Abstract. Floodplains exert profound control on catchment water quality by transiently storing, transforming, and releasing solutes and particulate matter as they flow through the river corridor. These dynamic environments are shaped by periodic floods that increase hydrologic connectivity, linking shallow floodplain soils to groundwater and surface water and driving abrupt shifts in solute mobility. While floodplain inundation is often assumed to flush accumulated solutes toward groundwater and surface water, floods can arise through several different mechanisms — including overbank flow, rising groundwater levels, and rainfall- or snowmelt-induced ponding — each of which likely has a distinct impact on solute transport. Here, we combine field observations with reactive transport simulations to evaluate how distinct forms of inundation impact solute mobilization from floodplains. Results from a dye infiltration experiment reveal that precipitation-driven, top-down inundation events (such as rainfall in excess of infiltration capacity) induce preferential flow through macropores. This floodwater bypasses the soil matrix and results in minimal solute exchange. In contrast, observations from a groundwater-driven, bottom-up flood show rapid increases in solute concentrations as groundwater rose into the soil profile and dissolved evaporites within the soil matrix. To generalize beyond these field observations, we use dual permeability reactive transport simulations to test how inundation type, magnitude, and timing affect net solute exchange between the soil and underlying aquifer. Simulations show that groundwater-driven, bottom-up floods drive a net gain of solutes from the aquifer to the floodplain. Top-down floods, on the other hand, lead to solute loss from the floodplain to the aquifer, but this loss can be outweighed by summer plant water demand, which limits downward percolation of floodwater. Collectively, these results reveal that floodplain inundation cannot be interpreted as a simple flushing process. Instead, net solute exchange depends on the type of inundation event, the extent of preferential flow, and the seasonal timing of flooding with respect to plant transpiration.

Soil hydraulic properties, such as water retention and hydrodynamics, play a pivotal role in regulating belowground carbon (C) storage by influencing microbial activity and nutrient availability. However, empirical measurements of these properties are labor-intensive and often fail to replicate field conditions in laboratory settings. Standardizing and increasing the throughput of hydraulic property measurements is essential to improve model predictions of ecosystem-scale soil C dynamics. To address this need, we investigated the hydraulic properties of intact field-collected soil cores and laboratory-repacked soil columns to assess how soil structure impacts hydraulic measurements and subsequent model predictions of soil respiration. Using four distinct soil textures (sandy loam, silt loam, loam, and silt clay) sampled as part of the Molecular Observation Network (MONet), we compared water retention curves derived from both methods to publicly available HiHydroSoil v2.0 database values. We then applied the Millennial model to simulate soil respiration rates and total C stocks based on measured hydraulic properties. Our experimental results show the largest differences in hydraulic properties between intact and repacked approach for the silty soil texture, and the smallest differences in the sandy soil texture. The model predicted increased respiration in repacked sandy loam and loam cores (~6% and ~9%), while repacked silt loam and silty clay showed ~17% lower respiration vs. intact cores. Respiration in sandy loam and loam soils showed higher respiration in repacked associated with lower SOC stocks compared to intact. However, silt loam and silty clay in repacked cores had ~12–19% higher total C stocks as compared to intact, consistent with SOC protection by clay. These uncertainties in model predictions also varied with whether intact or repacked hydraulic properties were used, emphasizing the need for reliable measurements that account for environmental and anthropogenic impacts on soil structure, with implications for both empirical and modeling efforts.

