Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “ecosystem function”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
NASA NTRS1994

Application of remote sensing in regional scale estimates of vegetation carbon budgets: The Belfix project

A concept for coupling the remote sensing derived fraction of the absorbed photosynthetic active radiation (FAPAR) with a functional ecosystem model was developed. The study was named the Belfix procedure. The quantification of changes in carbon dynamics at the ecosystem level is a key issue in studies of global climatic change effects at the vegetation atmosphere interface. An operational procedure, for the determination of carbon fluxes at the regional scale (Belgian territory), is presented. The approach allows for the determination of the sink function of vegetation for carbon (dioxide). The phyto- and litter mass, photosynthetic assimilation, autotroph and heterotroph carbon fluxes and net ecosystem exchange (NEE) of carbon, were evaluated. The results suggest that a single solution can be obtained for ecosystem rates and states, applying an iterative procedure, based on minimizing the change in maximal seasonal green phytomass in function of yearly FAPAR temporal profiles. Total phytomass values obtained are in close range with those obtained by ground sampling.

Veroustraete, Frank↗
DOE OSTI2025

Earlier snowmelt increases the strength of the carbon sink in montane meadows unequally across the growing season

1. Warming temperatures are changing winters, leading to earlier snowmelt. This shift can lead to an earlier and potentially longer growing season, which in turn may affect various plant-mediated ecosystem functions. Despite its relevance in the carbon cycle, we still know little about how earlier snowmelt impacts the carbon balance in ecosystems over the growing season, for example, does it only shift phenology, or does it affect the overall carbon uptake? Most studies rely on interannual variability in snowmelt timing, making it difficult to isolate snowmelt effects from other confounding variables, for example, temperature and moisture anomalies. To address this uncertainty, we investigated how experimentally advancing snowmelt affects the carbon cycling of montane meadows across the growing season. 2. We experimentally advanced the snowmelt date in a montane meadow by approximately 12 days and collected data every 2 weeks throughout the growing season, including net ecosystem exchange (NEE), gross primary productivity (GPP), ecosystem respiration (ER), plant composition, and shrub, graminoid, and forb biomass. 3. Early in the growing season, GPP was higher in the early snowmelt plots, though this effect decreased as the growing season progressed. Our modelling of cumulative NEE showed a possible 22% increase in the carbon sink strength with earlier snowmelt. The effect was strongest in the early spring and diminished as the growing season progressed, with control plots being a greater carbon sink in the later season. Graminoid biomass was 47% higher in plots with earlier snowmelt, but there was no change in total biomass. 4. Synthesis. As winters warm and snowmelt occurs earlier, plant productivity will shift earlier in the growing season, and montane meadows may become a stronger carbon sink. However, this effect will differ seasonally, altering the carbon balance in montane meadows.

carbon cycle↗
NASA NTRS2007

Maintenance of Ecosystem Nitrogen Limitation by Ephemeral Forest Disturbance: An Assessment using MODIS, Hyperion, and Landsat ETM+

Ephemeral disturbances, such as non-lethal insect defoliations and crown damage from meteorological events, can significantly affect the delivery of ecosystem services by helping maintain nitrogen (N) limitation in temperate forest ecosystems. However, the impacts of these disturbances are difficult to observe across the broad-scales at which they affect ecosystem function. Using remotely sensed measures and field data, we find support for the hypothesis that ephemeral disturbances help maintain landscape-wide ecosystem N limitation. Specifically, a phenology-based defoliation index derived from daily MODIS satellite imagery predicts three ecosystem responses from oak-dominated forested watersheds: elevated stream water N export (R(exp 2) = 0.48), decreased foliar N (R(exp 2) = 0.69, assessed with Hyperion imagery), and reduced vegetation growth vigor (R(exp 2) = 0.49, assessed with Landsat ETM+ imagery). The results indicate that ephemeral disturbances and other forest stressors may sustain N limitation by reducing the ability of trees to compete for--and retain--soil available N.

