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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

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↗
DOE OSTI2022

Plant-Soil Relationships Influence Observed Trends Between Manganese and Carbon Across Biomes

Manganese (Mn) is an essential plant micronutrient that plays a critical role in the litter decomposition by oxidizing and degrading complex organic molecules. Previous studies report a negative correlation between Mn concentrations and carbon (C) storage in organic horizons and suggest that high Mn concentrations in leaf litter reduce soil C storage in forest ecosystems, presumably by stimulating the oxidation of lignin by fungal enzymes. Yet, the relationship between Mn and C in the litter layer and organic soil remains poorly understood and restricted to a few biomes, hampering our ability to improve mechanistic understanding of soil C accumulation. Here, to examine plant-soil interactions that underlie observed relationships between Mn and C across a wide range of biomes, we extracted biogeochemical data reported for plants and soils from the National Ecological Observatory Network (NEON) database. We found that increased C and nitrogen (N) storage in organic horizons were associated with declines in Mn concentrations across diverse ecosystems at the continental scale, and this relationship was associated with the degree of organic matter decomposition (i.e., O i , O e , and O a ). Carbon and N stocks were more strongly correlated with Mn than with climatic variables (i.e., temperature and precipitation). Foliar Mn was strongly correlated with foliar lignin, and both these parameters increased with a decrease in soil pH, indicating links between soil pH, foliar chemistry, and litter decomposability. Our observations suggest that increased Mn bioavailability and accumulation in foliage under moderately acidic soil conditions support fungal decomposition of lignin-rich litter and contributes to lower soil C stocks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

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↗
DOE OSTI2022

Year-around survey and manipulation experiments reveal differential sensitivities of soil prokaryotic and fungal communities to saltwater intrusion in Florida Everglades wetlands

Global sea-level rise is transforming coastal ecosystems, especially freshwater wetlands, in part due to increased episodic or chronic saltwater exposure, leading to shifts in biogeochemistry, plant- and microbial communities, as well as ecological services. Yet, it is still difficult to predict how soil microbial communities respond to the saltwater exposure because of poorly understood microbial sensitivity within complex wetland soil microbial communities, as well as the high spatial and temporal heterogeneity of wetland soils and saltwater exposure. To address this, we first conducted a two-year survey of microbial community structure and bottom water chemistry in submerged surface soils from 14 wetland sites across the Florida Everglades. We identified ecosystem-specific microbial biomarker taxa primarily associated with variation in salinity. Bacterial, archaeal and fungal community composition differed between freshwater, mangrove, and marine seagrass meadow sites, irrespective of soil type or season. Especially, methanogens, putative denitrifying methanotrophs and sulfate reducers shifted in relative abundance and/or composition between wetland types. Methanogens and putative denitrifying methanotrophs declined in relative abundance from freshwater to marine wetlands, whereas sulfate reducers showed the opposite trend. A four-year experimental simulation of salt-water intrusion in a pristine freshwater site and a previously saltwater-impacted site corroborated the highest sensitivity and relative increase of sulfate reducers, as well as taxon-specific sensitivity of methanogens, in response to continuously pulsing of saltwater treatment. Collectively, these results suggest that besides increased salinity, saltwater-mediated increased sulfate availability leads to displacement of methanogens by sulfate reducers even at low or temporal salt exposure. In conclusion, these changes of microbial composition could affect organic matter degradation pathways in coastal freshwater wetlands exposed to sea-level rise, with potential consequences, such as loss of stored soil organic carbon.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Remote Sensing of Tundra Ecosystems Using High Spectral Resolution Reflectance: Opportunities and Challenges

