Anoxic Soil Research Articles

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.

Root porosity contributes to root trait space of wetland monocotyledons independently of economics traits

AimsRoot aerenchyma, a key adaptive trait to anoxic soils has rarely been integrated into trait-based plant ecology. This study aims to evaluate the relationship between root porosity and root economics-related traits among wetland plants, focusing on the effect of aerenchyma on root tissue density, a central trait in plant economics spectrum.MethodsRoot porosity, root tissue density with air-space included (RTD) or excluded (RTDA), and other root traits such as root dry matter content (root dry mass to fresh mass ratio) were measured separately for adventitious and lateral roots of 16 garden-grown Ontario wetland monocots with contrasting root longevities.ResultsPrincipal component analysis showed that in the root adaptive trait space of wetland plants, the first dimension is defined by economics-related traits, the second dimension by lateral root porosity and the ratio of lateral to adventitious root length, and the third dimension by adventitious root porosity. Interspecific variation in root porosity was unrelated to root economics traits. Consequently, root tissue density excluding air space (RTDA) better differentiated between species with contrasting root longevities than RTD did, consistently both for adventitious and lateral roots. Root dry matter content accurately predicted RTDA.ConclusionsInterspecific variation in root porosity is independent of root economics: Wetland plants can construct economically conservative or acquisitive roots of any porosity. Consequently, to consistently express root functional relationships among wetland plant species, root tissue density should be expressed with excluding the air space (i.e., RTDA), or with the more easily measured root dry matter content.

Demethylation of the Antibiotic Methylarsenite is Coupled to Denitrification in Anoxic Paddy Soil.

Arsenic (As) biomethylation is an important component of the As biogeochemical cycle, which produces methylarsenite [MAs(III)] as an intermediate product. Its high toxicity is used by some microbes as an antibiotic to kill off other microbes and gain a competitive advantage. Some aerobic microbes have evolved a detoxification mechanism to demethylate MAs(III) via the dioxygenase C-As lyase ArsI. How MAs(III) is demethylated under anoxic conditions is unclear. We found that nitrate addition to a flooded paddy soil enhanced MAs(III) demethylation. A facultative anaerobe Bacillus sp. CZDM1 isolated from the soil was able to demethylate MAs(III) under anoxic nitrate-reducing conditions. A putative C-As lyase gene (BcarsI) was identified in the genome of strain CZDM1. The expression of BcarsI in the As-sensitive Escherichia coli AW3110 conferred the bacterium the ability to demethylate MAs(III) under anoxic nitrate-reducing condition and enhanced its resistance to MAs(III). Both Bacillus sp. CZDM1 and E. coli AW3110 harboring BcarsI could not demethylate MAs(III) under fermentative conditions. Five conserved amino acid resides of cysteine, histidine, and glutamic acid are essential for MAs(III) demethylation under anoxic nitrate-reducing conditions. Putative arsI genes are widely present in denitrifying bacteria, with 75% of the sequenced genomes containing arsI, also possessing dissimilatory nitrate reductase genes narG or napA. These results reveal a novel mechanism in which MAs(III) is demethylated via ArsI by coupling to denitrification, and such a mechanism is likely to be common in an anoxic environment such as paddy soils and wetlands.

Consistent controls on trace metal micronutrient speciation in wetland soils and stream sediments