Organic compounds such as urea and cyanate can serve as nitrogen (N) sources for nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Here we investigated metagenome-assembled genomes (MAGs) for all four nitrifier guilds generated from hydrologically variable floodplain sediments of the Wind River Basin (WRB; Riverton, WY, USA) for their genetic potential to utilize organic N compounds. A vast majority of WRB nitrifier MAGs harbored urease (ure) and at least one urea transporter (utp, urt, dur3). AOA were the most abundant and phylogenetically diverse nitrifiers in WRB floodplain sediments. Several AOA MAGs encoded cyanase (cynS), nitrilase (nit1), omega-amidase (nit2), nitrile hydratase (nthA), and genes related to purine degradation, including biuret hydrolase (biuH), oxamic transcarbamylase (allFGH), and catabolic carbamate kinase (allK). AOA often encoded an uncharacterized amidohydrolase collocated with biuH, rather than allophanate hydrolase (atzF). A small number of AOA encoded atzF, functioning in an unknown pathway. AOB and comammox were of relatively low abundance and taxonomic diversity and were present only at certain depths in WRB; however, they encoded triuret/biuret degradation genes (trtA, biuH, and atzH), and in comammox, these genes were also collocated with allFGHK. The genetic potential of ammonia oxidizers in the WRB floodplain suggests that organic N may support nitrification in this system. The proposed pathways for utilizing purine degradation products other than urea potentially expand the known metabolic capabilities of AOA, AOB, and comammox bacteria and reveal the possibility for cryptic N cycling between microbial community members. IMPORTANCE:Floodplains are critical ecosystems where terrestrial and riverine systems meet. Floodplain sediments experience many, sometimes dramatic, changes in moisture and oxygen concentrations because of changes in water table height, flooding, and drought, leading to active microbial cycling of contaminants and nutrients. Nitrogen is one such nutrient that is not only essential for the building blocks of life but can also be used as an energy source by some microorganisms. Microorganisms that oxidize ammonia and nitrite are a crucial part of the nitrogen cycle and can lead to eventual nitrogen loss from a system. Investigating the genes present in microorganisms responsible for nitrification in a dynamic floodplain suggests that organic nitrogen-from decaying plants or potentially other sources, such as fertilizers, grazing livestock feces, or contaminants (e.g., pesticides, pharmaceuticals)-is an important nitrogen source to these microorganisms. This study identifies genes not previously described in nitrifying microorganisms, expanding their potential metabolic substrates.

The chemodiversity of dissolved organic matter (DOM) in soil has been proposed to influence the microbial metabolism and fate of belowground organic carbon (C). However, integrating DOM chemistry into soil C cycle models to improve predictions of C stocks and fluxes-beyond simply considering DOM pool size-remains a challenge. While recent research suggests that incorporating DOM chemodiversity into models can improve predictions of microbial respiration, there is still a lack of mechanistic understanding describing how DOM chemodiversity affects microbial metabolism and soil respiration. We evaluated whether DOM chemodiversity was a determinant of soil respiration using paired measurements of high-resolution DOM chemistry, obtained from Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and potential soil respiration rates from across the United States (U.S.), all data provided by the Molecular Observation Network. Our objectives were to (1) assess statistical relationships between DOM chemodiversity and microbial respiration, and (2) evaluate the ability of kinetic models to leverage DOM chemistry to explain empirical relationships found in statistical models. Statistical regressions revealed that DOM chemodiversity (alpha diversity) was nonlinearly related to potential soil respiration rates, both independently and through its interactions with DOM and total C concentrations. In soils with relatively high DOM but low total C concentrations, potential soil respiration rates were negatively correlated with DOM alpha diversity, whereas in soils with relatively low DOM and high total C concentrations showed the opposite trend. However, when metabolic transition theory kinetic models were modified to include chemodiversity, their performance was comparable to traditional Monod kinetics approaches, which simulate respiration rates as a function of DOM concentration. The inability to account for nonlinearities in DOM chemodiversity-respiration relationships highlight an opportunity to advance substrate uptake kinetics by establishing causal links between DOM chemodiversity, microbial metabolism trade-offs, and potential interactions under varied environmental conditions.

