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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Calcium promotes persistent soil organic matter by altering microbial transformation of plant litter

Abstract Calcium (Ca) can contribute to soil organic carbon (SOC) persistence by mediating physico-chemical interactions between organic compounds and minerals. Yet, Ca is also crucial for microbial adhesion, potentially affecting colonization of plant and mineral surfaces. The importance of Ca as a mediator of microbe-mineral-organic matter interactions and resulting SOC transformation has been largely overlooked. We incubated 44 Ca labeled soils with 13 C 15 N labeled leaf litter to study how Ca affects microbial transformation of litter and formation of mineral associated organic matter. Here we show that Ca additions promote hyphae-forming bacteria, which often specialize in colonizing surfaces, and increase incorporation of litter into microbial biomass and carbon use efficiency by approximately 45% each. Ca additions reduce cumulative CO 2 production by 4%, while promoting associations between minerals and microbial byproducts of plant litter. These findings expand the role of Ca in SOC persistence from solely a driver of physico-chemical reactions to a mediator of coupled abiotic-biotic cycling of SOC.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Latitudinal shifts of soil microbial biomass seasonality

Soil microbes ultimately drive the mineralization of soil organic carbon and thus ecosystem functions. We compiled a dataset of the seasonality of microbial biomass carbon (MBC) and developed a semi-mechanistic model to map monthly MBC across the globe. MBC exhibits an equatorially symmetric seasonality between the Northern and Southern Hemispheres. In the Northern Hemisphere, MBC peaks in autumn and is minimal in spring at low latitudes (<25°N), peaks in the spring and is minimal in autumn at mid-latitudes (25°N to 50°N), while peaks in autumn and is minimal in spring at high latitudes (>50°N). This latitudinal shift of MBC seasonality is attributed to an interaction of soil temperature, soil moisture, and substrate availability. The MBC seasonality is inconsistent with patterns of heterotrophic respiration, indicating that MBC as a proxy for microbial activity is inappropriate at this resolution. This study highlights the need to explicitly represent microbial physiology in microbial models. The interactive controls of environments and substrate on microbial seasonality provide insights for better representing microbial mechanisms in simulating ecosystem functions at the seasonal scale.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods

Microbial communities are a key driver of the carbon cycle through the breakdown of complex polysaccharides in diverse environments including soil, marine systems, and the mammalian gut. However, due to the complexity of these communities, the species-species interactions that impact community structure and ultimately shape the rate of decomposition are difficult to define.

microbial interactions↗
DOE OSTI2025

Distinct Fracture Mineralogy That is Out of Equilibrium With Modern Groundwaters Provides Important Context for Subsurface Life

Rock fracture surfaces in the crust are essential habitat for microorganisms. Fracture‐groundwater interfaces provide physical substrates for biofilm growth and are sources of carbon, nutrients, and electron donors and acceptors. To better understand geochemical processes impacting fracture surfaces and the subsurface microbiome, we identified fractures in archived rock cores from the Soudan formation, which is known to host saline groundwaters and isolated microbial communities dependent on rock‐water interactions. Cores with open fractures were thin sectioned and studied via electron microprobe and synchrotron X‐ray fluorescence microprobe. Most fracture surfaces had mineralogy distinct from that of the bulk rock. Chlorite minerals were abundant on fracture surfaces and had elemental compositions suggesting deposition during late‐stage hydrothermal alteration. Fracture‐lining chlorites likely limit access to iron oxide and sulfide minerals that are active in subsurface biogeochemical cycles. Calcium‐rich rinds were also observed along fracture edges. These rinds were too thin and poorly ordered to be identified via light microscopy or X‐ray diffraction; however, Ca K‐edge micro‐X‐ray absorption near‐edge structure spectroscopy identified them as carbonates, minerals not observed in the bulk rock. Thermodynamic modeling shows that carbonate precipitation is largely unfavorable in Soudan groundwaters, indicating that fracture edge conditions differed from those in modern water samples. Because of the low carbon concentrations in Soudan groundwaters, carbonate rinds likely play an important role in subsurface carbon cycling and may mark fracture surfaces that once hosted biofilms. Overall, this study suggests that fracture alteration can both play an active role in and suppress rock‐water interactions essential to subsurface life.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Syntrophic bacterial and host–microbe interactions in bacterial vaginosis

Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host–bacteria and bacteria–bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.

bacterial vaginosis↗
DOE OSTI2020

Ecological Assembly Processes Are Coordinated between Bacterial and Viral Communities in Fractured Shale Ecosystems

The ecological drivers that concurrently act upon both a virus and its host and that drive community assembly are poorly understood despite known interactions between viral populations and their microbial hosts. Hydraulically fractured shale environments provide access to a closed ecosystem in the deep subsurface where constrained microbial and viral community assembly processes can be examined. Here, we used metagenomic analyses of time-resolved-produced fluid samples from two wells in the Appalachian Basin to track viral and host dynamics and to investigate community assembly processes. Hypersaline conditions within these ecosystems should drive microbial community structure to a similar configuration through time in response to common osmotic stress. However, viral predation appears to counterbalance this potentially strong homogeneous selection and pushes the microbial community toward undominated assembly. In comparison, while the viral community was also influenced by substantial undominated processes, it assembled, in part, due to homogeneous selection. When the overall assembly processes acting upon both these communities were directly compared with each other, a significant relationship was revealed, suggesting an association between microbial and viral community development despite differing selective pressures. These results reveal a potentially important balance of ecological dynamics that must be in maintained within this deep subsurface ecosystem in order for the microbial community to persist over extended time periods. More broadly, this relationship begins to provide knowledge underlying metacommunity development across trophic levels.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

ELM-Wet: Inclusion of a wetland landunit with sub-grid representation of eco-hydrological patches and hydrological forcing in E3SM Land Model (ELM)

Wetlands emit the most biogenic methane (CH4) and present the greatest uncertainty in the global CH4 budget. Modeling these emissions is challenging due to the temporal and spatial variability in wetland structure and CH4 flux rates, along with complex interactions among hydrological, ecological, meteorological, and microbial processes that govern CH4 dynamics. To address these issues, we aim to enhance the accuracy of wetland representation in the U.S. Department of Energy’s Exascale Earth System Model (E3SM) Land Model, ELM. This effort led to the development of ELM-Wet, which incorporates a dedicated wetland landunit with subgrid representation of eco-hydrological patch types. We implement wetland-specific hydrology by imposing site-specific constraints on surface water levels, thereby allowing different patches to sustain varying depths of inundation. Additionally, we refined the calculation of aerenchyma transport diffusivity based on observed conductance across different vegetation types. We validated these enhancements through site-specific simulations of a coastal freshwater wetland, the Salvador WMA Freshwater Marsh (Ameriflux, site ID US-LA2), located in the coast of Louisiana (29.85N,90.29W) at an elevation of 0 m. The site was simulated with ELM-Wet and the default version ELMv1. We use Bayesian Optimization to parameterize CO2 and CH4 fluxes. Eddy covariance observations of CO2 and CH4 fluxes from 2012-2013 were used to train the model and data from 2021 were used for validation. In this repository, we include all the output of all the simulations performed using different versions of ELMv1 and ELM-Wet, all input required to the model, and the Matlab scripts we used to processed the output data. ELM-Wet_flmd.csv includes a detailed description of the datasets files.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Abstract Our current knowledge of host–virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria. However, natural biofilms are diverse and chiefly composed of uncultured bacteria and archaea with no viral infection patterns and lifestyle predictions described to date. Herein, we predict the first DNA sequence-based host–virus interactions in a natural biofilm. Using single-cell genomics and metagenomics applied to a hot spring mat of the Cone Pool in Mono County, California, we provide insights into virus–host range, lifestyle and distribution across different mat layers. Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species. Analysis of single-cell amplification kinetics revealed a lack of active viral replication on the single-cell level. These findings were further supported by mapping metagenomic reads from different mat layers to the obtained host–virus pairs, which indicated a low copy number of viral genomes compared to their hosts. Lastly, the metagenomic data revealed high layer specificity of viruses, suggesting limited diffusion to other mat layers. Taken together, these observations indicate that in low mobility environments with high microbial abundance, lysogeny is the predominant viral lifestyle, in line with the previously proposed “Piggyback-the-Winner” theory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts

