Anoxic Soil Research Articles

Redox Gradient Shapes the Chemical Composition of Peatland Microbial Communities.

The response of soil carbon to climate change and anthropogenic forcing depends on the relationship between the physicochemical variables of the environment and microbial communities. In anoxic soils that store large amounts of organic carbon, it can be hypothesized that the low amount of catabolic energy available leads microbial organisms to minimize the energy costs of biosynthesis, which may shape the composition of microbial communities. To test this hypothesis, thermodynamic modeling was used to assess the link between redox gradients in the ombrotrophic peatland of the Marcell Experimental Forest (Minnesota, USA) and the chemical and taxonomic composition of microbial communities. The average amino acid composition of community-level proteins, called hereafter model proteins, was calculated from shotgun metagenomic sequencing. The carbon oxidation state of model proteins decreases linearly from -0.14 at 10 cm depth to -0.17 at 150 cm depth. Calculating equilibrium activities of model proteins for a wide range of chemical conditions allows identification of the redox potential of maximum chemical activity. Consistent with redox measurements across peat soils, this model Eh decreases logarithmically from an average value of 300 mV at 10 cm depth, close to the stability domain of goethite relative to Fe2+, to an average value of -200 mV at 150 cm, within the stability domain of CH4 relative to CO2. The correlation identified between the taxonomic abundance and the carbon oxidation state of model proteins enables predicting the evolution of taxonomic abundance as a function of model Eh. The model taxonomic abundance is consistent with the measured gene and taxonomic abundance, which evolves from aerobic bacteria at the surface including Acidobacteria, Proteobacteria, and Verrumicrobia, to anaerobes at depth dominated by Crenarchaeota. These results indicate that the thermodynamic forcing imposed by redox gradient across peat soils shapes both the chemical and taxonomic composition of microbial communities. By providing a mechanistic understanding of the relationship between microbial community and environmental conditions, this work sheds new light on the mechanisms that govern soil microbial life and opens up prospects for predicting geochemical and microbial evolution in changing environments.

Physiological and biochemical responses of the achachairu tree (Garcinia humilis) to prolonged flooding

Flooding and waterlogging create hypoxic or anoxic soil conditions that negatively affect the physiology of wild and cultivated tropical fruit trees. The achachairu (Garcinia humilis) is a slow-growing tropical fruit tree endemic to the Bolivian Amazon region. Like many tropical trees, G. humilis is increasingly affected by flooding events that may threaten its natural and cultivated areas, but its physiological and biochemical responses to prolonged flooding have not been reported. This study assessed the physiological, biochemical, and morphological responses of G. humilis to prolonged flooding of different durations for up to 30 d Physiological variables measured included leaf gas exchange [net CO2 assimilation (A), stomatal conductance of H2O (gs), and intercellular CO2 concentration (Ci)], leaf chlorophyll index (LCI), and the ratio of variable to maximum chlorophyll fluorescence (Fv/Fm). Antioxidant responses, such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX), glutathione (GSH), glutathione reductase (GTR), dehydroascorbate reductase (DHAR), monodehydroascorbate reductase (MDAR), ascorbic acid (AsA), and glutathione (GSH); reactive oxygen species (ROS); and lipid peroxidation indicated by malondialdehyde (MDA) were also measured. Results indicate that G. humilis is very tolerant of flooding periods of at least 30 d, which causes approximately a 50 % reduction in net A but no measurable negative impact on other physiological variables, including LCI and Fv/Fm. Flooding caused an increase in ROS and malonaldehyde (MDA), which were countered by a robust antioxidant response that possibly contributed to improved flooding tolerance. Plants continued to grow during the flooding period, and A recovered to nearly pre-flooding levels 90 d after plants were unflooded.

Leaf Gas Film 1 promotes glycerol ester accumulation and formation of a tight root barrier to radial O2 loss in rice.