Trace metal are essential for microbially-mediated biogeochemical processes occurring in anoxic wetland soils and stream bed sediments, but low availability of these elements may inhibit anaerobic element cycling and transformations. Solid-phase speciation is likely a critical control on trace metal availability but has seen limited study in anoxic systems having concentrations similar to geological background levels, where metal limitations may be most prevalent. We have investigated trace metal concentrations and solid-phase speciation in three freshwater subsurface aquatic systems: marsh wetland soils, riparian wetland soils, and the sediments of a streambed. These systems displayed low solid-phase trace metal concentrations, generally at or below geological background levels, which generally followed the trend Zn > Cu ≈ Ni > Co and showed no correlation with major element compositions. All soils and sediments were dominated by quartz but varied in clay mineralogy as well as the organic matter, total sulfur, and total iron contents. X-ray absorption near-edge structure (XANES) spectroscopy shows that sulfur speciation in both wetlands is dominated by organic sulfur. Elemental sulfur and iron sulfides together made up <25% of the sulfur in the wetland soils, but the distribution between inorganic and organic forms was reversed in the stream sediments. Ferrous and ferric iron in clay minerals were common species identified by both XANES and extended X-ray absorption fine structure (EXAFS) spectroscopies at all sites. Iron(III) oxides were substantial components in all but the marsh wetland soils. Quantitative analysis of copper, nickel, and zinc XANES spectra revealed similar metal speciation across all sites. Copper speciation was dominated by sulfides, adsorbed species, and minor amounts of copper bound to organic matter; no metallic copper was detected. Nickel speciation also varied little and was dominated by nickel in clay mineral octahedral sheets and nickel sulfide, with adsorbed species also present. Zinc speciation was slightly more varied, with the marsh wetland soils and stream bed sediments containing adsorbed species, zinc associated with clay mineral structures, and zinc bound to reduced sulfur groups on organic matter, whereas the riparian wetland soils lacked clay-associated zinc but contained zinc sulfide. Trace metals bound to reduced sulfur occurred at every site, with a greater sulfur-bound fraction for copper. The fractional abundance of sulfur-bound species showed no relationship with soil or sediment total sulfur content, which varied by two orders of magnitude. More broadly, the observations in this study suggest that trace metal speciation in freshwater wetland soils and stream sediments is consistently dominated by a small set of recurring components which are distinct for each metal. This may represent a general geochemical phenomenon in anoxic soils and sediments containing trace metals at background concentrations (as low as 3 µg g−1) that was not predicted from systems that are contaminated with or naturally-enriched in copper, nickel, or zinc.

Oxygen matters: Short- and medium-term effects of aeration on hydrolytic enzymes in a paddy soil

Rapid exposure of anoxic microbial communities to oxygen (O2) can have unpredictable effects, including strong suppression of their enzymatic activity. Nonetheless, most medium- and long-term incubation studies on soil organic matter transformations fail to consider aeration effects during sample post-processing and/or assays. Moreover, it remains unclear whether anoxic enzymatic systems are adapted to quick switch to oxic conditions. We evaluated the effects of short-term (2-h oxic (+O2) vs. anoxic (–O2) assays) and medium-term aeration (after 10-day oxic vs. anoxic pre-incubation) on the kinetic parameters (Vmax, Km) of phosphomonoesterase, β-glucosidase, and leucine aminopeptidase in top bulk, rooted, and bottom bulk paddy soil of flooded rice mesocosms. We hypothesized contrasting short- and medium-term responses of hydrolytic enzyme activities to aeration (i) a negative short-term effect caused by reactive O2 species toxicity and/or other mechanisms, and (ii) adaptation of anoxic microbial communities to medium-term aeration reducing the impact of ongoing O2 exposure.Overall, 2-h aeration suppressed Vmax values by 7–43% and catalytic efficiency Ka (Vmax/Km) by 3–22%, and extended the substrate turnover time Tt (7–33%) of three tested enzymes in all soil compartments pre-incubated without O2. In contrast, no short-term suppressive effect of O2 was observed on three tested enzymes after oxic pre-incubation. Medium-term aeration increased Vmax (by 12–253%) and Ka (by 3–78%) of the enzymes and shortened Tt (4–42%) as compared to the anoxic counterpart. These findings support our hypothesis about anoxic microbial community adaptation over the medium-term aeration. Accordingly, the sensitivity of anoxic hydrolytic enzymes to a short-term O2 exposure and the O2 adaptation mechanisms require strong consideration (i) for enzyme assays of anoxic soils and (ii) for understanding the soil organic matter dynamics in environments with O2 fluctuations.

Enhanced mobilization of Cd from commercial pigments in the rhizosphere of flooded lowland rice

