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At least 379 records · Page 21

Simulating environmentally-sensitive tree recruitment in vegetation demographic models

Vegetation demographic models (VDMs) endeavor to predict how global forests will respond to climate change. This requires simulating which trees, if any, are able to recruit under changing environmental conditions. We present a new recruitment scheme for VDMs in which functional-type-specific recruitment rates are sensitive to light, soil moisture and the productivity of reproductive trees. We evaluate the scheme by predicting tree recruitment for four tropical tree functional types under varying meteorology and canopy structure at Barro Colorado Island, Panama. We compare predictions to those of a current VDM, quantitative observations and ecological expectations. We find that the scheme improves the magnitude and rank order of recruitment rates among functional types and captures recruitment limitations in response to variable understory light, soil moisture and precipitation regimes. Furthermore, our results indicate that adopting this framework will improve VDM capacity to predict functional-type-specific tree recruitment in response to climate change, thereby improving predictions of future forest distribution, composition and function.

59 BASIC BIOLOGICAL SCIENCES↗

Responses of Boreal Forest Ecosystems and Permafrost to Climate Change and Disturbances: A Modeling Perspective

The north circumpolar region contains a large amount of carbon. This carbon storage is vulnerable due to permafrost degradation and wildfire disturbances under ongoing and projected climate change. Climate warming and wildfires change soil organic horizons gradually or abruptly, and modify permafrost thermal-hydrology and biogeochemistry, ecosystem structures, functions, and capability of sequestrating rising atmospheric CO2. Land models do not fully take accounts of these interactions and its complexity in the high latitude. This chapter describes a terrestrial ecosystem model with dynamic organic soil module (DOS-TEM) and its unique freezing-thawing algorithm, and presents key results of its applications mainly in boreal forests of Alaska. The DOS-TEM explicitly considers interactions of soil thermal and hydrological processes, permafrost degradation and the direct and indirect effects of wildfire disturbances, in addition to soil–plant C and N cycles. We first introduce four modules of DOS-TEM, focusing on its disturbance module and coupling with a dynamic organic soil module. Then we describe and validate DOS-TEM’s freezing-thawing algorithm and development based on two-directional Stefan algorithm (TDSA). Finally, we apply the DOS-TEM at site and region scales, with a focus on model ability to dynamically simulate soil organic thickness under warming and wildfires, and consequent impacts on permafrost in the Yukon River Basin. We conclude that land surface model development is urgently needed to include other critical landscape processes, such as thermalkarst and other disturbances, to synchronize thermal-hydrological-biogeochemical processes, and to incorporate an advanced understanding of biospheric feedbacks to atmosphere and ecosystems. Such a complexity of modeling scope is plausible with advancement of high performance computing.

Yi, Shuhua↗

Raw seedling and sapling census data collected from June 2015 - April 2019 within a tropical wet forest in Puerto Rico

This data package contains data used to evaluate the effects of experimental warming (4˚C above ambient), drought, and hurricane disturbance on species richness, diversity, and composition of understory plant communities across ontogeny at the Tropical Responses to Altered Climate Experiment (TRACE) in Luquillo, Puerto Rico. The raw data in this package include a file for the species composition matrix of woody seedlings (>10 cm and <20 cm height; TRACE_composition_seedling.csv) and saplings (>20 cm height; TRACE_composition_sapling.csv) within the six TRACE plots, collected during six census dates from June 2015 to April 2019. Also included is also a file with the species names associated with the species codes found in the composition files (TRACE_species_codes.csv), and a data dictionary file describing the columns in the composition files (data_dictionary_composition_files.csv). All data files are in csv format, with the exception of the metadata which is in xml format.

54 ENVIRONMENTAL SCIENCES↗

Intensified Soil Moisture Extremes Decrease Soil Organic Carbon Decomposition: A Mechanistic Modeling Analysis

Earth system models have predicted that there will be more frequent and severe precipitation and drought events in terrestrial ecosystems. Microbially mediated decomposition of soil organic carbon (SOC) tends to increase as soils wet and decrease as soils dry. However, the long-term SOC change under intensified moisture extremes remains poorly known as it depends on the frequency and intensity of soil drying and wetting. In this study, we explored long-term SOC dynamics under scenarios of alternating drying-wetting cycles using the Microbial-ENzyme Decomposition model, a mechanistic microbial model. The model was parameterized with 11 years of observations from a temperate deciduous broadleaf forest site, showing satisfactory model performance in both model calibration (R 2 = 0.67) and validation (R 2 = 0.69) against heterotrophic respiration. We then used the model to simulate the long-term SOC dynamics under five scenarios of alternating drying-wetting cycles with different frequencies and severities over a period of 100 years. Results showed that the changes in active microbial biomass C and the corresponding turnover rates of SOC pools were more sensitive to soil drying than soil wetting. As a result, the cumulative soil carbon emission from microbial respiration decreased by 433.7 g C m -2 after the 100-year simulation in the highest frequency and intensity moisture scenario, but was not significantly affected by the lowest frequency and intensity scenario. This study emphasizes the nonlinear response of SOC decomposition to soil moisture changes, which causes decreased decomposition by microbes under drying that is, not compensated by increased decomposition under wetting conditions.

