Results for “Microbiome” — Page 26

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2023

Data for EMSL Project 60929 from October 2023: PI Goemann MONet Request

Just as humans rely on a healthy gut microbiome for resilience to illness, plants rely on a healthy root microbiome for resilience to environmental abiotic stress (heat, drought). To achieve a healthy root microbiome, plants release carbon (C)-rich compounds as root exudates to stimulate microbial activity and increase local nutrient mineralization. However, the enhanced performance comes at a cost: up to 44% of a plant’s C can be lost to root exudates, diverting C from plant growth and respiration. Critical knowledge gaps include how the ‘C cost’ is managed and how root exudates alter the microbiome under different environmental conditions. In addition, historical climate conditions, particularly mean annual precipitation, is known to shape local soil microbiomes and alter their sensitivity to drought. Therefore, studies that better characterize the plant-microbe responses to environmental stress will aid in efforts to harness the microbiome to improve crop resilience. However, current knowledge gaps make it challenging to engineer beneficial plant-microbe interactions to improve plant productivity in agricultural systems and to predict how increased climate variability will alter terrestrial C fluxes and climate feedbacks. To fill this knowledge gap our research group at Montana State University – Bozeman is currently studying blue grama (Bouteloua gracilis), a prairie grass native across the Northern Great Plains, as a model for drought tolerance. Our goal is to investigate the above- and belowground responses of blue grama to drought and heat stress to improve our understanding of stress-induced carbon allocation and plant-microbe interactions. Most recently, we investigated the influence of climate history on the blue grama drought response. We collected soil from three blue grama-dominated sites (those proposed to sample here) across a 150 mm mean annual precipitation gradient in SW Montana, USA, to use as inoculum for a greenhouse drought experiment. Preliminary results indicate that soil climate history has a strong influence on the blue grama physiological response to drought as well as on the chemical composition of root exudates and rhizosphere microbiome composition. Metabarcoding data from this experiment is scheduled to be submitted to public databases within the next year. Having in-depth analyses of the soil biogeochemistry and metagenomic composition through the MONet project at each of the field sites associated with this experiment will allow us to link underlying ecological processes with observed patterns of plant growth and productivity at each site. In addition, we plan to utilize the MONet database for future meta-analyses to compare the genomic and biogeochemical signatures of our field sites to others across a wider precipitation gradient throughout the native range of blue grama. This will further provide critical insights into the mechanisms that drive ecosystem functioning and resilience to drought stress.

Peyton, Brent↗

DOE OSTI2024

Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs

Shifts in host-associated microbiomes can impact both host and microbes. It is of interest to understand how perturbations, like the introduction of exogenous chemicals, impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense. These alkaloids are antimicrobial; however, their effect on the frogs’ skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. Further, to better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice

There are known associations between opioids, obesity, and the gut microbiome, but the molecular connection/mediation of these relationships is not understood. To better clarify the interplay of physiological, genetic, and microbial factors, this study investigated the microbiome and host inflammatory responses to chronic opioid administration in genetically obese, diet-induced obese, and lean mice. Samples of feces, urine, colon tissue, and plasma were analyzed using targeted LC-MS/MS quantification of metabolites, immunoassays of inflammatory cytokine levels, genome-resolved metagenomics, and metaproteomics. Genetic obesity, diet-induced obesity, and morphine treatment in lean mice each showed increases in distinct inflammatory cytokines. Metagenomic assembly and binning uncovered over 400 novel gut bacterial genomes and species. Morphine administration impacted the microbiome’s composition and function, with the strongest effect observed in lean mice. This microbiome effect was less pronounced than either diet or genetically driven obesity. Based on inferred microbial physiology from the metaproteome datasets, a high-fat diet transitioned constituent microbes away from harvesting diet-derived nutrients and towards nutrients present in the host mucosal layer. Considered together, these results identified novel host-dependent phenotypes, differentiated the effects of genetic obesity versus diet induced obesity on gut microbiome composition and function, and showed that chronic morphine administration altered the gut microbiome.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Coordinating and Assisting Research at the SARS-CoV-2/Microbiome Nexus

