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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Using neural network ensembles to separate ocean biogeochemical and physical drivers of phytoplankton biogeography in Earth system models

Abstract. Earth system models (ESMs) are useful tools for predicting and understanding past and future aspects of the climate system. However, the biological and physical parameters used in ESMs can have wide variations in their estimates. Even small changes in these parameters can yield unexpected results without a clear explanation of how a particular outcome was reached. The standard method for estimating ESM sensitivity is to compare spatiotemporal distributions of variables from different runs of a single ESM. However, a potential pitfall of this method is that ESM output could match observational patterns because of compensating errors. For example, if a model predicts overly weak upwelling and low nutrient concentrations, it might compensate for this by allowing phytoplankton to have a high sensitivity to nutrients. Recently, we demonstrated that neural network ensembles (NNEs) are capable of extracting relationships between predictor and target variables within ocean biogeochemical models. Being able to view the relationships between variables, along with spatiotemporal distributions, allows for a more mechanistically based examination of ESM outputs. Here, we investigated whether we could apply NNEs to help us determine why different ESMs produce different spatiotemporal distributions of phytoplankton biomass. We tested this using three cases. The first and second case used different runs of the same ESM, except that the physical circulations differed between them in the first case, while the biological equations differed between them in the second. Our results indicated that the NNEs were capable of extracting the relationships between variables for different runs of a single ESM, allowing us to distinguish between differences due to changes in circulation (which do not change relationships) from changes in biogeochemical formulation (which do change relationships). In the third case, we applied NNEs to two different ESMs. The results of the third case highlighted the capability of NNEs to contrast the apparent relationships of different ESMs and some of the challenges it presents. Although applied specifically to the ocean components of an ESM, our study demonstrates that Earth system modelers can use NNEs to separate the contributions of different components of ESMs. Specifically, this allows modelers to compare the apparent relationships across different ESMs and observational datasets.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1989

The historic biogeography of India: isolation or contact?

Geophysical maps depicting continental movement have consistently shown India, as it moved northward, to be located far out in the Tethys Sea. India split off from the African east coast about 148 m.y.a. From that time onward, according to almost all geophysical accounts, India was isolated from all of other continents until the early Miocene when it made contact with Eurasia. But the biological data, both fossil and Recent, indicate that this concept cannot be correct. If India had really existed as an isolated, oceanic continent for about 100 m.y., it should have developed a peculiar biota with many endemic genera and families in its terrestrial and shallow marine habitats. But there are virtually no remains of organisms indicating that India was isolated for any substantial time (millions of years). Instead, we find that almost all Indian taxa were possessed in common with other continents. As time went on, the northern relationships became stronger and the southern ones weaker. Most of the recent geophysical accounts show India not making contact with Eurasia until the early Miocene, but fossil materials show that this event must have taken place by the early Eocene. It has been postulated that, as India moved northward, it created a biogeographic barrier that separated marine fish populations and resulted in the east-west provinces that are now apparent in the Indian Ocean. At the same time, the barrier effect was supposed to have resulted in the formation of sister species that are now located far apart. Information currently available indicates that most living, tropical marine species are probably not over 3 m.y. old. Consequently, the northward movement of India, which took place primarily between 148 and 50 m.y.a., could have no bearing on the relationships of modern species.

NASA Discipline Exobiology↗
NASA NTRS2010

Quantitative Measures of Immersion in Cloud and the Biogeography of Cloud Forests

Sites described as tropical montane cloud forests differ greatly, in part because observers tend to differ in their opinion as to what constitutes frequent and prolonged immersion in cloud. This definitional difficulty interferes with hydrologic analyses, assessments of environmental impacts on ecosystems, and biogeographical analyses of cloud forest communities and species. Quantitative measurements of cloud immersion can be obtained on site, but the observations are necessarily spatially limited, although well-placed observers can examine 10 50 km of a mountain range under rainless conditions. Regional analyses, however, require observations at a broader scale. This chapter discusses remote sensing and modeling approaches that can provide quantitative measures of the spatiotemporal patterns of cloud cover and cloud immersion in tropical mountain ranges. These approaches integrate remote sensing tools of various spatial resolutions and frequencies of observation, digital elevation models, regional atmospheric models, and ground-based observations to provide measures of cloud cover, cloud base height, and the intersection of cloud and terrain. This combined approach was applied to the Monteverde region of northern Costa Rica to illustrate how the proportion of time the forest is immersed in cloud may vary spatially and temporally. The observed spatial variation was largely due to patterns of airflow over the mountains. The temporal variation reflected the diurnal rise and fall of the orographic cloud base, which was influenced in turn by synoptic weather conditions, the seasonal movement of the Intertropical Convergence Zone and the north-easterly trade winds. Knowledge of the proportion of the time that sites are immersed in clouds should facilitate ecological comparisons and biogeographical analyses, as well as land use planning and hydrologic assessments in areas where intensive on-site work is not feasible.