Rice (Oryza sativa L.) and many other wetland plants form an apoplastic barrier in the outer parts of the roots to restrict radial O2 loss to the rhizosphere during soil flooding. This barrier facilitates longitudinal internal O2 diffusion via gas-filled tissues from shoot to root apices, enabling root growth in anoxic soils. We tested the hypothesis that Leaf Gas Film 1 (LGF1), which influences leaf hydrophobicity in rice, plays a crucial role in tight outer apoplastic barriers formation in rice roots. We examined the roots of a rice mutant (dripping wet leaf 7, drp7) lacking functional LGF1, its wild type, and an LGF1 overexpression line for their capacity to develop outer apoplastic barriers that restrict radial O2 loss. We quantified the chemical composition of the outer part of the root and measured radial O2 diffusion from intact roots. The drp7 mutant exhibited a weak barrier to radial O2 loss compared to the wild type. However, introducing functional LGF1 into the mutant fully restored tight barrier function. The formation of a tight barrier to radial O2 loss was associated with increased glycerol ester levels in exodermal cells, rather than differences in total root suberization or lignification. These results demonstrate that, in addition to its role in leaf hydrophobicity regulation, LGF1 plays an important role in controlling the function of the outer apoplastic barriers in roots. Our study suggests that increased deposition of glycerol esters in the suberized root exodermis establishes a tight barrier to radial O2 loss in rice roots.

Millennial-aged organic matter preservation in anoxic and sulfidic mangrove soils: Insights from isotopic and molecular analyses

Mangrove forests are known as coastal carbon sinks, but the long-term (millennium-scale) preservation processes of organic matter (OM) in their soils and the role of sulphur in these processes are still not fully understood. These processes are crucial for better estimating the impact of sea-level variations on the carbon dynamics in mangrove forests, which are particularly sensitive to sea-level changes due to their direct hydrological interactions with coastal waters. This study focuses on a soil layer enriched in mangrove-derived OM that accumulated during a stable sea-level period of the Holocene in New Caledonia (South Pacific). Radiocarbon dating situates this enriched layer at approximately 4000 cal BP. The aim of this study is to characterize the enriched OM layer using bulk (Rock-Eval), isotopic (δ13C and δ15N), and molecular (lignin and neutral carbohydrates) analyses. This OM has undergone diagenetic processes such as dehydrogenation, and the loss of components such as the main neutral carbohydrates: glucose, xylose, and galactose. However, some Rock-Eval parameters, the total lignin content, and carbon and nitrogen isotopic ratios are characteristic of well-preserved OM, suggesting differential decomposition/preservation processes. In addition, SEM observations highlighted the presence of pyrite associated to preserved root material. Along with high Sorg/TOC ratio, these results suggest potential processes of OM sulfurization preserving it from decomposition. Prolonged sea-level stability in addition to anoxic and sulfidic soil conditions enhanced OM accumulation and long-term sequestration in mangrove soils.

Clostridium omnivorum sp. nov., isolated from anoxic soil under the treatment of reductive soil disinfestation.

Reductive soil disinfestation (RSD), also known as biological soil disinfestation, is a bioremediation method used to suppress soil-borne plant pathogens by stimulating the activity of indigenous anaerobic bacteria in the soil. An anaerobic bacterial strain (E14T) was isolated from an anoxic soil sample subjected to RSD treatment and then comprehensively characterized. Cells of the strain were Gram-stain-positive, curved to sigmoid, and spore-forming rods. Cells were motile with a polar flagellum. Strain E14T grew in peptone-yeast extract broth, indicating that it utilized proteinous compounds. Strain E14T was also saccharolytic and produced acetate, isobutyrate, butyrate, isovalerate and gases (H2 and CO2) as fermentation products. The strain did not decompose any of examined polysaccharides except for starch. The major cellular fatty acids of strain E14T were iso-C15:0 and iso-C15:0 DMA. The closest relative to strain E14T, based on 16S rRNA gene sequences, was Clostridium thermarum SYSU GA15002T (96.2 %) in the Clostridiaceae. Whole-genome analysis of strain E14T showed that its genome was 4.66 Mb long with a genomic DNA G+C content of 32.5 mol%. The average nucleotide identity (ANIb) between strain E14T and C. thermarum SYSU GA15002T was 69.0 %. The presence of the genes encoding glycolysis and butyrate production via the acetyl-CoA pathway was confirmed through genome analysis. Based on the obtained phylogenetic, genomic and phenotypic data, we propose that strain E14T should be assigned to the genus Clostridium in the family Clostridiaceae as Clostridium omnivorum sp. nov. The type strain is E14T (=NBRC 115133T=DSM 114974T).

Sequestration of Labile Organic Matter by Secondary Fe Minerals from Chemodenitrification: Insight into Mineral Protection Mechanisms.

