Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “ECOLOGY”

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 1,513 records · Page 84
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Overcoming persistent challenges in putting environmental flow policy into practice: a systematic review and bibliometric analysis

The implementation of environmental flows (e-flows) aims to reduce the negative impacts of hydrological alteration on freshwater ecosystems. Despite the growing attention to the importance of e-flows since the 1970s, actual implementation has lagged. Therefore, we explore the limitations in e-flows implementation, their systemic reasons, and solutions. We conducted a systematic review and a bibliometric analysis to identify peer-reviewed articles published on the topic of e-flows implementation research in the last two decades, resulting in 68 research and review papers. Co-occurrence of terms, and geographic and temporal trends were analyzed to identify the gaps in environmental water management and propose recommendations to address limitations on e-flows implementation. We identify the underlying causes and potential solutions to such challenges in environmental water management. The limitations to e-flow implementation identified were categorized into 21 classes. The most recognized limitation was the competing priorities of human uses of water (n = 29). Many secondary limitations, generally co-occurring in co-causation, were identified as limiting factors, especially for implementing more nuanced and sophisticated e-flows. The lack of adequate hydrological data (n = 24) and ecological data (n = 28) were among the most mentioned, and ultimately lead to difficulties in starting or continuing monitoring/adaptive management (n = 28) efforts. The lack of resource/capacity (n = 21), experimentation (n = 19), regulatory enforcement (n = 17), and differing authorities involved (n = 18) were also recurrent problems, driven by the deficiencies in the relative importance given to e-flows when facing other human priorities. In order to provide a clearer path for successful e-flow implementation, system mapping can be used as a starting point and general-purpose resource for understanding the sociohydrological problems, interactions, and inherited complexity of river systems. Secondly, we recommend a system analysis approach to address competing demands, especially with the use of coupled water-energy modeling tools to support decision-making when hydropower generation is involved. Such approaches can better assess the complex interactions among the hydrologic, ecological, socioeconomic, and engineering dimensions of water resource systems and their effective management. Lastly, given the complexities in environmental water allocation, implementation requires both scientific rigor and proven utility. Consequently, and where possible, we recommend a move from simplistic flow allocations to a more holistic approach informed by hydroecological principles. To ease conflicts between competing water demands, water managers can realize more 'pop per drop' by supporting key components of a flow regime that include functional attributes and processes that enhance biogeochemical cycling, structural habitat formation, and ecosystem maintenance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

ABSTRACT Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Pathogenic budding yeasts isolated outside of clinical settings

Budding yeasts are distributed across a wide range of habitats, including as human commensals. However, under some conditions, these commensals can cause superficial, invasive, and even lethal infections. Despite their importance to human health, little is known about the ecology of these opportunistic pathogens, aside from their associations with mammals and clinical environments. During a survey of approximately 1000 non-clinical samples across the United States of America, we isolated 54 strains of budding yeast species considered opportunistic pathogens, including Candida albicans and Candida (Nakaseomyces) glabrata . We report that, as a group, pathogenic yeasts were positively associated with fruits and soil environments, whereas the species Pichia kudriavzevii (syn. Candida krusei syn. Issatchenkia orientalis ) had a significant association with plants. Of the four species that cause 95% of candidiasis, we found a positive association with soil. These results indicate that pathogenic yeast ecology is more complex and diverse than is currently appreciated and raises the possibility that these additional environments could be a point of contact for human infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle↗
DOE OSTI2024

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes

Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Architecture of Metabolism Maximizes Biosynthetic Diversity in the Largest Class of Fungi

Abstract Ecological diversity in fungi is largely defined by metabolic traits, including the ability to produce secondary or “specialized” metabolites (SMs) that mediate interactions with other organisms. Fungal SM pathways are frequently encoded in biosynthetic gene clusters (BGCs), which facilitate the identification and characterization of metabolic pathways. Variation in BGC composition reflects the diversity of their SM products. Recent studies have documented surprising diversity of BGC repertoires among isolates of the same fungal species, yet little is known about how this population-level variation is inherited across macroevolutionary timescales. Here, we applied a novel linkage-based algorithm to reveal previously unexplored dimensions of diversity in BGC composition, distribution, and repertoire across 101 species of Dothideomycetes, which are considered the most phylogenetically diverse class of fungi and known to produce many SMs. We predicted both complementary and overlapping sets of clustered genes compared with existing methods and identified novel gene pairs that associate with known secondary metabolite genes. We found that variation among sets of BGCs in individual genomes is due to nonoverlapping BGC combinations and that several BGCs have biased ecological distributions, consistent with niche-specific selection. We observed that total BGC diversity scales linearly with increasing repertoire size, suggesting that secondary metabolites have little structural redundancy in individual fungi. We project that there is substantial unsampled BGC diversity across specific families of Dothideomycetes, which will provide a roadmap for future sampling efforts. Our approach and findings lend new insight into how BGC diversity is generated and maintained across an entire fungal taxonomic class.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mixotrophic microbes create carbon tipping points under warming

