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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Uncovering the dominant role of root metabolism in shaping rhizosphere metabolome under drought in tropical rainforest plants

Plant-soil-microbe interactions are crucial for driving rhizosphere processes that contribute to metabolite turnover and nutrient cycling. With the increasing frequency and severity of water scarcity due to climate warming, understanding how plant-mediated processes, such as root exudation, influence soil organic matter turnover in the rhizosphere is essential. In this study, we used 16S rRNA gene amplicon sequencing, rhizosphere metabolomics, and position-specific 13 C-pyruvate labeling to examine the effects of three different plant species (Piper auritum, Hibiscus rosa sinensis, and Clitoria fairchildiana) and their associated microbial communities on soil organic carbon turnover in the rhizosphere. Here, our findings indicate that in these tropical plants, the rhizosphere metabolome is primarily shaped by the response of roots to drought rather than direct shifts in the rhizosphere bacterial community composition. Specifically, the reduced exudation of plant roots had a notable effect on the metabolome of the rhizosphere of P. auritum, with less reliance on neighboring microbes. Contrary to P. auritum, H. rosa sinensis and C. fairchildiana experienced changes in their exudate composition during drought, causing alterations to the bacterial communities in the rhizosphere. This, in turn, had a collective impact on the rhizosphere's metabolome. Furthermore, the exclusion of phylogenetically distant microbes from the rhizosphere led to shifts in its metabolome. Additionally, C. fairchildiana appeared to be associated with only a subset of symbiotic bacteria under drought conditions. These results indicate that plant species-specific microbial interactions systematically change with the root metabolome. As roots respond to drought, their associated microbial communities adapt, potentially reinforcing the drought tolerance strategies of plant roots. These findings have significant implications for maintaining plant health and preference during drought stress and improving plant performance under climate change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2000

Dynamics of Molecular Hydrogen in Hypersaline Microbial Mars

Early Earth microbial communities that centered around the anaerobic decomposition of organic molecular hydrogen as a carrier of electrons, regulator of energy metabolism, and facilitator of syntroph'c microbial interactions. The advent of oxygenic photosynthetic organisms added a highly dynamic and potentially dominant term to the hydrogen economy of these communities. We have examined the daily variations of hydrogen concentrations in cyanobacteria-dominated microbial mats from hypersaline ponds in Baja California Sur, Mexico. These mats bring together phototrophic and anaerobic bacteria (along with virtually all other trophic groups) in a spatially ordered and chemically dynamic matrix that provides a good analog for early Earth microbial ecosystems. Hydrogen concentrations in the photic zone of the mat can be three orders of magnitude or more higher than in the photic zone, which are, in turn, an order of magnitude higher than in the unconsolidated sediments underlying the mat community. Within the photic zone, hydrogen concentrations can fluctuate dramatically during the diel (24 hour day-night) cycle, ranging from less than 0.001% during the day to nearly 10% at night. The resultant nighttime flux of hydrogen from the mat to the environment was up to 17% of the daytime oxygen flux. The daily pattern observed is highly dependent on cyanobacterial species composition within the mat, with Lyngbya-dominated systems having a much greater dynamic range than those dominated by Microcoleus; this may relate largely to differing degrees of nitrogen-fixing and fermentative activity in the two mats. The greatest H2 concentrations and fluxes were observed in the absence of oxygen, suggesting an important potential feedback control in the context of the evolution of atmospheric composition. The impact of adding this highly dynamic photosynthetic term to the hydrogen economy of early microbial ecosystems must have been substantial. From an evolutionary standpoint, the H2 generated in mats could have represented a very important new source of electrons and energy - but one that could not be harnessed without substantial adaptation to the highly variable chemistry of the mat surface. In addition, the emergent chemistry of anaerobic communities is often highly dependent on ambient hydrogen concentrations, so that incorporation of these communities into photosynthetic mats could have significantly affected the composition and flux of reduced "biosignature' gases to the environment.

