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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Unraveling the ecological success of Iodidimonas in a bioreactor treating oil and gas produced water

Iodidimonas sp., a bacterium found in bioreactors treating oil and gas produced water as well as iodide-rich brines, has garnered attention for its unique ability to oxidize iodine. However, little is known about the metabolic capabilities that enable Iodidimonas sp. to thrive in certain unique ecological niches. In this study, we isolated, characterized, and sequenced three strains belonging to the Iodidimonas genus from the sludge of a membrane bioreactor used for produced water treatment. We investigated the genomic features of these isolates and compared them with the four publicly available isolate genomes from this genus, as well as a metagenome-assembled genome from the source bioreactor. Our Iodidimonas isolates had several genes associated with mitigating salinity, heavy metal, and organic compound stress, which likely help these bacteria to survive in produced water. Phenotyping tests revealed that while the isolates could utilize a wide variety of simple carbon substrates, they failed to degrade aliphatic or aromatic hydrocarbons, consistent with the lack of genes associated with common hydrocarbon degradation pathways in their genomes. We hypothesize that these microbes may lead a scavenging lifestyle in the bioreactor and similar iodide-rich brines. IMPORTANCE: Occupying a niche habitat and having few representative isolates, the genus Iodidimonas is a relatively understudied alphaproteobacterial group. Its ability to corrode pipes in iodine production facilities has economic implications, and its ability to generate potentially carcinogenic iodinated organic compounds during treatment of oil and gas produced water may cause environmental and health concerns with the recycling of treated water. Therefore, detailed characterization of the metabolic potential of the Iodidimonas isolates in this study both sheds light on their adaptation to the environmental conditions they inhabit and has environmental and economic significance.

Acharya, Shwetha M↗
DOE OSTI2022

Successional adaptive strategies revealed by correlating arbuscular mycorrhizal fungal abundance with host plant gene expression

The shifts in adaptive strategies revealed by ecological succession and the mechanisms that facilitate these shifts are fundamental to ecology. These adaptive strategies could be particularly important in communities of arbuscular mycorrhizal fungi (AMF) mutualistic with sorghum, where strong AMF succession replaces initially ruderal species with competitive ones and where the strongest plant response to drought is to manage these AMF. Although most studies of agriculturally important fungi focus on parasites, the mutualistic symbionts, AMF, constitute a research system of human-associated fungi whose relative simplicity and synchrony are conducive to experimental ecology. First, we hypothesize that, when irrigation is stopped to mimic drought, competitive AMF species should be replaced by AMF species tolerant to drought stress. We then, for the first time, correlate AMF abundance and host plant transcription to test two novel hypotheses about the mechanisms behind the shift from ruderal to competitive AMF. Surprisingly, despite imposing drought stress, we found no stress-tolerant AMF, probably due to our agricultural system having been irrigated for nearly six decades. Remarkably, we found strong and differential correlation between the successional shift from ruderal to competitive AMF and sorghum genes whose products (i) produce and release strigolactone signals, (ii) perceive mycorrhizal-lipochitinoligosaccharide (Myc-LCO) signals, (iii) provide plant lipid and sugar to AMF, and (iv) import minerals and water provided by AMF. These novel insights frame new hypotheses about AMF adaptive evolution and suggest a rationale for selecting AMF to reduce inputs and maximize yields in commercial agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Transportome remodeling of a symbiotic microalga inside a planktonic host

