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Models test our understanding of processes and can reach beyond the spatial and temporal scales of measurements. Multi-component Reactive Transport Models (RTMs), initially developed more than three decades ago, have been used extensively to explore the interactions of geothermal, hydrologic, geochemical, and geobiological processes in subsurface systems. Driven by extensive data sets now available from intensive measurement efforts, there is a pressing need to couple RTMs with other community models to explore non-linear interactions among the atmosphere, hydrosphere, biosphere, and geosphere. Here we briefly review the history of RTM development, summarize the current state of RTM approaches, and identify new research directions, opportunities, and infrastructure needs to broaden the use of RTMs. In particular, we envision the expanded use of RTMs in advancing process understanding in the Critical Zone, the veneer of the Earth that extends from the top of vegetation to the bottom of groundwater. We argue that, although parsimonious models are essential at larger scales, process-based models offer tools to explore the highly nonlinear coupling that characterizes natural systems. We present seven testable hypotheses that emphasize the unique capabilities of process-based RTMs for (1) elucidating chemical weathering and its physical and biogeochemical drivers; (2) understanding the interactions among roots, micro-organisms, carbon, water, and minerals in the rhizosphere; (3) assessing the effects of heterogeneity across spatial and temporal scales; and (4) integrating the vast quantity of novel data, including “omics” data (genomics, transcriptomics, proteomics, metabolomics), elemental concentration and speciation data, and isotope data into our understanding of complex earth surface systems. With strong support from data-driven sciences, we are now in an exciting era where integration of RTM framework into other community models will facilitate process understanding across disciplines and across scales.

The development of a dynamic cell model of the abundant Geobacter sulfurreducens has shown that a kinetic representation of key components of cell metabolism has matched microbial growth dynamics seen in chemostat experiments. The studies have shown that simplified model representations of microbial dynamics in the subsurface that depended on extracellular conditions are derived by parameterizing emerging properties of the kinetic cell model.

A dynamic environment and diverse interactions with marine plankton is reflected in the genomes in bacterioplankton of the marine Roseobacter clade. It is suggested that a significant fraction of marine bacterioplankton communities together account for 30% of the bacterioplankton in most ocean surface waters.

Coxiella burnetii is an underreported zoonotic pathogen in many rural regions globally. We investigated C. burnetii exposure in a remote indigenous tribe residing in the Sierra Nevada de Santa Marta, Colombia. The high seroprevalence of 35% (95% CI, 27-43%) demonstrates the need for One Health studies to identify risk factors, clinical impact, and potential medical, veterinary, and environmental interventions.

Intertidal sands are global hotspots of terrestrial and marine carbon cycling with strong hydrodynamic forcing by waves and tides and high macrofaunal activity. Yet, the relative importance of hydrodynamics and macrofauna in controlling these ecosystems remains unclear. Here, we compare geochemical gradients and bacterial, archaeal, and eukaryotic gene sequences in intertidal sands dominated by subsurface deposit-feeding worms ( Abarenicola pacifica ) to adjacent worm-free areas. We show that hydrodynamic forcing controls organismal assemblages in surface sediments, while in deeper layers selective feeding by worms on fine, algae-rich particles strongly decreases the abundance and richness of all three domains. In these deeper layers, bacterial and eukaryotic network connectivity decreases, while percentages of clades involved in degradation of refractory organic matter, oxidative nitrogen, and sulfur cycling increase. Our findings reveal macrofaunal activity as the key driver of biological community structure and functioning, that in turn influence carbon cycling in intertidal sands below the mainly physically controlled surface layer., (© The Author(s) 2022. Published by Oxford University Press on behalf of National Academy of Sciences.)

