. Lawrence estuary salt marsh

Salt marshes have the ability to store large amounts of ‘blue carbon’, potentially mitigating some of the effects of climate change. Salt marsh carbon storage may be partially offset by emissions of CH4, a highly potent greenhouse gas. Sea level rise and invasive vegetation may cause shifts between different elevation and vegetation zones in salt marsh ecosystems. Elevation zones have distinct soil properties, plant traits and rhizosphere characteristics, which affect CH4 fluxes. We investigated differences in CH4 emissions between four elevation zones (mudflat, Spartina alterniflora, Spartina patens and invasive Phragmites australis) typical of salt marshes in the northern Northwest Atlantic. CH4 emissions were significantly higher from the S. alterniflora zone (17.7 ± 9.7 mg C m−2h−1) compared to the other three zones, where emissions were negligible (<0.3 mg C m−2h−1). These emissions were high for salt marshes and were similar to those typically found in oligohaline marshes with lower salinities. CH4 fluxes were significantly correlated with soil properties (salinity, water table depth, bulk density and temperature), plant traits (rhizome volume and biomass, root volume and dead biomass volume all at 0–15 cm) and CO2 fluxes. The relationships between CH4 emissions, and rhizome and root volume suggest that the aerenchyma tissues in these plants may be a major transport mechanism of CH4 from anoxic soils to the atmosphere. This may have major implications for the mitigation potential carbon sink from salt marshes globally, especially as S. alterniflora is widespread. This study shows CH4 fluxes can vary over orders of magnitude from different vegetation in the same system, therefore, specific emissions factors may need to be used in future climate models and for more accurate carbon budgeting depending on vegetation type.

Keep oxygen in check: An improved in-situ zymography approach for mapping anoxic hydrolytic enzyme activities in a paddy soil

Paddy soils regularly experience redox oscillations during the wetting and draining stages, yet the effects of short-term presence of oxygen (O2) on in-situ microbial hotspots and enzyme activities in anoxic ecosystems remain unclear. To fill this knowledge gap, we applied soil zymography to localize hotspots and activities of phosphomonoesterase (PME), β-glucosidase (BG), and leucine aminopeptidase (LAP) in three compartments of rice-planted rhizoboxes (top bulk, rooted, and bottom bulk paddy soil) under oxic (+O2) and anoxic (O2) conditions. Short-term (35 min) aeration decreased PME activity by 13–49 %, BG by 4–52 %, and LAP by 12–61 % as compared with O2 in three soil compartments. The percentage of hotspot area was higher by 3–110 % for PME, by 10–60 % for BG, and by 12–158 % for LAP under +O2 vs. O2 conditions depending on a rice growth stage. Irrespective of the aeration conditions, the rhizosphere extent of rice plants for three enzymes was generally greater under higher moisture conditions and at earlier growth stage. Higher O2 sensitivity for the tested enzymes at bottom bulk soil versus other compartments suggested that short-term aeration during conventional zymography may lead to underestimation of nutrient mobilization in subsoil compared to top bulk soil. The intolerance of anaerobic microorganisms against the toxicity of O2 in the cells and the shift of microbial metabolic pathways may explain such a short-term suppression by O2. Our findings, therefore, show that anoxic conditions and soil moisture should be kept during zymography and probably other in-situ soil imaging methods when studying anoxic systems.

Coupled dynamics of aqueous biogeochemistry in contrasting floodplain environments: Implications for Critical Zone carbon sequestration along redox gradients