Although yellow Cd pigments (Cd-YP), widely used in industrial colorants, are considered inert, increasing evidence suggests once released into the environment, photobleaching/weathering mobilizes Cd from these pigments posing a pollution threat. Although general redox conditions and biotic/microbial activity are known to be important factors in determining Cd release, how spatial trends and specific soil processes regulate the Cd-YP behavior are poorly understood. Using plant rhizotrons in controlled environmental conditions, this study investigated the behavior of Cd-YP amendments matched to levels (15 mg kg−1) representative of contaminated soils in Yixing, China. Using high-resolution two-dimensional diffusive-gradient-in-thin-films (HR-2D-DGT), planar-optode (PO) multilayer systems alongside targeted soil and porewater sampling for chemical analysis the biogeochemistry associated with Cd mobilization from Cd-YP rice rhizospheres were determined. The results showed that there was a significant release of Cd into soil porewaters (51.5 μg L−1), but this reduced by 90.9% and stabilized over time (after 6-days). HR-2D-DGT ion-maps revealed pronounced spatial variances. The flux-maxima for Cd, which located within aerobic-rhizosphere zones, was 9 to 19-fold higher than in associated anoxic bulk soil. In general, zones of radial O2 loss (ROL)/higher redox conditions and lower pH were associated with Cd release, with S2− to SO42− transitions marking the boundaries of high-flux areas. Some isolated colocalization of Fe and Cd hotspots were observed in lateral root regions, but on-the-whole Fe/Mn and Cd release were not linked. In addition, microniche development was also an important feature of Cd mobilization due to soil heterogeneity.

A coupled function of biochar as geobattery and geoconductor leads to stimulation of microbial Fe(III) reduction and methanogenesis in a paddy soil enrichment culture

Biochar can participate in biogeochemical electron transfer processes due to its electron-accepting and donating capabilities (i.e., geobattery) and electron conductivity (i.e., geoconductor). These two functions were separately demonstrated to play a role in biogeochemical iron cycling and methane formation. Yet, little is known about the coupled effect of both electron transfer mechanisms, even though naturally occurring electron transfer through biochar is expected to simultaneously rely on both geobattery and geoconductor mechanisms. Here, we incubated an anoxic paddy soil enrichment culture with acetate as the substrate to investigate how biochar's coupled electron transfer mechanisms influence the electron transfer pathways between microbes and Fe(III) minerals and how it impacts the soil microbial community composition. We found that biochar simultaneously stimulated microbial Fe(III) reduction and methanogenesis by 2.6 and 2.3 fold, but these processes were spatially decoupled. Small biochar particles (5–20 μm) caused higher Fe(III) reduction and methanogenesis rates than large particles (50–100 μm). The addition of biochar enriched a syntrophic acetate-oxidizing co-culture with dominating Fe(III)-reducing Geobacteraceae taxa and acetoclastic methanogenic Methanosarcina taxa. After acetoclastic methanogenesis stopped, the observed continuing methanogenesis was likely due to interspecies electron transfer caused by biochar functioning as a geoconductor transferring electrons from Geobacteraceae to Methanosarcina. In summary, the simultaneous occurrence of Fe(III) reduction and methanogenesis leads to the formation of a cell-biochar-mineral battery network and a cell-biochar-cell conductive network in an enrichment culture from a paddy soil.

Reduction of antimony mobility from Sb-rich smelting slag by Shewanella oneidensis: Integrated biosorption and precipitation

The dissimilatory Fe(III)-reducing bacteria play a significant role in the mobility of antimony (Sb) under reducing environment. Sb-rich smelting slag is iron (Fe)-containing antimonic mine waste, which is one of the main sources of antimony pollution. In this study, the soluble antimony reacted with Fe(III) by S. oneidensis (Shewanella oneidensis strain MR-1) was performed in reduction condition, then the dissolution behavior of the Sb-rich smelting slag with S. oneidensis was investigated. The results showed that the released Sb was immobilized by S. oneidensis and the strain adsorbed Sb(III) preferentially. Sb(V) can be reduced by S. oneidensis without aqueous Fe. In the presence of Fe(III), S. oneidensis mediated Sb bio-adsorption and the chemical redox of Sb-Fe occurred simultaneously. Sb was co-precipitated with Fe to form the Sb(V)-O-Fe(III) secondary mineral, which was identified as the bidentate mononuclear edge-sharing structure by extended X-ray absorption fine structure (EXAFS) analysis. These results suggest that S. oneidensis has a positive effect on the immobilization and minimizing toxicity of antimony in anoxic soil and groundwater, which provides a theoretical basis for the treatment of antimony contamination.

Anaerocolumna chitinilytica sp. nov., a chitin-decomposing anaerobic bacterium isolated from anoxic soil subjected to biological soil disinfestation.