About 382 Tg yr -1 of methane rising through the seafloor is oxidized anaerobically (W. S. Reeburgh, Chem Rev 107:486-513, 2007, https://doi.org/10.1021/cr050362v), preventing it from reaching the atmosphere, where it acts as a strong greenhouse gas. Microbial consortia composed of anaerobic methanotrophic archaea and sulfate-reducing bacteria couple the oxidation of methane to the reduction of sulfate under anaerobic conditions via a syntrophic process. Recent experimental studies and modeling efforts indicate that direct interspecies electron transfer (DIET) is involved in this syntrophy. Here, we explore a fluorescent in situ hybridization-nanoscale secondary ion mass spectrometry data set of large, segregated anaerobic oxidation of methane (AOM) consortia that reveal a decline in metabolic activity away from the archaeal-bacterial interface and use a process-based model to identify the physiological controls on rates of AOM. Simulations reproducing the observational data reveal that ohmic resistance and activation loss are the two main factors causing the declining metabolic activity, where activation loss dominated at a distance of <8 μm. These voltage losses limit the maximum spatial distance between syntrophic partners with model simulations, indicating that sulfate-reducing bacterial cells can remain metabolically active up to ∼30 μm away from the archaeal-bacterial interface. Model simulations further predict that a hybrid metabolism that combines DIET with a small contribution of diffusive exchange of electron donors can offer energetic advantages for syntrophic consortia. IMPORTANCE Anaerobic oxidation of methane is a globally important, microbially mediated process reducing the emission of methane, a potent greenhouse gas. In this study, we investigate the mechanism of how a microbial consortium consisting of archaea and bacteria carries out this process and how these organisms interact with each other through the sharing of electrons. We present a process-based model validated by novel experimental measurements of the metabolic activity of individual, phylogenetically identified cells in very large (>20-μm-diameter) microbial aggregates. Model simulations indicate that extracellular electron transfer between archaeal and bacterial cells within a consortium is limited by potential losses and suggest that a flexible use of electron donors can provide energetic advantages for syntrophic consortia., (Copyright © 2021 He et al.)

Through a process called "bioturbation," burrowing macrofauna have altered the seafloor habitat and modified global carbon cycling since the Cambrian. However, the impact of macrofauna on the community structure of microorganisms is poorly understood. Here, we show that microbial communities across bioturbated, but geochemically and sedimentologically divergent, continental margin sites are highly similar but differ clearly from those in nonbioturbated surface and underlying subsurface sediments. Solid- and solute-phase geochemical analyses combined with modeled bioturbation activities reveal that dissolved O 2 introduction by burrow ventilation is the major driver of archaeal community structure. By contrast, solid-phase reworking, which regulates the distribution of fresh, algal organic matter, is the main control of bacterial community structure. In nonbioturbated surface sediments and in subsurface sediments, bacterial and archaeal communities are more divergent between locations and appear mainly driven by site-specific differences in organic carbon sources., Competing Interests: The authors declare no competing interest., (Copyright © 2020 the Author(s). Published by PNAS.)

Reactions mediated by microorganisms determine the fate of many chemicals in natural porous media. At the pore scale, the distribution of chemicals and microorganisms is not homogeneous, leading to heterogeneous distribution of microbial activities at the pore scale. We conducted pore scale reactive transport simulations to investigate the scaling of microbially mediated consumption reaction rates under a range of flow and reaction conditions. The results reveal that the scaling effects largely depended on Péclet and Damköhler numbers. Consumption rate estimates based on volume-averaged concentrations and reaction kinetics overestimated the true volumetric reaction rates, and large-sized biomass aggregates intensified these scaling errors. In contrast, the macroscopic rates estimated via flux-weighted concentrations underestimated the true volumetric reaction rates, with large microbial aggregates reducing scaling errors. This study also demonstrated that macroscopic rate estimates can be improved by combining information on the reaction kinetics with the flux-weighted concentrations., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Proposed syntrophic interactions between the archaeal and bacterial cells mediating anaerobic oxidation of methane coupled with sulfate reduction include electron transfer through (1) the exchange of H 2 or small organic molecules between methane-oxidizing archaea and sulfate-reducing bacteria, (2) the delivery of disulfide from methane-oxidizing archaea to bacteria for disproportionation and (3) direct interspecies electron transfer. Each of these mechanisms was implemented in a reactive transport model. The simulated activities across different arrangements of archaeal and bacterial cells and aggregate sizes were compared to empirical data for AOM rates and intra-aggregate spatial patterns of cell-specific anabolic activity determined by FISH-nanoSIMS. Simulation results showed that rates for chemical diffusion by mechanism (1) were limited by the build-up of metabolites, while mechanisms (2) and (3) yielded cell specific rates and archaeal activity distributions that were consistent with observations from single cell resolved FISH-nanoSIMS analyses. The novel integration of both intra-aggregate and environmental data provided powerful constraints on the model results, but the similarities in model outcomes for mechanisms (2) and (3) highlight the need for additional observational data (e.g. genomic or physiological) on electron transfer and metabolic functioning of these globally important methanotrophic consortia., (© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.)