McNeil, Brenden E.↗
NASA NTRS2003

Effects of litter addition on ectomycorrhizal associates of a lodgepole pine (Pinus contorta) stand in Yellowstone National Park

Increasing soil nutrients through litter manipulation, pollution, or fertilization can adversely affect ectomycorrhizal (EM) communities by inhibiting fungal growth. In this study, we used molecular genetic methods to determine the effects of litter addition on the EM community of a Pinus contorta stand in Yellowstone National Park that regenerated after a stand-replacing fire. Two controls were used; in unmodified control plots nothing was added to the soil, and in perlite plots perlite, a chemically neutral substance, was added to maintain soil moisture and temperature at levels similar to those under litter. We found that (i) species richness did not change significantly following perlite addition (2.6 +/- 0.3 species/core in control plots, compared with 2.3 +/- 0.3 species/core in perlite plots) but decreased significantly (P < 0.05) following litter addition (1.8 +/- 0.3 species/core); (ii) EM infection was not affected by the addition of perlite but increased significantly (P < 0.001) in response to litter addition, and the increase occurred only in the upper soil layer, directly adjacent to the added litter; and (iii) Suillus granulatus, Wilcoxina mikolae, and agaricoid DD were the dominant organisms in controls, but the levels of W. mikolae and agaricoid DD decreased significantly in response to both perlite and litter addition. The relative levels of S. granulatus and a fourth fungus, Cortinariaceae species 2, increased significantly (P < 0.01 and P < 0.05, respectively) following litter addition. Thus, litter addition resulted in some negative effects that may be attributable to moisture-temperature relationships rather than to the increased nutrients associated with litter. Some species respond positively to litter addition, indicating that there are differences in their physiologies. Hence, changes in the EM community induced by litter accumulation also may affect ecosystem function.

Fungi/classification/growth & development↗
DOE OSTI2025

Filling the Gaps: A Bayesian Mixture Model for Imputing Missing Soil Water Content Data

ABSTRACT Soil water content (SWC) data are central to evaluating how soil moisture varies over time and space and influences critical plant and ecosystem functions, especially in water‐limited drylands. However, sensors that record SWC at high frequencies often malfunction, leading to incomplete timeseries and limiting our understanding of dryland ecosystem dynamics. We developed an analytical approach to impute missing SWC data, which we tested at six eddy flux tower sites along an elevation gradient in the southwestern United States. We impute missing data as a mixture of linearly interpolated SWC between the observed endpoints of a missing data gap and SWC simulated by an ecosystem water balance model (SOILWAT2). Within a Bayesian framework, we allowed the relative utility (mixture weight) of each component (linearly interpolated vs. SOILWAT2) to vary by depth, site and gap characteristics. We explored “fixed” weights versus “dynamic” weights that vary as a function of cumulative precipitation, average temperature, and time since the start of the gap. Both models estimated missing SWC data well ( R 2 = 0.70–0.88 vs. 0.75–0.91 for fixed vs. dynamic weights, respectively), but the utility of linearly interpolated versus SOILWAT2 values depended on site and depth. SOILWAT2 was more useful for more arid sites, shallower depths, longer and warmer gaps and gaps that received greater precipitation. Overall, the mixture model reliably gap‐fills SWC, while lending insight into processes governing SWC dynamics. This approach to impute missing data could be adapted to accommodate more than two mixture components and other types of environmental timeseries.

Ogle, Kiona [School of Informatics, Computing, and↗
NASA NTRS1994

Overview of the Oregon Transect Ecosystem Research Project

The Oregon Transect Ecosystem Research (OTTER) project is a study of ecosystem functions in coniferous forests using the methods of computer modeling, experimental and theoretical remote sensing, and ecological field and laboratory techniques. The study is focused on predicting the major fluxes of carbon, nitrogen, and water, and the factors that dynamically regulate them. The OTTER project was conceived to test two major questions: (1) Can a generalized ecosystem simulation model, designed to use mainly parameters available from remote sensing, predict the functioning of forests across an environmentally variable region? and (2) To what extent can the variables required by this model be derived from remotely sensed data? The scientific objectives and scope of the project demanded that a coordinated effort be made to link ground measurements with remote sensing and modeling requirements. OTTER was selected as a focus for a National Aeronautics and Space Administration (NASA)-sponsored Multi-sensor Aircraft Campaign (MAC; combining NASA aircraft and sensors with those of others) on the basis of experience gained in past ecosystem studies and remote-sensing projects, and the importance of the OTTER objectives to NASA's long-range science goals and plans. Having several independent approaches available, both on the ground and from various remote-sensing platforms, proved valuable in estimating and validating many of the critical variables. This experience and cross comparison should help simplify future studies of a similar nature. Edited data sets from the OTTER project are now available to the scientific community on optical disks or via on-line data banks at NASA (Washington, D.C., USA) and Oregon State University (Corvallis, Oregon, USA).