Labile organic matter (OM) immobilized by secondary iron (Fe) minerals from chemodenitrification may be an effective way to immobilize organic carbon (OC). However, the underlying mechanisms of coupled chemodenitrification and OC sequestration are poorly understood. Here, OM immobilization by secondary Fe minerals from chemodenitrification was investigated at different C/Fe ratios. Kinetics of Fe(II) oxidation and nitrite reduction rates decreased with increasing C/Fe ratios. Despite efficient sequestration, the immobilization efficiency of OM by secondary minerals varied with the C/Fe ratios. Higher C/Fe ratios were conducive to the formation of ferrihydrite and lepidocrocite, with defects and nanopores. Three contributions, including inner-core Fe-O and edge- and corner-shared Fe-Fe interactions, constituted the local coordination environment of mineral-organic composites. Microscopic analysis at the molecular scale uncovered that labile OM was more likely to combine with secondary minerals with poor crystallinity to enhance its stability, and OM distributed within nanopores and defects had a higher oxidation state. After chemodenitrification, high molecular weight substances and substances high in unsaturation or O/C ratios including phenols, polycyclic aromatics, and carboxylic compounds exhibited a stronger affinity to Fe minerals in the treatments with lower C/Fe ratios. Collectively, labile OM immobilization can occur during chemodenitrification. The findings on OM sequestration coupled with chemodenitrification have significant implications for understanding the long-term cycling of Fe, C, and N, providing a potential strategy for OM immobilization in anoxic soils and sediments.

Microbial central carbon metabolism in a tidal freshwater marsh and an upland mixed conifer soil under oxic and anoxic conditions.

The central carbon (C) metabolic network is responsible for most of the production of energy and biosynthesis in microorganisms and is therefore key to a mechanistic understanding of microbial life in soil communities. Many upland soil communities have shown a relatively high C flux through the pentose phosphate (PP) or the Entner-Doudoroff (ED) pathway, thought to be related to oxidative damage control. We tested the hypothesis that the metabolic organization of the central C metabolic network differed between two ecosystems, an anoxic marsh soil and oxic upland soil, and would be affected by altering oxygen concentrations. We expected there to be high PP/ED pathway activity under high oxygen concentrations and in oxic soils and low PP/ED activity in reduced oxygen concentrations and in marsh soil. Although we found high PP/ED activity in the upland soil and low activity in the marsh soil, lowering the oxygen concentration for the upland soil did not reduce the relative PP/ED pathway activity as hypothesized, nor did increasing the oxygen concentration in the marsh soil increase the PP/ED pathway activity. We speculate that the high PP/ED activity in the upland soil, even when exposed to low oxygen concentrations, was related to a high demand for NADPH for biosynthesis, thus reflecting higher microbial growth rates in C-rich soils than in C-poor sediments. Further studies are needed to explain the observed metabolic diversity among soil ecosystems and determine whether it is related to microbial growth rates.IMPORTANCEWe observed that the organization of the central carbon (C) metabolic processes differed between oxic and anoxic soil. However, we also found that the pentose phosphate pathway/Entner-Doudoroff (PP/ED) pathway activity remained high after reducing the oxygen concentration for the upland soil and did not increase in response to an increase in oxygen concentration in the marsh soil. These observations contradicted the hypothesis that oxidative stress is a main driver for high PP/ED activity in soil communities. We suggest that the high PP/ED activity and NADPH production reflect higher anabolic activities and growth rates in the upland soil compared to the anaerobic marsh soil. A greater understanding of the molecular and biochemical processes in soil communities is needed to develop a mechanistic perspective on microbial activities and their relationship to soil C and nutrient cycling. Such an increased mechanistic perspective is ecologically relevant, given that the central carbon metabolic network is intimately tied to the energy metabolism of microbes, the efficiency of new microbial biomass production, and soil organic matter formation.

Colloidal fraction on pomelo peel-derived biochar plays a dual role as electron shuttle and adsorbent in controlling arsenic transformation in anoxic paddy soil

Arsenic release and reduction in anoxic environments can be mitigated or facilitated by biochar amendment. However, the key fractions in biochars and how they control arsenic transformation remain poorly understood. In this study, a biochar produced from pomelo peel was rich in colloids and was used to evaluate the roles of the colloidal and residual fractions of biochar in arsenic transformation in anoxic paddy soil. Bulk biochar showed a markedly higher maximum adsorption capacity for As(III) at 1732 mg/kg than for As(V) at 75.7 mg/kg, mainly because of the colloidal fraction on the surface. When compared with the control and treatments with the colloidal/residual fraction, the addition of bulk biochar facilitated As(V) reduction and release in the soil during days 0–12, but decreased the dissolved As(III) concentration during days 12–20. The colloidal fraction revealed significantly higher electron donating capacity (8.26 μmole−/g) than that of bulk biochar (0.88 μmole−/g) and residual fraction (0.65 μmole−/g), acting as electron shuttle to promote As(V) reduction. Because the colloidal fraction was rich in aliphatic carbon, fulvic acid-like compounds, potassium, and calcium, it favored As(III) adsorption when more As(III) was released, probably via organic-cation-As(III) complexation. These findings provide deeper insight into the role of the colloidal fraction of biochar in controlling anaerobic arsenic transformation, which will be helpful for the practical application of biochar in arsenic-contaminated environments.

