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At least 145 records · Page 8

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DOE OSTI2023

Contrasting effects of bioenergy crops on biodiversity

Agriculture is driving biodiversity loss, and future bioenergy cropping systems have the potential to ameliorate or exacerbate these effects. Using a long-term experimental array of 10 bioenergy cropping systems, we quantified diversity of plants, invertebrates, vertebrates, and microbes in each crop. For many taxonomic groups, alternative annual cropping systems provided no biodiversity benefits when compared to corn (the business-as-usual bioenergy crop in the United States), and simple perennial grass–based systems provided only modest gains. In contrast, for most animal groups, richness in plant-diverse perennial systems was much higher than in annual crops or simple perennial systems. Microbial richness patterns were more eclectic, although some groups responded positively to plant diversity. Future agricultural landscapes incorporating plant-diverse perennial bioenergy cropping systems could be of high conservation value. However, increased use of annual crops will continue to have negative effects, and simple perennial grass systems may provide little improvement over annual crops.

09 BIOMASS FUELS↗

DOE OSTI2024

Agent-based modeling to evaluate the effects of harvesting biomass and hunting on ring-necked pheasant ( Phasianus colchicus ) populations

As the US strives to divest from fossil fuels, dedicated energy crops have increased in popularity because of their potential to serve as a renewable source of transportation fuel and biomass-generated electricity. Whereas the impacts of crop agriculture on biodiversity have been well-documented, less is known about the potential impacts that growing bioenergy crops could have on wildlife. Here we look specifically at the ring-necked pheasant (Phasianus colchicus) and how pheasant populations may be influenced by growing and harvesting bioenergy crops. We explored effects of temporal harvest strategies at the field scale on biomass yield and pheasant population size. To investigate, we developed an agent-based model (ABM) that simulates ring-necked pheasants, tractors, hunters, and vegetation classes. One such vegetation class is land that is enrolled in a Conservation Reserve Program (CRP) plan specifically targeting pheasant conservation. Using this ABM, we assessed four different landscapes—corn-dominated, CRP-dominated, grassland-dominated, and mixed landscape—under strategies that varied the time of harvest. We also used ecological valuation to compare scenario outcomes from an economic perspective. We determined that biomass yield and pheasant population size were sensitive to harvesting times. Our scenarios totaled between ~$931,000 (minimum) and $3.8 million (maximum) over all landscapes, though on average harvesting in late spring generated the most value ($2.45 million) and harvesting in fall was a close second in terms of profitability ($2.39 million).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Landscape fragmentation overturns classical metapopulation thinking

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally (“residents”) were often more resilient to fragmentation than long-ranging “migrants.” This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Can large herbivores enhance ecosystem carbon persistence?

There is growing interest in aligning the wildlife conservation and restoration agenda with climate change mitigation goals. However, the presence of large herbivores tends to reduce aboveground biomass in some open-canopy ecosystems, leading to the possibility that large herbivore restoration may negatively influence ecosystem carbon storage. Furthermore, belowground carbon storage is often ignored in these systems, despite the wide recognition of soils as the largest actively-cycling terrestrial carbon pool. Here, we suggest a shift away from a main focus on vegetation carbon stocks, towards inclusion of whole ecosystem carbon persistence, in future assessments of large herbivore effects on long-term carbon storage. Failure to do so may lead to counterproductive biodiversity and climate impacts of land management actions.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Knitting while Australia burns

A global biodiversity hotspot, Australia has reached a tipping point from which many of its forests may never recover. Record-breaking heat, drought and windy conditions have burned at least 10 million hectares. Halfway through the season, fires have persisted for months with no end in sight. Here, the continent faces an exponential rise in future wildfire risk as the climate warms and dries.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Land‐based climate solutions for the United States

