Biology subjects

Stegen, J. C.

Publications and source records attributed to Stegen, J. C..

At least 19 recordsLinked to original sources

bioRxiv2025

Harnessing artificial intelligence to automate environmental predictions

Predicting heterogeneous and non-linear processes remains a fundamental challenge in Earth sciences. Here, we present an artificial intelligence (AI)-guided framework that iteratively combines predictive modeling with targeted field sampling to rapidly improve environmental predictions. We demonstrate our workflow by predicting oxygen consumption, a key process of stream metabolism, across the contiguous United States (CONUS). Our approach consisted of 18 iterative loops of measurements and models, combining distributed participatory field sampling, lab analysis, automated machine learning (ML) predictions, and error and distinctiveness analyses to autonomously guide the next sampling at optimal site locations. Through our approach, we increased the predictive power of sediment oxygen consumption across CONUS by over fifteenfold between the first and last iteration. Relative to our last sampling iteration, our first sampling missed sites with high rates and underestimated median oxygen consumption rates by 68%. In addition to identifying areas of high oxygen consumption rates, iterations enabled refinement of laboratory and data handling methods, and engagement with a broad community of field researchers. We conclude that AI-guided iterative loops between targeted sampling and predictive modeling are a powerful and efficient approach for improving predictions of heterogeneous environmental processes.

ecology↗

bioRxiv2025

A uniform stress response of stream microbiomes in the hyporheic zone across North America

BackgroundStream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental stressors. ResultsBased on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies. ConclusionsThe hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems.

microbiology↗

bioRxiv2024

Modeling Microbial Regulatory Feedback in Organic Matter Decomposition Identifies Copiotrophic Traits as Key Drivers of Positive Priming

Microbial decomposition of complex soil organic matter (OM) is often regulated by labile organic carbon inputs, a phenomenon known as priming, which plays a critical role in belowground biogeochemical cycling. However, the strength and direction of microbial priming of soil OM pools varies significantly across ecosystems. A generalizable mechanistic framework explaining the factors that lead to accelerated (positive priming) or impeded (negative priming) rates of OM decomposition is still lacking. In this work, we conceptualize priming as a microbial feedback loop that optimizes the costs and benefits of maximizing growth rate, specifically, the cost of exoenzyme synthesis for decomposing complex OM versus the benefit of energy acquisition from labile OM. We examined the impacts of microbial growth traits and interactions on priming by employing a cybernetic modelling approach, which predicts complex microbial growth patterns by accounting for dynamic metabolic regulations. We simulated microbial priming across ecological community configurations composed of degraders and non-degraders with either oligotrophic or copiotrophic growth traits, resulting in seven combinations that included both single functional groups (degraders with either growth trait) and binary functional groups (combinations of degraders and non-degraders, or degraders only, with differing or common traits). Configurations with only non-degraders were excluded, as they are irrelevant for studying priming in OM decomposition. Monte Carlo simulations for these scenarios revealed: (1) positive priming is prevalent, while negative priming occurs sporadically under specific parameter settings; (2) positive priming is more frequently observed in microbial systems with copiotrophic degraders than those with oligotrophic degraders; (3) the presence of copiotrophic non-degraders suppresses positive priming, whereas the presence of oligotrophic non-degraders promotes it; and (4) the temporal dynamics of priming is also influenced by microbial growth traits and interactions. These findings highlight the driving role of microbial functional traits and interactions in priming. Most strikingly, our simulations predicted a dramatic positive priming effect triggered by the addition of a small amount (i.e., less than 10%) of labile OM, with no notable changes observed beyond this point. As we used a generalized microbial model, we hypothesize that our findings may reflect common features of OM priming across diverse microbial systems and environments. Overall, this work, combining new theories and models, significantly enhances our understanding of priming by providing model-generated and empirically testable hypotheses on the mechanisms governing it.

systems biology↗

bioRxiv2024

Sediment-associated processes drive spatial variation in ecosystem respiration in the Yakima River basin

