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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Dynamic microbial assembly processes correspond to soil fertility in sustainable paddy agroecosystems

1. Microorganisms underpin the sustainability of agroecosystems, but we have a poor understanding of how the assembly processes that govern microbial community structure interact through time to maintain soil fertility. 2. Ancient rice paddies have a history of cultivation spanning hundreds or thousands of years and provide an ideal opportunity to explore relationships between community assembly processes and long-term agroecosystem sustainability. We used statistical null models to evaluate temporal patterns of bacterial community assembly processes across rice cultivation years and their associations with increases in soil fertility in paddy agroecosystems. 3. We found that stochasticity was a persistent force structuring paddy soil microbial communities, putatively due to frequent flooding that facilities dispersal. However, determinism gradually increased over centuries of agriculture and corresponded to increases in soil fertility. Accordingly, multifunctionality, calculated using enzymes catalyzing key soil functions in carbon, nitrogen, phosphorous and sulfur cycling significantly increased along rice cultivation years. We therefore propose that balanced assembly processes preserve a diverse array of traits that can dominate under various circumstances (stochasticity) while allowing for traits relevant to soil fertility to be selected for by soil fertility (determinism), thus supporting multifunctionality that underlies sustainable agroecosystems. 4. In total, our results highlight that knowledge on temporal microbial assembly processes, community composition, and ecological function in context of soil fertility is key to understanding ecological mechanisms maintaining agroecosystems sustainability.

Liu, Wenjing↗
DOE OSTI2021

Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity

How soil is managed, particularly for agriculture, exerts stresses upon soil microbiomes, resulting in altered community structures and functional states. Understanding how soil microbiomes respond to combined stresses is important for predicting system performance under different land use scenarios, aids in identification of the most environmentally benign managements, and provides insight into how system function can be recovered in degraded soils. We use a long-established field experiment to study the effects of combined chronic (press) disturbance of the magnitude of organic carbon inputs with acute (pulse) effects of physical disturbance by tillage and chemical disturbance due to inorganic fertilization and pesticide application. We show that because of the variety of ways it can be assessed, biodiversity—here based on microbial small subunit rRNA gene phylotypes—does not provide a consistent view of community change. In contrast, aggregated traits associated with soil microbiomes indicate general loss of function, measured as a reduction of average genome lengths, associated with chronic reduction of organic inputs in arable or bare fallow soils and altered growth strategies associated with rRNA operon copy number in prokaryotes, as well as a switch to pathogenicity in fungal communities. In addition, pulse disturbance by soil tillage is associated with an increased influence of stochastic processes upon prokaryote community assembly, but fungicide used in arable soils results in niche assembly of fungal communities compared to untilled grassland. Overall, bacteria, archaea, and fungi do not share a common response to land management change, and estimates of biodiversity do not capture important facets of community adaptation to stresses adequately.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile

Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/ Q 10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity ( V max ) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. V max and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/ Q 10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Benefits of symbiotic ectomycorrhizal fungi to plant water relations depend on plant genotype in pinyon pine

Rhizosphere microbes, such as root-associated fungi, can improve plant access to soil resources, affecting plant health, productivity, and stress tolerance. While mycorrhizal associations are ubiquitous, plant–microbe interactions can be species specific. Here we show that the specificity of the effects of microbial symbionts on plant function can go beyond species level: colonization of roots by ectomycorrhizal fungi (EMF) of the genus Geopora has opposite effects on water uptake, and stomatal control of desiccation in drought tolerant and intolerant genotypes of pinyon pine (Pinus edulis Engelm.). These results demonstrate, for the first time, that microorganisms can have significant and opposite effects on important plant functional traits like stomatal control of desiccation that are associated with differential mortality and growth in nature. They also highlight that appropriate pairing of plant genotypes and microbial associates will be important for mitigating climate change impacts on vegetation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Enhancing climate-smart crop performance in arid agrivoltaics systems: effects of photovoltaic shading and soil amendments on tepary bean growth, yield, and associated soil microbiome