Peterson, David L.↗
DOE OSTI2026

Innovative Biomonitoring and Remediation of Heavy Metals Using Phytotechnologies at the Savannah River Site (SRS) Coal Combustion Product (CCP) Impoundment Sites

The Savannah River Site (SRS) contains legacy coal combustion product (CCP) impoundments that are impacted by elevated concentrations of heavy metals and radionuclides, posing long-term risks to soil health, ecosystem functioning, and environmental sustainability. Traditional environmental monitoring approaches rely primarily on chemical analyses to quantify contaminant concentrations but often provide limited information regarding biological responses or ecosystem recovery. This project addressed these limitations by integrating environmental chemistry, microbial ecology, artificial intelligence (AI), and bioremediation into a comprehensive framework for environmental diagnostics and restoration of contaminated soils. The overarching goal of this collaborative project between Florida A&M University (FAMU) and the University of Georgia's Savannah River Ecology Laboratory (SREL) was to develop innovative biomonitoring and remediation strategies for heavy metal-contaminated CCP impoundment sites at the Savannah River Site. Specifically, the project sought to (i) characterize heavy metal contamination, (ii) determine microbial responses to contamination, (iii) isolate indigenous heavy metal-resistant microorganisms for remediation applications, (iv) develop a microbial ecological health index using machine learning, and (v) optimize fungal-mediated bioremediation using artificial intelligence.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2026

Vegetation responses to air dryness amplify future land surface warming

Temperature exerts a first-order control on vegetation photosynthesis and transpiration. Yet most studies investigating temperature impacts on plants rely on near-surface air temperature, rather than canopy temperature—the temperature plants actually experience. Because canopy temperature directly regulates ecosystem function, it provides a more accurate measure of vegetation–climate interactions. Combining Earth System Model (ESM) simulations and satellite observations in a dual emergent constraint, here we show that canopy temperature is projected to increase substantially more than air temperature (~0.11-degrees more or a 16% increase in their difference) over the 21st century. The ESM ensemble median fails to capture these stronger increases in the majority of vegetated regions. We find that the largest projected increases in the difference between canopy and air temperature are predicted to occur in regions where elevating moisture stress—particularly rising vapor pressure deficit—increasingly constrains vegetation growth and transpiration. This implies that future warming will impose stronger constraints on plant function than currently estimated. Relying on air temperature alone will therefore lead to systematic underestimation of temperature effects on photosynthesis, vegetation growth, and the land carbon sink. Accurate representation of canopy temperature in ESMs is thus essential to improve projections of ecosystem responses and feedbacks to climate change.

Green, Julia K↗
DOE OSTI2025

Ecovoltaic solar energy development can promote grassland bird communities

Ecologically informed photovoltaic (PV) developments that co-prioritize PV electricity generation with ecosystem function (‘ecovoltaics’) have emerged as a promising land sharing strategy to minimize ecological conflicts associated with PV solar energy development. While habitat-focused ecovoltaic designs can conceptually benefit biodiversity by offsetting or enhancing impacts of PV development, foundational field research is needed to examine how wildlife respond to these novel ecosystems. We conducted passive acoustic monitoring (PAM) in 2023 and 2024 at 13 solar facilities and paired control sites to investigate avian community responses to ecovoltaic facilities in the Midwestern United States. Compared to control sites (row crop agricultural fields), we found that ecovoltaic sites supported more grassland bird species throughout a 17-week monitoring period between May and September. Grassland bird communities on ecovoltaic sites were also more stable than on agricultural controls, as measured by the Jaccard dissimilarity index. We also used PAM-based weekly species occurrences in an occupancy-modelling framework to investigate the influence of PV development and other landscape variables on grassland bird occupancy. 10 out of 13 modelled grassland bird species had greater predicted occupancy probabilities (ψ) on PV sites than control sites. Synthesis and applications. Our findings suggest that properly sited and developed ecovoltaic solar facilities in human altered landscapes can improve habitat for birds and other wildlife, but further research is needed to understand which species may benefit most from these novel ecosystems.

