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At least 55 records · Page 3

Synthetic soils for ecological and synthetic biology applications

Soils are heterogeneous and dynamic systems characterized by complex physical, chemical, and biological interactions. Understanding these interactions is critical, as they influence plant productivity, global biogeochemical cycles, and ecosystem resilience. While ecologists have long studied soils in field, greenhouse, and laboratory settings, their complexity and heterogeneity make it challenging to pinpoint key properties driving biological processes and derive mechanistic insights. Advancements in synthetic biology, which seeks to engineer and control biological processes in soils, have increased the demand for standardized and controllable experimental platforms. These platforms, referred to here as ‘synthetic soils’, are systems designed to reproduce selected physicochemical characteristics of natural soils in a simplified and defined format, allowing scientists to systematically change soil physicochemical properties (i.e. texture, mineralogy, pH) to study how biological components (i.e. microbes, plants, soil fauna, etc.) respond to, modify, or interact within these controlled environments. This review explores existing synthetic soils, their advantages, limitations, and applications in ecology and synthetic biology, and discusses potential directions for their future development.

artificial soils↗

Evaluation and modification of ELM seasonal deciduous phenology against observations in a southern boreal peatland forest

Phenological transitions determine the timing of changes in land surface properties and the seasonality of exchanges of biosphere-atmosphere energy, water, and carbon. Accurate mechanistic modeling of phenological processes is therefore critical to understand and correctly predict terrestrial ecosystem feedbacks with changing atmospheric and climate conditions. However, the phenological components in the land model of the US Department of Energy's (DOE) Energy Exascale Earth System Model (ELM of E3SM) were previously unable to accurately capture the observed phenological responses to environmental conditions in a well-studied boreal peatland forest. In this research, we introduced new seasonal-deciduous phenology schemes into version 1.0 of ELM and evaluated their performance against the PhenoCam observations at the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment in northern Minnesota from 2015 to 2018. We found that phenology simulated by the revised ELM (i.e., earlier spring onsets and stronger warming responses of spring onsets and autumn senescence) was closer to observations than simulations from the original algorithms for both the deciduous conifer (Larix laricina) and mixed shrub layers. Moreover, the revised ELM generally produced higher carbon and water fluxes (e.g., photosynthesis and evapotranspiration) during the growing season and stronger flux responses to warming than the default ELM. A parameter sensitivity analysis further indicated the significant contribution of phenology parameters to uncertainty in key carbon and water cycle variables, underscoring the importance of precise phenology parameterization. Furthermore, this phenological modeling effort demonstrates the potential to enhance the E3SM representation of land-climate interactions at broader spatiotemporal scales, especially under anticipated elevated CO 2 and warming conditions.

54 ENVIRONMENTAL SCIENCES↗

Biochemical processes in sagebrush ecosystems: Interactions with terrain

The objectives of a biogeochemical study of sagebrush ecosystems in Wyoming and their interactions with terrain are as follows: to describe the vegetational pattern on the landscape and elucidate controlling variables, to measure the soil properties and chemical cycling properties associated with the vegetation units, to associate soil properties with vegetation properties as measured on the ground, to develop remote sensing capabilities for vegetation and surface characteristics of the sagebrush landscape, to develop a system of sensing snow cover and indexing seasonal soil to moisture; and to develop relationships between temporal Thematic Mapper (TM) data and vegetation phenological state.

