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At least 73 records · Page 4

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↗

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↗

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↗

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↗

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↗

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↗

Climate warming enhances microbial network complexity and stability

Unravelling the relationships between network complexity and stability under changing climate is a challenging topic in theoretical ecology that remains understudied in the field of microbial ecology. Here, we examined the effects of long-term experimental warming on the complexity and stability of molecular ecological networks in grassland soil microbial communities. Warming significantly increased network complexity, including network size, connectivity, connectance, average clustering coefficient, relative modularity and number of keystone species, as compared with the ambient control. Molecular ecological networks under warming became significantly more robust, with network stability strongly correlated with network complexity, supporting the central ecological belief that complexity begets stability. Furthermore, warming significantly strengthened the relationships of network structure to community functional potentials and key ecosystem functioning. Furthermore, these results indicate that preserving microbial ‘interactions’ is critical for ecosystem management and for projecting ecological consequences of future climate warming.

54 ENVIRONMENTAL SCIENCES↗

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↗

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↗

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↗

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↗

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↗

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↗

Widespread bacterial diversity within the bacteriome of fungi

Abstract Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗

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↗

Studying microbially induced corrosion on glass using ToF-SIMS

Microbially induced corrosion (MIC) is an emerging topic that has huge environmental impacts, such as long-term evaluation of microbial interactions with radioactive waste glass, environmental cleanup and disposal of radioactive material, and weathering effects of microbes. Time-of-flight secondary ion mass spectrometry (ToF-SIMS), a powerful mass spectral imaging technique with high surface sensitivity, mass resolution, and mass accuracy, can be used to study biofilm effects on different substrates. Understanding how to prepare biofilms on MIC susceptible substrates is critical for proper analysis via ToF-SIMS. We present here a step-by-step protocol for preparing bacterial biofilms for ToF-SIMS analysis, comparing three biofilm preparation techniques: no desalination, centrifugal spinning (CS), and water submersion (WS). Comparisons of two desalinating methods, CS and WS, show a decrease in the media peaks up to 99% using CS and 55% using WS, respectively. Proper desalination methods also can increase biological signals by over four times for fatty acids using WS, for example. ToF-SIMS spectral results show chemical compositional changes of the glass exposed in a Paenibacillus polymyxa SCE2 biofilm, indicating its capability to probe microbiologically induced corrosion of solid surfaces. This represents the proper desalination technique to use without significantly altering biofilm structure and substrate for ToF-SIMS analysis. ToF-SIMS spectral results showed chemical compositional changes of the glass exposed by a Paenibacillus bacterial biofilm over 3-month inoculation. Finally, possible MIC products include various phosphate phase molecules not observed in any control samples with the highest percent increases when experimental samples were compared with biofilm control samples.

36 MATERIALS SCIENCE↗

Carbon-phosphorus cycle models overestimate CO 2 enrichment response in a mature Eucalyptus forest

The importance of phosphorus (P) in regulating ecosystem responses to climate change has fostered P-cycle implementation in land surface models, but their CO 2 effects predictions have not been evaluated against measurements. Here, we perform a data-driven model evaluation where simulations of eight widely used P-enabled models were confronted with observations from a long-term free-air CO 2 enrichment experiment in a mature, P-limited Eucalyptus forest. We show that most models predicted the correct sign and magnitude of the CO 2 effect on ecosystem carbon (C) sequestration, but they generally overestimated the effects on plant C uptake and growth. We identify leaf-to-canopy scaling of photosynthesis, plant tissue stoichiometry, plant belowground C allocation, and the subsequent consequences for plant-microbial interaction as key areas in which models of ecosystem C-P interaction can be improved. Together, this data-model intercomparison reveals data-driven insights into the performance and functionality of P-enabled models and adds to the existing evidence that the global CO 2 -driven carbon sink is overestimated by models.

54 ENVIRONMENTAL SCIENCES↗