A 1 Ma sedimentary ancient DNA (sedaDNA) record of catchment vegetation changes and the developmental history of tropical Lake Towuti (Sulawesi, Indonesia).

Studying past ecosystems from ancient environmental DNA preserved in lake sediments (sedaDNA) is a rapidly expanding field. This research has mainly involved Holocene sediments from lakes in cool climates, with little known about the suitability of sedaDNA to reconstruct substantially older ecosystems in the warm tropics. Here, we report the successful recovery of chloroplast trnL (UAA) sequences (trnL-P6 loop) from the sedimentary record of Lake Towuti (Sulawesi, Indonesia) to elucidate changes in regional tropical vegetation assemblages during the lake's Late Quaternary paleodepositional history. After the stringent removal of contaminants and sequence artifacts, taxonomic assignment of the remaining genuine trnL-P6 reads showed that native nitrogen-fixing legumes, C3 grasses, and shallow wetland vegetation (Alocasia) were most strongly associated with >1-million-year-old (>1 Ma) peats and silts (114-98.8 m composite depth; mcd), which were deposited in a landscape of active river channels, shallow lakes, and peat-swamps. A statistically significant shift toward partly submerged shoreline vegetation that was likely rooted in anoxic muddy soils (i.e., peatland forest trees and wetland C3 grasses (Oryzaceae) and nutrient-demanding aquatic herbs (presumably Oenanthe javanica)) occurred at 76 mcd (~0.8 Ma), ~0.2 Ma after the transition into a permanent lake. This wetland vegetation was most strongly associated with diatom ooze (46-37 mcd), thought to be deposited during maximum nutrient availability and primary productivity. Herbs (Brassicaceae), trees/shrubs (Fabaceae and Theaceae), and C3 grasses correlated with inorganic parameters, indicating increased drainage of ultramafic sediments and laterite soils from the lakes' catchment, particularly at times of inferred drying. Downcore variability in trnL-P6 from tropical forest trees (Toona), shady ground cover herbs (Zingiberaceae), and tree orchids (Luisia) most strongly correlated with sediments of a predominantly felsic signature considered to be originating from the catchment of the Loeha River draining into Lake Towuti during wetter climate conditions. However, the co-correlation with dry climate-adapted trees (i.e., Castanopsis or Lithocarpus) plus C4 grasses suggests that increased precipitation seasonality also contributed to the increased drainage of felsic Loeha River sediments. This multiproxy approach shows that despite elevated insitu temperatures, tropical lake sediments potentially comprise long-term archives of ancient environmental DNA for reconstructing ecosystems, which warrants further exploration.

Reduction and transformation of Cr(VI)-associated ferrihydrite by Shewanella oneidensis MR-1: Kinetics and secondary minerals

Hexavalent chromium (Cr(VI)) could be sequestrated by soils via microbial reduction to Cr(III) and association with minerals, however, quantitative understanding of metal reducing bacteria on the coupled kinetics of Cr and Fe minerals is still lacking. Here, microbial-mediated ferrihydrite transformation and reductive sequestration of Cr(VI) were investigated with Shewanella oneidensis MR-1 under varying Cr/Fe ratios. Quantitative results depicted that the contents of magnetite from ferrihydrite transformation decreased from 70 % to 22 % after 288 h as Cr/Fe ratios increased from 0 to 8 × 10−3, and reductive transformation rates increased with decreasing Cr/Fe ratio. Elemental mapping and line scan analyses at nano-scale revealed that Cr(VI) was evenly combined within fresh ferrihydrite, and a part of produced Cr(III) was doped into the crystal lattice of magnetite and goethite. Cr may be sequestrated by secondary Fe minerals via structural substitution, surface complexation, and physical encapsulation. Microscopy-based results exhibited that more Fe minerals adsorbed on the surface of cell and less cells were lysed at low Cr/Fe ratios. Confocal laser scanning microscopy depicted that less cells were alive at high Cr/Fe ratios. The amplification of extracellular electron transfer-associated genes was downregulated as Cr/Fe ratios increased. The Cr/Fe ratios could affect cell activity, the combination with Fe minerals, and Mtr gene expression, thus controlling the reductive sequestration of Cr(VI) and phase transformation of ferrihydrite. A kinetic model has been established by combining elementary reductions, and it could well describe Cr(VI) reduction and Cr(III) incorporation under various Cr/Fe ratios during dissimilatory Fe reduction process. These findings could broaden our knowledge of quantifying the migration and transport of Cr in anoxic Cr-contaminated soil environments, and could be useful for simulating Cr dynamic behaviors in the natural soil, aquatic, and sediment environments.