Abstract Metabolic exchange is one of the foundations of symbiotic associations between organisms and is a driving force in evolution. In the ocean, photosymbiosis between heterotrophic hosts and microalgae is powered by photosynthesis and relies on the transfer of organic carbon to the host (e.g. sugars). Yet, the identity of transferred carbohydrates as well as the molecular mechanisms that drive this exchange remain largely unknown, especially in unicellular photosymbioses that are widespread in the open ocean. Combining genomics, single-holobiont transcriptomics, and environmental metatranscriptomics, we revealed the transportome of the marine microalga Phaeocystis in symbiosis within acantharia, with a focus on sugar transporters. At the genomic level, the sugar transportome of Phaeocystis is comparable to non-symbiotic haptophytes. By contrast, we found significant remodeling of the expression of the transportome in symbiotic microalgae compared to the free-living stage. More particularly, 36% of sugar transporter genes were differentially expressed. Several of them, such as GLUTs, TPTs, and aquaporins, with glucose, triose-phosphate sugars, and glycerol as potential substrates, were upregulated at the holobiont and community level. We also showed that algal sugar transporter genes exhibit distinct temporal expression patterns during the day. This reprogramed transportome indicates that symbiosis has a major impact on sugar fluxes within and outside the algal cell, and highlights the complexity and the dynamics of metabolic exchanges between partners. This study improves our understanding of the molecular players of the metabolic connectivity underlying the ecological success of planktonic photosymbiosis and paves the way for more studies on transporters across photosymbiotic models.

Environmental Sciences & Ecology↗
DOE OSTI2024

Characterizing suburban soil and microbial properties along a soil age chronosequence

Abstract Rapid urbanization is drastically altering ecosystem processes in landscapes around the world. In particular, suburban residential neighborhoods comprise novel ecosystems with water and nutrient inputs that differ greatly from the surrounding land area. These impacts generate concern over the sustainability of urban ecosystems, especially whether they will be characterized by net carbon gain or loss over time. To address this knowledge gap, we established a chronosequence of residential yards in Southern California to test how urban soils change after development. We predicted that urbanized soils would experience shifts in physical characteristics and microbial function over time consistent with ecological succession theory, but residential soils would maintain novel moisture and nutrient regimes compared to undeveloped soils, never “recovering” to a pre‐developed state. We compared different vegetation types to quantify impacts of homeowner landscaping choices and characterized yard soils and their microbial communities. We found that yard soils were nutrient‐ and moisture‐enriched compared to an adjacent undeveloped ecosystem, and turfgrass was associated with higher levels of water and nitrogen. Despite high respiration rates, yard soils accumulated carbon and nitrogen over time. We conclude that suburban residential soils comprise dynamic and heterogeneous ecosystems that are highly influenced by landscaping choices and management practices, and warrant closer study at small management‐relevant scales.

Suratt, Andie [Department of Ecology and Evolution↗
DOE OSTI2020

Management opportunities for soil carbon sequestration following agricultural land abandonment

The widespread historical and ongoing abandonment of agricultural lands worldwide presents important opportunities for promoting climate change mitigation through carbon sequestration. The default management outcome of abandonment is natural regeneration through ecological succession. However, several different management strategies and new land uses for abandoned agricultural lands have been recommended by the scientific community in recent years. This paper reviews the foremost proposed strategies and compares their soil carbon sequestration potentials. Six major categories have been proposed globally. Each proposal has positive and negative outcomes depending on site-specific factors and management objectives. Accordingly, no single strategy is ideal in all scenarios and a combination of strategies addresses multiple rural development goals concurrently. A combination of passive and active management techniques is the most effective approach for maximizing soil carbon sequestration over large geographic scales, while other strategies can be designed to also promote low-carbon land use practices and fossil fuel substitution. The implications of each proposal highlighted here demonstrates the positive role that abandoned agricultural lands can serve in climate change mitigation efforts, supporting policymakers tasked with planning the future of regions undergoing abandonment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Do Cell Wall Esters Facilitate Forest Response to Climate?