14 SOLAR ENERGY↗
NASA NTRS2024

Effects of Water Limitation and Competition on Tree Carbon Allocation in an Earth System Modeling Framework

Earth system models (ESMs) have a limited capacity to represent plant functional diversity and shifts in trait distributions. Approaches to improving the representation of this complexity in ESMs include (i) optimality-based approaches that predict trait–environment responses and (ii) explicitly modelling coexistence and community assembly. These approaches are expected to converge only when optimality-based approaches identify competitively dominant strategies, which often differ from strategies that maximize ecosystem functioning or fitness components in monoculture. We used two models, LM3-PPA (a vegetation demographic model designed as an ESM component) and BiomeE (a computationally efficient analog for LM3-PPA), to explore how water limitation affects carbon allocation strategies of canopy trees. We compared competitive allocation strategies and those that maximize biomass or productivity in monoculture. We did not explicitly model coexistence or community assembly. Rather, we used model experiments to identify competitive and maximizing strategies in a two-dimensional trait space under different precipitation and mortality scenarios. At 10 eastern US locations, we simulated historical, wet and dry climate scenarios, novel drought and three different mortality scenarios (low, medium or high sensitivity to water deficit). For each site and scenario, we identified the competitive strategy and three maximizing strategies (maximum biomass, productivity or drought-tolerance). Root: leaf ratios tended to increase and leaf area tended to decrease with increasing water stress (increasing water limitation and its effects on mortality). However, relative to maximizing strategies, competitive strategies shifted towards greater allocation to roots and leaves with increasing water stress. Competitive overinvestments (greater allocation to roots and leaves by competitive strategies compared with maximizing strategies) were robust across different modelling contexts, including vegetation parameter sets (Acer vs. Populus), models (LM3-PPA vs. BiomeE) and uncalibrated vs. calibrated BiomeE versions. Synthesis: The theoretical prediction that competitive and maximizing allocation strategies differ under water limitation is confirmed for a demographic model designed as an ESM component. Optimality-based trait predictions can simplify representing trait diversity in ESMs but do not always correspond to competitive outcomes. Explicitly modelling coexistence and community assembly in ESMs is challenging but is likely the most general approach to representing trait diversity.

vegetation demographic model↗
DOE OSTI2024

A functional microbiome catalogue crowdsourced from North American rivers

Predicting elemental cycles and maintaining water quality under increasing anthropogenic influence requires knowledge of the spatial drivers of river microbiomes. However, understanding of the core microbial processes governing river biogeochemistry is hindered by a lack of genome-resolved functional insights and sampling across multiple rivers. Here we used a community science effort to accelerate the sampling, sequencing and genome-resolved analyses of river microbiomes to create the Genome Resolved Open Watersheds database (GROWdb). GROWdb profiles the identity, distribution, function and expression of microbial genomes across river surface waters covering 90% of United States watersheds. Specifically, GROWdb encompasses microbial lineages from 27 phyla, including novel members from 10 families and 128 genera, and defines the core river microbiome at the genome level. GROWdb analyses coupled to extensive geospatial information reveals local and regional drivers of microbial community structuring, while also presenting foundational hypotheses about ecosystem function. Building on the previously conceived River Continuum Concept, we layer on microbial functional trait expression, which suggests that the structure and function of river microbiomes is predictable. We make GROWdb available through various collaborative cyberinfrastructures, so that it can be widely accessed across disciplines for watershed predictive modelling and microbiome-based management practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Island influences on plant functional traits and trait–trait associations across species‐ and community‐scales

The island rule predicts gigantism or dwarfism in body size of island species relative to their mainland counterparts. However, whether other functional traits shift and whether trait–trait associations on islands differ between species and community levels remains unclear. We measured 13 carbon- and water-related functional traits in 37 shared tree species across 35 eastern Chinese islands and 66 nearby mainland plots. We examined species-level trait value shifts and associations under the island rule and compared trait associations between species and communities. Most size-related, wood-anatomical, and hydraulic traits shifted on islands, with large values decreasing and small values increasing; yet, their associations remained stable, aligning with the global trait spectrum and trait–trait coevolution. This stability, despite trait value shifts, suggests evolutionary integration of functional strategies. By contrast, island community-scale trait associations diverged from shared species-level patterns and sometimes reversed, such as positive relationships between wood density and resource-acquisitive traits. Community-level trait associations were stronger on islands, likely reflecting constrained environmental filtering and migration limitation. These contrasting patterns suggest that dominant species can restructure trait associations at the community level, with implications for ecosystem functioning and carbon storage, thereby advancing understanding of plant trait strategies in island systems.