Vegetation Loss Following Vertical Drowning of Mississippi River Deltaic Wetlands Leads to Faster Microbial Decomposition and Decreases in Soil Carbon

AbstractWetland ecosystems hold nearly a third of the global soil carbon pool, but as wetlands rapidly disappear the fate of this stored soil carbon is unclear. The aim of this study was to quantify and then link potential rates of microbial decomposition after vertical drowning of vegetated tidal marshes in coastal Louisiana to known drivers of anaerobic decomposition altered by vegetation loss. Profiles of potential CH4 and CO2 production (surface to 60 cm deep) were measured during anaerobic incubations, organic matter chemistry was assessed with infrared spectroscopy, and soil porewater nutrients and redox potentials were measured in the field along a chronosequence of wetland loss. After vertical drowning, pond soils had lower redox potentials, higher pH values, lower soil carbon and nitrogen concentrations, lower lignin: polysaccharide ratios, more NH4+ and PO43−, and higher rates of potential CO2 release than vegetated marsh soils. Potential CH4 production was similar in vegetated marshes and open water ponds, with depth‐dependent decreases in CH4 production as soil carbon concentrations increased. In these anoxic soils, vegetation loss exerts a primary control on decomposition rates because flooding drives sustained increases in porewater nutrient availability (NH4+ and PO43, dissolved organic carbon) and decreases in redox potential (from −150 to −500 mV) that lead to higher potential CO2 fluxes within a few years. Without new carbon inputs following wetland loss, the sustained decomposition in open water ponds may lead to losses of stored soil carbon and could influence global carbon budgets.

Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments

Abstract. Formate is energetically equivalent to hydrogen and thus is an important intermediate during the breakdown of organic matter in anoxic rice paddy soils and lake sediments. Formate is a common substrate for methanogenesis, homoacetogenesis and sulfate reduction. However, how much these processes contribute to formate degradation and fractionate carbon stable isotopes is largely unknown. Therefore, we measured the conversion of formate to acetate, CH4 and CO2 and the δ13C of these compounds in samples of paddy soils from Vercelli, Italy, and the International Rice Research Institute (IRRI) in the Philippines and of sediments from the NE and SW basins of Lake Fuchskuhle, Germany. The samples were suspended in a phosphate buffer (pH 7.0) in both the absence and presence of sulfate (gypsum) and of methyl fluoride (CH3F), an inhibitor of aceticlastic methanogenesis. In the paddy soils, formate was mainly converted to acetate under both methanogenic and sulfidogenic conditions. Methane was only a minor product and was mainly formed from the acetate. In the lake sediments, the product spectrum was similar but only under methanogenic conditions. In the presence of sulfate, however, acetate and CH4 were only minor products. The isotopic enrichment factors (εform) of formate consumption, determined by Mariotti plots, were in the low range of −8 ‰ to −2.5 ‰ when sulfate was absent, and formate was mainly converted to acetate and CH4. However, no enrichment factor was detectable when formate was degraded with sulfate to mainly CO2. The δ13C of acetate was by about 25 ‰–50 ‰ more negative than that of formate, indicating acetate production by chemolithotrophic homoacetogenesis. Hence, formate seems to be an excellent substrate for homoacetogenesis in anoxic soils and sediments, so that this process is competing well with methanogenesis and sulfate reduction.

Exogenous abscisic acid induces the formation of a suberized barrier to radial oxygen loss in adventitious roots of barley (Hordeum vulgare).