This study contributes to our evolving understanding of how coupled biogeochemical dynamics of Fe and Mn along the redox gradients affect C cycling and sequestration at Critical Zones. A 12-month monitoring of the in-situ soil pore-water biogeochemistry and redox gradients across the floodplain at the White Clay Creek Watershed in the Christina River Basin - Critical Zone Observatory was investigated. Topographically, eastern floodplain was narrow with a steep hillslope connected to the agricultural field while western floodplain was flat and wide. Soil profile consisted of post-colonial oxic deposits, pre-colonial anoxic buried wetland soils underlain by suboxic valley-bottom gravel. Contrasting soil pore-water chemistry including DOM quality, DOC, Fe and Mn, δ18O and δD profiles, and redox potentials were observed between the eastern and western floodplains due to seasonal fluctuations, divergent topographic and hydrologic settings. We observed diverse types of C pools across the floodplain from short (labile) to long term (recalcitrant) C forms: microbial origin DOM at eastern versus terrestrial or plant-derived DOM at western buried wetland soil pore-waters. Gravel was linked to the soluble microbial byproduct-like fractions indicating bioavailable DOM and microbial activity. Gravel beds may act as a natural filter (or C sink) of terrestrial DOM via adsorption and precipitation with Mn- and Fe (hydr)oxides, stimulating the long-term sequestration of sedimentary OC while retaining the microbially-derived DOM in the pore-water. In contrast, reductive dissolution of Mn- and Fe (hydr)oxides may result in re-mobilization of aromatic DOM and increase of DOC flux (C source) to the stream. Future studies are needed to improve our understanding of how in-situ redox gradients and/or microbial activity transform OC-mineral complexes and the coupled C dynamics at Critical Zones.

The Novel Role of Tyrosinase Enzymes in the Storage of Globally Significant Amounts of Carbon in Wetland Ecosystems.

Over the last millennia, wetlands have been sequestering carbon from the atmosphere via photosynthesis at a higher rate than releasing it and, therefore, have globally accumulated 550 × 1015 g of carbon, which is equivalent to 73% of the atmospheric carbon pool. The accumulation of organic carbon in wetlands is effectuated by phenolic compounds, which suppress the degradation of soil organic matter by inhibiting the activity of organic-matter-degrading enzymes. The enzymatic removal of phenolic compounds by bacterial tyrosinases has historically been blocked by anoxic conditions in wetland soils, resulting from waterlogging. Bacterial tyrosinases are a subgroup of oxidoreductases that oxidatively remove phenolic compounds, coupled to the reduction of molecular oxygen to water. The biochemical properties of bacterial tyrosinases have been investigated thoroughly in vitro within recent decades, while investigations focused on carbon fluxes in wetlands on a macroscopic level have remained a thriving yet separated research area so far. In the wake of climate change, however, anoxic conditions in wetland soils are threatened by reduced rainfall and prolonged summer drought. This potentially allows tyrosinase enzymes to reduce the concentration of phenolic compounds, which in turn will increase the release of stored carbon back into the atmosphere. To offer compelling evidence for the novel concept that bacterial tyrosinases are among the key enzymes influencing carbon cycling in wetland ecosystems first, bacterial organisms indigenous to wetland ecosystems that harbor a TYR gene within their respective genome (tyr+) have been identified, which revealed a phylogenetically diverse community of tyr+ bacteria indigenous to wetlands based on genomic sequencing data. Bacterial TYR host organisms covering seven phyla (Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Nitrospirae, Planctomycetes, and Proteobacteria) have been identified within various wetland ecosystems (peatlands, marshes, mangrove forests, bogs, and alkaline soda lakes) which cover a climatic continuum ranging from high arctic to tropic ecosystems. Second, it is demonstrated that (in vitro) bacterial TYR activity is commonly observed at pH values characteristic for wetland ecosystems (ranging from pH 3.5 in peatlands and freshwater swamps to pH 9.0 in soda lakes and freshwater marshes) and toward phenolic compounds naturally present within wetland environments (p-coumaric acid, gallic acid, protocatechuic acid, p-hydroxybenzoic acid, caffeic acid, catechin, and epicatechin). Third, analyzing the available data confirmed that bacterial host organisms tend to exhibit in vitro growth optima at pH values similar to their respective wetland habitats. Based on these findings, it is concluded that, following increased aeration of previously anoxic wetland soils due to climate change, TYRs are among the enzymes capable of reducing the concentration of phenolic compounds present within wetland ecosystems, which will potentially destabilize vast amounts of carbon stored in these ecosystems. Finally, promising approaches to mitigate the detrimental effects of increased TYR activity in wetland ecosystems and the requirement of future investigations of the abundance and activity of TYRs in an environmental setting are presented.