Mixotrophs are ubiquitous and integral to microbial food webs, but their impacts on the dynamics and functioning of broader ecosystems are largely unresolved. Here, we show that mixotrophy produces a unique type of food web module that exhibits unusual ecological dynamics, with surprising consequences for carbon flux under warming. We develop a generalizable model of a mixotrophic food web module that incorporates dynamic switching between phototrophy and phagotrophy to assess ecological dynamics and total system CO 2 flux. We find that warming switches mixotrophic systems between alternative stable carbon states—including a phototrophy-dominant carbon sink state, a phagotrophy-dominant carbon source state and cycling between these two. Moreover, warming always shifts this mixotrophic system from a carbon sink state to a carbon source state, but a coordinated increase in nutrients can erase early warning signals of this transition and expand hysteresis. This suggests that mixotrophs can generate critical carbon tipping points under warming that will be more abrupt and less reversible when combined with increased nutrient levels, having widespread implications for ecosystem functioning in the face of rapid global change.

54 ENVIRONMENTAL SCIENCES↗
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↗
DOE OSTI2018

A century of genetic variation inferred from a persistent soil‐stored seed bank

Abstract Stratigraphic accretion of dormant propagules in soil can result in natural archives useful for studying ecological and evolutionary responses to environmental change. Few attempts have been made, however, to use soil‐stored seed banks as natural archives, in part because of concerns over nonrandom attrition and mixed stratification. Here, we examine the persistent seed bank of Schoenoplectus americanus , a foundational brackish marsh sedge, to determine whether it can serve as a resource for reconstructing historical records of demographic and population genetic variation. After assembling profiles of the seed bank from radionuclide‐dated soil cores, we germinated seeds to “resurrect” cohorts spanning the 20th century. Using microsatellite markers, we assessed genetic diversity and differentiation among depth cohorts, drawing comparisons to extant plants at the study site and in nearby and more distant marshes. We found that seed density peaked at intermediate soil depths. We also detected genotypic differences among cohorts as well as between cohorts and extant plants. Genetic diversity did not decline with depth, indicating that the observed pattern of differentiation is not due to attrition. Patterns of differentiation within and among extant marshes also suggest that local populations persist as aggregates of small clones, likely reflecting repeated seedling recruitment and low immigration from admixed regional gene pools. These findings indicate that persistent and stratified soil‐stored seed banks merit further consideration as resources for reconstructing decadal‐ to century‐long records that can lend insight into the tempo and nature of ecological and evolutionary processes that shape populations over time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Anticipating global terrestrial ecosystem state change using FLUXNET

Ecosystems can be characterized as complex systems that traverse a variety of functional and structural states in response to changing bioclimatic forcings. A central challenge of global change biology is the robust empirical description of these states and state transitions. An ecosystem's functional state can be empirically described using Process Networks (PN) that use timeseries observations to determine the strength of process-level functional couplings between ecosystem components. A globally extensive source of in-situ observations of terrestrial ecosystem dynamics is the FLUXNET eddy-covariance network that provides standardized observations of micrometeorology and carbon, water, and energy flux dynamics. We employ the LaThuile FLUXNET synthesis dataset to delineate each month's functional state for 204 sites, yielding the LaThuile PN version 1.0 database that describes the strength of an ecosystem's functional couplings from air temperature and precipitation to carbon fluxes during each site-month. Then we calculate the elasticity of these couplings to seasonal scale forcings: air temperature, precipitation, solar radiation, and phenophase. Finally, we train artificial neural networks to extrapolate these elasticities from 204 sites to the globe, yielding maps of the estimated functional elasticity of every terrestrial ecosystem's functional states to changing seasonal bioclimatic forcings. These maps provide theoretically novel resource that can be used to anticipate ecological state transitions in response to climate change and to validate process-based models of ecological change. These elasticity maps show that each ecosystem can be expected to respond uniquely to changing forcings. Tropical forests, hot deserts, savannas, and high elevations are most elastic to climate change, and elasticity of ecosystems to seasonal air temperature is on average an order of magnitude higher than elasticity to other bioclimatic forcings. We also observe a reasonable amount of moderate relationships between functional elasticity and structural state change across different ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Cryptic phenology in plants: case studies, implications and recommendations