Terrestrial ecosystem dynamics are strongly modified by stresses associated with climate change, impacting plant growth and development, mortality, and ecological succession. Finally, we highlight the potential role of plant cell wall esters to link changes in cell wall structure and function with biosphere-atmosphere fluxes of methanol, acetic acid, carbon dioxide (CO 2 ), and water (H 2 O).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mechanisms and heterogeneity of in situ mineral processing by the marine nitrogen fixer Trichodesmium revealed by single-colony metaproteomics

The keystone marine nitrogen fixer Trichodesmium thrives in high-dust environments. While laboratory investigations have observed that Trichodesmium colonies can access the essential nutrient iron from dust particles, less clear are the biochemical strategies underlying particle–colony interactions in nature. Here we demonstrate that Trichodesmium colonies engage with mineral particles in the wild with distinct molecular responses. We encountered particle-laden Trichodesmium colonies at a sampling location in the Southern Caribbean Sea; microscopy and synchrotron-based imaging then demonstrated heterogeneous associations with iron oxide and iron-silicate minerals. Metaproteomic analysis of individual colonies by a new low-biomass approach revealed responses in biogeochemically relevant proteins including photosynthesis proteins and metalloproteins containing iron, nickel, copper, and zinc. The iron-storage protein ferritin was particularly enriched implying accumulation of mineral-derived iron, and multiple iron acquisition pathways including Fe(II), Fe(III), and Fe-siderophore transporters were engaged. While the particles provided key trace metals such as iron and nickel, there was also evidence that Trichodesmium was altering its strategy to confront increased superoxide production and metal exposure. Chemotaxis regulators also responded to mineral presence suggesting involvement in particle entrainment. These molecular responses are fundamental to Trichodesmium’s ecological success and global biogeochemical impact, and may contribute to the leaching of particulate trace metals with implications for global iron and carbon cycling.

Held, Noelle A.↗
DOE OSTI2024

Aridity and forest age mediate landscape scale patterns of tropical forest resistance to cyclonic storms

Abstract Cyclonic storms, or hurricanes, are expected to intensify as ocean heat energy rises due to climate change. Ecological theory suggests that tropical forest resistance to hurricanes should increase with forest age and wood density. However, most data on hurricane effects on tropical forests come from a limited number of well‐studied long‐term monitoring sites, restricting our capacity to evaluate the resistance of tropical forests to hurricanes across broad environmental gradients. In this study, we assessed whether forest age and aridity mediate the effects of hurricanes Irma and Maria in Puerto Rico, Vieques and Culebra islands. We leveraged functional trait data for 410 tree species, remotely sensed measurements of canopy height and cover, along with data on forest stand characteristics of 180 of 338 forest monitoring plots, each covering an area of 0.067 ha. The plots represent a broad mean annual precipitation (MAP) gradient from 701 to 4598 mm and a complex mosaic of forest age from 5 to around 85 years since deforestation. Hurricanes resulted in a 25% increase in basal area mortality rates, a 45% decrease in canopy height and a 21% reduction in canopy cover. These effects intensified with forest age, even after considering proximity to the hurricane path. The links between forest age and hurricane disturbances were likely due the prevalence of tall canopies. Tall forest canopies were strongly linked with low community‐weighted wood density (WD). These characteristics were on average more common in moist and wet forests (MAP >1250 mm). Conversely, dry forests were dominated by short species with high wood density (WD > 0.6 g cm −3 ) and did not show significant increases in basal area mortality rates after the hurricanes. Synthesis . Our findings show that selection towards drought‐tolerant traits across aridity gradients, such as short stature and dense wood, enhances resistance to hurricanes. However, forest age modulated responses to hurricanes, with older forests being less resistant across the islands. This evidence highlights the importance of considering the intricate links between ecological succession and plant function when forecasting tropical forests’ responses to increasingly strong hurricanes.

Vargas G., German↗
DOE OSTI2020

2020 State of the Science Report, Chapter 6: Changes in Benthic and Pelagic Habitats Caused by Marine Renewable Energy Devices

Most marine renewable energy (MRE) devices must be attached to the seafloor in some way, either through gravity foundations, pilings, or anchors, and with mooring lines, transmission cables, and devices themselves in the water column. Physical changes in benthic and pelagic habitats have the potential to alter species occurrence or abundance at a localized scale, lead to some level of habitat loss, provide opportunities for colonization by non-native species, alter patterns of ecological succession, modify ecosystem functioning, and affect behavioral responses of marine organisms. The transformation of the seafloor and/or water column habitat to new hard substratum because of the presence of the MRE devices may also lead to artificial reef effects or changes in animal behavior. While there is no indication that MRE devices affect marine habitats differently than other structures currently and historically placed in the ocean, regulators and stakeholders may continue to have concerns. https://tethys.pnnl.gov/publications/state-of-the-science-2020-chapter-6-habitat-changes