In coastal marsh ecosystems, porewater salinity strongly affects vegetation distribution and productivity. To simulate marsh porewater salinity, an integrated, spatially explicit model was developed, accounting for tidal inundation, evaporation, and precipitation, as well as lateral and vertical exchanges in both surface waters and the subsurface. It was applied to the Duplin River marsh, Sapelo Island, USA, over a 3-year period, which covered both drought and wet conditions. Simulated porewater salinity in the low and high marsh correlated with Duplin River salinity, with evapotranspiration and precipitation leading to substantial variations in porewater salinities across seasons, in particular in the high marsh. The model revealed substantial interannual variability in marsh soil conditions, and-due to its process-based approach linked to external forcings-can be used to explore effects of sea level rise and changes in hydrological forcings on marsh soil conditions., Competing Interests: Christof Meile is an Academic Editor for PeerJ.

Ferrous iron (Fe II ) oxidation is an important pathway for generating reactive Fe III phases in soils, which can affect organic carbon (OC) persistence/decomposition. We explored how pO 2 concentration influences Fe II oxidation rates and Fe III mineral composition, and how this impacts the subsequent Fe III reduction and anaerobic OC mineralization following a transition from oxic to anoxic conditions. We conducted batch soil slurry experiments within a humid tropical forest soil amended with isotopically labeled 57 Fe II . The slurries were oxidized with either 21% or 1% pO 2 for 9 days and then incubated for 20 days under anoxic conditions. Exposure to 21% pO 2 led to faster Fe II oxidation rates and greater partitioning of the amended 57 Fe into low-crystallinity Fe III -(oxyhydr)oxides (based on Mössbauer analysis) than exposure to 1% pO 2 . During the subsequent anoxic period, low-crystallinity Fe III -(oxyhydr)oxides were preferentially reduced relative to more crystalline forms with higher net rates of anoxic Fe II and CO 2 production-which were well correlated-following exposure to 21% pO 2 than to 1% pO 2 . This study illustrates that in redox-dynamic systems, the magnitude of O 2 fluctuations can influence the coupled iron and organic carbon cycling in soils and more broadly, that reaction rates during periods of anoxia depend on the characteristics of prior oxidation events.

Iron oxides are important structural and biogeochemical components of soils that can be strongly altered by redox-driven processes. This study examined the influence of temporal oxygen variations on Fe speciation in soils from the Luquillo Critical Zone Observatory (Puerto Rico). We incubated soils under cycles of oxic-anoxic conditions (τ oxic :τ anoxic = 1:6) at three frequencies with and without phosphate addition. Fe(II) production, P availability, and Fe mineral composition were monitored using batch analytical and spectroscopic techniques. The rate of soil Fe(II) production increased from ∼3 to >45 mmol Fe(II) kg -1 d -1 over the experiment with a concomitant increase of an Fe(II) concentration plateau within each anoxic period. The apparent maximum in Fe(II) produced is similar in all treatments, but was hastened by P-amendment. Numerical modeling suggests the Fe(II) dynamics can be explained by the formation of a rapidly reducible Fe(III) phases derived from the progressive dissolution and re-oxidation of native Fe(III) oxides accompanied by minor increases in Fe reducer populations. The shift in Fe(III) reactivity is evident from Fe-reducibility assays using Shewanella sp., however was undetectable by chemical extractions, Mössbauer or X-ray Absorption spectroscopies. More broadly, our findings suggest Fe reduction rates are strongly coupled to redox dynamics of the recent past, and that frequent shifts in redox conditions can prime a soil for rapid Fe-reduction.