Sulfur Geochemistry Destabilizes Population Oscillations of Wild Rice (Zizania palustris)

AbstractElevated inputs of sulfate to freshwater systems can increase sulfide concentrations in anoxic soils and subsequently destabilize aquatic plant populations, but the interactions between sulfate, other geochemical cycles, and interannual plant population cycles are poorly understood. Increased sulfate loading increases mineralization of nitrogen from litter, but the sulfide produced during this process can limit nitrogen uptake by plants. In some cases, iron may mitigate sulfide's impacts on plants by precipitating iron sulfide. We examined the interannual effects of sulfate loading on mesocosm populations of wild rice, an emergent aquatic plant that undergoes population oscillations and is sensitive to sulfide. Using experimental mesocosms with self‐perpetuating populations, we investigated how population dynamics respond to manipulations of surface water sulfate (10 mg L−1 or 300 mg L−1), sediment iron (4.3 mg g−1 or 10.9 mg g−1 dry weight), and shoot litter (present or removed). Populations exposed to constant 10 mg L−1 sulfate concentrations had stable biomass oscillations of approximately 3‐year periods, consistent with previous studies that demonstrated litter‐driven oscillations in nitrogen availability. Populations exposed to 300 mg L−1 sulfate concentrations produced fewer and smaller seeds and declined to extinction in 6 years or less. We did not find a strong effect of iron loading or litter removal on wild rice biomass or seed production. Our observations show the potential of elevated surface water sulfate to rapidly destabilize wild rice populations under varying iron and organic carbon concentrations.

Stronger link of nosZI than nosZII to the higher total N2O consumption in anoxic paddy surface soils

Rice paddy surface soils emit substantial amounts of atmospheric nitrous oxide (N2O). However, the soil can also act as sites for the abiotic and biological consumption of some of the N2O produced in the soil profile, thus, reducing net N2O emissions. Determining the proportion of N2O consumed in the soil, as well as the amount of N2O microbially reduced to nitrogen (N2) is critical for developing N2O mitigating strategies in paddy soils. However, few studies have focused on these processes. Furthermore, the association of microorganisms containing nosZI and nosZII genes with variations in biological N2O consumption potential remains largely unexplored. Here, moisture-controlled (60% gravimetric water content, GWC) and completely anoxic (helium [He] system) microcosm experiments were conducted on paddy surface soils (0–5 cm deep) treated with N2O. During a 96-h incubation period, the N2O cumulative emissions were monitored, the total N2O consumption and N2 production were quantified, and the population sizes of nosZI- and nosZII-containing microorganisms were analyzed. The results showed that 97.87%–99.99% of the N2O that accumulated in the 5 cm soil profile were consumed before emission, and the N2 increase in these soils accounted for 64.50%–82.44% of the total N2O consumption, indicating that the total N2O consumption potential and biological N2O sink capacity of paddy surface soils were considerable under experimental conditions. Furthermore, the production of N2 from N2O seemed to be positively related to soil pH, with less N2 being produced in more acidic soil. In addition, nosZI gene abundance had a strong positive correlation with N2 production, while nosZII had a much weaker correlation. Considering the positive correlation between N2 production and soil dissolved organic carbon (DOC) consumption and available potassium content (AK), it is speculated that complete denitrification by nosZI-N2O reducers dominate the N2O biological sink capacity of the paddy surface soils investigated in this study.