An obligately anaerobic bacterial strain (CTTWT) belonging to the family Lachnospiraceae within the class Clostridia was isolated from an anoxic soil sample subjected to biological or reductive soil disinfestation. Cells of the strain were Gram-stain-positive, short rods with peritrichous flagella. The strain was saccharolytic and decomposed polysaccharides, chitin, xylan and β-1,3-glucan. Strain CTTWT decomposed cell biomass and cell-wall preparations of an ascomycete plant pathogen, Fusarium oxysporum f. sp. spinaciae. The strain produced acetate, ethanol, H2 and CO2 as fermentation products from the utilized substrates. The major cellular fatty acids of the strain were C16 : 1 ω7c dimethylacetal (DMA), C16 : 0 DMA and C18 : 1 ω7c DMA. The closely related species of strain CTTWT based on the 16S rRNA gene sequences were species in the genus Anaerocolumna with sequence similarities of 95.2-97.6 %. Results of genome analyses of strain CTTWT indicated that the genome size of the strain was 5.62 Mb and the genomic DNA G+C content was 38.3 mol%. Six 16S rRNA genes with five different sequences from each other were found in the genome. Strain CTTWT had genes encoding chitinase, xylanase, cellulase, β-glucosidase and nitrogenase as characteristic genes in the genome. Homologous genes encoding these proteins were found in the genomes of the related Anaerocolumna species, but the genomic and phenotypic properties of strain CTTWT were distinct from them. Based on the phylogenetic, genomic and phenotypic analyses, the name Anaerocolumna chitinilytica sp. nov., in the family Lachnospiraceae is proposed for strain CTTWT (=NBRC 112102T=DSM 110036T).

Subsurface aeration of tidal wetland soils: Root-system structure and aerenchyma connectivity in Spartina (Poaceae)

Root-aerenchyma in wetland plants facilitate transport of oxygen from aboveground sources (atmosphere and photosynthesis) to belowground roots and rhizomes, where oxygen can leak out and oxygenate the otherwise anoxic soils. In salt marshes, the soil oxygenation capacity varies among different Spartina-taxa, but little is known about structural pattern and connectivity of root-aerenchyma that facilitates this gas transport. Both environmental conditions and ploidy level play a role for the root-system morphology. Root-system morphology of polyploid Spartina-taxa was studied, quantifying root-tissue volume and root-aerenchyma volume of hexaploid Spartina alterniflora, Spartina maritima, and Spartina × townsendii as well as dodecaploid Spartina anglica from different habitats. Computed tomography (CT)-scan image analysis was applied to quantify the volume of roots and aerenchyma, and to determine the root-system structure (ratio of aerenchyma to root-tissue volumes) and aerenchyma connectivity. On average, Spartina-roots accounted for 12% (v/v) and root-aerenchyma accounted for 1% (v/v) of the soil volume in the pioneer marsh. About 90% (v/v) of all roots were associated with aerenchyma. Root-system structures of S. × townsendii and S. anglica differed and showed clear responses to habitat conditions, such as flooding regime and redox potential. The development of large well-connected aerenchyma fragments were specifically shown in S. anglica and to a minor extend in S. maritima. Aerenchyma in S. alterniflora and S. × townsendii consisted only of smaller fragments. Spartina-dominated tidal marsh soils show high connectivity with the atmosphere via root-aerenchyma. The high ploidy level in S. anglica comes along with high connectivity in root-aerenchyma.

Nitrogen processing by treatment wetlands in a tropical catchment dominated by agricultural landuse

Agriculture is a major contributor to marine nitrogen pollution, and treatment wetlands can be a strategy to reduce it. However, few studies have assessed the potential of treatment wetlands to mitigate nitrogen pollution in tropical regions. We quantify the nitrogen removal rates of four recently constructed treatment wetlands in tropical Australia. We measured denitrification potential (Dt), the inflow-outflow of nutrients, and tested whether the environment in these tropical catchments is favourable for nitrogen removal. Dt was detected in three of the four systems with rates between 2.0 and 12.0 mg m-2 h−1; the highest rates were measured in anoxic soils (ORP −100 to 300 mV) that were rich in carbon and nitrogen (>2% and >0.2%, respectively). The highest nitrogen removal rates were measured when NO3−-N concentrations were >0.4 mg L−1 and when water flows were slow. Treatment wetlands in tropical regions can deliver high removal rates of nitrogen and other pollutants when adequately managed. This strategy can reduce nutrient loads and their impacts on sensitive coastal zones such as the Great Barrier Reef.

Organic Matter from Redoximorphic Soils Accelerates and Sustains Microbial Fe(III) Reduction.