Abstract Observing the environment in the vast regions of Earth through remote sensing platforms provides the tools to measure ecological dynamics. The Arctic tundra biome, one of the largest inaccessible terrestrial biomes on Earth, requires remote sensing across multiple spatial and temporal scales, from towers to satellites, particularly those equipped for imaging spectroscopy (IS). We describe a rationale for using IS derived from advances in our understanding of Arctic tundra vegetation communities and their interaction with the environment. To best leverage ongoing and forthcoming IS resources, including National Aeronautics and Space Administration’s Surface Biology and Geology mission, we identify a series of opportunities and challenges based on intrinsic spectral dimensionality analysis and a review of current data and literature that illustrates the unique attributes of the Arctic tundra biome. These opportunities and challenges include thematic vegetation mapping, complicated by low‐stature plants and very fine‐scale surface composition heterogeneity; development of scalable algorithms for retrieval of canopy and leaf traits; nuanced variation in vegetation growth and composition that complicates detection of long‐term trends; and rapid phenological changes across brief growing seasons that may go undetected due to low revisit frequency or be obscured by snow cover and clouds. We recommend improvements to future field campaigns and satellite missions, advocating for research that combines multi‐scale spectroscopy, from lab studies to satellites that enable frequent and continuous long‐term monitoring, to inform statistical and biophysical approaches to model vegetation dynamics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

First observation of potential phoresy between Planorbarius metidjensis and Ancylus fluviatilis (Gastropoda: Planorbidae) in Algeria

Phoresy, an ecological phenomenon in which one organism attaches itself to another for dispersal, has been observed in various species. In this study, we describe the potential occurrence of phoresy between Ancylus fluviatilis and Planorbarius metidjensis in Algerian freshwater. Through field observations, we provide evidence to suggest that P. metidjensis may serve as a transport host for A. fluviatilis, facilitating its movement within aquatic ecosystems. Additionally, juvenile P. metidjensis were observed attached to adults of the same species, which may be a case of intraspecific phoresy. This interaction has implications for understanding the ecology and dispersal mechanisms of freshwater molluscs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Microbial Community Shifts Reflect Losses of Native Soil Carbon with Pyrogenic and Fresh Organic Matter Additions and Are Greatest in Low-Carbon Soils

ABSTRACT Soil organic carbon (SOC) plays an important role in regulating global climate change, carbon and nutrient cycling in soils, and soil moisture. Organic matter (OM) additions to soils can affect the rate at which SOC is mineralized by microbes, with potentially important effects on SOC stocks. Understanding how pyrogenic organic matter (PyOM) affects the cycling of native SOC (nSOC) and the soil microbes responsible for these effects is important for fire-affected ecosystems as well as for biochar-amended systems. We used an incubation trial with five different soils from National Ecological Observatory Network sites across the United States and 13 C-labeled 350°C corn stover PyOM and fresh corn stover OM to trace nSOC-derived CO 2 emissions with and without PyOM and OM amendments. We used high-throughput sequencing of rRNA genes to characterize bacterial, archaeal, and fungal communities and their responses to PyOM and OM in soils that were previously stored at −80°C. We found that the effects of amendments on nSOC-derived CO 2 reflected the unamended soil C status, where relative increases in C mineralization were greatest in low-C soils. OM additions produced much greater effects on nSOC-CO 2 emissions than PyOM additions. Furthermore, the magnitude of the microbial community composition change mirrored the magnitude of increases in nSOC-CO 2 , indicating that a specific subset of microbes was likely responsible for the observed changes in nSOC mineralization. However, PyOM responders differed across soils and did not necessarily reflect a common “charosphere.” Overall, this study suggests that soils that already have low SOC may be particularly vulnerable to short-term increases in SOC loss with OM or PyOM additions. IMPORTANCE Soil organic matter (SOM) has an important role in global climate change, carbon and nutrient cycling in soils, and soil moisture dynamics. Understanding the processes that affect SOM stocks is important for managing these functions. Recently, understanding how fire-affected organic matter (or “pyrogenic” organic matter [PyOM]) affects existing SOM stocks has become increasingly important, due to both changing fire regimes and interest in “biochar,” pyrogenic organic matter that is produced intentionally for carbon management or as an agricultural soil amendment. We found that soils with less SOM were more prone to increased losses with PyOM (and fresh organic matter) additions and that soil microbial communities changed more in soils that also had greater SOM losses with PyOM additions. This suggests that soils that already have low SOM content may be particularly vulnerable to short-term increases in SOM loss and that a subset of the soil microbial community is likely responsible for these effects.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Identification of Effector Metabolites Using Exometabolite Profiling of Diverse Microalgae