Hoehler, Tori M.↗
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↗
NASA NTRS2004

Microbial Characterization and Comparison of Isolates During the Mir and ISS Missions

Spacecraft represent a semi-closed ecosystem that provides a unique model of microbial interaction with other microbes, potential hosts, and their environment. Environmental samples from the Mir Space Station (1995-1998) and the International Space Station (ISS) (2000-Present) were collected and processed to provide insight into the characterization of microbial diversity aboard spacecraft over time and assess any potential health risks to the crew. All microbiota were isolated using standard media-based methodologies. Isolates from Mir and ISS were processed using various methods of analysis, including VITEK biochemical analysis, 16s ribosomal identification, and fingerprinting using rep-PCR analysis. Over the first 41 months of habitation, the diversity of the microbiota from air and surface samples aboard ISS increased from an initial six to 53 different bacterial species. During the same period, fungal diversity increased from 2 to 24 species. Based upon rep-PCR analysis, the majority of isolates were unique suggesting the need for increased sampling frequency and a more thorough analysis of samples to properly characterize the ISS microbiota. This limited fungal and bacterial data from environmental samples acquired during monitoring currently do not indicate a microbial hazard to ISS or any trends suggesting potential health risks.

Fontenot, Sondra L.↗
DOE OSTI2022

High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

We present Microbe-seq, a high-throughput single-microbe method that yields strain-resolved genomes from complex microbial communities. We encapsulate individual microbes into droplets with microfluidics and liberate their DNA, which we amplify, tag with droplet-specific barcodes, and sequence. We use Microbe-seq to explore the human gut microbiome; we collect stool samples from a single individual, sequence over 20,000 microbes, and reconstruct nearly-complete genomes of almost 100 bacterial species, including several with multiple subspecies strains. We use these genomes to probe genomic signatures of microbial interactions: we reconstruct the horizontal gene transfer (HGT) network within the individual and observe far greater exchange within the same bacterial phylum than between different phyla. We probe bacteria-virus interactions; unexpectedly, we identify a significant in vivo association between crAssphage, an abundant bacteriophage, and a single strain of Bacteroides vulgatus. Microbe-seq contributes high-throughput culture-free capabilities to investigate genomic blueprints of complex microbial communities with single-microbe resolution.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2014

Spaceflight Microbiology: Benefits for Long Duration Spaceflight and Our Understanding of Microorganisms on Earth

Spaceflight microbiology is composed of both operational and experimental components that complement each other in our understanding of microbial interactions and their responses in the microgravity of spaceflight. Operationally, efforts to mitigate microbiological risk to the crew and the spacecraft have historically focused on minimizing the number of detectable organisms, relying heavily on preventative measures, including appropriate vehicle design, crew quarantine prior to flight, and stringent microbial monitoring. Preflight monitoring targets have included the astronauts, spaceflight foods, potable water systems, the vehicle air and surfaces, and the cargo carried aboard the spacecraft. This approach has been very successful for earlier missions; however, the construction and long-term habitation of the International Space Station (ISS) has created the need for additional inflight monitoring of the environment and potable water systems using hardware designed for both in-flight microbial enumeration and sample collection and return to Earth. In addition to operational activities, the ISS is providing a research platform to advance our understanding of microbiomes in the built environment. Adding to the research possibilities of this system are multiple reports of unique changes in microbial gene expression and phenotypic responses, including virulence and biofilm formation, in response to spaceflight culture. The tremendous potential of the ISS research platform led the National Research Council to recommend that NASA utilize the ISS as a microbial observatory. Collectively, the findings from operational and research activities on the ISS are expected to both enable future space exploration and translate to basic and applied research on Earth.

