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At least 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Desiccation induces varied responses within a soil bacterial genus

Abstract Desiccation impacts a suite of physiological processes in microbes by elevating levels of damaging reactive oxygen species and inducing DNA strand breaks. In response to desiccation‐induced stress, microbes have evolved specialized mechanisms to help them survive. Here, we performed a 128‐day lab desiccation experiment on nine strains from three clades of an abundant soil bacterium, Curtobacterium . We sequenced RNA from each strain at three time points to investigate their response. Curtobacterium was highly resistant to desiccation, outlasting both Escherichia coli and a famously DNA damage‐resistant bacterium, Deinococcus radiodurans . However, within the genus, there were also 10‐fold differences in survival rates among strains. Transcriptomic profiling revealed responses shared within the genus including up‐regulation of genes involved in DNA damage repair, osmolyte production, and efflux pumps, but also up‐regulation of pathways and genes unique to the three clades. For example, trehalose synthesis gene otsB , the chaperone groEL , and the oxygen scavenger katA were all found in either one or two clades but not the third. Here, we provide evidence of considerable variation in closely related strains, and further elucidation of the phylogenetic conservation of desiccation tolerance remains an important goal for microbial ecologists.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Protistan community composition and metabolism in the North Pacific Subtropical Gyre: Influences of mesoscale eddies and depth

Abstract Marine protists and their metabolic activities are intricately tied to the cycling of nutrients and the flow of energy through microbial food webs. Physiochemical changes in the environment, such as those that result from mesoscale eddies, may impact protistan communities, but the effects that such changes have on protists are poorly known. A metatranscriptomic study was conducted to investigate how eddies affected protists at adjacent cyclonic and anticyclonic eddy sites in the oligotrophic ocean at four depths from 25 to 250 m. Eddy polarity impacted protists at all depths sampled, although the effects of eddy polarity were secondary to the impact of depth across the depth range. Eddy‐induced vertical shifts in the water column yielded differences in the cyclonic and anticyclonic eddy protistan communities, and these differences were the most pronounced at and just below the deep chlorophyll maximum. An analysis of transcripts associated with protistan nutritional physiology at 150 m revealed that cyclonic eddies may support a more heterotrophic community, while anticyclonic eddies promote a more phototrophic community. The results of this study indicate that eddies alter the metabolism of protists particularly in the lower euphotic zone and may therefore impact carbon export from the euphotic zone.

Microbiology↗
DOE OSTI2024

Utilization of formic acid by extremely thermoacidophilic archaea species

The exploration of novel hosts with the ability to assimilate formic acid, a C1 substrate that can be produced from renewable electrons and CO 2 , is of great relevance for developing novel and sustainable biomanufacturing platforms. Formatotrophs can use formic acid or formate as a carbon and/or reducing power source. Formatotrophy has typically been studied in neutrophilic microorganisms because formic acid toxicity increases in acidic environments below the pKa of 3.75 (25°C). Because of this toxicity challenge, utilization of formic acid as either a carbon or energy source has been largely unexplored in thermoacidophiles, species that possess the ability to produce a variety of metabolites and enzymes of high biotechnological relevance. Here we investigate the capacity of several thermoacidophilic archaea species from the Sulfolobales order to tolerate and metabolize formic acid. Metallosphaera prunae, Sulfolobus metallicus and Sulfolobus acidocaldarium were found to metabolize and grow with 1–2 mM of formic acid in batch cultivations. Formic acid was co-utilized by this species alongside physiological electron donors, including ferrous iron. To enhance formic acid utilization while maintaining aqueous concentrations below the toxicity threshold, we developed a bioreactor culturing method based on a sequential formic acid feeding strategy. By dosing small amounts of formic acid sequentially and feeding H 2 as co-substrate, M. prunae could utilize a total of 16.3 mM of formic acid and grow to higher cell densities than when H 2 was supplied as a sole electron donor. These results demonstrate the viability of culturing thermoacidophilic species with formic acid as an auxiliary substrate in bioreactors to obtain higher cell densities than those yielded by conventional autotrophic conditions. Our work underscores the significance of formic acid metabolism in extreme habitats and holds promise for biotechnological applications in the realm of sustainable energy production and environmental remediation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural bases for stoichiometry‐selective calcium potentiation of a neuronal nicotinic receptor

