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All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance

Abstract Background Microbe-microbe interactions between members of the plant rhizosphere are important but remain poorly understood. A more comprehensive understanding of the molecular mechanisms used by microbes to cooperate, compete, and persist has been challenging because of the complexity of natural ecosystems and the limited control over environmental factors. One strategy to address this challenge relies on studying complexity in a progressive manner, by first building a detailed understanding of relatively simple subsets of the community and then achieving high predictive power through combining different building blocks (e.g., hosts, community members) for different environments. Herein, we coupled this reductionist approach with high-resolution mass spectrometry-based metaproteomics to study molecular mechanisms driving community assembly, adaptation, and functionality for a defined community of ten taxonomically diverse bacterial members of Populus deltoides rhizosphere co-cultured either in a complex or defined medium. Results Metaproteomics showed this defined community assembled into distinct microbiomes based on growth media that eventually exhibit composition and functional stability over time. The community grown in two different media showed variation in composition, yet both were dominated by only a few microbial strains. Proteome-wide interrogation provided detailed insights into the functional behavior of each dominant member as they adjust to changing community compositions and environments. The emergence and persistence of select microbes in these communities were driven by specialization in strategies including motility, antibiotic production, altered metabolism, and dormancy. Protein-level interrogation identified post-translational modifications that provided additional insights into regulatory mechanisms influencing microbial adaptation in the changing environments. Conclusions This study provides high-resolution proteome-level insights into our understanding of microbe-microbe interactions and highlights specialized biological processes carried out by specific members of assembled microbiomes to compete and persist in changing environmental conditions. Emergent properties observed in these lower complexity communities can then be re-evaluated as more complex systems are studied and, when a particular property becomes less relevant, higher-order interactions can be identified.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Filling gaps in our understanding of belowground plant traits across the world: an introduction to a Virtual Issue

The belowground world is one of the final frontiers in terrestrial ecology. The tangling of plant roots with the surrounding soil below is a lifeline for the humble forbs and towering trees above, and roots play a key role in shaping ecosystem carbon, water and nutrient cycling (Bardgett et al., 2014). Ecologists have long sought to better understand the ecosystem-scale consequences of differing plant strategies, above- and belowground, by relating plant characteristics, or traits, to plant function (Grime, 1977; Pregitzer, 2002). While developing trait–function linkages is arguably more difficult for plant traits that are hidden belowground, root and rhizosphere ecologists continue to fan out across grasslands and forests with their shovels, isotopes, and specialized cameras, seeking a better understanding of the secret lives of roots. Over the years, New Phytologist has served as a virtual town square for scientists to discuss their hard-won observations on the interplay among belowground plant traits, microbial activity, and edaphic and environmental conditions from biomes around the world (Norby & Jackson, 2000; Pregitzer, 2002; Matamala & Stover, 2013; Norby & Iversen, 2017). In this Editorial we highlight the newest papers that update and add to our understanding of the role of root and rhizosphere traits in broader ecosystem processes. We focused on papers published in New Phytologist between 1 January 2019 and 31 December 2020 and extended this window to papers still in ‘early view’ up to the time of writing. Because of the overwhelming number of papers, we did not include those with a decidedly genomic focus or that served primarily as data syntheses, reviews, insights or commentaries.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome

Microbiomes are important contributors to many ecosystems, including ones where nutrient cycling is stimulated by aeration control. Optimizing cyclic aeration helps reduce energy needs and maximize microbiome performance during wastewater treatment; however, little is known about how most microbial community members respond to these alternating conditions.

transcription factors↗
DOE OSTI2025

Data from a throughfall exclusion experiment: Fine root dynamics, morphology, chemistry, and AMF colonization across four lowland Panamanian forests