Ott, C. Mark↗
DOE OSTI2025

Root exudate lipids: Uncovering chemodiversity and carbon stability potential

Root-derived carbon has been shown to contribute more to soil carbon stocks than aboveground litter. Yet the molecular chemodiversity of root exudates remains poorly understood due to limited characterization and annotation. In this study, we characterized the molecular chemodiversity and production of metabolites and lipids in root exudates from field grown mature tall wheatgrass (Thinopyrum ponticum). We discovered a diversity of lipids, including substantial levels of triacylglycerols (∼19 μg/g fresh root per min), fatty acyls, sphingolipids, sterol lipids, and glycerophospholipids, some of which have not been previously documented in root exudates. By integrating tandem mass spectral library searching and deep learning-based chemical class assignment, our metabo-lipidomics approach significantly expanded the known molecular diversity of root exudates. Rates of lipid derived carbon production were approximately double that of polar metabolites (lipids: 81.52 ± 13.81 vs polar metabolites: 38.41 ± 5.93 μg C g −1 fresh root mass min −1 ) with an order of magnitude higher carbon to nitrogen ratios (lipids: 459 ± 90 vs polar metabolites: 14.40 ± 0.58). Exudate lipids displayed highly negative nominal oxidation state of carbon (−1.182 to −1.909), indicating that these compounds may be less favorable for microbial decomposition. Together our results suggest the potential of root exudate lipids to contribute to stable carbon pools in soil, supporting long-term carbon storage. This work advances understanding of plant-derived lipid inputs to soil and underscores the need for future studies on the functional roles of lipids in shaping root-microbe-soil interactions, microbial activity, soil structure, and nutrient availability – contributing to soil health.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The quality of organic amendments affects soil microbiome and nitrogen-cycling bacteria in an organic farming system

Organic amendments are applied in organic farming systems to provide nutrients for crop uptake and to improve soil health. Compost is often favored over fresh manure for food safety reasons, while fresh manure can be a valuable source of readily available nitrogen (N). However, the potential for fresh versus composted manure to differentially affect soil microbial and N-cycling functional communities over multiple seasons remains unknown. We compared the effect of composted vs. fresh cattle manure on soil microbial communities using taxonomic and functional approaches. Soils were collected from field plots with three organic N treatments: control (no amendment), composted manure (compost, 224 kg/ha total N), and fresh manure (manure, 224 kg/ha total N) in an organic production system. Illumina amplicon sequencing was used to comprehensively assess the bacterial community (16S rRNA genes), fungal community (ITS), ureolytic community ( ureC ), chitinolytic community ( chiA ), bacterial ammonia oxidizers (AOB amoA ), and nitrite oxidizers ( Nitrospira nxrB ). The results showed that both compost and manure treatment significantly changed the soil microbial communities. Manure had a stronger effect than compost on soil bacterial and fungal community composition, as well as on the ureolytic and chitinolytic communities, while compost treated soils had higher microbial richness than manure treated soils. Both taxonomic and functional approaches showed that the microbial community was more responsive to fresh manure than to compost. Manure treated soil also had more complex microbial interactions than compost treated soil. The abundance and community composition of N-cycling functional groups often played more limited roles than soil chemical properties (soil organic carbon, extractable organic carbon, and pH) in driving N-cycling processes. Results from our study may guide strategies for the management of organic amendments in organic farming systems and provide insights into the linkages between soil microbial communities and soil function.

Ouyang, Yang↗
DOE OSTI2025

Dissection of Carbon and Nitrogen Cycling in Post-Fire Soil Environments using a Genome- Informed Experimental Community (Final Technical Report)

Wildfires are a natural part of many forest ecosystems, with globally important carbon (C) storage and nutrient cycling consequences, and they are increasing in frequency and severity in Western North America. Forest fires affect soil C stocks in complex ways; some C is released into the atmosphere through combustion, while a large percentage of the C is added to the soil in the form of pyrogenic organic matter. Worldwide, it is estimated that 16% of soil organic matter is pyrogenic, while locally, this number may be as high as 80%. Understanding how wildfires affect soil organic matter cycling requires understanding how microbes respond to pyrogenic organic matter and other post-fire soil conditions. However, our understanding of microbial interactions within post-fire soil was in its infancy at the time of our proposal. Outstanding questions included: Which microbes are capable of degrading pyrogenic organic matter? What are the relevant genes and metabolites associated with this degradation? What are the key interactions among post-fire microbes? Key highlights of outcomes supported by this grant included training eleven early-career scientists and two early-career PIs, publication of twelve peer-reviewed papers, cross-lab collaborations that empowered complex scientific approaches, the development of an open-source automated gas sampler to drive novel insights in C cycling, enhanced understanding of post-fire microbial community dynamics, and novel genetic and molecular insights into microbial responses to fire.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Considering Soil Biota and Symbioses in Forest Management and Ecosystem Restoration