As climate change expands the world’s arid and semiarid regions, sustainable systems that integrate food and energy production are becoming increasingly critical. Agrivoltaics—co-locating crops with photovoltaic (PV) panels—offers a dual land-use strategy that mitigates environmental stress by shading crops, conserving soil moisture, and enhancing PV efficiency. While climate-smart crops like the tepary bean ( Phaseolus acutifolius ) are well adapted to heat and drought, little is known about how these crops and their associated soil microbiomes respond to the unique microclimates created by PV shading. This study evaluated tepary bean performance and plant–microbial interactions under PV-shade vs. no shade across three soil amendment treatments at two experimental sites. We assessed plant traits including germination, phenology, biomass, height, as well as yield and bean morphology, alongside shifts in soil microbial composition and functional potential. Plants grown under PV-shade were generally taller, with extended reproductive periods and higher yields: 42% of shaded plants produced beans compared to only 8% under full sun. Shaded plants also produced rounder, higher-quality beans, whereas non-shaded plants yielded flatter, less developed beans. Microbial community composition was more strongly influenced by amendment and site conditions than by shading alone. Key microbial taxa (e.g., Glomeromycetes, Desulfobacterota ) and predicted functions (e.g., denitrification, nitrogen-respiration, sulfate reduction) were associated with differences in plant performance. Finally, combining agrivoltaic systems with targeted soil amendments can enhance crop yield and soil microbial functionality—offering a promising strategy for sustainable agriculture in arid landscapes.

14 SOLAR ENERGY↗
DOE OSTI2021

Natural soil microbiome variation affects spring foliar phenology with consequences for plant productivity and climate-driven range shifts

Identifying the potential for natural soil microbial communities to predictably affect complex plant traits is an important frontier in climate change research. Plant phenology varies with environmental and genetic factors, but few studies have examined if the soil microbiome interacts with plant population differentiation to affect phenology and ecosystem function. We compared soil microbial variation in a widespread tree species (Populus angustifolia) with different soil inoculum treatments in a common garden environment to test how the soil microbiome affects spring foliar phenology and subsequent biomass growth. We hypothesized and show that: 1) soil bacterial and fungal communities vary with tree conditioning from different populations and elevations, 2) this soil community variation influences patterns of foliar phenology and plant growth across populations and elevation gradients, and 3) transferring lower elevation plant genotypes to higher elevation soil communities delayed foliar phenology, thereby shortening the growing season and reducing annual biomass production. Our findings show the importance of plant-soil interactions that help shape the timing of tree foliar phenology and productivity. Here, these geographic patterns in plant population x microbiome interactions also broaden our understanding of how soil communities impact plant phenotypic variation across key climate change gradients, with consequences for ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Differential Response of Bacterial Microdiversity to Simulated Global Change

Microbial communities play an integral role in global biogeochemical cycling, but our understanding of how global change will affect microbial community structure and functioning remains limited. Microbiome analyses typically aggregate large amounts of genetic diversity which may obscure finer variation in traits.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Testing the contribution of dispersal to microbial succession following a wildfire

ABSTRACT Given increased wildfire activity, there is growing interest in understanding the drivers of microbial succession after fire. Dispersal may be especially important to post-fire succession as biotic communities can be more susceptible to invasion following a disturbance. Here, we experimentally manipulated dispersal into disturbed leaf litter communities collected following a wildfire and tracked bacterial and fungal dispersal assemblages over time. We show that the identity and source of microbes immigrating into the soil surface post-fire change across time with seasonal shifts and the reemergence of aboveground vegetation. Further, dispersal significantly contributed to the reassembly of leaf litter microbial communities after the fire, producing an increasingly distinct assembly trajectory. The effect of dispersal on α-diversity and β-diversity was ecosystem dependent but, unexpectedly, influenced bacterial and fungal communities in a similar manner within ecosystems. Collectively, these results demonstrate that dispersal explicitly alters the course of microbial community succession following a wildfire and may impact bacteria and fungi in parallel ways, despite differing in traits expected to alter dispersal patterns. IMPORTANCE Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Macroecological distributions of gene variants highlight the functional organization of soil microbial systems

Abstract The recent application of macroecological tools and concepts has made it possible to identify consistent patterns in the distribution of microbial biodiversity, which greatly improved our understanding of the microbial world at large scales. However, the distribution of microbial functions remains largely uncharted from the macroecological point of view. Here, we used macroecological models to examine how the genes encoding the functional capabilities of microorganisms are distributed within and across soil systems. Models built using functional gene array data from 818 soil microbial communities showed that the occupancy-frequency distributions of genes were bimodal in every studied site, and that their rank-abundance distributions were best described by a lognormal model. In addition, the relationships between gene occupancy and abundance were positive in all sites. This allowed us to identify genes with high abundance and ubiquitous distribution (core) and genes with low abundance and limited spatial distribution (satellites), and to show that they encode different sets of microbial traits. Common genes encode microbial traits related to the main biogeochemical cycles (C, N, P and S) while rare genes encode traits related to adaptation to environmental stresses, such as nutrient limitation, resistance to heavy metals and degradation of xenobiotics. Overall, this study characterized for the first time the distribution of microbial functional genes within soil systems, and highlight the interest of macroecological models for understanding the functional organization of microbial systems across spatial scales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Population-level control of two manganese oxidases expands the niche for bacterial manganese biomineralization