Sponges are ancient sessile metazoans, which form with their associated microbial symbionts a complex functional unit called a holobiont. Sponges are a rich source of chemical diversity; however, there is limited knowledge of which holobiont members produce certain metabolites and how they may contribute to chemical interactions. To address this issue, we applied non-targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) and gas chromatography mass spectrometry (GC-MS) to either whole sponge tissue or fractionated microbial cells from six different, co-occurring sponge species. Several metabolites were commonly found or enriched in whole sponge tissue, supporting the notion that sponge cells produce them. These include 2-methylbutyryl-carnitine, hexanoyl-carnitine and various carbohydrates, which may be potential food sources for microorganisms, as well as the antagonistic compounds hymenialdisine and eicosatrienoic acid methyl ester. Metabolites that were mostly observed or enriched in microbial cells include the antioxidant didodecyl 3,3'-thiodipropionate, the antagonistic compounds docosatetraenoic acid, and immune-suppressor phenylethylamide. This suggests that these compounds are mainly produced by the microbial members in the sponge holobiont, and are potentially either involved in inter-microbial competitions or in defenses against intruding organisms. This study shows how different chemical functionality is compartmentalized between sponge hosts and their microbial symbionts and provides new insights into how chemical interactions underpin the function of sponge holobionts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

CarbStor: Development, Analysis and Modification of Carbon Storing Model Soil Communities

Soil microbial communities carry out a number of key processes including plant growth promotion, bioremediation and cycling of nutrients. Carbon cycling is among the most important of these nutrients that are metabolized and processed by the soil microbial community. Many of the carbon inputs are converted to alternative organic forms of carbon that can be used by plants or act as biomass for microbial growth. However, inorganic forms of carbon can also be produced by soil microbial communities including calcium carbonate (CaCO 3 ). Production of calcium carbonate is beneficial for the ecosystem in several ways: it can stabilize soils and improve soil health, especially denser soils with high clay content, it can act as a method of bioremediation, it can serve as an alternative carbon source for plants and it can be a way to store carbon in soil in a stable, inorganic manner for the long term. While the chemistry surrounding individual species carrying out this process is well known what is lacking is an understanding of how species interact in a community to drive carbonate production. As all microbial species in soil exist in a community setting gaining this knowledge is critical to our predicting and controlling this microbial phenotype to greatly improve soil health. The CarbStor project is focused on developing, analyzing and modifying defined microbial soil consortia that express phenotypes at both the species and community level to convert carbon into recalcitrant stable sources such as precipitated carbonate or microbial necromass. To take full advantage of the soil community for this process we will need to fill several key knowledge gaps (KG), three of which are the focus of CarbStor. KG1: Whether and to what degree microbial communities can be developed that produce precipitated carbon via microbial metabolism. KG2: What interspecies interactions drive the individual member phenotypes in defined communities that lead to carbon precipitation. KG3: How can these interactions be modified to enhance carbon sequestration beyond what native communities are capable of. We hypothesize that in a carbon sequestering community only a subset of species will express phenotypes related to carbon storage processes. We also hypothesize that these phenotypes are expressed as a result of interactions with other species in the community that are not involved in carbon storage processes and that these interactions can be harnessed to enhance community carbon sequestration.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Dynamic interactions at the mineral–organic matter interface