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

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass

Abstract Nitrogen (N) is frequently limiting to plant growth, in part because most soil N is present as polymeric organic compounds that are not readily taken up by plants. Microbial depolymerization of these large macromolecular N-substrates gradually releases available inorganic N. While many studies have researched and modeled controls on soil organic matter formation and bulk N mineralization, the ecological—spatial, temporal and phylogenetic—patterns underlying organic N degradation remain unclear. We analyzed 48 time-resolved metatranscriptomes and quantified N-depolymerization gene expression to resolve differential expression by soil habitat and time in specific taxonomic groups and gene-based guilds. We observed much higher expression of extracellular serine-type proteases than other extracellular N-degrading enzymes, with protease expression of predatory bacteria declining with time and other taxonomic patterns driven by the presence (Gammaproteobacteria) or absence (Thermoproteota) of live roots and root detritus (Deltaproteobacteria and Fungi). The primary chitinase chit1 gene was more highly expressed by eukaryotes near root detritus, suggesting predation of fungi. In some lineages, increased gene expression over time suggests increased competitiveness with rhizosphere age (Chloroflexi). Phylotypes from some genera had protease expression patterns that could benefit plant N nutrition, for example, we identified a Janthinobacterium phylotype and two Burkholderiales that depolymerize organic N near young roots and a Rhizobacter with elevated protease levels near mature roots. These taxon-resolved gene expression results provide an ecological read-out of microbial interactions and controls on N dynamics in specific soil microhabitats and could be used to target potential plant N bioaugmentation strategies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2016

Pick-and-Eat Salad-Crop Productivity, Nutritional Value, and Acceptability to Supplement the ISS Food System

The capability to grow nutritious, palatable food for crew consumption during spaceflight has the potential to provide health-promoting, bioavailable nutrients, enhance the dietary experience, and reduce launch mass as we move toward longer-duration missions. However, studies of edible produce during spaceflight have been limited, leaving a significant knowledge gap in the methods required to grow safe, acceptable, nutritious crops for consumption in space. Researchers from Kennedy Space Center, Johnson Space Center, Purdue University and ORBITEC have teamed up to explore the potential for plant growth and food production on the International Space Station (ISS) and future exploration missions. KSC, Purdue, and ORBITEC bring a history of plant and plant-microbial interaction research for ISS and for future bioregenerative life support systems. JSC brings expertise in Advanced Food Technology (AFT), Behavioral Health and Performance (BHP), and statistics. The Veggie vegetable-production system on the ISS offers an opportunity to develop a pick-and-eat fresh vegetable component to the ISS food system as a first step to bioregenerative supplemental food production. We propose growing salad plants in the Veggie unit during spaceflight, focusing on the impact of light quality and fertilizer formulation on crop morphology, edible biomass yield, microbial food safety, organoleptic acceptability, nutritional value, and behavioral health benefits of the fresh produce. The first phase of the project will involve flight tests using leafy greens, with a small Chinese cabbage variety, Tokyo bekana, previously down selected through a series of research tests as a suitable candidate. The second phase will focus on dwarf tomato. Down selection of candidate varieties have been performed, and the dwarf cultivar Red Robin has been selected as the test crop. Four light treatments and three fertilizer treatments will be tested for each crop on the ground, to down select to two light treatments and one fertilizer treatment to test on ISS. Our work will help define light colors, levels, and horticultural best practices to achieve high yields of safe, nutritious leafy greens and tomatoes to supplement a space diet of prepackaged food. Our final deliverable will be the development of growth protocols for these crops in a spaceflight vegetable production system. With this work, and potentially with other pending joint projects, we will continue the synergistic research to help close gaps in the human research roadmap, and enable humans to venture to Mars and beyond. This research was co-funded by the Human Research Program and Space Biology (MTL1075) in the ILSRA 2015 NRA call.