Abstract Meeting end‐of‐century global warming targets requires aggressive action on multiple fronts. Recent reports note the futility of addressing mitigation goals without fully engaging the agricultural sector, yet no available assessments combine both nature‐based solutions (reforestation, grassland and wetland protection, and agricultural practice change) and cellulosic bioenergy for a single geographic region. Collectively, these solutions might offer a suite of climate, biodiversity, and other benefits greater than either alone. Nature‐based solutions are largely constrained by the duration of carbon accrual in soils and forest biomass; each of these carbon pools will eventually saturate. Bioenergy solutions can last indefinitely but carry significant environmental risk if carelessly deployed. We detail a simplified scenario for the United States that illustrates the benefits of combining approaches. We assign a portion of non‐forested former cropland to bioenergy sufficient to meet projected mid‐century transportation needs, with the remainder assigned to nature‐based solutions such as reforestation. Bottom‐up mitigation potentials for the aggregate contributions of crop, grazing, forest, and bioenergy lands are assessed by including in a Monte Carlo model conservative ranges for cost‐effective local mitigation capacities, together with ranges for (a) areal extents that avoid double counting and include realistic adoption rates and (b) the projected duration of different carbon sinks. The projected duration illustrates the net effect of eventually saturating soil carbon pools in the case of most strategies, and additionally saturating biomass carbon pools in the case of forest management. Results show a conservative end‐of‐century mitigation capacity of 110 (57–178) Gt CO 2 e for the U.S., ~50% higher than existing estimates that prioritize nature‐based or bioenergy solutions separately. Further research is needed to shrink uncertainties, but there is sufficient confidence in the general magnitude and direction of a combined approach to plan for deployment now.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs

Shifts in host-associated microbiomes can impact both host and microbes. It is of interest to understand how perturbations, like the introduction of exogenous chemicals, impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense. These alkaloids are antimicrobial; however, their effect on the frogs’ skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. Further, to better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Data from: Land-based climate solutions for the United States

Meeting end-of-century global warming targets requires aggressive action on multiple fronts. Recent reports note the futility of addressing mitigation goals without fully engaging the agricultural sector, yet no available assessments combine both nature-based solutions (reforestation, grassland and wetland protection, and agricultural practice change) and cellulosic bioenergy for a single geographic region. Collectively, these solutions might offer a suite of climate, biodiversity, and other benefits greater than either alone. Nature-based solutions are largely constrained by the duration of carbon accrual in soils and forest biomass; each of these carbon pools will eventually saturate. Bioenergy solutions can last indefinitely but carry significant environmental risk if carelessly deployed. We detail a simplified scenario for the U.S. that illustrates the benefits of combining approaches. We assign a portion of non-forested former cropland to bioenergy sufficient to meet projected mid-century transportation needs, with the remainder assigned to nature-based solutions such as reforestation. Bottom-up mitigation potentials for the aggregate contributions of crop, grazing, forest, and bioenergy lands are assessed by including in a Monte Carlo model conservative ranges for cost-effective local mitigation capacities, together with ranges for (a) areal extents that avoid double counting and include realistic adoption rates and (b) the projected duration of different carbon sinks. The projected duration illustrates the net effect of eventually saturating soil carbon pools in the case of most strategies, and additionally saturating biomass carbon pools in the case of reforestation. Results show a conservative end-of-century mitigation capacity of 110 (57 – 178) Gt CO2e for the U.S., ~50% higher than existing estimates that prioritize nature-based or bioenergy solutions separately. Further research is needed to shrink uncertainties but there is sufficient confidence in the general magnitude and direction of a combined approach to plan for deployment now.

09 BIOMASS FUELS↗

DOE OSTI2025

Functional but not taxonomic diversity increases productivity of Populus in the southeastern United States