Hyporheic zones (HZ) can contribute substantially to total stream ecosystem respiration (ERtot). HZ-focused process-based models may, therefore, effectively predict ERtot across sites, yet this remains untested under variable environmental conditions. Here we evaluate whether spatial variation in HZ respiration predicted via a process-based model explains spatial variation in field-estimates of ERtot across 33 sites in the Yakima River basin in Washington State, USA. We found that HZ respiration predictions did not explain spatial variation in field estimates of ERtot. To investigate further, we partitioned ERtot contributions into water column respiration (ERwc) and sediment-associated respiration (ERsed). ERsed contributed >50% of ERtot at 88% of sites, though relative contributions varied substantially. Despite this dominance, modeled HZ respiration explained neither spatial variation in ERtot nor in ERsed, suggesting that the HZ model alone does not capture the drivers of sediment-associated respiration across these sites. Instead, ERsed spatial variation was primarily explained by gross primary production, stream slope, velocity, and total dissolved nitrogen rather than median grain size, a primary control of HZ respiration predicted by the process-based model. Consistent with recent studies, our results indicate that improving basin-scale ERtot predictions requires integrating hydrologic and biogeochemical processes across hyporheic, benthic, and water column zones.

ecology↗

bioRxiv2024

Meta-metabolome ecology reveals that geochemistry and microbial functional potential are linked to organic matter development across seven rivers

Rivers receive substantial dissolved organic matter (DOM) input from the land and transport it to the ocean. As DOM travels through watersheds, it undergoes biotic and abiotic transformations that impact biogeochemical cycles and any subsequent CO2 release into the atmosphere. While recent research has increased our mechanistic knowledge of DOM composition within watersheds, DOM development across broad spatial distances and within divergent biomes is under investigated. Here, we combined DOM characterization, geochemical analyses, and shotgun metagenomics to analyze samples from seven rivers ranging from the U.S. Pacific Northwest to Berlin, Germany. Initial analyses revealed that many DOM properties were distinguished by river type (e.g., wastewater, headwater) and that geochemistry often explained variation across rivers. At a global scale, analyses rooted in meta-metabolome ecology indicated that DOM was structured overwhelmingly by deterministic selection. When controlling for scale, however, analyses indicated that ecological assembly dynamics were again partially structured by river type. Finally, microbial analyses revealed that many riverine microbes from our systems shared core metabolic functional potential while differing in peripheral capabilities in across the rivers. Further analysis of the carbon degradation potential for recovered metagenomically assembled genomes indicated that the sampled rivers had strong taxonomically conserved niche differentiation and that carbon degradation potential diversity was significantly related to organic matter diversity. Together, these results help us uncover interconnections between the development of DOM, riverine geochemistry, and microbial functional potential.

ecology↗

bioRxiv2022

Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments

Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to global greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, microbial roles in these climatically relevant systems are mostly inferred from 16S rRNA amplicon surveys, which are not sufficiently resolved to inform biogeochemical models. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated dataset of over 30 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome assembled genomes (MAGs), which we dereplicated into 55 unique genomes spanning 12 bacterial and archaeal phyla. We also reconstructed 2482 viral genomic contigs, which were dereplicated into 111 viral MAGs >10kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovers new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. Integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen we show how these metabolic pathways could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral genomes to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. ImportanceHere we created HUM-V (Hyporheic Uncultured Microbial and Viral), an annotated microbial and viral genome catalog that captures the strain and functional diversity encoded in river sediments. Demonstrating its utility, this genomic inventory encompasses multiple representatives of the most dominant microbial and archaeal phyla reported in river sediments and provides novel viral genomes that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these genomes and reconstruct their active roles in river sediment biogeochemical cycling. We show the power of genome resolved, multi-omics to uncover the organismal interactions and chemical handoffs shaping an intertwined carbon and nitrogen metabolic network and create a framework that can be extended to other river sediments. The accessible microbial and viral genomes in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these and related freshwater terrestrial-aquatic ecosystems.