Ventilation Systems in Wetland Plant Species

Molecular oxygen and carbon dioxide may be limited for aquatic plants, but they have various mechanisms for acquiring these gases from the atmosphere, soil, or metabolic processes. The most common adaptations of aquatic plants involve various aerenchymatic structures, which occur in various organs, and enable the throughflow of gases. These gases can be transferred in emergent plants by molecular diffusion, pressurized gas flow, and Venturi-induced convection. In submerged species, the direct exchange of gases between submerged above-ground tissues and water occurs, as well as the transfer of gases via aerenchyma. Photosynthetic O2 streams to the rhizosphere, while soil CO2 streams towards leaves where it may be used for photosynthesis. In floating-leaved plants anchored in the anoxic sediment, two strategies have developed. In water lilies, air enters through the stomata of young leaves, and streams through channels towards rhizomes and roots, and back through older leaves, while in lotus, two-way flow in separate air canals in the petioles occurs. In Nypa Steck palm, aeration takes place via leaf bases with lenticels. Mangroves solve the problem of oxygen shortage with root structures such as pneumatophores, knee roots, and stilt roots. Some grasses have layers of air on hydrophobic leaf surfaces, which can improve the exchange of gases during submergence. Air spaces in wetland species also facilitate the release of greenhouse gases, with CH4 and N2O released from anoxic soil, which has important implications for global warming.

Stimulating Effect of Trichococcus flocculiformis on a Coculture of Syntrophomonas wolfei and Methanospirillum hungatei.

ABSTRACTSyntrophic anaerobic consortia comprised of fatty acid-degrading bacteria and hydrogen/formate-scavenging methanogenic archaea are of central importance for balanced and resilient natural and manufactured ecosystems: anoxic sediments, soils, and wastewater treatment bioreactors. Previously published studies investigated interaction between the syntrophic bi-cultures, but little information is available on the influence of fermentative bacteria on syntrophic fatty acid oxidation, even though fermentative organisms are always present together with syntrophic partners in the above-mentioned ecosystems. Here, we present experimental observations of stimulated butyrate oxidation and methane generation by a coculture of Syntrophomonas wolfei with any of the following methanogens: Methanospirillum hungatei, Methanobrevibacter arboriphilus, or Methanobacterium formicicum due to the addition of a fermentative Trichococcus flocculiformis strain ES5. The addition of T. flocculiformis ES5 to the syntrophic cocultures led to an increase in the rates of butyrate consumption (120%) and volumetric methane production (150%). Scanning electron microscopy of the most positively affected coculture (S. wolfei, M. hungatei, and T. flocculiformis ES5) revealed a tendency of T. flocculiformis ES5 to aggregate with the syntrophic partners. Analysis of coculture’s proteome with or without addition of the fermentative bacterium points to a potential link with signal transducing systems of M. hungatei, as well as activation of additional butyryl coenzyme A dehydrogenase and an electron transfer flavoprotein in S. wolfei.IMPORTANCE Results from the present study open doors to fascinating research on complex microbial cultures in anaerobic environments (of biotechnological and ecological relevance). Such studies of defined mixed populations are critical to understanding the highly intertwined natural and engineered microbial systems and to developing more reliable and trustable metabolic models. By investigating the existing cultured microbial consortia, like the ones described here, we can acquire knowledge on microbial interactions that go beyond “who feeds whom” relations but yet benefit the parties involved. Transfer of signaling compounds and stimulation of gene expression are examples of indirect influence that members of mixed communities can exert on each other. Understanding such microbial relationships will enable development of new sustainable biotechnologies with mixed microbial cocultures and contribute to the general understanding of the complex natural microbial interactions.