Background and Purpose α4β2 nicotinic acetylcholine (nACh) receptors assemble in two stoichiometric forms, one of which is potentiated by calcium. The sites of calcium binding that underpin potentiation are not known. Experimental Approach To identify calcium binding sites, we applied cryo‐electron microscopy (cryo‐EM) and molecular dynamics (MD) simulations to each stoichiometric form of the α4β2 nACh receptor in the presence of calcium ions. To test whether the identified calcium sites are linked to potentiation, we generated mutants of anionic residues at the sites, expressed wild type and mutant receptors in clonal mammalian fibroblasts, and recorded ACh‐elicited single‐channel currents with or without calcium. Key Results Both cryo‐EM and MD simulations show calcium bound to a site between the extracellular and transmembrane domains of each α4 subunit (ECD‐TMD site). Substituting alanine for anionic residues at the ECD‐TMD site abolishes stoichiometry‐selective calcium potentiation, as monitored by single‐channel patch clamp electrophysiology. Additionally, MD simulation reveals calcium association at subunit interfaces within the extracellular domain. Substituting alanine for anionic residues at the ECD sites reduces or abolishes stoichiometry‐selective calcium potentiation. Conclusions and Implications Stoichiometry‐selective calcium potentiation of the α4β2 nACh receptor is achieved by calcium association with topographically distinct sites framed by anionic residues within the α4 subunit and between the α4 and β2 subunits. Stoichiometry‐selective calcium potentiation could result from the greater number of calcium sites in the stoichiometric form with three rather than two α4 subunits. The results are relevant to modulation of signalling via α4β2 nACh receptors in physiological and pathophysiological conditions.

Pharmacology & Pharmacy↗
DOE OSTI2022

Revisiting the growth rate hypothesis: Towards a holistic stoichiometric understanding of growth

The growth rate hypothesis (GRH) posits that variation in organismal stoichiometry (C:P and N:P ratios) is driven by growth-dependent allocation of P to ribosomal RNA. The GRH has found broad but not uniform support in studies across diverse biota and habitats. We synthesise information on how and why the tripartite growth-RNA-P relationship predicted by the GRH may be uncoupled and outline paths for both theoretical and empirical work needed to broaden the working domain of the GRH. We found strong support for growth to RNA (r 2 = 0.59) and RNA-P to P (r 2 = 0.63) relationships across taxa, but growth to P relationships were relatively weaker (r 2 = 0.09). Together, the GRH was supported in ~50% of studies. Mechanisms behind GRH uncoupling were diverse but could generally be attributed to physiological (P accumulation in non-RNA pools, inactive ribosomes, translation elongation rates and protein turnover rates), ecological (limitation by resources other than P), and evolutionary (adaptation to different nutrient supply regimes) causes. These factors should be accounted for in empirical tests of the GRH and formalised mathematically to facilitate a predictive understanding of growth.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Investigating the eco‐evolutionary response of microbiomes to environmental change

Abstract Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free‐living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome–functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

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 OSTI2023

A genomic region associated with iteroparous spawning phenology is linked with age‐at‐maturity in female steelhead trout

Abstract Age‐at‐maturity and iteroparity are two life history variations of steelhead trout ( Oncorhynchus mykiss ) that are believed to increase population resilience and stability. While repeat‐spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat‐spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either “consecutive” (reproduce immediately the following season) or “skip” (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta ( ER β) and glycoprotein hormone beta‐5 ( GPHB5 ), which, in mammals, are estrogen‐sensitive and expressed in reproductive tissues. Allele frequencies in this ER β/ GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age‐at‐maturity. These observations contribute to growing evidence that age‐at‐maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways.

Willis, Stuart↗
DOE OSTI2020

Increased microbial growth, biomass, and turnover drive soil organic carbon accumulation at higher plant diversity

Species-rich plant communities have been shown to be more productive and to ­exhibit increased long-term soil organic carbon (SOC) storage. Soil microorganisms are central to the conversion of plant organic matter into SOC, yet the relationship between plant diversity, soil microbial growth, turnover as well as carbon use efficiency (CUE) and SOC accumulation is unknown. As heterotrophic soil microbes are primarily carbon limited, it is important to understand how they respond to increased plant-derived carbon inputs at higher plant species richness (PSR). We used the long-term grassland biodiversity experiment in Jena, Germany, to examine how microbial physiology responds to changes in plant diversity and how this affects SOC content. The Jena Experiment considers different numbers of species (1–60), functional groups (1–4) as well as functional identity (small herbs, tall herbs, grasses, and legumes). We found that PSR accelerated microbial growth and turnover and increased microbial biomass and necromass. PSR also accelerated microbial respiration, but this effect was less strong than for microbial growth. In contrast, PSR did not affect microbial CUE or biomass-specific respiration. Structural equation models revealed that PSR had direct positive effects on root biomass, and thereby on microbial growth and microbial biomass carbon. Finally, PSR increased SOC content via its positive influence on microbial biomass carbon. We suggest that PSR favors faster rates of microbial growth and turnover, likely due to greater plant productivity, resulting in higher amounts of microbial biomass and necromass that translate into the observed increase in SOC. We thus identify the microbial mechanism linking species-rich plant communities to a carbon cycle process of importance to Earth's climate system.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Microbial carbon limitation: The need for integrating microorganisms into our understanding of ecosystem carbon cycling