microbiology↗

bioRxiv2020

Disturbance Triggers Non-Linear Microbe-Environment Feedbacks

Conceptual frameworks linking microbial community membership, properties, and processes with the environment and emergent function have been proposed but remain untested. Here we refine and test a recent conceptual framework using hyporheic zone sediments exposed to wetting/drying transitions. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community--but not the whole community--responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter became less favorable for oxidation (an environmental component) and respiration decreased (a microbial process). While these responses were step functions of desiccation, we observed continuous monotonic relationships among community assembly, respiration, and organic matter thermodynamics. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance, mediated by thermodynamics, and that cause the impacts of disturbance to be dependent on the history of disturbance.

ecology↗

bioRxiv2020

Controls on and consequences of specific leaf area variation with permafrost depth in a boreal forest

Specific leaf area (SLA, leaf area per unit dry mass) is a key canopy structural characteristic, a measure of photosynthetic capacity, and an important input into many terrestrial process models. Although many studies have examined SLA variation, relatively few data exist from high latitude, climate-sensitive permafrost regions. We measured SLA and soil and topographic properties across a boreal forest permafrost transition, in which forest composition changed as permafrost deepened from 54 to >150 cm over 75 m hillslope transects in Caribou-Poker Creeks Research Watershed, Alaska. We characterized both linear and threshold relationships between topographic and edaphic variables and SLA and developed a conceptual model of these relationships. We found that the depth of the soil active layer above permafrost was significantly and positively correlated with SLA for both coniferous and deciduous boreal tree species. Intraspecific SLA variation was associated with a fivefold increase in net primary production, suggesting that changes in active layer depth due to permafrost thaw could strongly influence ecosystem productivity. While this is an exploratory study to begin understanding SLA variation in a non-contiguous permafrost system, our results indicate the need for more extensive evaluation across larger spatial domains. These empirical relationships and associated uncertainty can be incorporated into ecosystem models that use dynamic traits, improving our ability to predict ecosystem-level carbon cycling responses to ongoing climate change.

ecology↗

bioRxiv2020

Representing Organic Matter Thermodynamics in Biogeochemical Reactions via Substrate-Explicit Modeling

Predictive biogeochemical modeling requires data-model integration that enables explicit representation of the sophisticated roles of microbial processes that transform substrates. Data from high-resolution organic matter (OM) characterization are increasingly available and can serve as a critical resource for this purpose, but their incorporation into biogeochemical models is often prohibited due to an over-simplified description of reaction networks. To fill this gap, we proposed a new concept of biogeochemical modeling--termed substrate-explicit modeling--that enables parameterizing OM-specific oxidative degradation pathways and reaction rates based on the thermodynamic properties of OM pools. The resulting kinetic models are characterized by only two parameters regardless of the complexity of OM profiles, which can greatly facilitate the integration with reactive transport models for ecosystem simulations by alleviating the difficulty in parameter identification. For every detected organic molecule in a given sample, our approach provides a systematic way to formulate reaction kinetics from chemical formula, which enables the evaluation of the impact of OM character on biogeochemical processes across conditions. In a case study of two sites with distinct OM thermodynamics, our method not only predicted oxidative degradation to be primarily driven by thermodynamic efficiency of OM consistent with experimental rate measurements, but also revealed previously unknown critically important aspects of biogeochemical reactions, including their condition-specific response to carbon and/or oxygen limitations. Lastly, we showed that the proposed substrate-explicit modeling approach can be synergistically combined with enzyme-explicit approach to provide improved predictions. This result led us to present integrative biogeochemical modeling as a unifying framework that can ideally describe the dynamic interplay among microbes, enzymes, and substrates to address advanced questions and hypotheses in future studies. Altogether, the new modeling concept we propose in this work provides a foundational platform for unprecedented predictions of biogeochemical and ecosystem dynamics through enhanced integration with diverse experimental data and extant modeling approaches.