Chemodiversity of dissolved organic matter (DOM) has been proposed as an ecosystem property controlling the microbial metabolism; thus, the fate of carbon (C) in soils. Recent research suggests that accounting for DOM chemodiversity can improve the accuracy of process-based C cycling models; however, this approach has never been validated at continental U.S. scale. In this study, we used statistical and kinetic modeling approaches to evaluate how DOM chemodiversity affects soil respiration and whether incorporating it in kinetic models improves respiration prediction. We utilized paired high resolution FTICR-MS descriptions of DOM chemistry and soil respiration rate measurements from 63 topsoils across the USA, provided by the Molecular Observation Network. Regression analysis revealed that DOM alpha diversity (defined as the number of detected organic compounds) interacted nonlinearly with dissolved organic C (DOC) and water-extractable total nitrogen (WETN) concentrations. Soils with high DOC and WETN concentrations, showed decreased soil respiration with increasing alpha diversity, while soils with low DOC and WETN concentrations showed increased respiration. Therefore, DOM chemodiversity controlled the plausible tradeoff in microbial metabolism leading to either loss of C through respiration or SOM buildup through increased microbial growth. This finding implies that chemodiversity, as a parameter, has the potential to increase the accuracy of soil C cycling models. To evaluate respiration rate dependence on chemodiversity as a parameter, we tested three kinetic models: (1) as a function of DOC concentration only, (2) with model parameters informed by average DOM chemodiversity and (3) by chemodiversity calculated within chemical classes of DOM. All three models predicted respiration with similar accuracy. This inability suggests that current kinetic formulations do not adequately represent chemodiversity–microbial metabolism interactions. Therefore, we advise future studies to explore the effects of DOM chemodiversity, with consideration of its interactions with tradeoffs in microbial traits and environmental conditions.

Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.

High concentrations of Fe-rich colloids have been detected in the anoxic zones of our Slate River floodplain field site (CO, USA) since 2018. We speculated that the composition and abundance of the colloids is controlled by the seasonal dynamics and spatial heterogeneities of the subsurface. Therefore, our goals were to 1) decipher the structure and chemical composition of Fe-rich colloids, 2) identify mechanisms of colloid transformation and 3) understand their biogeochemical function.TEM analysis revealed nano-spheres and nano-assemblages that consist mainly of Fe, O, Si, and C, with lower contributions from Al, S and Ca. Based on this elemental distribution, we hypothesized that the colloids are composed of Fe minerals that are associated with organic matter and Si. This was further confirmed through Mössbauer spectroscopy and Fe-EXAFS that indicated the colloids consist ferrihydrite associated with organic matter and Si. NanoSIMS imaging detected co-localities of Fe, S, Si, and O, as well as C and N, which demonstrate once more that these are ferrihydrite-based colloids that are embedded in an organic matter-Si matrix. These findings are intriguing as they demonstrate high abundance of ferrihydrite-based colloids in anoxic depths of our field site. The stability of the colloids is likely attributed to the coating of organic matter and Si that serves as a protective layer against the reducing conditions. Nevertheless, our data also showed that colloids collected during snowmelt (Spring 2021) contained a higher proportion of Fe(II) than colloids collected during baseflow conditions (Summer 2021). XPS analysis measured higher atomic percentages of C and Si compared to Fe and O in baseflow versus snowmelt colloids, indicating a decrease in the organic-Si protective layer under baseflow conditions, allowing for Fe(II) oxidation and an increase in Fe(III)/ferrihydrite content. The fact that there is an occurrence of S species only in the more reduced snowmelt colloids illustrates the dynamic and delicate composition of these environmental colloids during seasonal changes in hydrology and porewater chemistry.We are also in the process of interpreting our seasonal data that will shed light on the controls over the seasonal dynamics of the colloids. We have already linked Fe(II) colloid abundance to lower vertical porewater velocities and higher organic matter levels, and are working on additional analyses including data acquired from FT-ICR-MS analysis of the organic composition of the colloids.

This study presents field experiments conducted in a contaminated aquifer in Rifle, CO, to determine the speciation and accumulation of uranium in sediments during in situ bioreduction. We applied synchrotron-based X-ray spectroscopy and imaging techniques as well as aqueous chemistry measurements to identify changes in U speciation in water and sediment in the first days follwing electron donor amendment. Limited changes in U solid speciation were observed throughout the duration of this study, and non-crystalline U(IV) was identified in all samples obtained. However, U accumulation rates strongly increased during in situ bioreduction, when the dominant microbial regime transitioned from iron- to sulfate-reducing conditions. Results suggest that uranium is enzymatically reduced during Fe reduction, as expected. Mineral grain coatings newly formed during sulfate reduction act as reduction hotspots, where numerous reductants can act as electron donors [Fe(II), S(II), and microbial extracellular polymeric substances] that bind and reduce U. The results have implications for identifying how changes in the dominant reducing mechanism, such as Fe versus sulfate reduction, affect trace metal speciation and accumulation. The outcomes from this study provide additional insights into uranium accumulation mechanisms in sediments that could be useful for the refinement of quantitative models describing redox processes and contaminant dynamics in floodplain aquifers.