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Restoring Soil Fertility on Degraded Lands to Meet Food, Fuel, and Climate Security Needs via Perennialization

A continuously growing pressure to increase food, fiber, and fuel production to meet worldwide demand and achieve zero hunger has put severe pressure on soil resources. Abandoned, degraded, and marginal lands with significant agricultural constraints—many still used for agricultural production—result from inappropriately intensive management, insufficient attention to soil conservation, and climate change. Continued use for agricultural production will often require ever more external inputs such as fertilizers and herbicides, further exacerbating soil degradation and impeding nutrient recycling and retention. Growing evidence suggests that degraded lands have a large potential for restoration, perhaps most effectively via perennial cropping systems that can simultaneously provide additional ecosystem services. Here we synthesize the advantages of and potentials for using perennial vegetation to restore soil fertility on degraded croplands, by summarizing the principal mechanisms underpinning soil carbon stabilization and nitrogen and phosphorus availability and retention. We illustrate restoration potentials with example systems that deliver climate mitigation (cellulosic bioenergy), animal production (intensive rotational grazing), and biodiversity conservation (natural ecological succession). Perennialization has substantial promise for restoring fertility to degraded croplands, helping to meet future food security needs.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

An Automated Method for Mapping Giant Kelp Canopy Dynamics from UAV

Satellite and aerial imagery have been used extensively for mapping the abundance and distribution of giant kelp ( Macrocystis pyrifera ) in southern California. There is now great potential for using unoccupied aerial vehicles (UAVs) to map kelp canopy at very high resolutions. However, tides and currents have been shown to affect the amount of floating kelp canopy on the water surface, and the impacts of these processes on remotely sensed kelp estimates in this region have not been fully quantified. UAVs were used to map fine-scale changes in canopy area due to tidal height and current speed at kelp forests off the coast of Palos Verdes, CA and Santa Barbara, CA. An automated method for detecting kelp canopy was developed that was 67% accurate using red-green-blue (RGB) UAV imagery and 93% accurate using multispectral UAV imagery across a range of weather, ocean, and illumination conditions. Increases in tidal height of 1 m reduced the amount of floating kelp canopy by 15% in Santa Barbara and by over 30% in Palos Verdes. The effect of current speed on visible kelp canopy was inconclusive, but there was a trend towards lower canopy area with increased current speed. Therefore, while tidal height and current speed can introduce significant variability to estimates of kelp abundance, the magnitude of this variability is site specific. Still, UAVs are a valuable tool for mapping of kelp canopy and can provide greater spatial resolution and temporal coverage than is possible from many satellite sensors. This data can provide insight into the patterns and drivers of high frequency fluctuations in kelp abundance.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data from: Soil carbon change in intensive agriculture after 25 years of conservation management

Changes in soil organic carbon (SOC) and nitrogen (SON) are strongly affected by land management, but few long-term comparative studies have surveyed changes throughout the whole soil profile. We quantified 25-year SOC and SON changes to 1 m in 10 replicate ecosystems at an Upper Midwest, USA site. We compared four annual cropping systems in maize ( Zea mays )-soybean ( Glycine max)-winter wheat ( Triticum aestivum ) rotations, each managed differently (Conventional, No-till, Reduced input, and Biologically based); in three managed perennial systems (hybrid Poplar ( Populus × euramericana ), Alfalfa ( Medicago sativa ), and Conifer ( Pinus spp.); and in three successional systems (Early, Mid- and Late succession undergoing a gradual change in species composition and structure over time).

agricultural sciences↗
DOE OSTI2024

The role of emerging scientists in restoration ecology: insights from a SER2023 conference workshop