Matson, P.↗

Using metacommunity ecology to understand environmental metabolomes

Abstract Environmental metabolomes are fundamentally coupled to microbially-linked biogeochemical processes within ecosystems. However, significant gaps exist in our understanding of their spatiotemporal organization, limiting our ability to uncover transferrable principles and predict ecosystem function. We propose that a theoretical paradigm, which integrates concepts from metacommunity ecology, is necessary to reveal underlying mechanisms governing metabolomes. We call this synthesis between ecology and metabolomics ‘meta-metabolome ecology’ and demonstrate its utility using a mass spectrometry dataset. We developed three relational metabolite dendrograms using molecular properties and putative biochemical transformations and performed ecological null modeling. Based upon null modeling results, we show that stochastic processes drove molecular properties while biochemical transformations were structured deterministically. We further suggest that potentially biochemically active metabolites were more deterministically assembled than less active metabolites. Understanding variation in the influences of stochasticity and determinism provides a way to focus attention on which meta-metabolomes and which parts of meta-metabolomes are most likely to be important to consider in mechanistic models. We propose that this paradigm will allow researchers to study the connections between ecological systems and their molecular processes in previously inaccessible detail.

54 ENVIRONMENTAL SCIENCES↗

Bio-Optical and Geochemical Properties of the South Atlantic Subtropical Gyre

An investigation of the bio-optical properties of the South Atlantic subtropical gyre (SASG) was conducted using data primarily from the UK Atlantic Meridional Transect (AMT) program and SeaWiFS. The AMT cruises extend from the UK to the Falklands Islands (sailing on the RRS James Clark Ross) with the purpose of improving our knowledge of surface layer hydrography, biogeochemical processes, ecosystem dynamics and food webs across basin scales in the Atlantic Ocean. Two objectives of the AMT program relevant to this study are the characterization of biogeochemical provinces and the analysis of optical and pigment parameters in connection with remote sensing ocean color data. The primary focus of this NASA Technical Memorandum is on the variability of the vertical distribution of phytoplankton pigments and associated absorption properties across the SASG, and their relevance to remote sensing algorithms. Therefore, a subset of the AMT data within the SASG from all available cruises was used in the analyses. One of the challenges addressed here is the determination of the SASG geographic boundaries. One of the major problems is to reconcile the properties of biogeochemical provinces. We use water mass analysis, dynamics of ocean currents, and meridional gradients of bio-optical properties, to identify the SASG boundaries.

Signorini, S. R.↗

ESD Reviews: Climate Feedbacks in the Earth System and Prospects for Their Evaluation

Earth system models (ESMs) are key tools for providing climate projections under different scenarios of human-induced forcing. ESMs include a large number of additional processes and feedbacks such as biogeochemical cycles that traditional physical climate models do not consider. Yet, some processes such as cloud dynamics and ecosystem functional response still have fairly high uncertainties. In this article, we present an overview of climate feedbacks for Earth system components currently included in state-of-the-art ESMs and discuss the challenges to evaluate and quantify them. Uncertainties in feedback quantification arise from the interdependencies of biogeochemical matter fluxes and physical properties, the spatial and temporal heterogeneity of processes, and the lack of long-term continuous observational data to constrain them. We present an outlook for promising approaches that can help to quantify and to constrain the large number of feedbacks in ESMs in the future. The target group for this article includes generalists with a background in natural sciences and an interest in climate change as well as experts working in interdisciplinary climate research (researchers, lecturers, and students). This study updates and significantly expands upon the last comprehensive overview of climate feedbacks in ESMs, which was produced 15 years ago (NRC, 2003).

Climate feedbacks↗

Long-Term Stochasticity Combines With Short-Term Variability in Assembly Processes to Underlie Rice Paddy Sustainability

Revealing temporal patterns of community assembly processes is important for understanding how microorganisms underlie the sustainability of agroecosystem. The ancient terraced rice paddies at Longji provide an ideal platform to study temporal dynamics of agroecosystem sustainability due to their chronosequential records of soil physicochemistry and well-archived microbial information along 630-year rice cultivation. We used statistical null models to evaluate microbial assembly processes along the soil chronosequences of Longji rice paddies through time. Stochastic and deterministic assembly processes jointly governed microbial community composition within successional eras (less than 250 years), and within-era determinism was mainly driven by soil fertility and redox conditions alone or in combination. Conversely, across successional eras (i.e., over 300 years), stochasticity linearly increased with increasing duration between eras and was eventually predominant for the whole 630 years. We suggest that the impact of stochasticity vs. determinism on assembly is timescale-dependent, and we propose that the importance of stochastic assembly of microbial community at longer timescales is due to the gradual changes in soil properties under long-term rice cultivation, which in turn contribute to the sustainability of paddy ecosystem by maintaining a diverse community of microorganisms with multi-functional traits. In total, our results indicate that knowledge on the timescales at which assembly processes govern microbial community composition is key to understanding the ecological mechanisms generating agroecosystem sustainability.