Fine roots regulate forest nutrient, carbon, and water cycling, yet their variation within and among tropical forests remains under-characterized. We quantified root productivity, disappearance, and stocks to 1 m using minirhizotron imaging, and we measured morphology, elemental composition [root carbon (C), root nitrogen (N), root phosphorus (P)], and arbuscular mycorrhizal fungi (AMF) colonization to 20 cm using ingrowth cores and sequential coring. Sampling took place in four distinct lowland Panamanian forests (32 plots; 8 per forest) from 2018 through 2022 under control and throughfall-exclusion (drought) treatments in the Panama Rainforest Changes with Experimental Drying (PARCHED) experiment.The dataset is presented as an Excel workbook with six tabs. The first tab is the data dictionary. Tab S1 contains ingrowth-core production and mortality, morphology and soil moisture. Tab S2 contains sequential-coring standing stocks with associated morphology and soil moisture. Tab S3 contains minirhizotron row data records to 1 m depth, including per-frame root length and diameter, normalized length metrics, and session timing. Tab S4 contains AMF colonization. Tab S5 contains fine-root chemistry at 0–10 cm, reporting %P, %C, %N, and C:N for samples collected via ingrowth cores and sequential-coring standing stocks. CSV mirrors for each tab are provided, and a KML file supplies coordinates for all 32 plots.Key variables span live and dead fine-root biomass (and coarse fractions where applicable), specific root length (SRL) and area (SRA), diameter, root tissue density (RTD), soil moisture, AMF colonization, root %N, %C, %P, and C:N, along with minirhizotron root length and diameter. Depth, season, treatment, and plot/site identifiers are included to support cross-tab integration and analysis from 0–100 cm (minirhizotron) and 0–20 cm (cores).Units are reported in-column and missing values are coded as NA. No special software is required to open or use the files (Excel, CSV, and KML compatible).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Community response of soil microorganisms to combined contamination of polycyclic aromatic hydrocarbons and potentially toxic elements in a typical coking plant

Both polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) of coking industries impose negative effects on the stability of soil ecosystem. Soil microbes are regarded as an essential moderator of biochemical processes and soil remediation, while their responses to PAHs-PTEs combined contamination are largely unknown. In the present study, soil microbial diversity and community composition in the typical coking plant under the chronic co-exposure of PAHs and PTEs were investigated and microbial interaction networks were built to reveal microbial co-occurrence patterns. The results indicated that the concentrations of PAHs in the soil inside the coking plant were significantly higher than those outside the plant. The mean concentration of ∑16PAHs was 2894.4 ng·g −1 , which is 5.58 times higher than that outside the plant. The average Hg concentration inside the coking plant was 22 times higher than the background value of Hebei province. The soil fungal community inside the coking plant showed lower richness compared with that of outside community, and there are significant difference in the bacterial and fungal community composition between inside and outside of coking plant ( p < 0.01). Predicted contribution of different environmental factors to each dominant species based on random forest identified 20 and 25 biomarkers in bacteria and fungi, respectively, that were highly sensitive to coking plant soil in operation, such as Betaproteobacteria，Sordariomycetes and Dothideomycetes . Bacterial and fungal communities were shaped by the soil chemical properties (pH), PTEs (Hg), and PAHs together in the coking plant soils. Furthermore, the bacterial and fungal interaction patterns were investigated separately or jointly by intradomain and interdomain networks. Competition is the main strategy based on the co-exclusion pattern in fungal community, and the competitive relationship inside the coking plant is more complex than that outside the plant. In contrast, cooperation is the dominant strategy in bacterial networks based on the co-occurrence pattern. The present study provided insights into microbial response strategies and the interactions between bacteria and fungi under long-term combined contamination.