systems biology↗

bioRxiv2020

Ecological theory applied to environmental metabolomes reveals compositional divergence despite conserved molecular properties

Stream and river systems transport and process substantial amounts of dissolved organic matter (DOM) from terrestrial and aquatic sources to the ocean, with global biogeochemical implications. However, the underlying mechanisms affecting the spatiotemporal organization of DOM composition are under-investigated. To understand the principles governing DOM composition, we leverage the recently proposed synthesis of metacommunity ecology and metabolomics, termed meta-metabolome ecology. Applying this novel approach to a freshwater ecosystem, we demonstrated that despite similar molecular properties across metabolomes, metabolite identity significantly diverged due to environmental filtering. We refer to this phenomenon as thermodynamic redundancy, which is analogous to the ecological concept of functional redundancy. We suggest that under thermodynamic redundancy, divergent metabolomes can support equivalent biogeochemical function just as divergent ecological communities can support equivalent ecosystem function. As these analyses are performed in additional ecosystems, potentially generalizable principles, like thermodynamic redundancy, can be revealed and provide insight into DOM dynamics.

ecology↗

bioRxiv2020

Unification of Environmental Metabolomics with Metacommunity Ecology

Environmental metabolomics, enabled by high-resolution mass spectrometric techniques, have demonstrated the biogeochemical importance of the metabolites which comprise natural organic matter (NOM). However, significant gaps exist in our understanding of the spatiotemporal organization of NOM composition. We suggest that the underlying mechanisms governing NOM can be revealed by applying tools and concepts from metacommunity ecology to environmental metabolomics. After illustrating the similarities between metabolomes and ecological communities, we call this conceptual synthesis meta-metabolome ecology and demonstrate its potential utility using a freshwater mass spectrometry dataset. Specifically, we developed three relational metabolite dendrograms using combinations of molecular properties (i.e., aromaticity index, double-bond equivalents, etc.) and putative biochemical transformations. Using these dendrograms, which are similar to phylogenetic or functional trait trees in ecological communities, we illustrate potential analytical techniques by investigating relationally-informed -diversity and {beta}-diversity metrics (e.g., MPD, MNTD, UniFrac), and null model analyses (e.g., NRI, NTI, and {beta}NTI). Furthermore, we demonstrate that this synthesis allows ecological communities (e.g., microbes) and the metabolites they produce and consume using the same framework. We propose that applying this framework to a broad range of ecosystems will reveal generalizable principles that can advance our predictive capabilities regarding NOM dynamics.

ecology↗

bioRxiv2020

Dissolved oxygen dynamics reveal biogeochemical tipping points driven by river corridor hydrology

Riverbeds can have an important impact on large-scale fluxes of biogeochemically active solutes in river corridor systems. The hyporheic zone is an important area of both hydrology and biogeochemistry, particularly in a hydropeaked river system where rapid variations in river stage height, hydraulic gradients, and residence times occur. We measured several biogeochemical and hydrological parameters at three different subsurface depths in the riverbed of the Columbia River in Washington state, a complex hydropeaked river system with significant subsurface heterogeneity. During the study, episodes of significant dissolved oxygen (DO) change were observed. The DO signal changes were the most apparent, compared to more modest changes in other biogeochemical markers. While DO is often associated with biological activity, we ultimately found that the notable DO excursions were associated with hydrologic gradients. Here we describe hydrologic perturbations and biogeochemical responses in terms of hydrobiogeochemical regimes. Two different forms of DO response to hydraulic gradient perturbation were observed, defining different hydrobiogeochemical regimes. The system tips abruptly from one regime to the other, exhibiting threshold behavior that is uncaptured in current estimations of cumulative influences of subsurface processes from reach to earth system scales. Plain language summaryThe water in a river is constantly flowing in and out of the rivers bed. While it is in the bed, microbes process environmentally and ecologically important nutrients and other compounds. The exchange of water between the river and the riverbed is largely controlled by the stage of the river. Many processes, both natural and human, can cause rapid changes in the river stage. These rapid stage changes can cause abrupt changes in the riverbeds ability to process nutrients and other compounds. In this study, we use dissolved oxygen as a window into riverbed microbial and chemical processing. We see that relatively rapid changes in river stage can cause abrupt changes in the concentrations of chemicals in the riverbed, indicating fundamental changes in how the riverbed processes are occurring. Understanding these abrupt and fundamental changes is important to our overall understanding of the ecological function of river corridor systems. 3 key pointsO_LIA hydrobiogeochemical regime is defined by the functional form of the relationship of a hydrologic perturbation and biogeochemical marker. C_LIO_LIShort-term hydrologic perturbations drive tipping points between distinct hydrobiogeochemical regimes. C_LIO_LILinear and hysteretic dissolved oxygen dynamics define distinct regimes as observed throughout the hyporheic zone. C_LI