Plant phenology – the timing of cyclic or recurrent biological events in plants – offers insight into the ecology, evolution, and seasonality of plant–mediated ecosystem processes. Traditionally studied phenologies are readily apparent, such as flowering events, germination timing, and season–initiating budbreak. However, a broad range of phenologies that are fundamental to the ecology and evolution of plants, and to global biogeochemical cycles and climate change predictions, have been neglected because they are “cryptic” – that is, hidden from view (e.g root production) or difficult to distinguish and interpret based on common measurements at typical scales of examination (e.g leaf turnover in evergreen forests). We illustrate how capturing cryptic phenology can advance scientific understanding with two case studies: wood phenology in a deciduous forest of the northeastern USA and leaf phenology in tropical evergreen forests of Amazonia. Drawing on these case studies and other literature, we argue that conceptualizing and characterizing cryptic plant phenology is needed for understanding and accurate prediction at many scales from organisms to ecosystems. As a result, we recommend avenues of empirical and modeling research to accelerate discovery of cryptic phenological patterns, to understand their causes and consequences, and to represent these processes in terrestrial biosphere models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Combining Observations and Models: A Review of the CARDAMOM Framework for Data‐Constrained Terrestrial Ecosystem Modeling

The rapid increase in the volume and variety of terrestrial biosphere observations (i.e., remote sensing data and in situ measurements) offers a unique opportunity to derive ecological insights, refine process‐based models, and improve forecasting for decision support. However, despite their potential, ecological observations have primarily been used to benchmark process‐based models, as many past and current models lack the capability to directly integrate observations and their associated uncertainties for parameterization. In contrast, data assimilation frameworks such as the CARbon DAta MOdel fraMework (CARDAMOM) and its suite of process‐based models, known as the Data Assimilation Linked Ecosystem Carbon Model (DALEC), are specifically designed for model‐data fusion. This review, motivated by a recent CARDAMOM community workshop, examines the development and applications of CARDAMOM, with an emphasis on its role in advancing ecosystem process understanding. CARDAMOM employs a Bayesian approach, using a Markov Chain Monte Carlo algorithm to enable data‐driven calibration of DALEC parameters and initial states (i.e., carbon pool sizes) through observation operators. CARDAMOM's unique ability to retrieve localized model process parameters from diverse datasets—ranging from in situ measurements to global satellite observations—makes it a highly flexible tool for analyzing spatially variable ecosystem responses to environmental change. However, assimilating these data also presents challenges, including data quality issues that propagate into model skill, as well as trade‐offs between model complexity, parameter equifinality, and predictive performance. We discuss potential solutions to these challenges, such as reducing parameter equifinality by incorporating new observations. This review also offers community recommendations for incorporating emerging datasets, integrating machine learning techniques, strengthening collaboration with remote sensing, field, and modeling communities, and expanding CARDAMOM's relevance for localized ecosystem monitoring and decision‐making. CARDAMOM enables a deep, mechanistic understanding of terrestrial ecosystem dynamics that cannot be achieved through empirical analyses of observational datasets or weakly constrained models alone.

Bayesian inference↗
DOE OSTI2020

Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs

The effects of plants on the biosphere, atmosphere and geosphere are key determinants of terrestrial ecosystem functioning. However, despite substantial progress made regarding plant belowground components, we are still only beginning to explore the complex relationships between root traits and functions. Drawing on the literature in plant physiology, ecophysiology, ecology, agronomy and soil science, we reviewed 24 aspects of plant and ecosystem functioning and their relationships with a number of root system traits, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, we critically evaluated the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology. Most importantly, we found that belowground traits with the broadest importance in plant and ecosystem functioning are not those most commonly measured. Also, the estimation of trait relative importance for functioning requires us to consider a more comprehensive range of functionally relevant traits from a diverse range of species, across environments and over time series. Finally, we also advocate that establishing causal hierarchical links among root traits will provide a hypothesis-based framework to identify the most parsimonious sets of traits with the strongest links on functions, and to link genotypes to plant and ecosystem functioning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2019

Life on the thermodynamic edge: Respiratory growth of an acetotrophic methanogen

Although two-thirds of the nearly 1 billion metric tons of methane produced annually in Earth’s biosphere derives from acetate, the in situ process has escaped rigorous understanding. The unresolved question concerns the mechanism by which the exceptionally marginal amount of available energy supports acetotrophic growth of methanogenic archaea in the environment. Here, we show that Methanosarcina acetivorans conserves energy by Fe(III)-dependent respiratory metabolism of acetate, augmenting production of the greenhouse gas methane. An extensively revised, ecologically relevant, biochemical pathway for acetotrophic growth is presented, in which the conservation of respiratory energy is maximized by electron bifurcation, a previously unknown mechanism of biological energy coupling. The results transform the ecological and biochemical understanding of methanogenesis and the role of iron in the mineralization of organic matter in anaerobic environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA gene amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCE Through highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.

16S RNA↗
DOE OSTI2025

Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake

The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) by Chlorobium and anaerobic respiration (electrogenic metabolism) by Geothrix, involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.

carbon emissions↗