Microbial reduction of Fe(III) minerals is a prominent process in redoximorphic soils and is strongly affected by organic matter (OM). We herein determined the rate and extent of microbial reduction of ferrihydrite (Fh) with either adsorbed or coprecipitated OM by Geobacter sulfurreducens. We focused on OM-mediated effects on electron uptake and alterations in Fh crystallinity. The OM was obtained from anoxic soil columns (effluent OM, efOM) and included-unlike water-extractable OM-compounds released by microbial activity under anoxic conditions. We found that organic molecules in efOM had generally no or only very low electron-accepting capacity and were incorporated into the Fh aggregates when coprecipitated with Fh. Compared to OM-free Fh, adsorption of efOM to Fh decelerated the microbial Fe(III) reduction by passivating the Fh surface toward electron uptake. In contrast, coprecipitation of Fh with efOM accelerated the microbial reduction, likely because efOM disrupted the Fh structure, as noted by Mössbauer spectroscopy. Additionally, the adsorbed and coprecipitated efOM resulted in a more sustained Fe(III) reduction, potentially because efOM could have effectively scavenged biogenic Fe(II) and prevented the passivation of the Fh surface by the adsorbed Fe(II). Fe(III)-OM coprecipitates forming at anoxic-oxic interfaces are thus likely readily reducible by Fe(III)-reducing bacteria in redoximorphic soils.

Extensive production of hydroxyl radicals during oxygenation of anoxic paddy soils: Implications to imidacloprid degradation

Hydroxyl radical (•OH) plays a critical role in driving organic pollutants degradation during redox fluctuations. Such processes have been frequently investigated in sedimentary environments, but rarely referred to the agricultural fields, such as paddy soils with frequent occurrence of redox fluctuations. Our findings demonstrated that extensive •OH (40.3–1061.4 μmol kg−1) was produced during oxygenation of anoxic paddy slurries under circumstance conditions. Wet chemical sequential extractions, Mössbauer spectra, and X-ray photoelectron spectroscopy characterizations collectively corroborated that 0.5 M HCl-extracted Fe(II) (i.e., surface-bound Fe and Fe in low-crystalline minerals) contributed to more •OH production than aqueous Fe2+. The produced •OH can efficiently induce the oxidative transformation of organic carbon and the degradation of imidacloprid (IMP), which in turn produced the by-products, such as IMP-urea, IMP-olefin, and 6-chloronicontinic acid, via •OH-attacking mechanisms. Quenching experiments showed that hydrogen peroxide (H2O2) was the important intermediate for •OH formation via Haber-Weiss mechanisms during oxygenation processes. These findings indicate that abundant •OH can be produced during the redox fluctuations of paddy soil, which might be of great significance to predict the removal of organic contaminants and the mineralization of organic carbon in paddy fields.

Novel functions of the root barrier to radial oxygen loss - radial diffusion resistance to H2 and water vapour.

The root barrier to radial O2 loss (ROL) is a trait enabling waterlogging tolerance of plants. The ROL barrier restricts O2 diffusion to the anoxic soil so that O2 is retained inside root tissues. We hypothesised that the ROL barrier can also restrict radial diffusion of other gases (H2 and water vapour) in rice roots with a barrier to ROL. We used O2 and H2 microsensors to measure ROL and permeability of rice roots, and gravimetric measurements to assess the influence of the ROL barrier on radial water loss (RWL). The ROL barrier greatly restricted radial diffusion of O2 as well as H2 . At 60kPa pO2 , we found no radial diffusion of O2 across the barrier, and for H2 the barrier reduced radial diffusion by 73%. Similarly, RWL was reduced by 93% in roots with a ROL barrier. Our study showed that the root barrier to ROL not only completely blocks radial O2 diffusion under steep concentration gradients but is also a diffusive barrier to H2 and to water vapour. The strong correlation between ROL and RWL presents a case in which simple measurements of RWL can be used to predict ROL in screening studies with a focus on waterlogging tolerance.