Dissolved exometabolites mediate algal interactions in aquatic ecosystems, but microalgal exometabolomes remain understudied. We conducted an untargeted metabolomic analysis of nonpolar exometabolites exuded from four phylogenetically and ecologically diverse eukaryotic microalgal strains grown in the laboratory, freshwater Chlamydomonas reinhardtii, brackish Desmodesmus sp., marine Phaeodactylum tricornutum, and marine Microchloropsis salina, to identify released metabolites based on relative enrichment in the exometabolomes compared to cell pellet metabolomes. Exudates from the different taxa were distinct, but we did not observe clear phylogenetic patterns. We used feature-based molecular networking to explore the identities of these metabolites, revealing several distinct di- and tripeptides secreted by each of the algae, lumichrome, a compound that is known to be involved in plant growth and bacterial quorum sensing, and novel prostaglandin-like compounds. We further investigated the impacts of exogenous additions of eight compounds selected based on exometabolome enrichment on algal growth. Of these compounds, five (lumichrome, 5'-S-methyl-5'-thioadenosine, 17-phenyl trinor prostaglandin A2, dodecanedioic acid, and aleuritic acid) impacted growth in at least one of the algal cultures. Two of these compounds (dodecanedioic acid and aleuritic acid) produced contrasting results, increasing growth in some algae and decreasing growth in others. Together, our results reveal new groups of microalgal exometabolites, some of which could alter algal growth when provided exogenously, suggesting potential roles in allelopathy and algal interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome

' Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus–host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, ' Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Investigating effects of soil chemicals on density of small mammal bioindicators using spatial capture-recapture models

Monitoring the ecological impacts of environmental pollution and the effectiveness of remediation efforts requires identifying relationships between contaminants and the disruption of biological processes in populations, communities, or ecosystems. Wildlife are useful bioindicators, but traditional comparative experimental approaches rely on a staunch and typically unverifiable assumption that, in the absence of contaminants, reference and contaminated sites would support the same densities of bioindicators, thereby inferring direct causation from indirect data. We demonstrate the utility of spatial capture-recapture (SCR) models for overcoming these issues, testing if community density of common small mammal bioindicators was directly influenced by soil chemical concentrations. By modeling density as an inhomogeneous Poisson point process, we found evidence for an inverse spatial relationship between Peromyscus density and soil mercury concentrations, but not other chemicals, such as polychlorinated biphenyls, at a site formerly occupied by a nuclear reactor. Although the coefficient point estimate supported Peromyscus density being lower where mercury concentrations were higher (β = –0.44), the 95% confidence interval overlapped zero, suggesting no effect was also compatible with our data. Estimated density from the most parsimonious model (2.88 mice/ha; 95% CI = 1.63–5.08), which did not support a density-chemical relationship, was within the range of reported densities for Peromyscus that did not inhabit contaminated sites elsewhere. Environmental pollution remains a global threat to biodiversity and ecosystem and human health, and our study provides an illustrative example of the utility of SCR models for investigating the effects that chemicals may have on wildlife bioindicator populations and communities.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Detection and Screening of Organic Contaminants in A Riverine System of Georgia Using Non-Targeted Analysis

Numerous organic chemicals exist within aquatic environments, yet effectively screening and prioritizing them is a huge challenge. This study provides a comprehensive investigation into the ecological dynamics of the North Oconee River within Athens-Clarke County, Georgia, with a specific focus on the distribution of 33 identified compounds, including a prominent pesticide. The research, conducted in the riverine ecosystems proximal to the Firefly trail, employs advanced analytical techniques to elucidate potential contamination sources arising from agricultural and urban runoff. Intriguingly, the study reveals North Oconee River near the Firefly Trail as a notable site for heightened pesticide contamination, warranting a meticulous exploration of its origins. Furthermore, the investigation unveils the intricate microbial degradation processes of malathion within the North Oconee River, elucidating the pivotal role played by microbial activity in river water. The detection of degradant byproducts prompts the considerations of bioavailability and toxicity, associating potential implications for the river’s overall ecological health. Ongoing research endeavors to precisely quantify environmental risks and unravel indigenous microbial degradation pathways, presenting pivotal contributions to the scientific community’s understanding of complex riverine ecosystems. This research serves as a foundational piece in informing sustainable environmental management practices and emphasizes the urgency of comprehensive stewardship in safeguarding aquatic ecosystems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here, in this work, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Breaking the Ice: A Review of Phages in Polar Ecosystems

Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. In this study, understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage–host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.