Shen, Qihui↗
DOE OSTI2021

Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition

Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800–3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2–3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. Furthermore, during a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Correlative Surface Imaging Reveals Chemical Signatures for Bacterial Hotspots on Plant Roots

The rhizosphere is arguably the most complex microbial habitat on earth, comprising an integrated network of plant roots, soil and a highly diverse microbial community (the rhizosphere microbiome)1. Understanding, predicting and controlling plant-microbe interactions in the rhizosphere will allow us to harness the plant microbiome as a means to increase or restore plant ecosystem productivity, improve plant responses to a wide range of environmental perturbations, and mitigate effects of climate change by designing ecosystems for long-term soil carbon storage1. To this end, it is imperative to develop new molecular approaches with high spatial resolution to capture interactions at the plant-microbe, microbe-microbe, and plant-plant interfaces. In this work, we designed an imaging sample holder that allows integrated surface imaging tools to map the same locations of a plant root-microbe interface with submicron lateral resolutions, providing novel in vivo analysis of root-microbe interactions. Specifically, confocal fluorescence microscopy, time-of-flight secondary ion mass spectrometry (ToF-SIMS), X-ray photoelectron spectroscopy (XPS), and scanning electron microscope (SEM) were used for the first time for correlative imaging of the Brachypodium distachyon root and its interaction with Pseudomonas SW25, a typical plant growth-promoting soil bacterium. Imaging data suggest that the root surface is inhomogeneous and that the interaction between Pseudomonas and Brachypodium roots was confined to only few spots along the sampled root segments and that the bacterial attachment spots were enriched in Na- and S-related and high-mass organic species. We conclude that attachment of the Pseudomonas cells to the root surface is outcompeted by strong root-soil mineral interactions but facilitated by formation of extracellular polymeric substances (EPS).

Plant root, Plant growth-promoting bacteria, soil,↗
DOE OSTI2021

Experimental warming and its legacy effects on root dynamics following two hurricane disturbances in a wet tropical forest

Abstract Tropical forests are expected to experience unprecedented warming and increases in hurricane disturbances in the coming decades; yet, our understanding of how these productive systems, especially their belowground component, will respond to the combined effects of varied environmental changes remains empirically limited. Here we evaluated the responses of root dynamics (production, mortality, and biomass) to soil and understory warming (+4°C) and after two consecutive tropical hurricanes in our in situ warming experiment in a tropical forest of Puerto Rico: Tropical Responses to Altered Climate Experiment (TRACE). We collected minirhizotron images from three warmed plots and three control plots of 12 m 2 . Following Hurricanes Irma and María in September 2017, the infrared heater warming treatment was suspended for repairs, which allowed us to explore potential legacy effects of prior warming on forest recovery. We found that warming significantly reduced root production and root biomass over time. Following hurricane disturbance, both root biomass and production increased substantially across all plots; the root biomass increased 2.8‐fold in controls but only 1.6‐fold in previously warmed plots. This pattern held true for both herbaceous and woody roots, suggesting that the consistent antecedent warming conditions reduced root capacity to recover following hurricane disturbance. Root production and mortality were both related to soil ammonium nitrogen and microbial biomass nitrogen before and after the hurricanes. This experiment has provided an unprecedented look at the complex interactive effects of disturbance and climate change on the root component of a tropical forested ecosystem. A decrease in root production in a warmer world and slower root recovery after a major hurricane disturbance, as observed here, are likely to have longer‐term consequences for tropical forest responses to future global change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Life history strategies among soil bacteria—dichotomy for few, continuum for many

Abstract Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O–H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms’ joint 18O–13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2012

Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of previously "shadowed" less abundant species available for PCR amplification. These PCR products obtained with and without PMA treatment will then be subjected to downstream diversity analyses such as sequencing and DNA microarray. It is expected that PMA-coupled PCR will amplify the "minority population" and help in understanding microbial diversity spectrum of an environmental sample at a much deeper level. This new protocol aims to overcome the major potential biases faced when analyzing microbial 16S rRNA gene diversity. This study will lead to a technological advancement and a commercial product that will aid microbial ecologists in understanding microbial diversity from various environmental niches. Implementation of this technique may lead to discoveries of novel microbes and their functions in sustenance of the ecosystem.