ABSTRACT We use metagenome-assembled genomes (MAGs) to understand single-carbon (C1) compound-cycling—particularly methane-cycling—microorganisms in montane riparian floodplain sediments. We generated 1,233 MAGs (>50% completeness and <10% contamination) from 50- to 150-cm depth below the sediment surface capturing the transition between oxic, unsaturated sediments and anoxic, saturated sediments in the Slate River (SR) floodplain (Crested Butte, CO, USA). We recovered genomes of putative methanogens, methanotrophs, and methylotrophs (n = 57). Methanogens, found only in deep, anoxic depths at SR, originate from three different clades (Methanoregulaceae, Methanotrichaceae, and Methanomassiliicoccales), each with a different methanogenesis pathway; putative methanotrophic MAGs originate from within the Archaea (Candidatus Methanoperedens) in anoxic depths and uncultured bacteria (Ca. Binatia) in oxic depths. Genomes for canonical aerobic methanotrophs were not recovered. Ca. Methanoperedens were exceptionally abundant (~1,400× coverage, >50% abundance in the MAG library) in one sample that also contained aceticlastic methanogens, indicating a potential C1/methane-cycling hotspot. Ca. Methylomirabilis MAGs from SR encode pathways for methylotrophy but do not harbor methane monooxygenase or nitrogen reduction genes. Comparative genomic analysis supports that one clade within the Ca. Methylomirabilis genus is not methanotrophic. The genetic potential for methylotrophy was widespread, with over 10% and 19% of SR MAGs encoding a methanol dehydrogenase or substrate-specific methyltransferase, respectively. MAGs from uncultured Thermoplasmata archaea in the Ca. Gimiplasmatales (UBA10834) contain pathways that may allow for anaerobic methylotrophic acetogenesis. Overall, MAGs from SR floodplain sediments reveal a potential for methane production and consumption in the system and a robust potential for methylotrophy.IMPORTANCEThe cycling of carbon by microorganisms in subsurface environments is of particular relevance in the face of global climate change. Riparian floodplain sediments contain high organic carbon that can be degraded into C1 compounds such as methane, methanol, and methylamines, the fate of which depends on the microbial metabolisms present as well as the hydrological conditions and availability of oxygen. In the present study, we generated over 1,000 MAGs from subsurface sediments from a montane river floodplain and recovered genomes for microorganisms that are capable of producing and consuming methane and other C1 compounds, highlighting a robust potential for C1 cycling in subsurface sediments both with and without oxygen. Archaea from the Ca. Methanoperedens genus were exceptionally abundant in one sample, indicating a potential C1/methane-cycling hotspot in the Slate River floodplain system.

[This corrects the article DOI: 10.1039/C9EN01427F.].

Soil zinc contamination is a major threat to water quality and sensitive ecosystems. While Zn itself is not redox-active in soils, transitions in soil redox conditions may promote mobilization of Zn from common Zn hosts, including Mn(IV)/Fe(III)-(hydr)oxides and sulfide precipitates, leading to elevated concentrations of dissolved Zn in surface and groundwater and thus a potential increase in Zn transport and uptake. Here, we examined the impacts of hydrologic fluctuations and coupled redox transitions on Zn partitioning in contaminated riparian soil in a mountain watershed. We found that oxygenation of the soil profile during low water conditions caused a spike in porewater Zn concentrations, driven by oxidative dissolution of amorphous ZnS and weak partitioning of Zn to Fe(III)-(hydr)oxides, hydroxy-interlayer vermiculite, and vermiculite. In contrast to Pb, released Zn did not immediately adsorb to Fe(III)-(hydr)oxides or particulate organic matter due to less-favorable sorption of Zn than that of Pb and, further, decreased Zn sorption at slightly acidic pH. As aridification intensifies and groundwater levels decline throughout the western United States, contaminated floodplain soils in mountain watersheds may be frequently oxygenated, leading to increased mobilization of dissolved Zn, which will amplify the threat Zn poses to water quality and ecosystem health.