Behavioral Health↗
DOE OSTI2022

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station

The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months. Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results. Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10 5 cfu/m 2 . Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Spatiotemporal Metabolic Network Models Reveal Complex Autotroph-Heterotroph Biofilm Interactions Governed by Photon Incidences

Autotroph-heterotroph interactions are ubiquitous in natural environment and play a key role in controlling various essential ecosystem functions, such as production and utilization of organic matter, cycling of nitrogen, sulfur, and other chemical elements. Understanding how these biofilm metabolic interactions are constrained in space and time remains challenging because fully predictive models designed for this purpose are currently limited. Toward filling this gap, here we developed community metabolic network models for two autotroph-heterotroph biofilm consortia (termed UCC-A and UCC-O), which share a suite of common heterotrophic members but have a single distinct photoautotrophic cyanobacterium (Phormidesmis priestleyi str. ANA and Phormidium sp. OSCR) that provides organic carbon and nitrogen sources to support the growth of heterotrophic partners. After determining model parameters by data fitting using the spatiotemporal distributions of microbial abundances, we comparatively analyzed the resulting biofilm models to examine any fundamental differences in microbial interactions between the two consortia under the variation of key environmental variables: CO2 and photon levels. The UCC-A model predicted generally expected responses, i.e., the autotroph population increased in response to elevated levels of CO2 and photon, followed by increase in the heterotroph population. In contrast, the UCC-O model showed somewhat complicated dynamics, e.g., higher photon incidence rates resulted in the increase in autotroph population but decrease in heterotroph population due to the lowered provision of glucose from the autotroph. A further analysis showed that species coexistence was governed by the photon incidences rather than the carbon availability for UCC-O, which was the opposite for UCC-A.

Phalak, Poonam↗
DOE OSTI2024

Potential applications of microbial genomics in nuclear non-proliferation

As nuclear technology evolves in response to increased demand for diversification and decarbonization of the energy sector, new and innovative approaches are needed to effectively identify and deter the proliferation of nuclear arms, while ensuring safe development of global nuclear energy resources. Preventing the use of nuclear material and technology for unsanctioned development of nuclear weapons has been a long-standing challenge for the International Atomic Energy Agency and signatories of the Treaty on the Non-Proliferation of Nuclear Weapons. Environmental swipe sampling has proven to be an effective technique for characterizing clandestine proliferation activities within and around known locations of nuclear facilities and sites. However, limited tools and techniques exist for detecting nuclear proliferation in unknown locations beyond the boundaries of declared nuclear fuel cycle facilities, representing a critical gap in non-proliferation safeguards. Microbiomes, defined as “characteristic communities of microorganisms” found in specific habitats with distinct physical and chemical properties, can provide valuable information about the conditions and activities occurring in the surrounding environment. Microorganisms are known to inhabit radionuclide-contaminated sites, spent nuclear fuel storage pools, and cooling systems of water-cooled nuclear reactors, where they can cause radionuclide migration and corrosion of critical structures. Microbial transformation of radionuclides is a well-established process that has been documented in numerous field and laboratory studies. These studies helped to identify key bacterial taxa and microbially-mediated processes that directly and indirectly control the transformation, mobility, and fate of radionuclides in the environment. Expanding on this work, other studies have used microbial genomics integrated with machine learning models to successfully monitor and predict the occurrence of heavy metals, radionuclides, and other process wastes in the environment, indicating the potential role of nuclear activities in shaping microbial community structure and function. Results of this previous body of work suggest fundamental geochemical-microbial interactions occurring at nuclear fuel cycle facilities could give rise to microbiomes that are characteristic of nuclear activities. These microbiomes could provide valuable information for monitoring nuclear fuel cycle facilities, planning environmental sampling campaigns, and developing biosensor technology for the detection of undisclosed fuel cycle activities and proliferation concerns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Risk Assessment of Industrial Microbes Using a Terrestrial Mesocosm Platform