Global modelling of soil carbonyl sulfide exchanges

Abstract. Carbonyl sulfide (COS) is an atmospheric trace gas of interest for C cycle research because COS uptake by continental vegetation is strongly related to terrestrial gross primary productivity (GPP), the largest and most uncertain flux in atmospheric CO2 budgets. However, to use atmospheric COS as an additional tracer of GPP, an accurate quantification of COS exchange by soils is also needed. At present, the atmospheric COS budget is unbalanced globally, with total COS flux estimates from oxic and anoxic soils that vary between −409 and −89 GgS yr−1. This uncertainty hampers the use of atmospheric COS concentrations to constrain GPP estimates through atmospheric transport inversions. In this study we implemented a mechanistic soil COS model in the ORCHIDEE (Organising Carbon and Hydrology In Dynamic Ecosystems) land surface model to simulate COS fluxes in oxic and anoxic soils. Evaluation of the model against flux measurements at seven sites yields a mean root mean square deviation of 1.6 pmol m−2 s−1, instead of 2 pmol m−2 s−1 when using a previous empirical approach that links soil COS uptake to soil heterotrophic respiration. However, soil COS model evaluation is still limited by the scarcity of observation sites and long-term measurement periods, with all sites located in a latitudinal band between 39 and 62∘ N and no observations during wintertime in this study. The new model predicts that, globally and over the 2009–2016 period, oxic soils act as a net uptake of −126 GgS yr−1 and anoxic soils are a source of +96 GgS yr−1, leading to a global net soil sink of only −30 GgS yr−1, i.e. much smaller than previous estimates. The small magnitude of the soil fluxes suggests that the error in the COS budget is dominated by the much larger fluxes from plants, oceans, and industrial activities. The predicted spatial distribution of soil COS fluxes, with large emissions from oxic (up to 68.2 pmol COS m−2 s−1) and anoxic (up to 36.8 pmol COS m−2 s−1) soils in the tropics, especially in India and in the Sahel region, marginally improves the latitudinal gradient of atmospheric COS concentrations, after transport by the LMDZ (Laboratoire de Météorologie Dynamique) atmospheric transport model. The impact of different soil COS flux representations on the latitudinal gradient of the atmospheric COS concentrations is strongest in the Northern Hemisphere. We also implemented spatiotemporal variations in near-ground atmospheric COS concentrations in the modelling of biospheric COS fluxes, which helped reduce the imbalance of the atmospheric COS budget by lowering soil COS uptake by 10 % and plant COS uptake by 8 % globally (with a revised mean vegetation budget of −576 GgS yr−1 over 2009–2016). Sensitivity analyses highlighted the different parameters to which each soil COS flux model is the most responsive, selected in a parameter optimization framework. Having both vegetation and soil COS fluxes modelled within ORCHIDEE opens the way for using observed ecosystem COS fluxes and larger-scale atmospheric COS mixing ratios to improve the simulated GPP, through data assimilation techniques.

Stabilization of Ferrihydrite and Lepidocrocite by Silicate during Fe(II)-Catalyzed Mineral Transformation: Impact on Particle Morphology and Silicate Distribution.

Interactions between aqueous ferrous iron (Fe(II)) and secondary Fe oxyhydroxides catalyze mineral recrystallization and/or transformation processes in anoxic soils and sediments, where oxyanions, such as silicate, are abundant. However, the effect and the fate of silicate during Fe mineral recrystallization and transformation are not entirely understood and especially remain unclear for lepidocrocite. In this study, we reacted (Si-)ferrihydrite (Si/Fe = 0, 0.05, and 0.18) and (Si-)lepidocrocite (Si/Fe = 0 and 0.08) with isotopically labeled 57Fe(II) (Fe(II)/Fe(III) = 0.02 and 0.2) at pH 7 for up to 4 weeks. We followed Fe mineral transformations with X-ray diffraction and tracked Fe atom exchange by measuring aqueous and solid phase Fe isotope fractions. Our results show that the extent of ferrihydrite transformation in the presence of Fe(II) was strongly influenced by the solid phase Si/Fe ratio, while increasing the Fe(II)/Fe(III) ratio (from 0.02 to 0.2) had only a minor effect. The presence of silicate increased the thickness of newly formed lepidocrocite crystallites, and elemental distribution maps of Fe(II)-reacted Si-ferrihydrites revealed that much more Si was associated with the remaining ferrihydrite than with the newly formed lepidocrocite. Pure lepidocrocite underwent recrystallization in the low Fe(II) treatment and transformed to magnetite at the high Fe(II)/Fe(III) ratio. Adsorbed silicate inactivated the lepidocrocite surfaces, which strongly reduced Fe atom exchange and inhibited mineral transformation. Collectively, the results of this study demonstrate that Fe(II)-catalyzed Si-ferrihydrite transformation leads to the redistribution of silicate in the solid phase and the formation of thicker lepidocrocite platelets, while lepidocrocite transformation can be completely inhibited by adsorbed silicate. Therefore, silicate is an important factor to include when considering Fe mineral dynamics in soils under reducing conditions.