Internal root aeration is essential for root growth in waterlogged conditions. Aerenchyma provides a path for oxygen to diffuse to the roots. In most wetland species, including rice, a barrier to radial oxygen loss (ROL) allows more of the oxygen to diffuse to the root tip, enabling root growth into anoxic soil. Most dryland crops, including barley, do not form a root ROL barrier. We previously found that abscisic acid (ABA) signalling is involved in the induction of ROL barrier formation in rice during waterlogging. Although rice typically does not form a tight ROL barrier in roots in aerated conditions, an ROL barrier with suberized exodermis was induced by application of exogenous ABA. Therefore, we hypothesized that ABA application could also trigger root ROL barrier formation with hypodermal suberization in barley. Formation of an ROL barrier was examined in roots in different exogenous ABA concentrations and at different time points using cylindrical electrodes and Methylene Blue staining. Additionally, we evaluated root porosity and observed suberin and lignin modification. Suberin, lignin and Casparian strips in the cell walls were observed by histochemical staining. We also evaluated the permeability of the apoplast to a tracer. Application of ABA induced suberization and ROL barrier formation in the adventitious roots of barley. The hypodermis also formed lignin-containing Casparian strips and a barrier to the infiltration of an apoplastic tracer (periodic acid). However, ABA application did not affect root porosity. Our results show that in artificial conditions, barley can induce the formation of ROL and apoplastic barriers in the outer part of roots if ABA is applied exogenously. The difference in ROL barrier inducibility between barley (an upland species) and rice (a wetland species) might be attributable to differences in ABA signalling in roots in response to waterlogging conditions.

Methane emissions and the microbial community in flooded paddies affected by the application of Fe-stabilized natural organic matter

Redox chemistry involving the quinone/phenol cycling of natural organic matter (NOM) is known to modulate microbial respiration. Complexation with metals or minerals can also affect NOM solubilization and stability. Inspired by these natural phenomena, a new soil amendment approach was suggested to effectively decrease methane emissions in flooded rice paddies. Structurally stable forms of NOM such as lignin and humic acids (HAs) were shown to decrease methane gas emissions in a vial experiment using different soil types and rice straw as a methanogenic substrate, and this inhibitory behavior was likely enhanced by ferric ion–NOM complexation. A mechanistic study using HAs revealed that complexation facilitated the slow release of the humic components. Interestingly, borohydride-based reduction, which transformed quinone moieties into phenols, caused the HAs to lose their inhibitory capacity, suggesting that the electron-accepting ability of HAs is vital for their inhibitory effect. In rice field tests, the humic–metal complexes were shown to successfully mitigate methane generation, while carbon dioxide emissions were relatively unchanged. Microbial community analysis of the rice fields by season revealed a decrease in specific cellulose-metabolizing and methanogenic genera associated with methane emissions. In contrast, the relative abundance of Thaumarchaeota and Actinomycetota, which are associated with NOM and recalcitrant organics, was higher in the presence of Fe-stabilized HAs. These microbial dynamics suggest that the slow release of humic components is effective in modulating the anoxic soil microbiome, possibly due to their electron-accepting ability. Given the simplicity, cost-effectiveness, and soil-friendly nature of complexation processes, Fe-stabilized NOM represents a promising approach for the mitigation of methane emissions from flooded rice paddies.

Emerging investigator series: Coprecipitation with glucuronic acid limits reductive dissolution and transformation of ferrihydrite in an anoxic soil.

Ferrihydrite, a poorly crystalline Fe(III)-oxyhydroxide, is abundant in soils and is often found associated with organic matter. Model studies consistently show that in the presence of aqueous Fe(II), organic carbon (OC)-associated ferrihydrite undergoes less transformation than OC-free ferrihydrite. Yet, these findings contrast microbial reductive dissolution studies in which the OC promotes the reductive dissolution of Fe(III) in ferrihydrite and leads to the release of associated OC. To shed light on these complex processes, we quantified the extent of reductive dissolution and transformation of native Fe minerals and added ferrihydrite in anoxic soil incubations where pure 57Fe-ferrihydrite (57Fh), pure 57Fe-ferrihydrite plus dissolved glucuronic acid (57Fh + GluCaq), a 57Fe-ferrihydrite-13C-glucuronic acid coprecipitate (57Fh13GluC), or only dissolved glucuronic acid (13GluCaq) were added. By tracking the transformation of the 57Fe-ferrihydrite in the solid phase with Mössbauer spectroscopy together with analysis of the iron isotope composition of the aqueous phase and chemical extractions with inductively coupled plasma-mass spectrometry, we show that the pure 57Fe-ferrihydrite underwent more reductive dissolution and transformation than the coprecipitated 57Fe-ferrihydrite when identical amounts of glucuronic acid were provided (57Fh + GluCaqversus57Fh13GluC treatments). In the absence of glucuronic acid, the pure 57Fe-ferrihydrite underwent the least reductive dissolution and transformation (57Fh). Comparing all treatments, the overall extent of Fe(III) reduction, including the added and native Fe minerals, determined with X-ray absorption spectroscopy, was highest in the 57Fh + GluCaq treatment. Collectively, our results suggest that the limited bioavailability of the coprecipitated OC restricts not only the reductive dissolution of the coprecipitated mineral, but it also limits the enhanced reduction of native soil Fe(III) minerals.