Saltwater intrusion affects nitrogen, phosphorus and iron transformations under oxic and anoxic conditions: an incubation experiment

Low-lying coastal ecosystems are rapidly salinizing due to sea level rise and associated saltwater intrusion (SWI). In agricultural soils, SWI can alter biogeochemical cycling of key nutrients such as nitrogen (N), phosphorus (P), and iron (Fe). The main objective of this study was to quantify the amount of nitrate–N (NO3–N), ammonium–N (NH4–N), soluble reactive P (SRP), and total dissolved iron (TDFe) released from agricultural soils undergoing SWI to determine their potential loss to downstream waterways. Agricultural soils were incubated for 0, 15, and 30 days (under oxic and anoxic conditions) with various salt solution combinations of sodium chloride (NaCl), sodium sulfate (Na2SO4), calcium sulfate (CaSO4), and Instant Ocean® to mimic (1) different ionic constituents of saltwater at different ionic strengths and (2) the presence or absence of gypsum, a soil amendment, through the addition of CaSO4. We also included a set of incubations treated with deionized water as a no ionic strength control (0.00 M). To increase statistical power, we grouped individual salt treatments based on our initial hypotheses at the end of the incubation period (day 30) to determine the effects of high (0.26–0.28 M) and low (0.03–0.04 M) ionic strength on inorganic N release and combinations of Ca and SO42− additions on SRP release to microcosm soil solution. Calcium additions decreased SRP release relative to saltwater that contained only NaCl additions under oxic and anoxic conditions. Additionally, high ionic strength treatments, which were about 7 times the ionic strength of low ionic strength treatments, released two times as much NH4–N to the soil solution, which suggests a non-linear relationship between ionic strength and NH4–N release. At day 30, anoxic microcosm soils treated with Instant Ocean® to simulate 15 parts per thousand seawater (ionic strength 0.26 M) released significantly more NH4–N (by 782 times), SRP (by 6 times), and TDFe (by 197 times) to the soil solution than oxic microcosm soils (P < 0.05). This treatment was designed to reflect a field inundated by brackish seawater for almost a month, which is representative of conditions on farm fields undergoing SWI. Under these anoxic conditions, as much as 22% of bioavailable soil P (as SRP) and 45% of total inorganic N (as NH4–N) could be released to overlying water when inundated with saltwater. Our work indicates that the influx of salts and inundation of SWI-affected farm fields could lead to a large export of N and P from agricultural soils and potentially affect downstream water quality.

Decrypting bacterial polyphenol metabolism in an anoxic wetland soil

Microorganisms play vital roles in modulating organic matter decomposition and nutrient cycling in soil ecosystems. The enzyme latch paradigm posits microbial degradation of polyphenols is hindered in anoxic peat leading to polyphenol accumulation, and consequently diminished microbial activity. This model assumes that polyphenols are microbially unavailable under anoxia, a supposition that has not been thoroughly investigated in any soil type. Here, we use anoxic soil reactors amended with and without a chemically defined polyphenol to test this hypothesis, employing metabolomics and genome-resolved metaproteomics to interrogate soil microbial polyphenol metabolism. Challenging the idea that polyphenols are not bioavailable under anoxia, we provide metabolite evidence that polyphenols are depolymerized, resulting in monomer accumulation, followed by the generation of small phenolic degradation products. Further, we show that soil microbiome function is maintained, and possibly enhanced, with polyphenol addition. In summary, this study provides chemical and enzymatic evidence that some soil microbiota can degrade polyphenols under anoxia and subvert the assumed polyphenol lock on soil microbial metabolism.

Differential effects of redox conditions on the decomposition of litter and soil organic matter

Soil redox conditions exert substantial influence on biogeochemical processes in terrestrial ecosystems. Humid tropical forest soils are often characterized by fluctuating redox, yet how these dynamics affect patterns of organic matter decomposition and associated CO2 fluxes remains poorly understood. We used a 13C-label incubation experiment in a humid tropical forest soil to follow the decomposition of plant litter and soil organic matter (SOM) in response to four redox regimes—static oxic or anoxic, and two oscillating treatments. We used high-resolution mass spectrometry to characterize the relative composition of organic compound classes in the water extractable OM. CO2 production from litter and SOM showed different responses to redox treatments. While cumulative production of SOM-derived CO2 was positively correlated with the length of oxic exposure (r = 0.89, n = 20), cumulative 13C-litter-derived CO2 production was not linked to oxygen availability. Litter-derived CO2 production was highest under static anoxic conditions in the first half of the experiment, and later dropped to the lowest rate amongst the treatments. In anoxic soils, we observed depletion of more oxidized water-extractable OM (especially amino sugar-, carbohydrate-, and protein-like compounds) over the second half of the experiment, which likely served as substrates for anaerobic CO2 production. Results from two-pool kinetic modeling showed that more frequent anoxic exposure limited decomposition of a slow-cycling C pool, but not a fast-cycling pool. These results suggest that aerobic and anaerobic heterotrophs were equally effective at degrading labile substrates released from fresh plant litter in this humid tropical forest soil, while aerobic decomposers were more effective in breaking down the potentially refractory compounds found in SOM.