Plant interactions like competition and facilitation impact ecosystem function and resilience. Improving our understanding of the relationships between these interactions and community productivity has important implications for managers of production systems in forestry and agriculture as well as conservation science. Populus spp. are an excellent model system for exploring how inter‐ and intraspecific interactions impact ecosystem functions, such as productivity, in forest plantations. In this study, we compared aboveground productivity of six Populus clones from three different taxa grown in monoclonal and mixed‐clonal plots. The different mixture treatments were intended to experimentally test aboveground biomass response to contrasting levels of taxonomic diversity and functional diversity based on nitrogen use characteristics of Populus clones. We hypothesize that functional diversity would be more important than taxonomic diversity in increasing aboveground productivity of mixed‐clonal plantings compared to monocultures. In addition, a subset of treatments was carried out on additional sites representing a productivity gradient in order to determine if the relationship between biodiversity and productivity in these systems diminished at more productive sites as suggested by the stress‐gradient hypothesis. We found that functionally diverse mixtures of clones had greater yield of aboveground biomass than the average of their constituent monocultures, while more taxonomically diverse mixes of clones did not differ from the average of their constituent monocultures. However, when reestablished on sites with extremely high or low productivity, the best performing clone mixture also did not differ from the average of its constituent monocultures. Our results suggest that intimate clone mixtures of Populus have the potential to significantly increase productivity, but results vary by mixture and by site. To capitalize on positive biodiversity effects on yield in production systems, targeted mixtures based on divergent functional traits linked to different use and acquisition strategies for site‐specific limiting resources are most likely to be successful.

BEF↗

DOE OSTI2023

Long-term, large-scale experiment reveals the effects of seed limitation, climate, and anthropogenic disturbance on restoration of plant communities in a biodiversity hotspot

Ecological restoration is essential for maintaining biodiversity in the face of dynamic, global changes in climate, human land use, and disturbance regimes. Effective restoration requires understanding bottlenecks in plant community recovery that exist today, while recognizing that these bottlenecks may relate to complex histories of environmental change. Such understanding has been a challenge because few long-term, well-replicated experiments exist to decipher the demographic processes influencing recovery for numerous species against the backdrop of multiyear variation in climate and management. Here we address this challenge through a long-term and geographically expansive experiment in longleaf pine savannas, an imperiled ecosystem and biodiversity hotspot in the southeastern United States. Using 48 sites at three locations spanning 480 km, the 8-y experiment manipulated initial seed arrival for 24 herbaceous plant species and presence of competitors to evaluate the impacts of climate variability and management actions (e.g., prescribed burning) on plant establishment and persistence. Adding seeds increased plant establishment of many species. Cool and wet climatic conditions, low tree density, and reduced litter depth also promoted establishment. Once established, most species persisted for the duration of the 8-y experiment. Plant traits were most predictive when tightly coupled to the process of establishment. Our results illustrate how seed additions can restore plant diversity and how interannual climatic variation affects the dynamics of plant communities across a large region. The significant effects of temperature and precipitation inform how future climate may affect restoration and conservation via large-scale changes in the fundamental processes of establishment and persistence.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Environmental RNA as a Tool for Marine Community Biodiversity Assessments

Abstract Microscopic organisms are often overlooked in traditional diversity assessments due to the difficulty of identifying them based on morphology. Metabarcoding is a method for rapidly identifying organisms where Environmental DNA (eDNA) is used as a template. However, legacy DNA is problematically detected from organisms no longer in the environment during sampling. Environmental RNA (eRNA), which is only produced by living organisms, can also be collected from environmental samples and used for metabarcoding. The aim of this study was to determine differences in community composition and diversity between eRNA and eDNA templates for metabarcoding. Using mesocosms containing field-collected communities from an estuary, RNA and DNA were co-extracted from sediment, libraries were prepared for two loci (18S and COI), and sequenced using an Illumina MiSeq. Results show a higher number of unique sequences detected from eRNA in both markers and higher α-diversity compared to eDNA. Significant differences between eRNA and eDNA for all β-diversity metrics were also detected. This study is the first to demonstrate community differences detected with eRNA compared to eDNA from an estuarine system and illustrates the broad applications of eRNA as a tool for assessing benthic community diversity, particularly for environmental conservation and management applications.