Lawton, R. O.↗
NASA NTRS2022

Increasing Threat of Wildfires: the Year 2020 in Perspective: A Global Ecology and Biogeography Special Issue

Each year, wild and managed fires burn roughly 4 million km2 [~400 million hectares (Mha)] of savanna, forest, grassland and agricultural ecosystems. Land use and climate change have altered fire regimes throughout the world, with a trend toward higher-severity fires found from Australia, the Americas, Europe and Asia, to the Arctic. In 2020, there were notable catastrophic fires in Australia (in the 2019/20 Austral fire season), the Western United States, South America and Siberia. These fires defined much of the global fire year and were compounded by the socio-economic disruption of the Coronavirus 2019 (COVID-19) pandemic.

Rachael H Nolan↗
DOE OSTI2023

Files and scripts to support manuscript Shuman et al 2023 FATES-SPITFIRE ecosystem assembly across tropics

The dataset includes the parameter and domain files, relevant output files, and scripts to generate simulations and perform analysis with Jupyter notebooks that support the manuscript Shuman, JK et al 2023 “Dynamic ecosystem assembly and escaping the “fire-trap” in the tropics: Insights from FATES_15.0.0”. We have adapted the fire-behavior and effects module, SPITFIRE, for use with the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a size-structured vegetation demographic model. We test how climate, fire regime and fire-tolerance plant traits interact to determine the biogeography of tropical forests and grasslands. We assign different fire-tolerance strategies based on crown, leaf and bark characteristics, which are key observed fire-tolerance traits across woody plants. For these simulations, three types of vegetation compete for resources: a fire-vulnerable tree with thin bark, a vulnerable deep crown and fire-intolerant foliage; a fire-tolerant tree with thick bark, a thin crown and fire-tolerant foliage; and a fire-promoting C4 grass. We explore the model sensitivity to a critical parameter governing fuel moisture, and show that drier fuels promote increased burning, an expansion of area for grass and fire-tolerant trees and a reduction of area for fire-vulnerable trees. This conversion to lower biomass or grass areas with increased fuel drying results in increased fire burned area and its effects, which could fee back to local climate variables. Simulated size-based fire mortality for trees less than 20 cm in diameter and those with fire-vulnerable traits is higher than that for larger and/or fire-tolerant trees, in agreement with observations. Fire-disturbed forests demonstrate reasonable productivity and capture observed patterns of aboveground biomass in areas dominated by natural vegetation for the recent historical period, but have a large bias in less disturbed areas. Though the model predicts a greater extent of burned fraction than observed in areas with grass dominance, the resulting biogeography of fire-tolerant, thick-bark trees and fire-vulnerable, thin-bark trees corresponds to observations across the tropics. In areas with more than 2500 mm of precipitation, simulated fire frequency and burned area are low, with fire intensities below 150 kW m-1, consistent with observed understory fire behavior across the Amazon. Areas drier than this demonstrate fire intensities consistent with those measured in savannas and grasslands, with high values up to 4000 kW m-1. The results support a positive grass-fire feedback across the region, and suggest that forests which have existed without frequent burning may be vulnerable at higher fire intensities, which is of greater concern under intensifying climate and land use pressures. The ability of FATES to capture the connection between fire disturbance and plant fire-tolerance strategies in determining biogeography provides a useful tool for assessing the vulnerability and resilience of these critical carbon storage areas under changing conditions across the tropics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Dynamic ecosystem assembly and escaping the “fire trap” in the tropics: insights from FATES_15.0.0