58 GEOSCIENCES↗

Dynamics and drivers of land use and land cover changes in Bangladesh

Abstract Bangladesh has undergone dramatic land use and land cover changes (LULCC) in recent years, but no quantitative analysis of LULCC drivers at the national scale exists so far. Here, we quantified the drivers of major LULCC in combination with biophysical and socioeconomic observations at the sub-district level. We used Landsat satellite data to interpret LULCC from 2000 to 2010 and employed a Global Surface Water Dataset to account for the influences of water seasonality. The results suggest that major LULCC in Bangladesh occur between agricultural land and waterbodies and between forest and shrubland. Exclusion of seasonal waterbodies can improve the accuracy of our LULCC results and driver analysis. Although the gross gain and loss of agricultural land are large on the local scale, the net change (gross gain minus gross loss) at a country scale is almost negligible. Climate dynamics and extreme events and changes in urban and rural households were driving the changes from forest to shrubland in the southeast region. The conversion from agricultural land to standing waterbodies in the southwest region was mainly driven by urban household dynamics, population growth, distance to cities and major roads, and precipitation dynamics. This study, which is the first effort accounting for water seasonality and quantifying biophysical and socioeconomic drivers of LULCC at the national scale, provides a perspective on overall LULCC and underlying drivers over a decadal time scale and national spatial scale and can serve as a scientific basis for developing land policies in Bangladesh.

54 ENVIRONMENTAL SCIENCES↗

Soil Carbon Dynamics Following Land Use Changes and Conversion to Oil Palm Plantations in Tropical Lowlands Inferred From Radiocarbon

We measured the 14C and 13C isotopic values of soil organic carbon in mineral soil from lowland tropical forests to provide insight into how quickly carbon is turning over in the soil following conversion of primary forests to oil palm plantations. In addition to areas converted to oil palm plantations in Peru, Indonesia, and Cameroon, we examine pastures and secondary forests in Peru as a comparison to the carbon cycling processes operating in the oil palm plantations.This dataset includes radiocarbon (Δ14C) and stable carbon (δ13C) isotopes of soil organic carbon in mineral soils from natural lowland forests and oil palm plantations in Peru, Indonesia, and Cameroon. We additionally examine plots of secondary forests following agricultural use and pastures on cleared natural forest in Peru. In addition to isotopic data, this dataset includes soil carbon and nitrogen concentrations and stock, soil texture (percent sand, silt, and clay), pH, ECEC (effective cation exchange capacity), base saturation, and bulk density. Soils were sampled in 4 depth increments to 100 cm depth.This dataset supports the publication Finstad et al., 2020. Finstad, K., van Straaten, O., Veldkamp, E., & McFarlane, K. (2020). Soil carbon dynamics following land use changes and conversion to oil palm plantations in tropical lowlands inferred from radiocarbon. Global Biogeochemical Cycles, 34, e2019GB006461. https://doi.org/10.1029/2019GB006461

54 ENVIRONMENTAL SCIENCES↗

Comparative Model Evaluation Studies of Biogenic Trace Gas Fluxes in Tropical Forests

Simulation modeling can play a number of important roles in large-scale ecosystem studies, including synthesis of patterns and changes in carbon and nutrient cycling dynamics, scaling up to regional estimates, and formulation of testable hypotheses for process studies. Recent comparative studies have shown that ecosystem models of soil trace gas exchange with the atmosphere are evolving into several distinct simulation approaches. Different levels of detail exist among process models in the treatment of physical controls on ecosystem nutrient fluxes and organic substrate transformations leading to gas emissions. These differences are is in part from distinct objectives of scaling and extrapolation. Parameter requirements for initialization scalings, boundary conditions, and time-series driven therefore vary among ecosystem simulation models, such that the design of field experiments for integration with modeling should consider a consolidated series of measurements that will satisfy most of the various model requirements. For example, variables that provide information on soil moisture holding capacity, moisture retention characteristics, potential evapotranspiration and drainage rates, and rooting depth appear to be of the first order in model evaluation trials for tropical moist forest ecosystems. The amount and nutrient content of labile organic matter in the soil, based on accurate plant production estimates, are also key parameters that determine emission model response. Based on comparative model results, it is possible to construct a preliminary evaluation matrix along categories of key diagnostic parameters and temporal domains. Nevertheless, as large-scale studied are planned, it is notable that few existing models age designed to simulate transient states of ecosystem change, a feature which will be essential for assessment of anthropogenic disturbance on regional gas budgets, and effects of long-term climate variability on biosphere-atmosphere exchange.