biochemistry↗

bioRxiv2019

Temporal dynamics of nitrogen cycle gene diversity in a hyporheic microbiome

Biodiversity is thought to prevent decline in community function in response to changing environmental conditions through replacement of organisms with similar functional capacity but different optimal growth characteristics. We examined how this concept translates to the within-gene level by exploring seasonal dynamics of within-gene diversity for genes involved in nitrogen cycling in hyporheic zone communities. Nitrification genes displayed low richness-- defined as the number of unique within-gene phylotypes--across seasons. Conversely, denitrification genes varied in both richness and the degree to which phylotypes were recruited or lost. These results demonstrate that there is not a universal mechanism for maintaining community functional potential for nitrogen cycling activities, even across seasonal environmental shifts to which communities would be expected to be well adapted. As such, extreme environmental changes could have very different effects on the stability of the different nitrogen cycle activities. These outcomes suggest a need to modify existing conceptual models that link biodiversity to microbiome function to incorporate within-gene diversity. Specifically, we suggest an expanded conceptualization that (1) recognizes component steps (genes) with low diversity as potential bottlenecks influencing pathway-level function, and (2) includes variation in both the number of entities (e.g. species, phylotypes) that can contribute to a given process and the turnover of those entities in response to shifting conditions. Building these concepts into process-based ecosystem models represents an exciting opportunity to connect within-gene-scale ecological dynamics to ecosystem-scale services.

ecology↗

bioRxiv2018

Multi omics comparison reveals metabolome biochemistry, not microbiome composition or gene expression, corresponds to elevated biogeochemical function in the hyporheic zone

Biogeochemical hotspots are pervasive at terrestrial-aquatic interfaces, particularly within groundwater-surface water mixing zones (hyporheic zones), and they are critical to understanding spatiotemporal variation in biogeochemical cycling. Here, we use multi omic comparisons of hotspots to low-activity sediments to gain mechanistic insight into hyporheic zone organic matter processing. We hypothesized that microbiome structure and function, as described by metagenomics and metaproteomics, would distinguish hotspots from low-activity sediments through a shift towards carbohydrate-utilizing metabolic pathways and elucidate discrete mechanisms governing organic matter processing in each location. We also expected these differences to be reflected in the metabolome, whereby hotspot carbon (C) pools and metabolite transformations therein would be enriched in sugar-associated compounds. In contrast to expectations, we found pronounced phenotypic plasticity in the hyporheic zone microbiome that was denoted by similar microbiome structure, functional potential, and expression across sediments with dissimilar metabolic rates. Instead, diverse nitrogenous metabolites and biochemical transformations characterized hotspots. Metabolomes also corresponded more strongly to aerobic metabolism than bulk C content only (explaining 67% vs. 42% of variation), and bulk C did not improve statistical models based on metabolome composition alone. These results point to organic nitrogen as a significant regulatory factor influencing hyporheic zone organic matter processing. Based on our findings, we propose incorporating knowledge of metabolic pathways associated with different chemical fractions of C pools into ecosystem models will enhance prediction accuracy.