Abstract. Fire is a fundamental part of the Earth system, with impacts on vegetation structure, biomass, and community composition, the latter mediated in part via key fire-tolerance traits, such as bark thickness. Due to anthropogenic climate change and land use pressure, fire regimes are changing across the world, and fire risk has already increased across much of the tropics. Projecting the impacts of these changes at global scales requires that we capture the selective force of fire on vegetation distribution through vegetation functional traits and size structure. We have adapted the fire behavior and effects module, SPITFIRE (SPread and InTensity of FIRE), for use with the Functionally Assembled Terrestrial Ecosystem Simulator (FATES), a size-structured vegetation demographic model. We test how climate, fire regime, and fire-tolerance plant traits interact to determine the biogeography of tropical forests and grasslands. We assign different fire-tolerance strategies based on crown, leaf, and bark characteristics, which are key observed fire-tolerance traits across woody plants. For these simulations, three types of vegetation compete for resources: a fire-vulnerable tree with thin bark, a vulnerable deep crown, and fire-intolerant foliage; a fire-tolerant tree with thick bark, a thin crown, and fire-tolerant foliage; and a fire-promoting C4 grass. We explore the model sensitivity to a critical parameter governing fuel moisture and show that drier fuels promote increased burning, an expansion of area for grass and fire-tolerant trees, and a reduction of area for fire-vulnerable trees. This conversion to lower biomass or grass areas with increased fuel drying results in increased fire-burned area and its effects, which could feed back to local climate variables. Simulated size-based fire mortality for trees less than 20 cm in diameter and those with fire-vulnerable traits is higher than that for larger and/or fire-tolerant trees, in agreement with observations. Fire-disturbed forests demonstrate reasonable productivity and capture observed patterns of aboveground biomass in areas dominated by natural vegetation for the recent historical period but have a large bias in less disturbed areas. Though the model predicts a greater extent of burned fraction than observed in areas with grass dominance, the resulting biogeography of fire-tolerant, thick-bark trees and fire-vulnerable, thin-bark trees corresponds to observations across the tropics. In areas with more than 2500 mm of precipitation, simulated fire frequency and burned area are low, with fire intensities below 150 kW m−1, consistent with observed understory fire behavior across the Amazon. Areas drier than this demonstrate fire intensities consistent with those measured in savannas and grasslands, with high values up to 4000 kW m−1. The results support a positive grass–fire feedback across the region and suggest that forests which have existed without frequent burning may be vulnerable at higher fire intensities, which is of greater concern under intensifying climate and land use pressures. The ability of FATES to capture the connection between fire disturbance and plant fire-tolerance strategies in determining biogeography provides a useful tool for assessing the vulnerability and resilience of these critical carbon storage areas under changing conditions across the tropics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Intraspecific Diversity in Thermal Performance Determines Phytoplankton Ecological Niche

ABSTRACT Temperature has a primary influence on phytoplankton physiology and ecology. We grew 12 strains of Gephyrocapsa huxleyi isolated from different‐temperature regions for ~45 generations (2 months) and characterised acclimated thermal response curves across a temperature range. Even with similar temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day −1 . Thermal niche widths varied from 16.7°C to 24.8°C, suggesting that strains use distinct thermal response mechanisms. We investigated the implications of this thermal intraspecific diversity using an ocean ecosystem simulation resolving phytoplankton thermal phenotypes. Model analogues of thermal ‘generalists’ and ‘specialists’ resulted in a distinctive global biogeography of thermal niche widths with a nonlinear latitudinal pattern. We leveraged model output to predict ranges of the 12 lab‐reared strains and demonstrated how this approach could broadly refine geographic range predictions. Our combination of observations and modelled biogeography highlights the capacity of diverse groups to survive temperature shifts.