Abstract The enzymatic oxidation of aqueous divalent manganese (Mn) is a widespread microbial trait that produces reactive Mn(III, IV) oxide minerals. These biominerals drive carbon, nutrient, and trace metal cycles, thus playing important environmental and ecological roles. However, the regulatory mechanisms and physiological functions of Mn biomineralization are unknown. This challenge arises from the common occurrence of multiple Mn oxidases within the same organism and the use of Mn oxides as indicators of combined gene activity. Through the detection of gene activation in individual cells, we discover that expression ofmnxGandmcoA, two Mn oxidase-encoding genes inPseudomonas putidaGB-1, is confined to subsets of cells within the population, with each gene showing distinct spatiotemporal patterns that reflect local microenvironments. These coordinated intra-population dynamics control Mn biomineralization and illuminate the strategies used by microbial communities to dictate the extent, location, and timing of biogeochemical transformations.

Biotechnology & Applied Microbiology↗
DOE OSTI2023

Quantitative, trait-based microbial ecology to accurately model the impacts of nitrogen deposition on soil carbon cycling in the Anthropocene (Final Technical Report)

Atmospheric nitrogen pollution has altered fundamental soil processes, challenging our understanding of the extent to which soils will continue to sequester carbon and slow the pace of future environmental change. While most evidence shows that increases in soil nitrogen have enhanced carbon storage in temperate forests, it remains unclear whether these effects will persist as nitrogen pollution continues to decline. Moreover, there remains uncertainty as to why some forests gain more carbon in response to nitrogen pollution than others. At the heart of this knowledge gap is a failure to link nitrogen–induced shifts in microbial biodiversity with gains or losses in their functional ability to decompose, assimilate, and ultimately stabilize soil carbon. Given that this uncertainty impedes the ability of predictive models to project future soil carbon stocks, there is a critical need to determine how key microbial traits drive soil carbon responses to nitrogen pollution. As such the goals of this project were to: (1) Quantify variation in taxon–specific and community–level microbial traits across gradients in microbial community composition, mycorrhizal symbioses, and nitrogen availability. (2) Integrate empirical data into a novel predictive framework that enhances our ability to project the regional soil carbon consequences of historical nitrogen pollution in temperate forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Climate-Driven Legacies in Simulated Microbial Communities Alter Litter Decomposition Rates

The mechanisms underlying diversity-functioning relationships have been a consistent area of inquiry in biogeochemistry since the 1950s. Though these mechanisms remain unresolved in soil microbiomes, many approaches at varying scales have pointed to the same notion—composition matters. Confronting the methodological challenge arising from the complexity of microbiomes, this study used the model DEMENTpy, a trait-based modeling framework, to explore trait-based drivers of microbiome-dependent litter decomposition. We parameterized DEMENTpy for five sites along a climate gradient in Southern California, United States, and conducted reciprocal transplant simulations analogous to a prior empirical study. The simulations demonstrated climate-dependent legacy effects of microbial communities on plant litter decomposition across the gradient. This result is consistent with the previous empirical study across the same gradient. An analysis of community-level traits further suggests that a 3-way tradeoff among resource acquisition, stress tolerance, and yield strategies influences community assembly. Simulated litter decomposition was predictable with two community traits (indicative of two of the three strategies) plus local environment, regardless of the system state (transient vs. equilibrium). Although more empirical confirmation is still needed, community traits plus local environmental factors (e.g., environment and litter chemistry) may robustly predict litter decomposition across spatial-temporal scales. In conclusion, this study offers a potential trait-based explanation for climate-dependent community effects on litter decomposition with implications for improved understanding of whole-ecosystem functioning across scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

The predictive power of phylogeny on growth rates in soil bacterial communities

Abstract Predicting ecosystem function is critical to assess and mitigate the impacts of climate change. Quantitative predictions of microbially mediated ecosystem processes are typically uninformed by microbial biodiversity. Yet new tools allow the measurement of taxon-specific traits within natural microbial communities. There is mounting evidence of a phylogenetic signal in these traits, which may support prediction and microbiome management frameworks. We investigated phylogeny-based trait prediction using bacterial growth rates from soil communities in Arctic, boreal, temperate, and tropical ecosystems. Here we show that phylogeny predicts growth rates of soil bacteria, explaining an average of 31%, and up to 58%, of the variation within ecosystems. Despite limited overlap in community composition across these ecosystems, shared nodes in the phylogeny enabled ancestral trait reconstruction and cross-ecosystem predictions. Phylogenetic relationships could explain up to 38% (averaging 14%) of the variation in growth rates across the highly disparate ecosystems studied. Our results suggest that shared evolutionary history contributes to similarity in the relative growth rates of related bacteria in the wild, allowing phylogeny-based predictions to explain a substantial amount of the variation in taxon-specific functional traits, within and across ecosystems.