Abstract Numerous studies have demonstrated that fertilization with nutrients such as nitrogen, phosphorus, and potassium increases plant productivity in both natural and managed ecosystems, demonstrating that primary productivity is nutrient limited in most terrestrial ecosystems. In contrast, it has been demonstrated that heterotrophic microbial communities in soil are primarily limited by organic carbon or energy. While this concept of contrasting limitations, that is, microbial carbon and plant nutrient limitation, is based on strong evidence that we review in this paper, it is often ignored in discussions of ecosystem response to global environment changes. The plant‐centric perspective has equated plant nutrient limitations with those of whole ecosystems, thereby ignoring the important role of the heterotrophs responsible for soil decomposition in driving ecosystem carbon storage. To truly integrate carbon and nutrient cycles in ecosystem science, we must account for the fact that while plant productivity may be nutrient limited, the secondary productivity by heterotrophic communities is inherently carbon limited. Ecosystem carbon cycling integrates the independent physiological responses of its individual components, as well as tightly coupled exchanges between autotrophs and heterotrophs. To the extent that the interacting autotrophic and heterotrophic processes are controlled by organisms that are limited by nutrient versus carbon accessibility, respectively, we propose that ecosystems by definition cannot be ‘limited’ by nutrients or carbon alone. Here, we outline how models aimed at predicting non‐steady state ecosystem responses over time can benefit from dissecting ecosystems into the organismal components and their inherent limitations to better represent plant–microbe interactions in coupled carbon and nutrient models.

Soong, Jennifer L.↗
DOE OSTI2020

Partitioning net carbon dioxide fluxes into photosynthesis and respiration using neural networks

The eddy covariance (EC) technique is used to measure the net ecosystem exchange (NEE) of CO 2 between ecosystems and the atmosphere, offering a unique opportunity to study ecosystem responses to climate change. NEE is the difference between the total CO 2 release due to all respiration processes (RECO), and the gross carbon uptake by photosynthesis (GPP). These two gross CO 2 fluxes are derived from EC measurements by applying partitioning methods that rely on physiologically based functional relationships with a limited number of environmental drivers. However, the partitioning methods applied in the global FLUXNET network of EC observations do not account for the multiple co-acting factors that modulate GPP and RECO flux dynamics. To overcome this limitation, we developed a hybrid data-driven approach based on combined neural networks (NN C-part ). NN C-part incorporates process knowledge by introducing a photosynthetic response based on the light-use efficiency (LUE) concept, and uses a comprehensive dataset of soil and micrometeorological variables as fluxes drivers. We applied the method to 36 sites from the FLUXNET2015 dataset and found a high consistency in the results with those derived from other standard partitioning methods for both GPP (R 2 > .94) and RECO (R 2 > .8). High consistency was also found for (a) the diurnal and seasonal patterns of fluxes and (b) the ecosystem functional responses. NNC-part performed more realistic than the traditional methods for predicting additional patterns of gross CO 2 fluxes, such as: (a) the GPP response to VPD, (b) direct effects of air temperature on GPP dynamics, (c) hysteresis in the diel cycle of gross CO 2 fluxes, (d) the sensitivity of LUE to the diffuse to direct radiation ratio, and (e) the post rain respiration pulse after a long dry period. In conclusion, NN C-part is a valid data-driven approach to provide GPP and RECO estimates and complementary to the existing partitioning methods.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Potential of hotspot solar‐induced chlorophyll fluorescence for better tracking terrestrial photosynthesis

Abstract Remote sensing of solar‐induced fluorescence (SIF) opens a new window for quantifying a key ecological variable, the terrestrial ecosystem gross primary production (GPP), because of the revealed strong SIF–GPP correlation. However, similar to many other remotely sensed metrics, SIF observations suffer from the sun‐sensor geometry effects, which may have important impacts on the SIF–GPP relationship but remain poorly understood. Here we used remotely sensed SIF, globally distributed tower GPP data, and a mechanistic model to provide a systematic analysis. Our results reveal that leaf physiology, canopy structure, and sun‐sensor geometries all affect the SIF–GPP relationship. In particular, we found that SIF observations in the sun‐tracking hotspot direction can be a better proxy of GPP due to the similar responses of light use efficiency and SIF escaping probability in the hotspot direction to the increasing incoming solar radiation. Such conclusions are supported by a variety of modeling simulations and satellite observations over various plant function types, at different time scales and with satellite observational modes. This study demonstrates the potential and advantage of normalizing SIF observations to the hotspot direction for better global GPP estimations. This study also demonstrates the great potentials of current and future spaceborne sun‐tracking satellite missions for a significant improvement in measuring and monitoring, at a wide range of spatial and temporal scales, the changes in terrestrial ecosystem GPP in response to anticipated changes in the Earth's environmental conditions.