Giroux, Marissa S.↗

DOE OSTI2020

The functional roles of species in metacommunities, as revealed by metanetwork analyses of bird–plant frugivory networks

Abstract Understanding how biodiversity and interaction networks change across environmental gradients is a major challenge in ecology. We integrated metacommunity and metanetwork perspectives to test species’ functional roles in bird–plant frugivory interactions in a fragmented forest landscape in Southwest China, with consequences for seed dispersal. Availability of fruit resources both on and under trees created vertical feeding stratification for frugivorous birds. Bird–plant interactions involving birds feeding only on‐the‐tree or both on and under‐the‐tree (shared) had a higher centrality and contributed more to metanetwork organisation than interactions involving birds feeding only under‐the‐tree. Moreover, bird–plant interactions associated with large‐seeded plants disproportionately contributed to metanetwork organisation and centrality. Consequently, on‐the‐tree and shared birds contributed more to metanetwork organisation whereas under‐the‐tree birds were more involved in local processes. We would expect that species’ roles in the metanetwork will translate into different conservation values for maintaining functioning of seed‐dispersal networks.

Li, Hai‐Dong↗

DOE OSTI2023

The importance of trait selection in ecology

Two recent publications have explored the importance of roots for understanding plant form and function but reached opposite conclusions on the basis of largely overlapping data. Carmona et al. concluded that their results “do not confirm the strong covariation between leaf and fine-root traits predicted by the plant economics spectrum hypothesis”. By contrast, Weigelt et al. concluded that “key leaf and fine-root traits were aligned along the expected [fast–slow] ‘conservation’ gradient of plant economic investment”. Furthermore, here we reflect on the causes for the apparent discrepancies of these studies and show that the rationale behind trait selection is vital for the conclusions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Rainforest-to-pasture conversion stimulates soil methanogenesis across the Brazilian Amazon

The Amazon rainforest is a biodiversity hotspot and large terrestrial carbon sink threatened by agricultural conversion. Rainforest-to-pasture conversion stimulates the release of methane, a potent greenhouse gas. The biotic methane cycle is driven by microorganisms; therefore, this study focused on active methane-cycling microorganisms and their functions across land-use types. We collected intact soil cores from three land use types (primary rainforest, pasture, and secondary rainforest) of two geographically distinct areas of the Brazilian Amazon (Santarém, Pará and Ariquemes, Rondônia) and performed DNA stable-isotope probing coupled with metagenomics to identify the active methanotrophs and methanogens. At both locations, we observed a significant change in the composition of the isotope-labeled methane-cycling microbial community across land use types, specifically an increase in the abundance and diversity of active methanogens in pastures. We conclude that a significant increase in the abundance and activity of methanogens in pasture soils could drive increased soil methane emissions. Furthermore, we found that secondary rainforests had decreased methanogenic activity similar to primary rainforests, and thus a potential to recover as methane sinks, making it conceivable for forest restoration to offset greenhouse gas emissions in the tropics. These findings are critical for informing land management practices and global tropical rainforest conservation.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Comparative genomics of Aspergillus nidulans and section Nidulantes

Aspergillus nidulans is an important model organism for eukaryotic biology and the reference for the section Nidulantes in comparative studies. In this study, we de novo sequenced the genomes of 25 species of this section. Whole-genome phylogeny of 34 Aspergillus species and Penicillium chrysogenum clarifies the position of clades inside section Nidulantes. Comparative genomics reveals a high genetic diversity between species with 684 up to 2433 unique protein families. Furthermore, we categorized 2118 secondary metabolite gene clusters (SMGC) into 603 families across Aspergilli, with at least 40 % of the families shared between Nidulantes species. Genetic dereplication of SMGC and subsequent synteny analysis provides evidence for horizontal gene transfer of a SMGC. Proteins that have been investigated in A. nidulans as well as its SMGC families are generally present in the section Nidulantes, supporting its role as model organism. The set of genes encoding plant biomass-related CAZymes is highly conserved in section Nidulantes, while there is remarkable diversity of organization of MAT-loci both within and between the different clades. This study provides a deeper understanding of the genomic conservation and diversity of this section and supports the position of A. nidulans as a reference species for cell biology.