Electrocatalytic method to quantify the redox reactivity of agricultural byproducts

Redox reaction is one of the determining fate pathways for biofertilizer, bio-stimulant, and other biomass-derived soil amendments. Versatile electrochemical method is in demand to screen redox reactivity of solid samples with minimal pretreatments to maintain the material integrity. This study employed reductive (anthraquinone-2,6-disulfonate) and oxidative (quercetin) mediators to visualize the electron donating and accepting functional groups in sugarcane mill mud, a potential bio-stimulant originating from raw sugar production. Mill mud was redox inert under the electrochemical conditions employed, and mediator was required to transfer electrons to and from the working electrodes. Peak areas of cyclic voltammograms were plotted as a function of sample weight, and the slope was used to compare samples. Higher redox reactivity was observed for aromatic, heat-treated (≈90 °C) mill mud samples, and those characteristics decreased by aging. Developed catalytic electrochemistry could be used to (1) screen organic carbon samples for plant growth stimulation in anoxic and sub-oxic soils and (2) monitor the life cycles of biomass feedstocks and value-added products for environmental fate pathways including redox transformation and photolysis.

Co-exposure of microplastics and polychlorinated biphenyls strongly influenced the cycling processes of typical biogenic elements in anoxic soil

The co-exposure of microplastics (MPs) and polychlorinated biphenyls (PCBs) in soil is inevitable, but their combined effect on cycles of typical biogenic elements (e.g. C, N, Fe, S) is still unclear. And the co-exposure of MPs and PCBs caused more severe effects than single exposure to pollution. Therefore, in this study, a 255-day anaerobic incubation experiment was conducted by adding polyethylene microplastics (PE MPs, including 30 ± 10 μm and 500 μm) and PCB138. The presence of PE MPs inhibited the PCB138 degradation. Also, PE MPs addition (1%, w/w) enhanced the methanogenesis, Fe(Ⅲ) reduction, and sulfate reduction while inhibited nitrate reduction and the biodegradation of PCB138. And PCB138 addition (10 mg·kg−1) promoted the methanogenesis and Fe(Ⅲ) reduction, but inhibited sulfate reduction and nitrate reduction. Strikingly, the presence of PE MPs significantly reduced the impact of PCB138 on the soil redox processes. The abundance changes of special microbial communities, including Anaeromyxobate, Geobacter, Bacillus, Desulfitobacterium, Thermodesulfovibrio, Metanobacterium, etc., were consistent with the changes in soil redox processes, revealing that the effect of PE MPs and/or PCB138 on the cycle of typical biogenic elements was mainly achieved by altering the functional microorganisms. This study improves the knowledge of studies on the impact of MPs and combined organic pollutants to soil redox processes, which is greatly important to the stabilization and balance of biogeochemical cycling in ecology.

Bacterial interference competition and environmental filtering reduce the fungal taxonomic and functional contribution to plant residue decomposition in anoxic paddy soils