Vaishampayan, Parag A.↗
DOE OSTI2024

Functional insights of novel Bathyarchaeia reveal metabolic versatility in their role in peatlands of the Peruvian Amazon

ABSTRACT The decomposition of soil organic carbon within tropical peatlands is influenced by the functional composition of the microbial community. In this study, building upon our previous work, we recovered a total of 28 metagenome-assembled genomes (MAGs) classified as Bathyarchaeia from the tropical peatlands of the Pastaza-Marañón Foreland Basin (PMFB) in the Amazon. Using phylogenomic analyses, we identified nine genus-level clades to have representatives from the PMFB, with four forming a putative novel family (“CandidatusPaludivitaceae”) endemic to peatlands. We focus on theCa. Paludivitaceae MAGs due to the novelty of this group and the limited understanding of their role within tropical peatlands. Functional analysis of these MAGs reveals that this putative family comprises facultative anaerobes, possessing the genetic potential for oxygen, sulfide, or nitrogen oxidation. This metabolic versatility can be coupled to the fermentation of acetoin, propanol, or proline. The other clades outsideCa. Paludivitaceae are putatively capable of acetogenesis andde novoamino acid biosynthesis and encode a high amount of Fe 3+ transporters. Crucially, theCa. Paludivitaceae are predicted to be carboxydotrophic, capable of utilizing CO for energy generation or biomass production. Through this metabolism, they could detoxify the environment from CO, a byproduct of methanogenesis, or produce methanogenic substrates like CO 2 and H 2 . Overall, our results show the complex metabolism and various lineages of Bathyarchaeia within tropical peatlands pointing to the need to further evaluate their role in these ecosystems. IMPORTANCE With the expansion of theCandidatusPaludivitaceae family by the assembly of 28 new metagenome assembled genomes, this study provides novel insights into their metabolic diversity and ecological significance in peatland ecosystems. From a comprehensive phylogenic and functional analysis, we have elucidated their putative unique facultative anaerobic capabilities and CO detoxification potential. This research highlights their crucial role in carbon cycling and greenhouse gas regulation. These findings are essential for resolving the microbial processes affecting peat soil stability, offering new perspectives on the ecological roles of previously underexplored and underrepresented archaeal populations.

Microbiology↗
DOE OSTI2021

Ecological stoichiometry as a foundation for omics-enabled biogeochemical models of soil organic matter decomposition

Coupled biogeochemical cycles drive ecosystem ecology by influencing individual-to-community scale behaviors; yet the development of process-based models that accurately capture these dynamics remains elusive. Soil organic matter (SOM) decomposition in particular is influenced by resource stoichiometry that dictates microbial nutrient acquisition (‘ecological stoichiometry’). Despite its basis in biogeochemical modeling, ecological stoichiometry is only implicitly considered in high-resolution microbial investigations and the metabolic models they inform. State-of-science SOM decomposition models in both fields have advanced largely separately, but they agree on a need to move beyond seminal pool-based models. This presents an opportunity and a challenge to maximize the strengths of various models across different scales and environmental contexts. To address this challenge, we contend that ecological stoichiometry provides a framework for merging biogeochemical and microbiological models, as both explicitly consider substrate chemistries that are the basis of ecological stoichiometry as applied to SOM decomposition. We highlight two gaps that limit our understanding of SOM decomposition: (1) understanding how individual microorganisms alter metabolic strategies in response to substrate stoichiometry and (2) translating this knowledge to the scale of biogeochemical models. We suggest iterative information exchange to refine the objectives of high-resolution investigations and to specify limited dynamics for representation in large-scale models, resulting in a new class of omics-enabled biogeochemical models. Assimilating theoretical and modelling frameworks from different scientific domains is the next frontier in SOM decomposition modelling; advancing technologies in the context of stoichiometric theory provides a consistent framework for interpreting molecular data, and further distilling this information into tractable SOM decomposition models.