Krinos, Arianna I. [Department of Biology Woods Ho↗
DOE OSTI2021

Metagenomic analysis reveals global-scale patterns of ocean nutrient limitation

Genomes reveal nutrient stress patterns Within the surface ocean, nitrogen, iron, and phosphorous can all be limiting nutrients for phytoplankton depending on location. Ustick et al. used the prevalence of Prochlorococcus genes involved in nutrient acquisition to develop maps of inferred nutrient stress across the global ocean (see the Perspective by Coleman). They found broad patterns of limitation consistent with an Earth system model and nutrient addition experiments. Leveraging metagenomic data in this manner is an appealing approach that will help to expand our understanding of the biogeochemistry in the vast open ocean. Science , this issue p. 287 ; see also p. 239

Science & Technology - Other Topics↗
DOE OSTI2022

Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China

Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Geological activity shapes the microbiome in deep-subsurface aquifers by advection

Subsurface environments host diverse microorganisms in fluid-filled fractures; however, little is known about how geological and hydrological processes shape the subterranean biosphere. Here, we sampled three flowing boreholes weekly for 10 mo in a 1478-m-deep fractured rock aquifer to study the role of fracture activity (defined as seismically or aseismically induced fracture aperture change) and advection on fluid-associated microbial community composition. We found that despite a largely stable deep-subsurface fluid microbiome, drastic community-level shifts occurred after events signifying physical changes in the permeable fracture network. The community-level shifts include the emergence of microbial families from undetected to over 50% relative abundance, as well as the replacement of the community in one borehole by the earlier community from a different borehole. Null-model analysis indicates that the observed spatial and temporal community turnover was primarily driven by stochastic processes (as opposed to deterministic processes). We, therefore, conclude that the observed community-level shifts resulted from the physical transport of distinct microbial communities from other fracture(s) that outpaced environmental selection. Given that geological activity is a major cause of fracture activity and that geological activity is ubiquitous across space and time on Earth, our findings suggest that advection induced by geological activity is a general mechanism shaping the microbial biogeography and diversity in deep-subsurface habitats across the globe.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Saccharomycotina yeasts defy long-standing macroecological patterns

The Saccharomycotina yeasts (“yeasts” hereafter) are a fungal clade of scientific, economic, and medical significance. Yeasts are highly ecologically diverse, found across a broad range of environments in every biome and continent on earth; however, little is known about what rules govern the macroecology of yeast species and their range limits in the wild. Here, we trained machine learning models on 12,816 terrestrial occurrence records and 96 environmental variables to infer global distribution maps at ~1 km2 resolution for 186 yeast species (~15% of described species from 75% of orders) and to test environmental drivers of yeast biogeography and macroecology. We found that predicted yeast diversity hotspots occur in mixed montane forests in temperate climates. Diversity in vegetation type and topography were some of the greatest predictors of yeast species richness, suggesting that microhabitats and environmental clines are key to yeast diversity. We further found that range limits in yeasts are significantly influenced by carbon niche breadth and range overlap with other yeast species, with carbon specialists and species in high-diversity environments exhibiting reduced geographic ranges. Finally, yeasts contravene many long-standing macroecological principles, including the latitudinal diversity gradient, temperature-dependent species richness, and a positive relationship between latitude and range size (Rapoport’s rule). These results unveil how the environment governs the global diversity and distribution of species in the yeast subphylum. These high-resolution models of yeast species distributions will facilitate the prediction of economically relevant and emerging pathogenic species under current and future climate scenarios.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Assessing biogeographic survey gaps in bacterial diversity knowledge: A global synthesis of freshwaters

Freshwaters account for 0.8% of Earth's surface area, yet support >10% of known plant and animal species making them disproportionately biodiverse. Modern molecular techniques have begun to reveal microbial diversity, but application of these approaches to address global microbial biogeography is relatively unknown in freshwaters. Our aim was to identify gaps in microbial data coverage along climatic and landscape disturbance gradients and among terrestrial biomes and hydrographic regions for all freshwater ecosystems and three freshwater habitat types: lakes and reservoirs (lentic); streams and rivers (lotic); and wetlands. We reviewed literature on microbial diversity in freshwaters surveyed using 16S ribosomal RNA sequencing which identify microbial taxa. We georeferenced survey locations and used a geographic information system to identify and map gaps in survey coverage using open-source data for climate, landscape disturbance, terrestrial biomes, and freshwater ecoregions. In our study, we compiled 3,425 georeferenced survey locations reported from 963 studies. Streams were surveyed most frequently (60.8% of survey locations), followed by lakes (33.5%) and wetlands (5.6%). Surveys were concentrated in North America, central and western Europe, and Southeast Asia; 35% of freshwater ecoregions were surveyed at least once across freshwater habitat types, whereas 23%, 23%, and 12% were surveyed at least once for lentic, lotic, and wetland habitat types, respectively. The climatic gap analysis indicated coverage is high for temperate regions but lacking in the tropics and Arctic, particularly for wetland ecosystems. Our assessment revealed high climatic coverage of freshwater microbial diversity knowledge, but expansive ecoregional gaps attributable to biased sampling near research institutions in North America, western Europe, and China. Future surveys should target ecoregions in Africa, South America, Central Asia, Australia, and Antarctica. An essential next step will be to curate and disseminate sequencing efforts to facilitate the study of processes driving global diversity patterns.