Archipelagos↗
DOE OSTI2021

Tradeoffs and Synergies in Tropical Forest Root Traits and Dynamics for Nutrient and Water Acquisition: Field and Modeling Advances

Vegetation processes are fundamentally limited by nutrient and water availability, the uptake of which is mediated by plant roots in terrestrial ecosystems. While tropical forests play a central role in global water, carbon, and nutrient cycling, we know very little about tradeoffs and synergies in root traits that respond to resource scarcity. Tropical trees face a unique set of resource limitations, with rock-derived nutrients and moisture seasonality governing many ecosystem functions, and nutrient versus water availability often separated spatially and temporally. Root traits that characterize biomass, depth distributions, production and phenology, morphology, physiology, chemistry, and symbiotic relationships can be predictive of plants’ capacities to access and acquire nutrients and water, with links to aboveground processes like transpiration, wood productivity, and leaf phenology. In this review, we identify an emerging trend in the literature that tropical fine root biomass and production in surface soils are greatest in infertile or sufficiently moist soils. We also identify interesting paradoxes in tropical forest root responses to changing resources that merit further exploration. For example, specific root length, which typically increases under resource scarcity to expand the volume of soil explored, instead can increase with greater base cation availability, both across natural tropical forest gradients and in fertilization experiments. Also, nutrient additions, rather than reducing mycorrhizal colonization of fine roots as might be expected, increased colonization rates under scenarios of water scarcity in some forests. Efforts to include fine root traits and functions in vegetation models have grown more sophisticated over time, yet there is a disconnect between the emphasis in models characterizing nutrient and water uptake rates and carbon costs versus the emphasis in field experiments on measuring root biomass, production, and morphology in response to changes in resource availability. Closer integration of field and modeling efforts could connect mechanistic investigation of fine-root dynamics to ecosystem-scale understanding of nutrient and water cycling, allowing us to better predict tropical forest-climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data for Stetten et al. (2025), "Biogeochemical controls on iron speciation and cycling across upland to shoreline gradients in freshwater and estuarine coastal soils (Lake Erie and Chesapeake Bay, United States)"

Coastal environments are dynamic interfaces that mediate carbon and nutrient exchanges between terrestrial landscapes and open waters, but it is unclear how biogeochemical reactions, in particular iron (Fe) redox transformations, affect the understanding and prediction of coastal ecosystem functions. This dataset includes measurements from two freshwater sites in the Western and Central basins of Lake Erie (Ohio, United States) and two estuarine sites in the Chesapeake Bay (Maryland, United States); the analytical results were reported by Stetten et al. (2025) in Science of the Total Environment. It was produced as part of the COMPASS-FME project, which seeks to advance a scalable, predictive understanding of the fundamental biogeochemical processes, ecological structure, and ecosystem dynamics that distinguish coastal terrestrial-aquatic interfaces from the purely terrestrial or aquatic systems to which they are coupled. The sites were sampled in November 2022 (CRC), December 2022 (MSM), February 2023 (GCW), and March 2023 (OWC); site codes follow those used by Pennington et al. (2025).The dataset consists of the following soil data:- Solid data (Fe concentration, etc.)- Porewater data (sulfate, sulfide, etc.)- Linear combination fitting results of X-ray absorption near edge structure (XANES) spectra; i.e., quantitative results of the oxidation state of Fe, indicated as a proportion of pure Fe(III) and Fe(II) model compounds- Linear combination fitting results of EXAFS (extended X-ray absorption fine structure) spectra, indicated as proportion of of Fe-model compounds (illite, smectite, etc.)Each data type has a single file in comma-separated value (CSV) format. No special software is required to read it.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1990