Hao, Dalei↗
DOE OSTI2021

Living on the edge: A continental-scale assessment of forest vulnerability to drought

Globally, forests are facing an increasing risk of mass tree mortality events associated with extreme droughts and higher temperatures. Hydraulic dysfunction is considered a key mechanism of drought-triggered dieback. By leveraging the climate breadth of the Australian landscape and a national network of research sites (Terrestrial Ecosystem Research Network), we conducted a continental-scale study of physiological and hydraulic traits of 33 native tree species from contrasting environments to disentangle the complexities of plant response to drought across communities. Here, we found strong relationships between key plant hydraulic traits and site aridity. Leaf turgor loss point and xylem embolism resistance were correlated with minimum water potential experienced by each species. Across the data set, there was a strong coordination between hydraulic traits, including those linked to hydraulic safety, stomatal regulation and the cost of carbon investment into woody tissue. These results illustrate that aridity has acted as a strong selective pressure, shaping hydraulic traits of tree species across the Australian landscape. Hydraulic safety margins were constrained across sites, with species from wetter sites tending to have smaller safety margin compared with species at drier sites, suggesting trees are operating close to their hydraulic thresholds and forest biomes across the spectrum may be susceptible to shifts in climate that result in the intensification of drought.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Reducing Model Uncertainty of Climate Change Impacts on High Latitude Carbon Assimilation

The Arctic Boreal Region (ABR) has a large impact on global vegetation-atmosphere interactions and is experiencing markedly greater warming than the rest of the planet, a trend that is projected to continue with anticipated future emissions of CO 2 . The ABR is a significant source of uncertainty in estimates of carbon uptake in terrestrial biosphere models (TBMs) such that reducing this uncertainty is critical for more accurately estimating global carbon cycling and understanding the response of the region to global change. Process representation and parameterization associated with gross primary productivity (GPP) drives a large amount of this model uncertainty, particularly within the next 50 years, where the response of existing vegetation to climate change will dominate estimates of GPP for the region. Furthermore, we review our current understanding and model representation of GPP in northern latitudes, focusing on vegetation composition, phenology and physiology, and consider how climate change alters these three components. We highlight challenges in the ABR for predicting GPP, but also focus on the unique opportunities for advancing knowledge and model representation, particularly through the combination of remote sensing and traditional boots-on-the-ground science.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Testing unified theories for ozone response in C 4 species

Abstract There is tremendous interspecific variability in O 3 sensitivity among C 3 species, but variation among C 4 species has been less clearly documented. It is also unclear whether stomatal conductance and leaf structure such as leaf mass per area (LMA) determine the variation in sensitivity to O 3 across species. In this study, we investigated leaf morphological, chemical, and photosynthetic responses of 22 genotypes of four C 4 bioenergy species (switchgrass, sorghum, maize, and miscanthus) to elevated O 3 in side‐by‐side field experiments using free‐air O 3 concentration enrichment (FACE). The C 4 species varied largely in leaf morphology, physiology, and nutrient composition. Elevated O 3 did not alter leaf morphology, nutrient content, stomatal conductance, chlorophyll fluorescence, and respiration in most genotypes but reduced net CO 2 assimilation in maize and photosynthetic capacity in sorghum and maize. Species with lower LMA and higher stomatal conductance tended to show greater losses in photosynthetic rate and capacity in elevated O 3 compared with species with higher LMA and lower stomatal conductance. Stomatal conductance was the strongest determinant of leaf photosynthetic rate and capacity. The response of both area‐ and mass‐based leaf photosynthetic rate and capacity to elevated O 3 were not affected by LMA directly but negatively influenced by LMA indirectly through stomatal conductance. These results demonstrate that there is significant variation in O 3 sensitivity among C 4 species with maize and sorghum showing greater sensitivity of photosynthesis to O 3 than switchgrass and miscanthus. Interspecific variation in O 3 sensitivity was determined by direct effects of stomatal conductance and indirect effects of LMA. This is the first study to provide a test of unifying theories explaining variation in O 3 sensitivity in C 4 bioenergy grasses. These findings advance understanding of O 3 tolerance in C 4 grasses and could aid in optimal placement of diverse C 4 bioenergy feedstock across a polluted landscape.

54 ENVIRONMENTAL SCIENCES↗