Exploring Key Soil Parameters Relevant to Arsenic and Cadmium Accumulation in Rice Grain in Southern China

Paddy soils in some areas of southern China are contaminated by arsenic (As) and cadmium (Cd), threatening human health via the consumption of As- and/or Cd-tainted rice. To date, a quantitative understanding of how soil characteristics control As and Cd accumulation in rice grains under field conditions is still deficient. Based on 31 paired soil-grain samples collected in southern China, we statistically explored which soil parameter or parameter combination from various soil analyses best estimates As and Cd in rice. We found that CaCl2 extraction of field-moist soil collected at rice harvest provided the best estimation (R2adj = 0.47–0.60) for grain Cd followed by dry soil CaCl2 extraction (R2adj = 0.38–0.49), where CaCl2 extractable Cd from moist or dry soil was the dominant soil parameter. Compared to soil totals, parameters from neither dry soil ascorbate-citrate extraction nor anoxic soil incubation improved model performance for grain As (R2adj ≤ 0.44), despite their closer relevance to soil redox conditions during plant As uptake. A key role of soil-available sulfur in controlling grain As was suggested by our models. Our approach and results may help develop potential soil amendment strategies for decreasing As and/or Cd accumulation from soils.

Groundwater-derived U and Ba exports from a coastal acid sulfate soil (CASS) catchment following rain events

Coastal acid sulfate soil (CASS) catchments are regions of enhanced weathering due to sulfur mineral oxidation following drainage of anoxic wetland soils. Heavy rainfall flushes CASS soils, releasing dissolved metals to nearby estuaries and the coastal ocean. The importance of CASS environments on the release of uranium (U) and barium (Ba) to the coastal ocean is not well understood. Here, we discuss daily observations of dissolved Ba and U in an extensively drained CASS system in Australia under contrasting hydrological conditions. Radon-traced groundwater discharge following rain events released trace metals to surface waters. Groundwater fluxes of Ba and U were on average 10% and 30% of the total surface fluxes in the Tuckean Swamp, respectively. The average local surface water fluxes from the Tuckean Swamp were 1692 and 1.6 μmol/m2/yr from the catchment. On a global scale, dissolved Ba and U derived from CASS systems may be equivalent to 1.0% and 2.5% of rivers, respectively, even though CASS cover only ∼0.1% of the global continental area. While CASS may not be a major contributor of dissolved Ba and U to the global ocean, fluxes on a square meter basis indicate that CASS may be highly important to regional U and Ba budgets.

Natural source of Cr(VI) in soil: The anoxic oxidation of Cr(III) by Mn oxides

Cr(VI) from oxidation of geogenic Cr(III) minerals is gradually becoming the primary source of Cr(VI) in soils and groundwater instead of direct emissions. Thermodynamically, natural oxidants of Cr(III) are limited to O2 and Mn oxides. The oxidation of Cr(III) occurs commonly in oxic soils but the difference in the oxidative dissolution of Cr(III) by Mn oxides in different redox soils (especially under anoxic conditions) is not fully understood and field evidence is lacking. Here, the relationship between Cr(VI) and Mn oxides in basalt-origin soil profiles under three different redox conditions (anoxic, suboxic and oxic) was studied. The oxidative dissolution of chromite was validated by synthesising δ-MnO2 that was close to biogenic Mn oxides under anoxic and oxic conditions. In anoxic soils, high levels of Cr(VI) were detected in the same horizons as those where Cr(III)-minerals co-existed with Mn(III/IV) oxides, suggesting an exclusive pathway for Cr(VI) generation through oxidation by Mn oxides where there was a deficiency of other oxidants, such as O2. In oxic soils, the highly abundant Fe oxides combined with Cr(III) to form Cr(III)-Fe(III) oxyhydroxides and Cr(VI) was generated mainly via slow oxidation by O2. The chromite oxidation experiment results also indicated that a high abundance of Mn oxides could promote chromite oxidative dissolution to generate Cr(VI), even under anoxic conditions. Additionally, the form of Cr and the reactivity and abundance of Mn oxides and reducing agents controlled the net content of Cr(VI) in the soil. This study showed that, even under reducing conditions, Cr(III) is readily oxidised by Mn oxides to generate Cr(VI) in reductant-deficient and Mn-rich soils, which may lead to the continuous introduction of Cr(VI) into groundwater and agricultural soils.