09 BIOMASS FUELS↗
DOE OSTI2021

Widespread co‐occurrence of Sebacinales and arbuscular mycorrhizal fungi in switchgrass roots and soils has limited dependence on soil carbon or nutrients

Societal Impact Statement This work addresses a novel group of Sebacinales mycorrhizal fungi being considered for development as inoculants in managed ecosystems because of their potential access to nutrients in soil organic matter. By comparing the diversity, distributions, and abundances of the Sebacinales with the more common arbuscular mycorrhizal fungi in switchgrass, a biofuel crop, we demonstrate that current suggestions for a Sebacinales revolution in agriculture should be tempered by their ecology. In particular, Sebacinales are rare compared to arbuscular mycorrhizal fungi, and are only weakly associated with soil carbon, suggesting that ideas about improved soil carbon cycling associated with Sebacinales need to be sufficiently studied across a range of environmental conditions prior to their consideration for broad‐spectrum soil inoculants. Summary Arbuscular mycorrhizal (AM) fungi are widespread and important root symbionts, but recent work suggests that Sebacinales fungi may play an equally important role in both plant success and ecosystem carbon and nutrient cycling based on their worldwide occurrence and putative access to organic matter. However, the ecological impacts of Sebacinales will depend on their abundance and distribution relative to AM fungi and environmental soil carbon and nutrient patterns, which remain unexplored. We characterized Glomeromycota and Sebacinales fungi in switchgrass ( Panicum virgatum L.) roots and soils across 14 sites with diverse soil conditions. We examined group richness differences, co‐occurrence patterns, and how the relative abundance of these fungi related to soil carbon, nutrient stoichiometry, and host size. Sebacinales were widespread, but less diverse, common, and abundant than Glomeromycota. Moreover, co‐occurrences were predominantly random, suggesting relatively few interactions between these groups. Sebacinales increased relative to Glomeromycota in soils with more carbon, but explanatory power was limited. Based on our findings, we suggest that Sebacinales are likely complementary to AM fungi in roots. Expectations that Sebacinales have large effects on soil carbon and nutrient cycling may need to be reconsidered, at least based on their limited abundances relative to AM fungi in switchgrass. This is an important consideration as Sebacinales are candidates for use as inoculants in managed ecosystems.

Lee, Marissa R.↗
DOE OSTI2021

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H 2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Landscape-scale characterization of Arctic tundra vegetation composition, structure, and function with a multi-sensor unoccupied aerial system

The Arctic is experiencing some of the most rapid climate change on Earth, with strong impacts on tundra ecosystems that are characterized by high land-surface and vegetation heterogeneity. Previous studies have explored this complexity using satellite remote sensing, however these typically coarse spatial resolution data have generally missed sub-pixel heterogeneity, leaving critical gaps in our understanding of tundra vegetation dynamics from the community to landscape scales. To address these gaps, we collected very high-resolution (1-5 cm) optical, structural, and thermal data at three low-Arctic tundra sites on the Seward Peninsula, Alaska, using a multi-sensor unoccupied aerial system (UAS). We examined the application of these data to studying tundra vegetation dynamics, by quantifying (1) canopy height and thermoregulation (leaf-air temperature) of representative plant functional types (PFTs), (2) fine-scale patterns of vegetation composition across landscapes, and (3) impacts of fine-scale vegetation composition on landscape-scale variation of canopy height and thermoregulation. Our results show that deciduous tall shrubs (those that can potentially grow >2 m) had a strong cooling effect, with canopy temperatures significantly lower than local air temperatures and other PFTs. Increased cover of tall shrubs also had the potential to reduce the cover of low-stature PFTs across the landscape, potentially associated with their closed canopy (i.e., increased light competition) and strong thermoregulation. To understand the connections between fine-scale vegetation composition and large-scale ecosystem processes, we produced a random forest model which showed that fine-scale PFT composition accounted for 86.8% and 74.2% of the landscape-scale variation in canopy height and thermoregulation, respectively. These findings highlight the importance of spatially detailed characterization of tundra PFTs to improve our ecological understanding and model representation of tundra vegetation, also transcend our study to show the need for continued collection of similar datasets to better understand the impacts of surface heterogeneity on the mapping and modeling of tundra ecosystem dynamics, as well as assist with conservation management and biodiversity monitoring strategies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Empirical Dynamic Modeling Reveals Complexity of Methane Fluxes in a Temperate Salt Marsh