Many microalgae induce an extracellular carbonic anhydrase (eCA), associated with the cell surface, at low carbon dioxide (CO2) concentrations. This enzyme is thought to aid inorganic carbon uptake by generating CO2 at the cell surface, but alternative roles have been proposed. We developed a new approach to quantify eCA activity in which a reaction-diffusion model is fit to data on (18)O removal from inorganic carbon. In contrast to previous methods, eCA activity is treated as a surface process, allowing the effects of eCA on cell boundary-layer chemistry to be assessed. Using this approach, we measured eCA activity in two marine diatoms (Thalassiosira pseudonana and Thalassiosira weissflogii), characterized the kinetics of this enzyme, and studied its regulation as a function of culture pH and CO2 concentration. In support of a role for eCA in CO2 supply, eCA activity specifically responded to low CO2 rather than to changes in pH or HCO3(-), and the rates of eCA activity are nearly optimal for maintaining cell surface CO2 concentrations near those in the bulk solution. Although the CO2 gradients abolished by eCA are small (less than 0.5 μm concentration difference between bulk and cell surface), CO2 uptake in these diatoms is a passive process driven by small concentration gradients. Analysis of the effects of short-term and long-term eCA inhibition on photosynthesis and growth indicates that eCA provides a small energetic benefit by reducing the surface-to-bulk CO2 gradient. Alternative roles for eCA in CO2 recovery as HCO3(-) and surface pH regulation were investigated, but eCA was found to have minimal effects on these processes.

Marine bacteria drive the biogeochemical processing of oceanic dissolved organic carbon (DOC), a 750-Tg C reservoir that is a critical component of the global C cycle. Catabolism of DOC is thought to be regulated by the biomass composition of heterotrophic bacteria, as cells maintain a C:N:P ratio of ∼50:10:1 during DOC processing. Yet a complicating factor in stoichiometry-based analyses is that bacteria can change the C:N:P ratio of their biomass in response to resource composition. We investigated the physiological mechanisms of resource-driven shifts in biomass stoichiometry in continuous cultures of the marine heterotrophic bacterium Ruegeria pomeroyi (a member of the Roseobacter clade) under four element limitation regimes (C, N, P, and S). Microarray analysis indicated that the bacterium scavenged for alternate sources of the scarce element when cells were C-, N-, or P-limited; reworked the ratios of biomolecules when C- and P- limited; and exerted tighter control over import/export and cytoplasmic pools when N-limited. Under S limitation, a scenario not existing naturally for surface ocean microbes, stress responses dominated transcriptional changes. Resource-driven changes in C:N ratios of up to 2.5-fold and in C:P ratios of up to sixfold were measured in R. pomeroyi biomass. These changes were best explained if the C and P content of the cells was flexible in the face of shifting resources but N content was not, achieved through the net balance of different transcriptional strategies. The cellular-level metabolic trade-offs that govern biomass stoichiometry in R. pomeroyi may have implications for global carbon cycling if extendable to other heterotrophic bacteria. Strong homeostatic responses to N limitation by marine bacteria would intensify competition with autotrophs. Modification of cellular inventories in C- and P-limited heterotrophs would vary the elemental ratio of particulate organic matter sequestered in the deep ocean.