Remote sensing of the biosphere; Proceedings of the Meeting, Orlando, FL, Apr. 19, 20, 1990

The global context and monitoring of the biological aspects relevant to the EOS program are addressed, the large-scale regional field experiments required to understand ecosystem functioning in more detail and to calibrate the application of remote-sensing techniques for extracting flux and state information are covered, and sensors of the proposed EOS platform are discussed. Attention is given to terrestrial productivity, both tropical-forest and semiarid environments, coastal environments, and global oceanic productivity. Focus is placed on the First International Field Experiment (FIFE) in Kansas, the HAPEX field experiment in France, the ABLE-2 experiment in the Amazon, and the Forest Ecosystem Study in Maine. The proposed electro-optical instruments for EOS including both MODIS-N and MODIS-T, the AIRS and MISR instruments, the ITIR, and ERBE calibration issues are considered.

Smith, James A.↗
DOE OSTI2025

Ecosystem consequences of a nitrogen-fixing proto-organelle

Microscale symbioses can be critical to ecosystem functions, but the mechanisms of these interactions in nature are often cryptic. Here, we use a combination of stable isotope imaging and tracing to reveal carbon (C) and nitrogen (N) exchanges among three symbiotic primary producers that fuel a salmon-bearing river food web. Bulk isotope analysis, nanoSIMS (secondary ion mass spectrometry) isotope imaging, and density centrifugation for quantitative stable isotope probing enabled quantification of organism-specific C- and N-fixation rates from the subcellular scale to the ecosystem. After winters with riverbed-scouring floods, the macroalga Cladophora glomerata uses nutrients in spring runoff to grow streamers up to 10 m long. During summer flow recession, riverine N concentrations wane and Cladophora becomes densely epiphytized by three species of Epithemia, diatoms with N-fixing endosymbionts (proto-organelles) descended from a free-living Crocosphaera cyanobacterium. Over summertime epiphyte succession on Cladophora, N-fixation rates increased as Epithemia spp. became dominant, Cladophora C-fixation declined to near zero, and Epithemia C-fixation increased. Carbon transfer to caddisflies grazing on Cladophora with high densities of Epithemia was 10-fold higher than C transfer to caddisflies grazing Cladophora with low Epithemia loads. In response to demand for N, Epithemia allocates high levels of newly fixed C to its endosymbiont. Consequently, these endosymbionts have the highest rates of C and N accumulation of any taxon in this tripartite symbiosis during the biologically productive season and can produce one of the highest areal rates of N-fixation reported in any river ecosystem.

Marks, Jane C. [Northern Arizona Univ., Flagstaff,↗
DOE OSTI2024

Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices

ABSTRACT Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding. IMPORTANCE Ecosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.

Biotechnology & Applied Microbiology↗
DOE OSTI2025

Unveiling the dark matter of riverine dissolved organic matter and its role in molecular chemodiversity

Chemodiversity of riverine dissolved organic matter (DOM) plays a crucial role in global elemental cycles and ecosystem function. However, DOM “dark matter”—molecules without assigned specific formulae—remain unexplored in the interpretation of chemodiversity. Here, we systematically investigated the characteristics and drivers of dark matter and its impacts on DOM chemodiversity using 551 river water and sediment samples. Compared to known matter with specific formulae, dark matter exhibited lower molecular weight and diversity, but higher compositional dissimilarity, with dissolved organic carbon (DOC) as the primary driver. Including dark matter into chemodiversity analysis changed mass, diversity, and compositional dissimilarity of DOM from –10.1 to –0.04 %, –0.7 to 4.9 %, and 0.4 to 28.8 % in waters, and from –17.5 to 5.7 %, –10.5 to 19.2 %, and –22.3 to 33.1 % in sediments, respectively. DOC mediated these ecosystem-dependent effects: lower DOC amplified the effects on chemodiversity in waters, whereas in sediments, the effects shifted from negative to positive with changing DOC. Furthermore, ignoring dark matter would overestimate the regulatory role of DOC on sediment DOM chemodiversity. In conclusion, collectively, our findings clarify the influence of dark matter on DOM chemodiversity assessments across environmental gradients, improving understanding of riverine DOM and refining its analytical framework.

Chemodiversity↗