Injection of acidic hydraulic fracture fluid (HFF) into shale formations for unconventional oil/gas production results in chemical reactions in the shale matrix that can alter fluid transport. Here, we report the results of set of experiments designed to evaluate the impact of calcite dissolution as a function of carbonate mineral content on matrix chemical reactivity and pore-space modification concomitant with imbibition. We tracked acidic HFF transport in four samples of Wolfcamp shale with calcite contents varying from 4% to 59% by monitoring the rate and spatial extent of bromide tracer transport using synchrotron-based X-ray fluorescence microprobe (XFM) imaging. Concurrently, we also carried out XFM imaging of the spatial distribution of Ca in the Wolfcamp shale cores (as a proxy of calcite distribution). Our approach thus yields a direct record of time-resolved selective ion transport resulting from the penetration of acidic HFF and the associated mineral transformations in the shale cores. We show that the variability in calcite content of Wolfcamp shale samples can directly affect the rate and spatial extent of imbibition. Although reaction of the acidic HFF with carbonates in shales enhances calcite dissolution and increases porosity, the spatial extent of calcite dissolution in the shale matrix is limited due to a rapid neutralization of pH. The relative abundance and spatial distribution of calcite control the chemical saturation state of the HFF progressing into the matrix. As a result, calcite has a major impact on the spatial extent and rate of matrix alteration and thus on HFF transport during subsurface reservoir stimulation. Consequently, increased calcite content in the shale matrix inhibits the spatial extent of the pore-volume increase and, by extension, the spatial extent and rate of imbibition. Our results thus show that the overall rates of calcite dissolution approach the rates of acidic HFF transport (i.e., Damköhler number ∼1), which could contribute to the efficiency of subsurface reservoir stimulation. A better understanding of HFF-calcite reaction rates is crucial for improving the prediction and optimization of fluid transport across HFF-shale interfaces during hydraulic fracturing.

Mobilization of naturally-occurring uranium(U) has been recognized to give rise to geogenic U groundwater contamination in aquifers. In addition to carbonate ligand complexation, nitrate has been demonstrated to play a role in controlling U mobility by altering uranium solubility through redox reactions. Nitrate is a common anthropogenic contaminant often prevalent at high concentrations in alluvial aquifers overlaying managed land. Alluvial deposition processes that form these aquifers create a lithologically heterogeneous subsurface with defined contacts between sands, silts, and clays. This leads to deposition of organic carbon and accumulation of reduced metals/radionuclides, including U(IV), in the finer grained silts and clays. The addition of high nitrate porewater into uranium-bearing alluvial aquifer silt sediments stimulated a nitrate reducing microbial community capable of catalyzing U(IV) oxidation and mobilization of U into porewaters. However, metadata from an aquifer wide study and a subsequent experiment revealed that this result is concentration dependent. Low concentrations of nitrate bearing pore-water added into organic-rich, uranium bearing sediments and resulted in a decrease in dissolved U(VI), consistent with reduction. XANES analysis of sediments supported U(VI) reduction with the precipitation of U(IV). U(VI) reduction activity occurred concurrent with an increase in dissolved organic carbon (DOC) and cell and virus abundance and activity. Metagenome assembled genomes from the microbial community revealed the metabolic potential indicating complex carbon degradation, fermentation, mineralization as well as the potential for anaerobic respiration of nitrate, metal/radionuclides, and sulfate. The virome recovered from the samples indicated a change in viral community in response to nitrate amendments and viral-encoded carbohydrate active enzymes were upregulated indicating a coupled response of both viral and microbial community regulating nitrate stimulated carbon biogeochemical cycling. These data together suggest that the addition of an electron acceptor in to organic carbon reduced sediments stimulates not only microbial but also viral activity leading to upregulation of genes associated with carbon biogeochemical cycling in sedimentary systems. While genes associated with metal oxidation are observed, net reduction of uranium prevails leading to uranium immobilization at low nitrate concentrations. Thus together these data indicate a tipping point whereby the influx of nitrate into the reduced environment can influence uranium mobility in DOC and carbon cycling supporting microbial activity and reducing conditions subsurface systems.