Theobald, Sebastian [Technical University of Denma↗

DOE OSTI2020

Climate regime shift and forest loss amplify fire in Amazonian forests

Frequent Amazonian fires over the last decade have raised the alarm about the fate of the Earth's most biodiverse forest. The increased fire frequency has been attributed to altered hydrological cycles. However, observations over the past few decades have demonstrated hydrological changes that may have opposing impacts on fire, including higher basin-wide precipitation and increased drought frequency and severity. Here, we use multiple satellite observations and climate reanalysis datasets to demonstrate compelling evidence of increased fire susceptibility in response to climate regime shifts across Amazonia. In this work, we show that accumulated forest loss since 2000 warmed and dried the lower atmosphere, which reduced moisture recycling and resulted in increased drought extent and severity, and subsequent fire. Extremely dry and wet events accompanied with hot days have been more frequent in Amazonia due to climate shift and forest loss. Simultaneously, intensified water vapor transport from the tropical Pacific and Atlantic increased high-altitude atmospheric humidity and heavy rainfall events, but those events did not alleviate severe and long-lasting droughts. Amazonia fire risk is most significant in the southeastern region where tropical savannas undergo long seasonally dry periods. We also find that fires have been expanding through the wet-dry transition season and northward to savanna-forest transition and tropical seasonal forest regions in response to increased forest loss at the "Arc of Deforestation." Tropical forests, which have adapted to historically moist conditions, are less resilient and easily tip into an alternative state. Our results imply forest conservation and fire protection options to reduce the stress from positive feedback between forest loss, climate change, and fire.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Description of a novel extremophile green algae, Chlamydomonas pacifica , and its potential as a biotechnology host

We present the comprehensive characterization of a newly identified microalga, Chlamydomonas pacifica , originally isolated from a soil sample in San Diego, CA, USA. This species showcases remarkable biological versatility, including a broad pH range tolerance (6–11.5), high thermal tolerance (up to 42 °C), and salinity resilience (up to 2 % NaCl). Its amenability to genetic manipulation and sexual reproduction via mating, particularly between the two opposing strains CC-5697 & CC-5699, now publicly available through the Chlamydomonas Resource Center, underscores its potential as a biotechnological chassis. The biological assessment of C. pacifica revealed versatile metabolic capabilities, including diverse nitrogen assimilation capability, motility and phototaxis. Genomic and transcriptomic analyses identified 17,829 genes within a 121 Mb genome, featuring a GC content of 61 %. The codon usage of C. pacifica closely mirrors that of C. reinhardtii , indicating a conserved genetic architecture that supports a trend in codon preference with minor variations. Phylogenetic analyses position C. pacifica within the core-Reinhardtinia clade yet distinct from known Volvocales species. The lipidomic data revealed an abundance of triacylglycerols (TAGs), promising for biofuel applications and lipids for health-related benefits. Our investigation lays the groundwork for exploiting C. pacifica in biotechnological applications, from biofuel generation to synthesizing biodegradable plastics, positioning it as a versatile host for future bioengineering endeavors.

Alkali tolerant↗

DOE OSTI2021

Effectiveness and outcomes of invasive species removal in Hawaiian streams

Despite aquatic invasive species (AIS) being a widely recognized threat to native biodiversity in streams on subtropical and tropical oceanic islands across the Pacific, AIS management has been constrained by concerns that methods of removal could result in more harm than good. In this study, we assessed the effectiveness and outcomes of combining hand-netting and streamside sequestration of native species with AIS removal via three-pass electrofishing tailored for Hawaiian Island watersheds. Removals were conducted in 13 watersheds on the island of O‘ahu following a before-after, control-impact design to assess how AIS removal and post-removal community reassembly varied by surface flow and target species of interest. We found that removals resulted in a sharp reduction in AIS densities without altering native species densities. Removal efficacy was greatest in streams with intermediate mean discharge irrespective of target group or pre-removal AIS densities. Long-term monitoring demonstrated that removals led to persistent shifts in community composition reflecting sustained reductions in AIS densities. These findings indicate that electrofishing can be a valuable tool for AIS management in Hawaiian and other subtropical Pacific island streams, so long as steps are taken to minimize potential harm to at-risk and culturally important native species.

59 BASIC BIOLOGICAL SCIENCES↗