Soil microbial communities-mediated bioattenuation in simulated aquifer storage and recovery (ASR) condition: Long-term study

This study evaluated the long-term organic removal performance and microbial community shift in simulated aquifer storage and recovery (ASR) conditions. For this purpose, anoxic soil box systems were operated at 15 °C for one year. The results showed that the assimilable organic carbon (AOC) concentration in the anoxic soil box systems was successfully decreased by 79.1%. The dissolved organic carbon (DOC) concentration increased during the initial operational periods; however, it subsequently decreased during long-term operation. Readily biodegradable organic fractions (i.e., low-molecular weight (LMW) neutrals and LMW acids) decreased along with time elapsed, whereas non-biodegradable fraction (i.e., humic substances) increased. Proteobacteria and Acidobacteriota were predominant in the anoxic box systems throughout the operational periods. Firmicutes and Bacteroidota suddenly increased during the initial operational period while Gemmatimonadota slightly increased during prolonged long-term operation. Interestingly, the microbial community structures were significantly shifted with respect to the operational periods while the effects of AOC/NO3− addition were negligible. Various bacterial species preferring low temperature or anoxic conditions were detected as predominant bacteria. Some denitrifying (i.e., Noviherbaspirillum denitrificans) and iron reducing bacteria (i.e., Geobacter spp.) appeared during the long-term operation; these bacterial communities also acted as organic degraders in the simulated ASR systems. The findings of this study suggest that the application of natural bioattenuation using indigenous soil microbial communities can be a promising option as an organic carbon management strategy in ASR systems.

Pulse labelling of deep soil layers in forest with 13CH4: testing a new method for tracing methane in the upper horizons, understorey vegetation and tree stems using laser-based spectrometry

Methane emissions from plants in wetlands are mainly due to internal transport, from the anoxic soil layers where methane is produced, to the atmosphere. This pathway has not yet been clearly demonstrated for upland forest vegetation, where methane can be produced in deep soil layers. We developed a new method to trace methane transfer from the deep soil. We conducted a 13CH4 pulse labelling at 40-cm soil depth and then monitored 13CH4 in the upper horizons, at the soil surface (with or without understorey vegetation) and emitted by tree stems until the total disappearance of the labelled gas. Most of the injected 13CH4 was oxidized in the soil despite high soil water content. The understorey vegetation did not contribute to 13CH4 emission by the soil. We prove that tree stems can emit methane produced in an upland forest soil, even when the said soil is a net methane sink. We conclude that pulse labelling with 13CH4 and tracing by laser-based spectrometry is a promising tool approach to study the transport of methane from production to emission.

Clothianidin decomposition in Missouri wetland soils.

Neonicotinoid pesticides can persist in soils for extended time periods; however, they also have a high potential to contaminate ground and surface waters. Studies have reported negative effects associated with neonicotinoids and nontarget taxa, including aquatic invertebrates, pollinating insect species, and insectivorous birds. This study evaluated factors associated with clothianidin (CTN) degradation and sorption in Missouri wetland soils to assess the potential for wetland soils to mitigate potential environmental risks associated with neonicotinoids. Solid-to-solution partition coefficients (Kd ) for CTN sorption to eight wetland soils were determined via single-point sorption experiments, and sorption isotherm experiments were conducted using the two most contrasting soils. Clothianidin degradation was determined under oxic and anoxic conditions over 60 d. Degradation data were fit to zero- and first-order kinetic decay models to determine CTN half-life (t0.5 ). Sorption results indicated CTN sorption to wetland soil was relatively weak (average Kd , 3.58 L kg-1 ); thus, CTN has the potential to be mobile and bioavailable within wetland soils. However, incubation results showed anoxic conditions significantly increased CTN degradation rates in wetland soils (anoxic average t0.5 , 27.2 d; oxic average t0.5 , 149.1 d). A significant negative correlation was observed between anoxic half-life values and soil organic C content (r2 =.782; p=.046). Greater CTN degradation rates in wetland soils under anoxic conditions suggest that managing wetlands to facilitate anoxic conditions could mitigate CTN presence in the environment and reduce exposure to nontarget organisms.