Members of the marine Roseobacter lineage have been characterized as ecological generalists, suggesting that there will be challenges in assigning well-delineated ecological roles and biogeochemical functions to the taxon. To address this issue, genome sequences of 32 Roseobacter isolates were analyzed for patterns in genome characteristics, gene inventory, and individual gene/pathway distribution using three predictive frameworks: phylogenetic relatedness, lifestyle strategy and environmental origin of the isolate. For the first framework, a phylogeny containing five deeply branching clades was obtained from a concatenation of 70 conserved single-copy genes. Somewhat surprisingly, phylogenetic tree topology was not the best model for organizing genome characteristics or distribution patterns of individual genes/pathways, although it provided some predictive power. The lifestyle framework, established by grouping isolates according to evidence for heterotrophy, photoheterotrophy or autotrophy, explained more of the gene repertoire in this lineage. The environment framework had a weak predictive power for the overall genome content of each strain, but explained the distribution of several individual genes/pathways, including those related to phosphorus acquisition, chemotaxis and aromatic compound degradation. Unassembled sequences in the Global Ocean Sampling metagenomic data independently verified this global-scale geographical signal in some Roseobacter genes. The primary findings emerging from this comparative genome analysis are that members of the lineage cannot be easily collapsed into just a few ecologically differentiated clusters (that is, there are almost as many clusters as isolates); the strongest framework for predicting genome content is trophic strategy, but no single framework gives robust predictions; and previously unknown homologs to genes for H(2) oxidation, proteorhodopsin-based phototrophy, xanthorhodpsin-based phototrophy, and CO(2) fixation by Form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) expand the possible mechanisms for energy and carbon acquisition in this remarkably versatile bacterial lineage.

Within soils, biogeochemical processes controlling elemental cycling are heterogeneously distributed owing, in large part, to the physical complexity of the media. Here we quantify how diffusive mass-transfer limitation at the soil aggregate scale controls the biogeochemical processes governing ferrihydrite reductive dissolution and secondary iron mineral formation. Artificial cm-scale aggregates made of ferrihydrite-coated sand inoculated with iron-reducing bacteria were placed in flow-through reactors, mimicking macro- and microporous soil environments. A reactive transport model was developed to delineate diffusively and advectively controlled regions, identify reaction zones and estimate kinetic parameters. Simulated iron (Fe) breakthrough-curves show good agreement with experimental results for a wide-range of flow rates and input lactate concentrations, with only a limited amount (< or =12%) of Fe lost in the reactor outflow over a 31 day period. Model simulations show substantial intra-aggregate, mm-scale radial variations in the secondary iron phase distributions, reproducing the trends observed experimentally where only limited transformation of ferrihydrite was found near the aggregate surface, whereas extensive formation of goethite/lepidocrocite and minor amounts of magnetite and/or siderite were observed toward the aggregate center. Our study highlights the important control of variations in transport intensities on microbially induced iron transformation at the soil aggregate scale.

A 1D reactive transport model (RTM) is used to obtain a mechanistic understanding of the fate of phosphorus (P) in the saturated zone of two contrasting aquifer systems. We use the field data from two oxic, electron donor-poor, wastewater-impacted, sandy Canadian aquifers, (Cambridge and Muskoka sites) as an example of a calcareous and non-calcareous groundwater system, respectively, to validate our reaction network. After approximately 10 years of wastewater infiltration, P is effectively attenuated within the first 10 m down-gradient of the source mainly through fast sorption onto calcite and Fe oxides. Slow, kinetic sorption contributes further to P removal, while precipitation of phosphate minerals (strengite, hydroxyapatite) is quantitatively unimportant in the saturated zone. Nitrogen (N) dynamics are also considered, but nitrate behaves essentially as a conservative tracer in both systems. The model-predicted advancement of the P plume upon continued wastewater discharge at the calcareous site is in line with field observations. Model results suggest that, upon removal of the wastewater source, the P plume at both sites will persist for at least 20 years, owing to desorption of P from aquifer solids and the slow rate of P mineral precipitation. Sensitivity analyses for the non-calcareous scenario (Muskoka) illustrate the importance of the sorption capacity of the aquifer solids for P in modulating groundwater N:P ratios in oxic groundwater. The model simulations predict the breakthrough of groundwater with high P concentrations and low N:P ratios after 17 years at 20 m from the source for an aquifer with low sorption capacity (<0.02% w/w Fe(OH)(3)). In this type of system, denitrification plays a minor role in lowering the N:P ratios because it is limited by the availability of labile dissolved organic matter.