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Soil microbiomes harbour unparalleled functional and phylogenetic diversity. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype does not lend itself to high-throughput screening. Here, we tackle the methylation of arsenic (As) in anoxic soils. As methylation was proposed to be catalysed by sulfate-reducing bacteria. However, to date, there are no available anaerobic isolates capable of As methylation, whether sulfate-reducing or otherwise. The isolation of such a microorganism has been thwarted by the fact that the anaerobic bacteria harbouring a functional arsenite S-adenosylmethionine methyltransferase (ArsM) tested to date did not methylate As in pure culture. Additionally, fortuitous As methylation can result from the release of non-specific methyltransferases upon lysis. Thus, we combined metagenomics, metatranscriptomics, and metaproteomics to identify the microorganisms actively methylating As in anoxic soil-derived microbial cultures. Based on the metagenome-assembled genomes of microorganisms expressing ArsM, we isolated Paraclostridium sp. strain EML, which was confirmed to actively methylate As anaerobically. This work is an example of the application of meta-omics to the isolation of elusive microorganisms.

Soil oxidoreductase zymography: Visualizing spatial distributions of peroxidase and phenol oxidase activities at the root-soil interface

Decomposition of organic material in the rhizosphere – the most dynamic microbial habitat in soil – involves arrays of oxidoreductase and hydrolytic enzymes. Spatial distributions of various hydrolytic activities in soil have already been explored by zymographic techniques. However, the distribution of oxidative activity in the rhizosphere remains to be studied. Thus, we extended a Time-Lapse Zymography technique, using Amplex Red® reagent, to visualize and quantify distributions of phenol oxidase and peroxidase activities in the rhizosphere of Zea mays L. growing in a Haplic Phaeozem and the non-rhizospheric soil. The gross oxidative activity was greatest at the root surfaces, and fell to background soil levels 1.26 and 0.73 mm from seminal (>1 mm diameter) and lateral (<0.5 mm diameter) roots, respectively. The rhizosphere extent relative to the root radius was 59% broader around lateral than around seminal roots. The greatest activities, up to 30 nmol cm−2 min−1, were peroxidase-dominated and closely associated with roots. The results confirm the utility of the approach for studying spatio-temporal distributions of oxidative activities in soil. However, actual activity of oxidoreductases in the field will be strongly controlled by fluctuating environmental conditions such as soil aeration and the gradient of reactive oxygen species, which need to be considered especially in anoxic soils.

Does Soil Drying in a Lab Affect Arsenic Speciation in Strongly Contaminated Soils?

This study examined the changes in extractability and fractionation of arsenic (As) that can be caused by the drying of strongly polluted anoxic soil samples. Two untreated and manure-amended soils were incubated for 7 and 21 days in flooded conditions. Thereafter, As water- and 1 M NH4NO3-extractability and As fractionation in a 5-step sequential extraction according to Wenzel were examined in fresh, oven-dried and air-dried samples. Soil treatment with manure considerably affected the results of the sequential extraction. Air-drying caused a significant decrease in As extractability with 1 M NH4NO3 and in As concentrations in the F1 fraction. The highest reduction of extractability (30–41%) was found in manure-treated soils. Oven-drying resulted in a smaller reduction (5–34%) of As extractability. These effects were explained by opposing processes of As mobilization and immobilization. Sequential extraction did not allow for balancing As redistribution due to drying, as As loss from the F1 fraction was smaller than the confidence intervals in the other fractions. The results showed that for the precise determination of As extractability in anoxic soils, fresh samples should be analyzed. However, oven-dried samples may be used for a rough assessment of environmental risk, As the order of magnitude of easily soluble As did not change due to drying.