59 BASIC BIOLOGICAL SCIENCES↗

NASA 1990 Multisensor Airborne Campaigns (MACs) for ecosystem and watershed studies

The Multisensor Airborne Campaign (MAC) focus within NASA's former Land Processes research program was conceived to achieve the following objectives: to acquire relatively complete, multisensor data sets for well-studied field sites, to add a strong remote sensing science component to ecology-, hydrology-, and geology-oriented field projects, to create a research environment that promotes strong interactions among scientists within the program, and to more efficiently utilize and compete for the NASA fleet of remote sensing aircraft. Four new MAC's were conducted in 1990: the Oregon Transect Ecosystem Research (OTTER) project along an east-west transect through central Oregon, the Forest Ecosystem Dynamics (FED) project at the Northern Experimental Forest in Howland, Maine, the MACHYDRO project in the Mahantango Creek watershed in central Pennsylvania, and the Walnut Gulch project near Tombstone, Arizona. The OTTER project is testing a model that estimates the major fluxes of carbon, nitrogen, and water through temperate coniferous forest ecosystems. The focus in the project is on short time-scale (days-year) variations in ecosystem function. The FED project is concerned with modeling vegetation changes of forest ecosystems using remotely sensed observations to extract biophysical properties of forest canopies. The focus in this project is on long time-scale (decades to millenia) changes in ecosystem structure. The MACHYDRO project is studying the role of soil moisture and its regulating effects on hydrologic processes. The focus of the study is to delineate soil moisture differences within a basin and their changes with respect to evapotranspiration, rainfall, and streamflow. The Walnut Gulch project is focused on the effects of soil moisture in the energy and water balance of arid and semiarid ecosystems and their feedbacks to the atmosphere via thermal forcing.

Wickland, Diane E.↗

Using mid-infrared spectroscopy to estimate soil microbial properties at the continental scale

Understanding microbial community properties is critical to improving the predictions of biogeochemical processes for enhancing soil carbon sequestration. Here, in this observational study, mid-infrared (MIR) spectroscopy and partial least squares regression was used to predict soil microbial and chemical properties from diverse ecosystems across the continental USA. Random calibration and validation demonstrated the prediction potential for soil properties using MIR spectra, with the strongest predictions for microbial respiration, followed by microbial biomass carbon and nitrogen, ß-glucosidase activity, as well as soil chemical properties including organic carbon and total nitrogen. Microbial properties were mainly positively correlated to spectral regions associated with aliphatic C-H groups and C=O stretches of polysaccharides and negatively correlated to quartz and silicate-associated regions. We conclude that MIR spectroscopy can characterize soil microbial functions and be useful for the improvement of continental-scale soil carbon modeling and prediction programs.

59 BASIC BIOLOGICAL SCIENCES↗

Carbon cycling across ecosystem succession in a north temperate forest: Controls and management implications