Walkup, Jeth (ORCID:0000000279082963)↗
DOE OSTI2020

Microbial macroecology: In search of mechanisms governing microbial biogeographic patterns

Abstract Introduction Rapidly advancing technologies and accumulating information about microbial communities across the globe allow the quantification of microbial properties and functions at a macro‐scale. These emerging microbial biogeographic patterns call for a practical macroecological approach to investigate their underlying mechanisms. Aims The primary aims of this paper are to review the advancements of microbial macroecology in seeking mechanisms governing microbial biogeographic patterns, and to further lay out a roadmap for microbial macroecology in 10 years. Methods We reviewed the progress of microbial macroecology and demonstrated the application of the microbial macroecological approach to microbial biogeographic patterns with three case studies. Results Microbial macroecology provides a platform for understanding microbial abundance, community structure, and functioning across space, time, and taxonomic hierarchy. It emphasizes the integral effects of environmental filtering, microbial responses, diversification, dispersal, and local extinction that drive the microbial biogeographic patterns. The microbial macroecological approach emphasizes the last two stages of the four‐stage scientific method applied to microbial ecology: (a) describing microbial traits across scales to reveal patterns, (b) mathematically representing these patterns, (c) developing and testing conceptual models to build a mechanistic understanding of these patterns from a macroecological perspective, (d) plugging the new knowledge into the theoretical advancements. Three case studies were used to demonstrate the microbial macroecological approach for understanding the global patterns of microbial biomass carbon, microbial composition (fungi : bacteria ratio), and microbial carbon use efficiency. Conclusions Microbial macroecology offers a platform for understanding the mechanisms that drive biogeographic patterns of microbial abundance, diversity and functions. It is likely that these patterns and mechanisms will be increasingly incorporated into predictive models that link climate, carbon dynamics, and biogeochemical processes. A roadmap is outlined for the growing microbial macroecology field; we expect significant progress will be made in five research directions over the next 10 years.

Xu, Xiaofeng↗
DOE OSTI2024

Multiplex characterization of microbial traits using dual barcoded nucleic acid fragment expression library

Disclosed herein are barcoded expression libraries comprising a plurality of expression vectors, wherein each expression vector comprises a nucleic acid fragment flanked by a first barcode and a second barcode. Further disclosed herein are methods of making the barcoded expression libraries and methods of conducting functional analysis using the barcoded expression libraries.

Mutalik, Vivek K.↗
DOE OSTI2021

Trade-Offs Between Growth Rate and Other Fungal Traits

If we better understand how fungal responses to global change are governed by their traits, we can improve predictions of fungal community composition and ecosystem function. Specifically, we can examine trade-offs among traits, in which the allocation of finite resources toward one trait reduces the investment in others. We hypothesized that trade-offs among fungal traits relating to rapid growth, resource capture, and stress tolerance sort fungal species into discrete life history strategies. We used the Biolog Filamentous Fungi database to calculate maximum growth rates of 37 fungal species and then compared them to their functional traits from the fun fun database. In partial support of our hypothesis, maximum growth rate displayed a negative relationship with traits related to resource capture. Moreover, maximum growth rate displayed a positive relationship with amino acid permease, forming a putative Fast Growth life history strategy. A second putative life history strategy is characterized by a positive relationship between extracellular enzymes, including cellobiohydrolase 6, cellobiohydrolase 7, crystalline cellulase AA9, and lignin peroxidase. These extracellular enzymes were negatively related to chitosanase 8, an enzyme that can break down a derivative of chitin. Chitosanase 8 displayed a positive relationship with many traits that were hypothesized to cluster separately, forming a putative Blended life history strategy characterized by certain resource capture, fast growth, and stress tolerance traits. These trait relationships complement previously explored microbial trait frameworks, such as the Competitor-Stress Tolerator-Ruderal and the Yield-Resource Acquisition-Stress Tolerance schemes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Data from TropiRoot 1.0 database: tropical root characteristics across environments

TropiRoot 1.0 is a new tropical root database with root characteristics across environment gradients. It has 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 includes root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology and root chemistry. This initiative represents an approximately 30% increase in the currently available data for tropical roots in the Fine Root Ecology Database (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 was available, including soil data, these data was either extracted and included in the database or their 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 the ones 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.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

59 BASIC BIOLOGICAL SCIENCES↗