Emerging professionals are crucial in advancing ecological restoration by connecting newcomers with established leaders and blending new ideas with traditional practices. This paper highlights the vital role emerging scientists play in restoration ecology and the Society for Ecological Restoration (SER). A survey conducted during the SER2023 conference workshop, organized by the Students and Emerging Professionals committee, showed that emerging professionals contribute significantly to every stage of scientific work, from planning to publication. However, participants emphasized the scarcity of funding opportunities for non‐senior scientists, which limits academic growth. The workshop underscored the importance of nurturing emerging professionals to develop future leaders for SER and ensure continuity. Fostering non‐hierarchical and inclusive networking is key to engaging and empowering these professionals, ultimately contributing to the long‐term success of ecological restoration efforts.

Weidlich, Emanuela W. A.↗
DOE OSTI2020

Soil organic carbon accumulation rates on Mediterranean abandoned agricultural lands

Secondary succession on abandoned agricultural lands can produce climate change mitigation co-benefits, such as soil carbon sequestration. However, the accumulation of soil organic carbon (SOC) in Mediterranean regions has been difficult to predict and is subject to multiple environmental and land management factors. Gains, losses, and no significant changes have all been reported. Here we compile chronosequence data (n = 113) from published studies and new field sites to assess the response of SOC to agricultural land abandonment in peninsular Spain. In this work we found an overall SOC accumulation rate of +2.3% yr -1 post-abandonment. SOC dynamics are highly variable and context-dependent. Minimal change occurs on abandoned cereal croplands compared to abandoned woody croplands (+4% yr -1 ). Accumulation is most prevalent within a Goldilocks climatic window of ~13–17 °C and ~450–900 mm precipitation, promoting >100% gains after three decades. Our secondary forest field sites accrued 40.8 Mg C ha -1 (+172%) following abandonment and displayed greater SOC and N depth heterogeneity than natural forests demonstrating the long-lasting impact of agriculture. Although changes in regional climate and crop types abandoned will impact future carbon sequestration, abandonment remains a low-cost, long-term natural climate solution best incorporated in tandem with other multipurpose sustainable land management strategies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Soil carbon change in intensive agriculture after 25 years of conservation management

Changes in soil organic carbon (SOC) and nitrogen (SON) are strongly affected by land management but few long-term comparative studies have surveyed changes throughout the whole soil profile. We quantified 25-year SOC and SON changes to 1 m in 10 replicate ecosystems at an Upper Midwest, USA site. We compared four annual cropping systems in maize (Zea mays)-soybean (Glycine max)-winter wheat (Triticum aestivum) rotations, each managed differently (Conventional, No-till, Reduced input, and Biologically based); in three managed perennial systems (hybrid Poplar (Populus × euramericana), Alfalfa (Medicago sativa), and Conifer (Pinus spp.); and in three successional systems (Early, Mid- and Late succession undergoing a gradual change in species composition and structure over time). Both Reduced input and Biologically based systems included winter cover crops. Neither SOC nor SON changed significantly in the Conventional or Late successional systems over 25 years. All other systems gained SOC and SON to different degrees. SOC accrual was fastest in the Early successional system (0.8 ± 0.1 Mg C ha –1 y –1 ) followed by Alfalfa and Conifer (avg. 0.7 ± 0.1 Mg C ha –1 y –1 ), Poplar, Reduced input, and Biologically based systems (avg. 0.4 ± 0.1 Mg C ha –1 y –1 ), and Mid-successional and No-till systems (0.3 and 0.2 Mg C ha –1 y –1 , respectively). Over the most recent 12 years, rates of SOC accrual slowed in all systems except Reduced input and Mid-successional. There was no evidence of SOC loss at depth in any system, including No-till. Rates of SON accrual ranged from 64.7 to 0.8 kg N ha –1 y –1 in the order Alfalfa ≥ Early successional > Reduced input and Biologically based ≥ Poplar > No-till and Conifer > Mid-successional systems. Pyrogenic C levels in the Conventional, Early, and Late successional systems were similar despite 17 years of annual burning in the Early successional system (~ 15 % of SOC to 50 cm, on average, and ~40 % of SOC from 50 to 100 cm). Results underscore the importance of cover crops, perennial crops, and no-till options for sequestering whole profile C in intensively managed croplands.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Considering Soil Biota and Symbioses in Forest Management and Ecosystem Restoration