Minerals are widely assumed to protect organic matter (OM) from degradation in the environment, promoting the persistence of carbon in soil and sediments. In this Review, we describe the mechanisms and processes operating at the mineral–organic interface as they relate to OM transformation dynamics. A broad set of interactions occur, with minerals adsorbing organic compounds to their surfaces and/or acting as catalysts for organic reactions. Minerals can serve as redox partners for OM through direct electron transfer or by generating reactive oxygen species, which then oxidize OM. Finally, the compartmentalization of soil and sediment by minerals creates unique microsites that host diverse microbial communities. Acknowledgement of this multiplicity of interactions suggests that the general assumption that the mineral matrix provides a protective function for OM is overly simplistic. Future work must recognize adsorption as a condition for further reactions instead of as a final destination for organic adsorbates, and should consider the spatial and functional complexity that is characteristic of the environments where mineral–OM interactions are observed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Development and implementation of an in situ high-resolution isotopic microscope for measuring metabolic interactions in soil mesocosms (Final Report)

Many of our planet’s ecosystems rely on the activities of soil microbial communities. These microbes have significant and wide-ranging effects: they metabolize carbon and other nutrients, interact with plants and fungi, and perform other processes important to soil health. However, our ability to directly observe the enzymatic and metabolic activities of microbes within soil is currently limited, not only by the complexity of soil microbial communities themselves, but also by the lack of experimental tools to study them and their molecular interactions in situ. These challenges hinder our understanding of the lifesustaining processes of biomass decomposition and the manner in which it contributes to the movement of freed carbon within soil ecosystems. Here we aim to develop a novel ultrahigh-resolution isotopic microscope that combines complementary imaging modalities to gain insights into metabolic cycling in soil. This final report covers the portion of this work that was completed at the University of North Carolina at Chapel Hill from 2018 to 2019; the research is continuing through 2022 at the University of Massachusetts Chan Medical School.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy

Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent. To characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO 2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members. Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration. Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Rhizosphere Carbon Turnover from Cradle to Grave: The Role of Microbe–Plant Interactions

Plant roots are the primary source of organic materials that become stabilized in soil. While most root carbon is decomposed into carbon dioxide (CO 2 ), the remainder typically undergoes multiple microbial transformations before it forms longer-term associations with soil minerals. However, the mechanisms by which roots affect microbial utilization of organic materials and subsequent mineral stabilization processes are poorly understood. It is well known that living roots increase the biomass of nearby microbial communities, and shape their population dynamics, diversity, and interactions. Community assembly and metabolic potential of these rhizosphere-enriched microorganisms are strongly influenced by the chemical composition of the exudates released by the host plant. The root exudate pools of plants undergo compositional changes as they grow, reproduce, and senesce. In the well-studied annual grasses Avena barbata and Avena fatua, this changing rhizosphere substrate pool and the “bloom” of organisms that respond are phylogenetically coherent; Acidobacteria and Actinobacteria are consistently depleted, whereas Alpha and Betaproteobacteria and Bacteroidetes are reliably enriched. When compared to non-root-influenced bulk soils, the responsive community is predictably less taxon-rich, yet forms more complex networks. Finally, these rhizosphere dynamics have significant downstream effects on the colonization of nearby soil minerals, degradation of prior season’s root litters, and the balance of stabilized versus lost soil carbon.

Pett-Ridge, Jennifer↗
DOE OSTI2021

Accessing the Subsurface Biosphere Within Rocks Undergoing Active Low-Temperature Serpentinization in the Samail Ophiolite (Oman Drilling Project)