Carbon cycling↗
DOE OSTI2023

Sticky roots--implications of widespread, cryptic, viral infection of plants in natural and managed ecosystems for soil carbon processing in the rhizosphere

Plants strongly influence soil properties through rhizodeposition, in which exudates diffuse from roots, additional secretions are actively released, and root cells are sloughed into the soil. This contribution by plants of carbon compounds belowground is at the core of soil health, water holding capacity, and the soil carbon storage that pulls carbon dioxide out of the atmosphere. Once in soil, organic matter can bind with minerals such as iron hydroxides, where it can be protected from microbial attack for millenia, preserving very large terrestrial soil carbon pools. However, those same compounds contributed by roots to soil may also destabilize the long-term protective associations of SOM with minerals, making that soil organic matter (SOM) more vulnerable to microbial attack and decomposition. Plant roots thus influence both the buildup and breakdown of soil carbon pools. DOE’s E3SM Land Model (ELM) includes a representation of soil carbon storage on minerals, but the potential vulnerability of SOM–mineral associations to effects of rhizodeposition is not yet represented in ELM. To begin testing for this effect of rhizodeposition on soil carbon storage and decomposition, we worked to develop a novel approach during this TES Exploratory project DE-SC0019142 – we harnessed the power of plant viral infection. We examined whether plant virus infection can serve as a tool to intensify rhizodeposition at the root surface, and therefore possibly intensify mobilization of SOM from minerals making it visible to our analytical techniques. Viral infection is widespread in terrestrial ecosystems; 25-70% of plants have virus infection, yet the influence of such infection on root traits and terrestrial soil carbon dynamics remains largely unexplored. We used two plant hosts: the annual Avena sativa (oats) and the genetically tractable, model grass Brachypodium distachyon. These grasses were infected with the broad host range virus Barley Yellow Dwarf Virus (BYDV) via aphids (Rhopalosiphum padi). BYDV infects at least 150 grass species in agricultural and natural ecosystems, and in previous experiments, oats infected with BYDV had roots that were very sticky to the touch, strongly suggesting that infection altered rhizodeposition. We developed this new experimental approach mostly in a one virus (Barley Yellow Dwarf Virus)–one plant (Avena sativa) system. (Several effects of infection in a Brachypodium-BYDV system were similar in nature to effects on Avena sativa, but were more variable.) In the BYDV-Avena system, we developed protocols for consistently infecting target plants (and avoiding infection of control plants) using aphid caging on leaves. We measured that infected plants exhibited reduced photosynthesis, plant (including root) biomass, and root:shoot ratio, as well as simplified root system architecture. We established procedures for sampling the organic compounds carried specifically in phloem (vascular tissue) of leaves and roots, using aphid stylectomy. We used FTICR-MS, Orbitrap GC-MS, and LC-MS/MS to analyze organic compounds in phloem, liquid around roots of plants grown hydroponically, and pore water around roots in soil, and found differences in the compounds in solution bathing roots when infected and uninfected plants were grown hydroponically. Finally, we synthesized isotopically-labeled mineral–organic matter (MAOM) associations in the lab and developed assays using them in solution and in soil. Assays quantified the extent and rate of mineralization of labeled MAOM that was mobilized by functionally distinct rhizodeposits and then attacked by microbes. Two mechanisms for MAOM mobilization emerged, with distinct dynamics. During “direct” mobilization, rhizodeposits such as the strong ligand oxalic acid could drive rapid dissolution of minerals, mobilizing MAOM. During “indirect” mobilization, rhizodeposits such as the simple sugar glucose did not attack minerals directly but instead intensified microbial activity, which led to mobilization via changes in e.g. pH, Eh, and microbial metabolite production (Li et al. 2021). Mechanistic understanding derived from these data and our ongoing experiments using these techniques will inform future development of ELM. Plant roots not only contribute newly fixed organic compounds to soils, but also root activities can drive mineralization of the carbon and nutrients mobilized off minerals via “indirect” or “direct” mechanisms. Using viral infection as a new tool, ongoing combined experimentation and modeling will explore the strength and larger-scale significance of the cascade of processes from rhizodeposition to MAOM mobilization for soil carbon storage and nutrient cycling in terrestrial ecosystems. And if viral infection leads quite generally to “sticky roots”, our perception of the potential importance of prevalent virus infection in terrestrial landscapes will be transformed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Microbial dispersal into surface soil is limited on a meter scale

Abstract Dispersal shapes microbial communities, yet it is largely unknown how fast or how far free-living microorganisms move in the environment. Here, we deployed microbial traps along transects spanning a grassland and neighboring shrubland to quantify the rate and distance at which microorganisms disperse into the soil surface. We found that bacteria disperse at a similar rate across the two ecosystems, and both bacteria and fungi exhibit a signature of dispersal limitation at a meter scale, indicating highly heterogeneous dispersal of microorganisms into soil.