Potter, C. S.↗

The bioclimatic extent and pattern of the cold edge of the boreal forest: the circumpolar taiga-tundra ecotone

Current configurations of forest structure at the cold edge of the boreal may help understand the future of ecosystem functioning in high northern latitudes. The circumpolar biome boundary at the boreal (taiga) forest and tundra interface is an ecological transition zone (taiga-tundra ecotone; TTE) experiencing changes that affect its forest structure. We accounted for the TTE's horizontal forest structure with an estimate of its extent and pattern as represented by tree canopy cover (TCC). We quantified TCC patterns with an algorithm that describes its spatial gradient, and summarized landscape patterns of structure to represent heterogeneity, capturing abrupt, diffuse, and uniform forest at mesoscales. We used these landscape patterns to constrain the spatial extent of sparse and open canopy forest, and non-forest (forest-adjacent) edge that defines the TTE extent. The resulting map of the TTE extent is based on forest structure spatial patterns resolved at 30 m, highlights structural variability across landscapes, and helps distinguish tundra from boreal domains. We classified 14 594 landscapes as those associated with the TTE within a circumpolar bioclimatic envelope (11.575 million km2), where 44.83% of the area of these landscapes were forest and non-forest edge, yet 36.43% contributed to the TTE extent. We report the overall extent of the TTE (3.032 million km2) across North America and Greenland (53%), and Eurasia (47%), where 0.697 million km2 is non-forest edge, 0.549 million km2 is sparse forest, and 1.787 million km2 is open canopy forest. Diffuse forest landscapes dominate the TTE (79%), and abrupt landscapes (~19%) indicate portions of the TTE where sparse forest and non-forest edge are the prevailing structural patterns. This account of the TTE quantifies the area of the cold edge of the boreal forest where previous global estimates show high discrepancies, and can help target monitoring and prediction of circumpolar dynamics.

Paul M Montesano↗

Expansion of high-latitude deciduous forests driven by interactions between climate warming and fire: Modeling Archive

This Modeling Archive is in support of an NGEE Arctic publication. More information in the related references. The dataset is a model (ecosys) output used in a study that examined the potential future shifts in high-latitude vegetation types (PFTs) driven by changes in 21st century climate and fire. The study highlights the importance of mechanistically representing differences in plant functional traits on current and possible 21st century trajectories of Alaskan PFTs. This dataset package includes 13 files in pdf, csv, and nc formats.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was 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↗

Overview of the Oregon Transect Ecosystem Research Project

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

Peterson, David L.↗

Enriched Background Isotope Study (EBIS): Analysis of 14C-Enriched Carbon Cycle in Soils and Litter at Forested Oak Ridge and AmeriFlux Sites, 2001-2011

These data provide a record of the multi-year, multi-institutional Enriched Background Isotope Studies (EBIS) projects that ran from 2000 through 2011. Elevated levels of 14C enriched CO2 in the air and soil atmosphere as well as leaf, stem, and root tissues were observed on the Oak Ridge Reservations (ORR) during the summer of 1999, and were attributed to local incinerator activities on and/or near the ORR (Trumbore et al. 2002). The isolated enrichment of the background levels of 14C in local forest ecosystem represented a unique opportunity to study unresolved carbon cycling processes such as the contribution of leaf versus root litter contributions to soil carbon accumulation, the rate of vertical transport of carbon into deep soil storage pools, and the differential contribution of physicochemical versus faunal driven processes to soil carbon cycling and sequestration. Leaf litter from the local enriched forest was transplanted to selected sites on the ORR and to selected AmeriFlux study sites to study soil C cycling across a range of soils and climates. The EBIS research projects provide data on C flux from litter sources to mineral soil sinks for United States eastern hardwood forests necessary for testing process hypotheses and judging efficacy of soil C cycling models. Experimental results from this study are being used to parameterize and refine existing carbon dynamics models, the quantification of the long-term fate of ecosystem carbon inputs and as a means to judge the potential for ecosystem carbon sequestration via enhance litter inputs to soil. EBIS observations support conclusions that intra- and inter-annual soil carbon cycling in hardwood forest soils should be characterized as a least a two-compartment system where surface leaf-litter and belowground root turnover represent primary carbon sources for organic-layer and mineral-soil carbon cycles, respectively. EBIS experiments were conducted to complete enriched litterfall maniplations in upland forests on Ultisol and Inceptisol soils of the Oak Ridge Reservation, Oak Ridge, Tennessee. We also collected additional14C-enriched materials for new experimental applications, and applied those materials to multiple AmeriFlux sites over a range of climatic, edaphic and biological conditions. The research provided data for addressing DOE's goal of understanding mechanisms controlling C flux, and for the improvement of models to be applied to policy discussions regarding the safe levels of greenhouse gases for the earth's system. There are 5 data files provided in comma separated (*.csv) format for vegetation, field litter, soil and air [C] and C isotope data from the EBIS studies and associated environmental data.