Despite decades of progress, much remains unknown about successional trajectories of carbon (C) cycling in north temperate forests. Drivers and mechanisms of these changes, including the role of different types of disturbances, are particularly elusive. To address this gap, we synthesized decades of data from experimental chronosequences and long-term monitoring at a well-studied, regionally representative field site in northern Michigan, USA. Our study provides a comprehensive assessment of changes in above- and belowground ecosystem components over two centuries of succession, links temporal dynamics in C pools and fluxes with underlying drivers, and offers several conceptual insights to the field of forest ecology. Our first advance shows how temporal dynamics in some ecosystem components are consistent across severe disturbances that reset succession and partial disturbances that slightly modify it: both of these disturbance types increase soil N availability, alter fungal community composition, and alter growth and competitive interactions between short-lived pioneer and longer-lived tree taxa. Further, these changes in turn affect soil C stocks, respiratory emissions, and other belowground processes. Second, we show that some other ecosystem components have effects on C cycling that are not consistent over the course of succession. For example, canopy structure does not influence C uptake early in succession but becomes important as stands develop, and the importance of individual structural properties changes over the course of two centuries of stand development. Third, we show that in recent decades, climate change is masking or overriding the influence of community composition on C uptake, while respiratory emissions are sensitive to both climatic and compositional change. In synthesis, we emphasize that time is not a driver of C cycling; it is a dimension within which ecosystem drivers such as canopy structure, tree and microbial community composition change. Changes in those drivers, not in forest age, are what control forest C trajectories, and those changes can happen quickly or slowly, through natural processes or deliberate intervention. Stemming from this view and a whole-ecosystem perspective on forest succession, we offer management applications from this work and assess its broader relevance to understanding long-term change in other north temperate forest ecosystems.

54 ENVIRONMENTAL SCIENCES↗

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 and variations in putative biochemical transformations. 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.

Danczak, Robert E.↗

Game-Theoretic Modeling of Vegetation Composition, Structure, and Dynamics: Physical Constraints, Fundamental Processes, and Emergent Properties

Vegetation structural and compositional dynamics emerge from plant physiological and demographic processes, individual-based competition, vegetation-soil feedbacks, and environmental variations and disturbance events. Predicting long-term changes in vegetation requires scaling plant individual behavior to large scale ecosystem processes. In this presentation, we summarize our studies in the modeling of vegetation demographic processes, competitively dominant plant traits, plant hydraulic processes, and stochastic disturbance effects on ecosystems, and illustrate the roles of the underlying ecological processes and eco-evolutionary optimization in vegetation modeling. With the case studies of evolutionarily stable strategy of allocation, leaf traits, and plant hydraulic processes, we show how the ecosystem processes and vegetation dynamics are determined by the individual-based plant competition and variations of soil and climate conditions. The predictions of ecosystem carbon dynamics can be greatly different with those from the traditional “single-tree” models. We also discuss the tradeoffs of plant traits and evolutionarily optimal strategies in the modeling of terrestrial ecosystem dynamics in an Earth system model.

vegetation models↗

Urbanization drives convergence in soil profile texture and carbon content

Urban development has driven extensive modification of the global landscape. This shift in land use and land cover alters ecological functioning, and thereby affects sustainable management agendas. Urbanization fundamentally reshapes the soils that underlay landscapes, and throughout the soil profile, extends impacts of urbanization far below the landscape surface. The impacts of urbanization on deeper soils that are beyond the reach of regular land management are largely unknown, and validation of general theories of convergent ecosystem properties are thwarted by a dearth of both level of measurement effort and the substantial heterogeneity in soils and urban landscapes. Here, we examined two soil properties with strong links to ecological functioning—carbon and mineral-fraction particle size—measured in urban soils, and compared them to their pre-urbanization conditions across a continental gradient encompassing global soil diversity. We hypothesized that urbanization drove convergence of soils properties from heterogeneous pre-urban conditions towards homogeneous urban conditions. Based on our observations, we confirm the hypothesis. Both soil carbon and particle size converged toward an intermediate value in the full data distribution, from pre-urban to urban conditions. These outcomes in urban soils were observed to uniformly be fine textured soils with overall lower carbon content. Although these properties are desirable for supporting urban infrastructure (e.g. buildings, pipes), they constrain the potential to render ecosystem services. Since soil profile texture and carbon content were convergent and observed across 11 cities, we suggest that these property profiles can be used as a universal urban soil profile to: 1) provide a clear prediction for how urbanization will shift soil properties from pre-urban conditions, 2) facilitate the adoption of commonly-accepted soil profiles for process models, and 3) offer a reference point to test against urban management strategies and how they impact soil resources.