Abstract Methane dynamics within salt marshes are complex because vegetation types, temperature, oscillating water levels, and changes in salinity and redox conditions influence CH 4 production, consumption, oxidation, and emissions. These non‐linear and complex interactions among variables affect the traditionally expected functional relationships and present challenges for interpreting and developing process‐based models. We employed empirical dynamic modeling (EDM) and convergent cross mapping (CCM) as a novel approach for characterizing seasonal/multiday and diurnal CH 4 dynamics by inferring causal variables, lags, and interconnections among multiple biophysical variables within a temperate salt marsh using 5 years of eddy covariance data. EDM/CCM is a nonparametric approach capable of quantifying the coupling between variables while determining time scales where variable interactions are the most relevant. We found that gross primary productivity, tidal creek dissolved oxygen, and temperature were important for seasonal/multiday dynamics (rho = 0.73–0.80), while water level was most important for diurnal dynamics during both the growing and dormancy phenoperiods (rho = 0.72 and 0.56, respectively). Lags for the top‐ranked variables (i.e., gross primary productivity, dissolved oxygen, temperature, water level) occurred between 1 and 5 weeks at the seasonal scale and 1–24 hr at the diurnal scale. The EDM had high prediction capabilities for intra‐/inter‐seasonal patterns and annual CH 4 sums but had limitations in representing large, infrequent fluxes. Results highlight the importance of non‐linearity, drivers, lag times, and interconnections among multiple biophysical variables that regulate CH 4 fluxes in tidal wetlands. This research introduces a novel approach to examining CH 4 fluxes, which will aid in evaluating current paradigms in wetlands and other ecosystems.

Environmental Sciences & Ecology↗
DOE OSTI2024

Variation in forest root image annotation by experts, novices, and AI

Abstract Background The manual study of root dynamics using images requires huge investments of time and resources and is prone to previously poorly quantified annotator bias. Artificial intelligence (AI) image-processing tools have been successful in overcoming limitations of manual annotation in homogeneous soils, but their efficiency and accuracy is yet to be widely tested on less homogenous, non-agricultural soil profiles, e.g., that of forests, from which data on root dynamics are key to understanding the carbon cycle. Here, we quantify variance in root length measured by human annotators with varying experience levels. We evaluate the application of a convolutional neural network (CNN) model, trained on a software accessible to researchers without a machine learning background, on a heterogeneous minirhizotron image dataset taken in a multispecies, mature, deciduous temperate forest. Results Less experienced annotators consistently identified more root length than experienced annotators. Root length annotation also varied between experienced annotators. The CNN root length results were neither precise nor accurate, taking ~ 10% of the time but significantly overestimating root length compared to expert manual annotation ( p = 0.01). The CNN net root length change results were closer to manual ( p = 0.08) but there remained substantial variation. Conclusions Manual root length annotation is contingent on the individual annotator. The only accessible CNN model cannot yet produce root data of sufficient accuracy and precision for ecological applications when applied to a complex, heterogeneous forest image dataset. A continuing evaluation and development of accessible CNNs for natural ecosystems is required.

Handy, Grace↗