Abstract Industrial microbes and bio-derived products have emerged as an integral component of the bioeconomy, with an array of agricultural, bioenergy, and biomedical applications. However, the rapid development of microbial biotechnology raises concerns related to environmental escape of laboratory microbes, detection and tracking thereof, and resultant impact upon native ecosystems. Indeed, though wild-type and genetically modified microbes are actively deployed in industrial bioprocesses, an understanding of microbial interactivity and impact upon the environment is severely lacking. In particular, the persistence and sustained ecosystem impact of industrial microbes following laboratory release or unintentional laboratory escape remains largely unexplored. Herein, we investigate the applicability of soil-sorghum mesocosms for the ecological risk assessment of the industrial microbe, Saccharomyces cerevisiae . We developed and applied a suite of diagnostic and bioinformatic analyses, including digital droplet PCR, microscopy, and phylogenomic analyses to assess the impacts of a terrestrial ecosystem perturbation event over a 30-day time course. The platform enables reproducible, high-sensitivity tracking of S. cerevisiae in a complex soil microbiome and analysis of the impact upon abiotic soil characteristics and soil microbiome population dynamics and diversity. The resultant data indicate that even though S. cerevisiae is relatively short-lived in the soil, a single perturbation event can have sustained impact upon mesocosm soil composition and underlying microbial populations in our system, underscoring the necessity for more comprehensive risk assessment and development of mitigation and biocontainment strategies in industrial bioprocesses.

09 BIOMASS FUELS↗
DOE OSTI2022

Transitions of foliar mycobiota community and transcriptome in response to pathogenic conifer needle interactions

Profiling the host–mycobiota interactions in healthy vs. diseased forest ecosystems helps understand the dynamics of understudied yet increasingly important threats to forest health that are emerging due to climate change. We analyzed the structural and functional changes of the mycobiota and the responses of Pinus contorta in the Lophodermella needle cast pathosystem through metabarcoding and metatranscriptomics. When needles transitioned from asymptomatic to symptomatic, dysbiosis of the mycobiota occurred, but with an enrichment of Lophodermella pathogens. Many pathogenicity-related genes were highly expressed by the mycobiota at the necrotrophic phase, showing an active pathogen response that are absent in asymptomatic needles. This study also revealed that Lophodermella spp. are members of a healthy needle mycobiota that have latent lifestyles suggesting that other pine needle pathogens may have similar biology. Interestingly, Pinus contorta upregulated defense genes in healthy needles, indicating response to fungal recognition, while a variety of biotic and abiotic stresses genes were activated in diseased needles. Further investigation to elucidate the possible antagonistic interplay of other biotic members leading to disease progression and/or suppression is warranted. This study provides insights into microbial interactions in non-model pathosystems and contributes to the development of new forest management strategies against emerging latent pathogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Decadal survival of tropical pioneer seeds in the soil seed bank is accompanied by fungal infection and dormancy release

Pioneer trees require high-light environments for successful seedling establishment. Consequently, seeds of these species often persist in the soil seed bank (SSB) for periods ranging from several weeks to decades. How they survive despite extensive pressure from seed predators and soil-borne pathogens remains an intriguing question. Here this study aims to test the hypotheses that decades-old seeds collected from the SSB in a lowland tropical forest remain viable by (i) escaping infection by fungi, which are major drivers of seed mortality in tropical soils, and/or (ii) maintaining high levels of seed dormancy and seed coat integrity when compared to inviable seeds. We collected seeds of Trema micrantha and Zanthoxylum ekmanii at Barro Colorado Island, Panama, from sites where adult trees previously occurred in the past 30 years. We used carbon dating to measure seed age and characterized seed coat integrity, seed dormancy and fungal communities. Viable seeds from the SSB ranged in age from 9 to 30 years for T. micrantha, and 5 to 33 years for Z. ekmanii. We found no evidence that decades-old seeds maintain high levels of seed dormancy or seed coat integrity. Fungi were rarely detected in fresh seeds (no soil contact), but phylogenetically diverse fungi were detected often in seeds from the SSB. Although fungal infections were more commonly detected in inviable seeds than in viable seeds, a lack of differences in fungal diversity and community composition between viable and inviable seeds suggested that viable seeds are not simply excluding fungal species to survive long periods in the SSB. Synthesis. Our findings reveal the importance of a previously understudied aspect of seed survival, where the impact of seed–microbial interactions may be critical to understand long-term persistence in the SSB.

54 ENVIRONMENTAL SCIENCES↗