54 ENVIRONMENTAL SCIENCES↗

NGEE Arctic Plant Traits: Fine Roots, Kougarok Road Mile Marker 64, Seward Peninsula, Alaska, 2016

Soil cores were collected from twelve vegetation biomass plots at the Kougarok hillslope in late July of 2016. The sampled plots were located across six ecotypes present at this site (n=2 replicates per ecotype). Soil cores were separated into depth intervals in the field and frozen for transport to Oak Ridge National Laboratory. Data package contains one *.csv and one *.pdf.Laboratory sample processing of these soils generated depth-specific data on soil properties as well as fine root biomass, length, %C, %N, delta13C, and delta15N. Only live fine roots were analyzed. Fine roots were not separated by species or plant functional type.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy’s Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy’s Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

NASA GRC ICME Schema for Materials Data Management: An Executive Summary

Integrated Computational Materials Engineering (ICME) has received a growing emphasis in attention due its potential impact on rapid material design, reduction in cost and time to market for new applications, and the promise of ‘fit-for-purpose’ materials coupled with recent advances in high performance computing and material characterization tools. However, for an organization to implement ICME practices for material discovery and design, a series of both technical and cultural challenges must be overcome to foster an environment that enables efficient, traceable, and predictive multiscale simulations of material behavior to enable virtual design of materials. In 2016, NASA sponsored a 2040 Vision study to define the potential 25-year future state required for integrated multiscale modeling of materials and systems to improve both the associated time and cost for aerospace and aeronautical innovation. The study envisions a cyber-physical-social ecosystem of experimentally validated computational models, tools, and techniques, along with the associated digital tapestry, that can enable rapid, optimized, ‘fit-for-purpose’ design of materials, components, and systems. A key requirement for such an ecosystem is the development of a robust information management system for materials across their full lifecycle, including material pedigree, experimental (real) and virtual (simulation) data, developed material models, and the implementation of models in engineering applications, such that process-structure-property-performance relationships can be established, thereby enabling the virtual design and optimization of materials. Such an information management system must be able to effectively capture: i) material information at each length scale; ii) test data and analysis; iii) associated material models; and iv) material and model deployment in engineering applications. These systems must also provide traceability between experimental and virtual representations of the material to ensure, when appropriate, the material digital twin is maintained. Additionally, this robust material information management system must be able to seamlessly connect with both commercial and an organization’s in-house software tools, be they analysis tools, other material databases, product lifecycle management (PLM) or simulation data management (SDM) tools, etc., such that automation of the design and analysis of a material across multiple length scales is possible. In this paper, an executive summary of the NASA GRC ICME Schema for materials information management is presented. The database best practices and schema design philosophy specifically for ICME materials data management and an overview description of each element in the schema is given, along with its associated role in an ICME workflow. Additionally, auxiliary tools that interact with the database and provide judicious automation with regards to importing, exporting, and analyzing materials data are presented. Such tools are critical to an ICME ecosystem, not only for their role in enabling optimization, but also in relieving users of tedious manual tasks, thus helping to promote adoption and combat the cultural challenges organizations face in enabling ICME.