molecular biology↗

bioRxiv2018

Forfeiting the founder effect: turnover defines biofilm community succession

Microbial community succession is a fundamental process that effects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the roles of founder species? We performed a succession experiment within a hypersaline microbial mat ecosystem to investigate how ecological processes contributed to the turnover of founder species. Bacterial and micro-eukaryotic founder species were identified from primary succession and tracked through a defined maturation period using 16S and 18S rRNA gene amplicon sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate basic functional capabilities. The majority of the founder species did not maintain high relative abundances in later stages of succession. Turnover (versus nestedness) was the dominant process shaping the final community structure. We also asked if different ecological processes acted on bacteria versus eukaryotes during successional stages and found that deterministic and stochastic forces corresponded more with eukaryote and bacterial colonization, respectively. Our results show that taxa from different kingdoms, that share habitat in the tight spatial confines of a biofilm, were influenced by different ecological forces and time scales of succession.

ecology↗

bioRxiv2018

Dispersal limitation and thermodynamic constraints govern spatial structure of permafrost microbial communities

Understanding drivers of permafrost microbial community composition is critical for understanding permafrost microbiology and predicting ecosystem responses to thaw, however studies describing ecological controls on these communities are lacking. We hypothesize that permafrost communities are uniquely shaped by constraints imposed by prolonged freezing, and decoupled from factors that influence non-permafrost soil communities. To test this hypothesis, we characterized patterns of environmental variation and microbial community composition in permafrost across an Alaskan boreal forest landscape. We used null modeling to estimate the relative importance of selective and neutral assembly processes on community composition, and identified environmental factors influencing ecological selection through regression and structural equation modeling (SEM). Proportionally, the strongest process influencing community composition was dispersal limitation (0.36), exceeding the influence of homogenous selection (0.21), variable selection (0.16), and homogenizing dispersal (0.05). Fe(II) content was the most important factor explaining variable selection, and was significantly associated with total selection by univariate regression (R2=0.14, p=0.003). SEM supported a model in which Fe(II) content mediated influences of the Gibbs free energy of the organic matter pool and organic acid concentration on total selection. These findings reveal that the processes shaping microbial communities in permafrost are distinct from those in non-permafrost soils, as the stability of the permafrost environment imposes dispersal and thermodynamic constraints on permafrost communities. Models of permafrost community composition will need to account for these unique drivers in order to predict community characteristics across permafrost landscapes, and in efforts to understand how pre-thaw conditions will influence post-thaw ecological and biogeochemical processes.

ecology↗

bioRxiv2017

Stochastic microbial community assembly decreases biogeochemical function

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative influence of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function, which we define generically to represent any biogeochemical reaction of interest. We used an ecological simulation model to evaluate this hypothesis. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by deterministic selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal rates high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer its biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.

ecology↗

bioRxiv2017

Riparian vegetation limits oxidation of thermodynamically unfavorable bound-carbon stocks along an aquatic interface

In light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here, we investigate the biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor using ultra-high resolution C characterization. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically -bound OC. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and--in direct conflict with the priming concept--that inputs of water-soluble and thermodynamically favorable terrestrial OC protects bound-OC from oxidation. In both environments, the most thermodynamically favorable compounds appear to be preferentially oxidized regardless of which OC pool microbiomes metabolize. In turn, we suggest that the extent of riparian vegetation causes sediment microbiomes to locally adapt to oxidize a particular pool of OC, but that common thermodynamic principles govern the oxidation of each pool (i.e., water-soluble or physically-bound). Finally, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.\n\nKey pointsO_LIRiparian vegetation protects bound-OC stocks\nC_LIO_LIBiochemical processes associated with OC oxidation vary with vegetation conditions\nC_LIO_LICommon thermodynamic principles underlie OC oxidation regardless of vegetation conditions\nC_LI

ecology↗