Environmental Sciences & Ecology↗
DOE OSTI2021

Permafrost thaw driven changes in hydrology and vegetation cover increase trace gas emissions and climate forcing in Stordalen Mire from 1970 to 2014

Permafrost thaw increases active layer thickness, changes landscape hydrology and influences vegetation species composition. These changes alter belowground microbial and geochemical processes, affecting production, consumption and net emission rates of climate forcing trace gases. Net carbon dioxide (CO 2 ) and methane (CH 4 ) fluxes determine the radiative forcing contribution from these climate-sensitive ecosystems. Permafrost peatlands may be a mosaic of dry frozen hummocks, semi-thawed or perched sphagnum dominated areas, wet permafrost-free sedge dominated sites and open water ponds. We revisited estimates of climate forcing made for 1970 and 2000 for Stordalen Mire in northern Sweden and found the trend of increasing forcing continued into 2014. The Mire continued to transition from dry permafrost to sedge and open water areas, increasing by 100% and 35%, respectively, over the 45-year period, causing the net radiative forcing of Stordalen Mire to shift from negative to positive. This trend is driven by transitioning vegetation community composition, improved estimates of annual CO 2 and CH 4 exchange and a 22% increase in the IPCC's 100-year global warming potential (GWP_100) value for CH 4 . These results indicate that discontinuous permafrost ecosystems, while still remaining a net overall sink of C, can become a positive feedback to climate change on decadal timescales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Lost and Found: Rediscovering Microbiome-Associated Phenotypes that Reshape Agricultural Sustainability

Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification—key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. Our findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture. ---- These maize root exduate metabolomics data are a subset of this larger project and make up a phenotyping for candidate lines.

Favela, Alonso [School of Plant Sciences, Universi↗
DOE OSTI2021

Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column

The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because of their immense metabolic and ecological potential. To obtain a comprehensive understanding on this aspect, we previously reported on the isolation and preliminary genomic characterization of three Pseudomonas species isolated from minced oyster tissue (P. alcaligenes strain OT69); oyster mantle fluid (P. stutzeri strain MF28) and the water collected from top of the oyster reef (P. aeruginosa strain WC55), respectively. In this comparative genomic analysis study conducted on these three targeted pseudomonads, native to the eastern oyster and its surrounding environment, provided further insights into their unique functional traits, conserved gene pools between the selected pseudomonads, as well as genes that render unique characteristics in context to metabolic traits recruited during their evolutionary history via horizontal gene transfer events as well as phage-mediated incorporation of genes. Moreover, the strains also supported extensively developed resistomes, which suggests that environmental microorganisms native to relatively pristine environments, such as Apalachicola Bay, Florida, have also recruited an arsenal of antibiotic resistant gene determinants, thus posing an emerging public health concern.

Pathak, Ashish↗
NASA NTRS1986

The ecology of microorganisms in a small closed system: Potential benefits and problems for space station

The inevitble presence on the space station of microorganisms associated with crew members and their environment will have the potential for both benefits and a range of problems including illness and corrosion of materials. This report reviews the literature presenting information about microorganisms pertinent to Environmental Control and Life Support (ECLS) on the space station. The perspective of the report is ecological, viewing the space station as an ecosystem in which biological relationships are affected by factors such as zero gravity and by closure of a small volume of space. Potential sites and activities of microorganisms on the space station and their environmental limits, microbial standards for the space station, monitoring and control methods, effects of space factors on microorganisms, and extraterrestrial contamination are discussed.

Rodgers, E. B.↗