Materials↗

Disturbance triggers non-linear microbe–environment feedbacks

Abstract. 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. Our refined framework includes relationships between cumulative properties of a microbial community (e.g., microbial membership, community assembly properties, and biogeochemical rates), environmental features (e.g., organic matter thermodynamics), and emergent ecosystem function. Our primary aim was to evaluate the hypothesized relationships that comprise the conceptual framework and contrast outcomes from the whole and putatively active bacterial and archaeal communities. Throughout the system we found threshold-like responses to the duration of desiccation. Membership of the putatively active community – but not the whole bacterial and archaeal community – responded due to enhanced deterministic selection (an emergent community property). Concurrently, the thermodynamic properties of organic matter (OM) became less favorable for oxidation (an environmental component), and respiration decreased (a microbial process). While these responses were step functions of desiccation, we found that in deterministically assembled active communities, respiration was lower and thermodynamic properties of OM were less favorable. Placing the results in context of our conceptual framework points to previously unrecognized internal feedbacks that are initiated by disturbance and mediated by thermodynamics and that cause the impacts of disturbance to be dependent on the history of disturbance.

59 BASIC BIOLOGICAL SCIENCES↗

Quantifying Drivers of Methane Hydrobiogeochemistry in a Tidal River Floodplain System

The influence of coastal ecosystems on global greenhouse gas (GHG) budgets and their response to increasing inundation and salinization remains poorly constrained. In this study, we have integrated an uncertainty quantification (UQ) and ensemble machine learning (ML) framework to identify and rank the most influential processes, properties, and conditions controlling methane behavior in a freshwater floodplain responding to recently restored seawater inundation. Our unique multivariate, multiyear, and multi-site dataset comprises tidal creek and floodplain porewater observations encompassing water level, salinity, pH, temperature, dissolved oxygen (DO), dissolved organic carbon (DOC), total dissolved nitrogen (TDN), partial pressure of carbon dioxide (pCO 2 ), nitrous oxide (pN 2 O), methane (pCH 4 ), and the stable isotopic composition of methane (δ 13 CH 4 ). Additionally, we incorporated topographical data, soil porosity, hydraulic conductivity, and water retention parameters for UQ analysis using a previously developed 3D variably saturated flow and transport floodplain model for a physical mechanistic understanding of factors influencing groundwater levels and salinity and, therefore, CH 4 . Principal component analysis revealed that groundwater level and salinity are the most significant predictors of overall biogeochemical variability. The ensemble ML models and UQ analyses identified DO, water level, salinity, and temperature as the most influential factors for porewater methane levels and indicated that approximately 80% of the total variability in hourly water levels and around 60% of the total variability in hourly salinity can be explained by permeability, creek water level, and two van Genuchten water retention function parameters: the air-entry suction parameter α and the pore size distribution parameter m. These findings provide insights on the physicochemical factors in methane behavior in coastal ecosystems and their representation in local- to global-scale Earth system models.

54 ENVIRONMENTAL SCIENCES↗

PhyLM: A Mission Design Concept for an Optical/Lidar Instrument to Measure Ocean Productivity and Aerosols from Space

The Physiology Lidar-Multispectral Mission (PhyLM) is intended to explore the complex ecosystems of our global oceans. New "inversion" methods and improved understanding of marine optics have opened the door to quantifying a range of critical ocean properties. This new information could revolutionize our understanding of global ocean processes, such as phytoplankton growth, harmful algal blooms, carbon fluxes between major pools and the productivity equation. The new science requires new measurements not addressed by currently planned space missions. PhyLM will combine active and advanced passive remote sensing technologies to quantify standing stocks and fluxes of climate-critical components of the Ocean carbon cycle to meet these science providing multispectral bands from the far UV through the near infrared (340 - 1250 nm) at a ground resolution of 250 m. Improved detectors, filters, mirrors, digitization and focal plane design will offer an overall higher-quality data product. The unprecedented accuracy and precision of the absolute water-leaving radiances will support inversion- based quantification of an expanded set of ocean carbon cycle components. The dual- wavelength (532 & 1064 nm) Nd:Yag Lidar will enhance the accuracy and precision of the passive data by providing aerosol profiles for atmospheric correction and coincident active measurements of backscattering. The Lidar will also examine dark-side fluorescence as an additional approach to quantifying phytoplankton biomass in highly productive regions.

Gervin, Janette C.↗