16S rRNA↗
DOE OSTI2026

Ecological and genomic variation in ectomycorrhizal fungal exploration types

Ectomycorrhizal fungi (EMF) produce mycelia with variable extension and complexity, which can be classified according to soil ‘exploration types’ (ETs). ETs have received attention as one of the few mycorrhizal trait frameworks, but without an empirical classification of ET functional diversity and environmental preferences, understanding and interpreting EMF biogeographic patterns has been difficult. We conducted a synthesis combining: comparative EMF genomics to describe functional divergence in decomposition and nutrient cycling genes across ETs; and EMF trait distribution modeling across continental Europe, pairing soil and root EMF surveys to establish biogeographic ET niche profiles. We demonstrate a signature of ETs encoded in EMF genomes, which is independent from phylogeny and linked to biomass production strategies. EMF ET relative abundances were separated by soil, root, and dominant tree leaf type habitats and exhibited unique correlations with forest biotic (e.g. plant productivity and plant pathogen densities) and abiotic (e.g. nitrogen deposition and soil pH) conditions. These findings support a theory that EMF niche partitioning can be partially explained by extraradical mycelial traits, with underlying variation in ET biogeography likely arising from distinct decomposition and nutrient cycling potentials. We also identify important limitations to this trait framework and provide a guided outlook for future research.

biogeography↗
DOE OSTI2021

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

Abstract Background Peatlands are expected to experience sustained yet fluctuating higher temperatures due to climate change, leading to increased microbial activity and greenhouse gas emissions. Despite mounting evidence for viral contributions to these processes in peatlands underlain with permafrost, little is known about viruses in other peatlands. More generally, soil viral biogeography and its potential drivers are poorly understood at both local and global scales. Here, 87 metagenomes and five viral size-fraction metagenomes (viromes) from a boreal peatland in northern Minnesota (the SPRUCE whole-ecosystem warming experiment and surrounding bog) were analyzed for dsDNA viral community ecological patterns, and the recovered viral populations (vOTUs) were compared with our curated PIGEON database of 266,125 vOTUs from diverse ecosystems. Results Within the SPRUCE experiment, viral community composition was significantly correlated with peat depth, water content, and carbon chemistry, including CH 4 and CO 2 concentrations, but not with temperature during the first 2 years of warming treatments. Peat vOTUs with aquatic-like signatures (shared predicted protein content with marine and/or freshwater vOTUs) were significantly enriched in more waterlogged surface peat depths. Predicted host ranges for SPRUCE vOTUs were relatively narrow, generally within a single bacterial genus. Of the 4326 SPRUCE vOTUs, 164 were previously detected in other soils, mostly peatlands. None of the previously identified 202,371 marine and freshwater vOTUs in our PIGEON database were detected in SPRUCE peat, but 0.4% of 80,714 viral clusters (VCs, grouped by predicted protein content) were shared between soil and aquatic environments. On a per-sample basis, vOTU recovery was 32 times higher from viromes compared with total metagenomes. Conclusions Results suggest strong viral “species” boundaries between terrestrial and aquatic ecosystems and to some extent between peat and other soils, with differences less pronounced at higher taxonomic levels. The significant enrichment of aquatic-like vOTUs in more waterlogged peat suggests that viruses may also exhibit niche partitioning on more local scales. These patterns are presumably driven in part by host ecology, consistent with the predicted narrow host ranges. Although more samples and increased sequencing depth improved vOTU recovery from total metagenomes, the substantially higher per-sample vOTU recovery after viral particle enrichment highlights the utility of soil viromics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

TropiRoot 1.0: Database of tropical root characteristics across environments

Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.

FRED↗