At the 16th Biennial Conference of Science & Management on the Colorado Plateau & Southwest Region on 12–15 September 2022, the authors hosted a symposium on the topic of “Considering host-microbial interactions in ecosystem restoration”. The goal of this symposium was to showcase studies that demonstrate how soil biota and symbioses can be used to promote forest restoration. Two key principles emerging from the symposium and research on this topic include the following: (1) diverse, native mixes of appropriate soil biota can meaningfully shift forests and plantings towards more successful and ecologically appropriate conditions; (2) context is important to consider in determining the appropriateness of plant and microbial pairings, including the similarity of source material and work sites across a variety of factors. To summarize the literature and discussion on this topic, we offer a graphical depiction of several of the factors to consider.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Genome, transcriptome and secretome analyses of the antagonistic, yeast-like fungus Aureobasidium pullulans to identify potential biocontrol genes

Aureobasidium pullulans is an extremotolerant, cosmopolitan yeast-like fungus that successfully colonises vastly different ecological niches. The species is widely used in biotechnology and successfully applied as a commercial biocontrol agent against postharvest diseases and fireblight. However, the exact mechanisms that are responsible for its antagonistic activity against diverse plant pathogens are not known at the molecular level. Thus, it is difficult to optimise and improve the biocontrol applications of this species. As a foundation for elucidating biocontrol mechanisms, we have de novo assembled a high-quality reference genome of a strongly antagonistic A. pullulans strain, performed dual RNA-seq experiments, and analysed proteins secreted during the interaction with the plant pathogen Fusarium oxysporum. Based on the genome annotation, potential biocontrol genes were predicted to encode secreted hydrolases or to be part of secondary metabolite clusters (e.g., NRPS-like, NRPS, T1PKS, terpene, and β-lactone clusters). Transcriptome and secretome analyses defined a subset of 79 A. pullulans genes (among the 10,925 annotated genes) that were transcriptionally upregulated or exclusively detected at the protein level during the competition with F. oxysporum. These potential biocontrol genes comprised predicted secreted hydrolases such as glycosylases, esterases, and proteases, as well as genes encoding enzymes, which are predicted to be involved in the synthesis of secondary metabolites. This study highlights the value of a sequential approach starting with genome mining and consecutive transcriptome and secretome analyses in order to identify a limited number of potential target genes for detailed, functional analyses.

transcriptome↗
DOE OSTI2023

Optimal reference genes for RNA tissue analysis in small animal models of hemorrhagic fever viruses

Abstract Reverse-transcription quantitative polymerase chain reaction assays are frequently used to evaluate gene expression in animal model studies. Data analyses depend on normalization using a suitable reference gene (RG) to minimize effects of variation due to sample collection, sample processing, or experimental set-up. Here, we investigated the suitability of nine potential RGs in laboratory animals commonly used to study viral hemorrhagic fever infection. Using tissues (liver, spleen, gonad [ovary or testis], kidney, heart, lung, eye, brain, and blood) collected from naïve animals and those infected with Crimean–Congo hemorrhagic fever (mice), Nipah (hamsters), or Lassa (guinea pigs) viruses, optimal species-specific RGs were identified based on five web-based algorithms to assess RG stability. Notably, the Ppia RG demonstrated stability across all rodent tissues tested. Optimal RG pairs that include Ppia were determined for each rodent species ( Ppia and Gusb for mice; Ppia and Hrpt for hamsters; and Ppia and Gapdh for guinea pigs). These RG pair assays were multiplexed with viral targets to improve assay turnaround time and economize sample usage. Finally, a pan-rodent Ppia assay capable of detecting Ppia across multiple rodent species was developed and successfully used in ecological investigations of field-caught rodents, further supporting its pan-species utility.

Davies, Katherine A.↗