The Oman Drilling Project established an “Active Alteration” multi-borehole observatory in peridotites undergoing low-temperature serpentinization in the Samail Ophiolite. The highly serpentinized rocks are in contact with strongly reducing fluids. Distinct hydrological regimes, governed by differences in rock porosity and fracture density, give rise to steep redox (Eh +200 to –750 mV) and pH (pH range 8.5–11.2) gradients within the 300–400 m deep boreholes. The serpentinites and fluids host an active subsurface ecosystem. Microbial cell abundances in serpentinite vary at least six orders of magnitude, from ≤3.5 × 10 1 to 2.9 × 10 7 cells/g. Low levels of biological sulfate reduction (2–1,000 fmol/cm 3 /day) can be detected in rock cores, particularly in rocks in contact with reduced groundwaters with pH < 10.5. Thermodesulfovibrio is the predominant sulfate reducer identified via metagenomic sequencing of adjacent groundwater communities. Here, we infer that transport and reaction of microbially generated sulfide with the serpentine and brucite assemblages gives rise to optical darkening and sulfide overprinting, including the formation of tochilinite-vallerite group minerals, potentially serving as an indicator that this system is inhabited by microbial life. Olivine mesh-cores replaced with ferroan brucite and minor awaruite, abundant veins containing hydroandradite garnet and polyhedral serpentine, and late-stage carbonate veins are suggested as targets for future spatially resolved life-detection investigations. The high-quality whole-round core samples that have been preserved can be further probed to define how life distributes itself and functions within a system where chemical disequilibria are sustained by low-temperature water/rock interaction, and how biosignatures of in situ microbial activity are generated.

58 GEOSCIENCES↗
DOE OSTI2026

Data for Genetic Variation in Zea mays Influences Microbial Nitrification and DeNitrification in Conventional Agroecosystems

Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N2O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds ( Z. mays ssp. mays ), ex-PVP hybrids ( Z. mays ssp. may s), and teosinte ( Z. mays ssp. mexicana and Z. mays ssp. parviglumis ). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N2O fluxes, with teosinte plots producing less GHG than maize plots. Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N2O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.

Nitrogen↗
NASA NTRSDate not supplied

SPACEFLIGHT-INDUCED CHANGES IN MICROBIAL VIRULENCE AND THE IMPACT TO THE HOST IMMUNE RESPONSE

INTRODUCTION Over the past 50 years, microorganisms have displayed unexpected responses relevant to infectious disease when grown in microgravity and microgravity analogue environments, including changes in final cell concentration, biofilm production, stress resistance, antibiotic sensitivity, gene expression, and virulence. In parallel, astronaut studies have characterized a persistent spaceflight-induced dysregulation of the human immune system; consisting of altered leukocyte distribution, reductions in T and NK cell function, altered cytokine profiles, and reactivation of latent herpesviruses. Further, astronauts have some degree of clinical incidence, primarily infectious disease episodes and atopic dermatitis. The impact of the microgravity environment on host-pathogen interactions and potential for clinical disease remains understudied and poorly characterized. SPECIFIC AIMS In the Host-Microorganism, Microbial Response aspect of this study, the following Specific Aims are being investigated, using the microbial pathogens, Salmonella enterica Enteritidis, Pseudomonas aeruginosa, Burkholderia cepacia, Streptococcus pneumoniae, and enterohemorrhagic Escherichia coli. Aim 1: Characterize the effect of spaceflight analogue culture on microbial pathogenesis-related stress responses and in vitro host-pathogen interactions. Analysis will include microbial stress responses as well as colonization and viability following pathogen challenge of three-dimensional (3-D) tissue co-culture models containing immune cells. We specifically selected obligate and opportunistic pathogens that are medically important and have been or are likely to be found aboard spacecraft. Aim 2: Characterize the effect of spaceflight analogue culture on the virulence potential of pathogenic microorganisms. Changes in virulence will be assessed using a mouse model of infection. SIGNIFICANCE The goal of this study is to use spaceflight analogue conditions to gain insight into the breadth of medically-significant International Space Station microorganisms that have altered virulence and the impact of those changes on the immune response of the host, including astronaut immune cells. This information will provide critical understanding into the impact of microgravity on potential alterations in microbial virulence and associated infectious disease risk to crew health during spaceflight missions.

C. M. Ott↗
DOE OSTI2025

Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere

Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, 13 C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant 13 CO 2 labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background. We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly 13 C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all 13 C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web. To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.

59 BASIC BIOLOGICAL SCIENCES↗