54 ENVIRONMENTAL SCIENCES↗

Flux Seasonality Metrics Database: A companion dataset for FLUXNET annual product

This dataset include standardized phenological transition dates, and derived season lengths of active, dormant and transition seasons of ecosystem carbon and energy fluxes, as reported in FLUXNET. Such metrics are unique in that they characterize the seasonal dynamics of these fluxes in their own terms rather than in reference to traditional phenology indicators that mostly relate to vegetation structural characteristics. The Flux Seasonality Metrics Database (FSMD) generated 17 standardized seasonality metrics for 4 different fluxes including gross primary productivity (GPP), ecosystem respiration (RE), latent heat (LE) and sensible heat (H) reported in FLUXNET2015 Dataset for about 200 sites and 1500 site-years of data globally. Each metric is reported as an estimate and a confidence interval, which is a function of data coverage and flux variability. We anticipate that the FSMD will facilitate new model validation exercises, and stimulate new research in global change and Earth science disciplines where land-atmosphere exchange dynamics play a central role.

54 ENVIRONMENTAL SCIENCES↗

Transition Zones at the Changing Coastal Terrestrial‐Aquatic Interface

Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience spatial and temporal variability in biogeochemical processes, driven by marsh‐to‐upland gradients and hydrological fluctuations. These fluctuations make it difficult to understand and predict biogeochemical processes in these highly dynamic systems. We studied coastal soil biogeochemistry and its variability (a) at regional scales and (b) across transects from upland forest to marsh, in two contrasting regions—Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity‐related analytes were a key source of variability in soil biogeochemistry, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI—however, contrary to expectations, transition soils were not consistently intermediate between upland and marsh endmembers; the non‐monotonic trends of C, P, Fe along our transects suggest that these do not behave as expected and may be difficult to model and predict—thus these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients (e.g., Ca, K, CEC, and TS) may act as precursors to ecosystem shifts. Our comprehensive soil characterization represents a snapshot of a single timepoint of surface soils and provides essential data for mechanistic modeling of ecosystem dynamics across coastal transects.

Patel, Kaizad F. [Pacific Northwest National Labor↗

Tracking seasonal variability in plant traits from spaceborne PRISMA and NEON AOP across forest types and ecoregions

Plant traits serve as critical indicators of how plants adapt to environmental changes and influence ecosystem functions. While airborne hyperspectral remote sensing effectively maps plant traits through detailed reflectance properties, it is limited by cost and scale, making large-scale and temporal studies challenging. The recently launched spaceborne hyperspectral imager, PRecursore IperSpettrale della Missione Applicativa (PRISMA), offers frequent, large scale and high-fidelity observations on a spatial resolution of 30 m and a revisit time of around 29 days, making it suitable for large-scale seasonal trait mapping. However, their potential remains largely unexplored. This study developed a multi-stage framework by leveraging the PRISMA spaceborne hyperspectral data and National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) hyperspectral data to investigate the seasonal dynamics of four key plant traits — chlorophyll content, carotenoid content, equivalent water thickness, and nitrogen content — across eleven NEON sites representing diverse forest types and ecoregions in the contiguous U.S. Our results demonstrated that PRISMA hyperspectral data can reliably track seasonal variability in plant traits, achieving overall R 2 values ranging from 0.78 to 0.88 and normalized root mean square error (NRMSE) values ranging from 5.4% to 8.4% for the four traits. Seasonal patterns revealed bell-shaped trajectories for chlorophyll and carotenoids, while equivalent water thickness decreased steadily across most sites, driven by structural changes during leaf maturation and senescence. Nitrogen content exhibited less pronounced seasonal variation but followed expected nutrient resorption patterns. Analysis of environmental drivers showed that seasonal variability is primarily controlled by solar radiation and day length in northern sites, vapor pressure in semi-arid regions, and temperature in mid-southeastern sites. Spatial variability, meanwhile, was primarily driven by soil properties, particularly during the peak growing season. However, the influence of soil variables slightly declines toward the end of the season at several sites, as climatic factors become more prominent. This study highlights the capability of PRISMA, and potentially other similar spaceborne hyperspectral data for large-scale, time-series plant trait mapping and provides valuable insights into the interactions between plant traits and environmental factors. In conclusion, these findings contribute to advancing our understanding of plant functional ecology and improving predictions of ecosystem responses to environmental changes.