Plant residue decomposition is central to soil organic matter formation. Fungi, bacteria, and archaea are all well-known agents of residue decomposition. However, their relative taxonomic and functional contributions to plant residue decomposition in anoxic paddy soils are not well understood, and neither are the factors that govern these contributions. Here, a series of microcosms inoculated with two distinct paddy soils and amended with 13C-labeled rice straw was set up. DNA stable-isotope probing (DNA-SIP) based shotgun metagenomic sequencing was performed to reveal the relative contributions of bacteria, archaea, and fungi in rice straw degradation. Furthermore, the possible underlying mechanisms were investigated, focusing on microbial interspecies interference competition. We found that bacteria and archaea collectively accounted for 96.2∼99.5% (in CS anoxic paddy soil) and 81.7∼96.0% (in YT anoxic paddy soil) of the total abundance, while fungi accounted for only 0.5∼3.8% and 4.0∼18.3%, respectively. Phylogenetic distribution of functional genes encoding the carbohydrate-active enzyme (CAZyme) revealed that 87.7% (in CS anoxic paddy soil) and 80.9% (in YT anoxic paddy soil) of these genes were derived from bacteria and archaea, the remainder (12.3% and 19.1%) coming from fungi. The bacteria-fungi antagonism experiment indicated that fungal growth was indeed markedly inhibited by members of the two well-known antimicrobial compounds producing bacterial groups present, the Actinobacteria and the Bacilli. This study indicates that bacterial interference competition and environmental filtering (i.e., low redox/oxygen conditions) may reduce the contribution of fungi to plant residue decomposition in anoxic paddy field environments. These outcomes are important when constructing models to forecast and/or quantitative the microbial contributions to the global carbon dynamics in anoxic paddy soils.

Root acclimations to soil flooding prime rice (Oryza sativa L.) for subsequent conditions of water deficit

Background and aimsThe root barrier to radial O2 loss is a trait induced during soil flooding restricting oxygen loss from the roots to the anoxic soil. It can also restrict radial water loss, potentially providing tolerance towards drought during conditions of water deficit. Several root traits (aerenchyma and xylem vessels area) respond in a similar way to soil flooding and low soil water potentials. Therefore, we hypothesised that root acclimations to soil flooding prime plants to withstand conditions of water deficit.MethodsWe raised plants in hydroponics mimicking contrasting soil water conditions (aerated controls for well-watered soils; stagnant, deoxygenated solutions for flooded soils, and aerated solutions with different PEG6000 concentrations to mimic conditions of water deficit). We used O2 microsensors and gravimetric measurements to characterize the formation of a barrier to radial O2 loss during conditions of water deficit, and measured key anatomical root traits using light microscopy.ResultsSeveral root traits were induced in stagnant conditions as well as in conditions of water deficit, including the barrier to radial O2 loss. The tightness of the barrier to water loss was similar in both stagnant and PEG6000 treatments. Moreover, plants growing in stagnant conditions tolerated a following severe condition of water deficit, whereas those growing in mimicked well-watered conditions did not.ConclusionsWe demonstrated that plants growing in stagnant conditions can withstand following severe conditions of water deficit. We propose that key root traits, such as the barrier to radial O2 loss, which are induced in stagnant conditions as well as mild conditions of water deficit, prime the plants for a following severe condition of water deficit.

Insights on biotic and abiotic 2,4-dichlorophenoxyacetic acid degradation by anaerobic iron-cycling bacteria.

The use of the phenoxy herbicide 2,4-dichlorophenoxyacetic acid (2,4-D) has been steadily increasing in recent years due to its selectivity against broad-leafed weeds and use on genetically modified crops resistant to 2,4-D. This increases the likelihood of 2,4-D persisting in agriculturally impacted soils, sediments, and aquatic systems. Aerobic microorganisms are capable of degrading 2,4-D enzymatically. Anaerobic degradation also occurs, though the enzymatic pathway is unclear. Iron-reducing bacteria (FeRB) have been hypothesized to augment anaerobic degradation through the production of a chemically reactive Fe(II) adsorbed to Fe(III) oxyhydroxides. To test whether this iron species can catalyze abiotic degradation of 2,4-D, an enrichment culture (BLA1) containing a photosynthetic Fe(II)-oxidizing bacterium (FeOB) "CandidatusChlorobium masyuteum" and the FeRB "CandidatusPseudopelobacter ferreus", both of which lacked known 2,4-D degradation genes was investigated. BLA1 produces Fe(II)-adsorbed to Fe(III) oxyhydroxides during alternating photoautotrophic iron oxidation and dark iron reduction (amended with acetate) cycles. No 2,4-D degradation occurred during iron oxidation byFeOB Ca.C. masyuteum or during iron reduction by FeRB Ca.P. ferreus under any incubation conditions tested (i.e., +/-Fe(II), +/-cells, and +/-light), or due to the presence of Fe(II) adsorbed to Fe(III) oxyhydroxides. Our results cast doubt on the hypothesis that the mineral-bound Fe(II) species augments the anaerobic degradation of 2,4-D in anoxic soils and waters by iron-cycling bacteria, and further justify the need to identify the genetic underpinnings of anaerobic 2,4-D degradation.