Microbial Community Structures and Methanogenic Functions in Wetland Peat Soils.

Methane metabolism in wetlands involves diverse groups of bacteria and archaea, which are responsible for the biological decomposition of organic matter under certain anoxic conditions. Recent advances in environmental omics revealed the phylogenetic diversity of novel microbial lineages, which have not been previously placed in the traditional tree of life. The present study aimed to verify the key players in methane production, either well-known archaeal members or recently identified lineages, in peat soils collected from wetland areas in Japan. Based on an ana­lysis of microbial communities using 16S rRNA gene sequencing and the mole­cular cloning of the functional gene, mcrA, a marker gene for methanogenesis, methanogenic archaea belonging to Methanomicrobiales, Methanosarcinales, Methanobacteriales, and Methanomassiliicoccales were detected in anoxic peat soils, suggesting the potential of CH4 production in this natural wetland. “Candidatus Bathyarchaeia”, archaea with vast metabolic capabilities that is widespread in anoxic environments, was abundant in subsurface peat soils (up to 96% of the archaeal community) based on microbial gene quantification by qPCR. These results emphasize the importance of discovering archaea members outside of traditional methanogenic lineages that may have significant functions in the wetland biogeochemical cycle.

Fractionation of stable carbon isotopes during acetate consumption by methanogenic and sulfidogenic microbial communities in rice paddy soils and lake sediments

Abstract. Acetate is an important intermediate during the degradation of organic matter in anoxic flooded soils and sediments. Acetate is disproportionated to CH4 and CO2 by methanogenic or is oxidized to CO2 by sulfate-reducing microorganisms. These reactions result in carbon isotope fractionation, depending on the microbial species and their particular carbon metabolism. To learn more about the magnitude of the isotopic enrichment factors (ε) involved, acetate conversion to CH4 and CO2 was measured in anoxic paddy soils from Vercelli (Italy) and the International Rice Research Institute (IRRI, the Philippines) and in anoxic lake sediments from the northeastern and the southwestern basins of Lake Fuchskuhle (Germany). Acetate consumption was measured using samples of paddy soil or lake sediment suspended in water or in phosphate buffer (pH 7.0), both in the absence and presence of sulfate (gypsum), and of methyl fluoride (CH3F), an inhibitor of aceticlastic methanogenesis. Under methanogenic conditions, values of εac for acetate consumption were always in a range of −21 ‰ to −17 ‰ but higher in the lake sediment from the southwestern basin (−11 ‰). Under sulfidogenic conditions εac values tended to be slightly lower (−26 ‰ to −19 ‰), especially when aceticlastic methanogenesis was inhibited. Again, εac in the lake sediment of the southwestern basin was higher (−18 ‰ to −14 ‰). Determination of εCH4 from the accumulation of 13C in CH4 resulted in much lower values (−37 ‰ to −27 ‰) than from the depletion of 13C in acetate (−21 ‰ to −17 ‰ ), especially when acetate degradation was measured in buffer suspensions. The microbial communities were characterized by sequencing the bacterial 16S rRNA (ribosomal ribonucleic acid) genes as well as the methanogenic mcrA and sulfidogenic dsrB genes. The microbial communities were quite different between lake sediments and paddy soils but were similar in the sediments of the two lake basins and in the soils from Vercelli and the IRRI, and they were similar after preincubation without and with addition of sulfate (gypsum). The different microbial compositions could hardly serve for the prediction of the magnitude of enrichment factors.