Environmental drivers↗

DeepPhenoMem V1.0: deep learning modelling of canopy greenness dynamics accounting for multi-variate meteorological memory effects on vegetation phenology

Abstract. Vegetation phenology plays a key role in controlling the seasonality of ecosystem processes that modulate carbon, water and energy fluxes between the biosphere and atmosphere. Accurate modelling of vegetation phenology in the interplay of Earth's surface and the atmosphere is thus crucial to understand how the coupled system will respond to and shape climatic changes. Phenology is controlled by meteorological conditions at different timescales: on the one hand, changes in key meteorological variables (temperature, water, radiation) can have immediate effects on the vegetation development; on the other hand, phenological changes can be driven by past environmental conditions, known as memory effects. However, the processes governing meteorological memory effects on phenology are not completely understood, resulting in their limited performance of vegetation phenology represented in land surface models. A deep learning model, specifically a long short-term memory network (LSTM), has the potential to capture and model the meteorological memory effects on vegetation phenology. Here, we apply the LSTM to model the vegetation phenology using meteorological drivers and high-temporal-resolution canopy greenness observations through digital repeat photography by the PhenoCam network. We compare a multiple linear regression model, a no-memory-effect LSTM model and a full-memory-effect LSTM model to predict the whole seasonal greenness trajectory and the corresponding phenological transition dates across 50 sites and 317 site years during 2009–2018, covering deciduous broadleaf forests, evergreen needleleaf forests and grasslands. Results show that the deep learning model outperforms the multiple linear regression model, and the full-memory-effect LSTM model performs better than the no-memory-effect model for all three plant function types (median R2 of 0.878, 0.957 and 0.955 for broadleaf forests, evergreen needleleaf forests and grasslands). We also find that the full-memory-effect LSTM model is capable of predicting the seasonal dynamic variations of canopy greenness and reproducing trends in shifting phenological transition dates. We also performed a sensitivity analysis of the full-memory-effect LSTM model to assess its plausibility, revealing its coherence with established knowledge of vegetation phenology sensitivity to meteorological conditions, particularly changes in temperature. Our study highlights that (1) multi-variate meteorological memory effects play a crucial role in vegetation phenology, and (2) deep learning opens up new avenues for improving the representation of vegetation phenological processes in land surface models via a hybrid modelling approach.

Geology↗

Evaluation of Atmospheric Boundary Layer Height From Wind Profiling Radar and Slab Models and Its Responses to Seasonality of Land Cover, Subsidence, and Advection

In this study, we evaluated the effect of land cover, atmospheric subsidence, and advection on the annual dynamics of atmospheric boundary layer (ABL) height from two contrasting sites. The first site is the Walker Branch forest, a deciduous forest of temperate climate, complex topography, and cloudy summers. The second site is the Sacramento-San Joaquin River Delta, a site of Mediterranean climate, flat terrain on a local scale, and clear summers. After testing a new algorithm to calculate ABL heights from 915 MHz radar wind profilers, we evaluated a hierarchy of three slab models to recreate the diurnal and annual patterns of ABL growth. We found that the lower ABL heights in the Delta, particularly during late summer, are driven by the combined effects of increased atmospheric subsidence and marine air advection. In both sites, the annual pattern of ABL height was strongly correlated to total daily incoming radiation, and in the Delta, the annual pattern of ABL height closely followed the seasonal patterns of sensible heat flux from a mosaic of different land covers. A land composite of latent and sensible heat fluxes obtained through a meso-network of eddy covariance measurements and the ECOsystem Spaceborne Thermal Radiometer Experiment on Space Station (ECOSTRESS) mission resulted in higher model skill, thus showing that land cover heterogeneity is an important driver of ABL growth. To conclude, model simulations show that in the Delta, restoring agricultural land to wetlands with large open water areas could result in a reduction of ABL height during those months with low subsidence and advection.

54 ENVIRONMENTAL SCIENCES↗

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.

Cenococcum geophilum↗