Although the COVID-19 pandemic is caused by a single virus, the rest of the human microbiome appears to be involved in the disease and could influence vaccine responses while offering opportunities for microbiome-directed therapeutics. The newly formed Microbiome Centers Consortium (MCC) surveyed its membership and identified four ways to leverage the strengths and experience of microbiome centers in the response to the COVID-19 pandemic. To meet these needs, the MCC will provide a platform to coordinate clinical and environmental research, assist with practical obstacles, and help communicate the connections between the microbiome and COVID-19. We ask that microbiome researchers join us in these efforts to address the ongoing pandemic.

59 BASIC BIOLOGICAL SCIENCES↗

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 OSTI2021

Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles

Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO 2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO 2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO 2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Depth dependence of climatic controls on soil microbial community activity and composition

Abstract Subsoil microbiomes play important roles in soil carbon and nutrient cycling, yet our understanding of the controls on subsoil microbial communities is limited. Here, we investigated the direct (mean annual temperature and precipitation) and indirect (soil chemistry) effects of climate on microbiome composition and extracellular enzyme activity throughout the soil profile across two elevation-bioclimatic gradients in central California, USA. We found that microbiome composition changes and activity decreases with depth. Across these sites, the direct influence of climate on microbiome composition and activity was relatively lower at depth. Furthermore, we found that certain microbial taxa change in relative abundance over large temperature and precipitation gradients only in specific soil horizons, highlighting the depth dependence of the climatic controls on microbiome composition. Our finding that the direct impacts of climate are muted at depth suggests that deep soil microbiomes may lag in their acclimation to new temperatures with a changing climate.

16S rRNA↗

DOE OSTI2021

Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities

ABSTRACT Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Metagenomic insights into the taxonomy, function, and dysbiosis of prokaryotic communities in octocorals

Background. In octocorals (Cnidaria Octocorallia), the functional relationship between host health and its symbiotic consortium has yet to be determined. Here, we employed comparative metagenomics to uncover the distinct functional and phylogenetic features of the microbiomes of healthy Eunicella gazella, Eunicella verrucosa, and Leptogorgia sarmentosa tissues, in contrast with the microbiomes found in seawater and sediments. We further explored how the octocoral microbiome shifts to a pathobiome state in E. gazella. Results. Multivariate analyses based on 16S rRNA genes, Clusters of Orthologous Groups of proteins (COGs), Protein families (Pfams), and secondary metabolite-biosynthetic gene clusters annotated from 20 Illumina-sequenced metagenomes each revealed separate clustering of the prokaryotic communities of healthy tissue samples of the three octocoral species from those of necrotic E. gazella tissue and surrounding environments. While the healthy octocoral microbiome was distinguished by so-far uncultivated Endozoicomonadaceae, Oceanospirillales, and Alteromonadales phylotypes in all host species, a pronounced increase of Flavobacteriaceae and Alphaproteobacteria, originating from seawater, was observed in necrotic E. gazella tissue. Increased abundances of eukaryotic-like proteins, exonucleases, restriction endonucleases, CRISPR/Cas proteins, and genes encoding for heat-shock proteins, inorganic ion transport, and iron storage distinguished the prokaryotic communities of healthy octocoral tissue regardless of the host species. An increase of arginase and nitric oxide reductase genes, observed in necrotic E. gazella tissues, suggests the existence of a mechanism for suppression of nitrite oxide production by which octocoral pathogens may overcome the host’s immune system. Conclusions. This is the first study to employ primer-less, shotgun metagenome sequencing to unveil the taxonomic, functional, and secondary metabolism features of prokaryotic communities in octocorals. Our analyses reveal that the octocoral microbiome is distinct from those of the environmental surroundings, is host genus (but not species) specific, and undergoes large, complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defense arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. We argue that these features collectively contribute to the stabilization of symbiosis in the octocoral holobiont and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1â€“13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

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, N 2 O 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. mays), 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 N 2 O 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 N 2 O 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.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Microbial Drivers of Plant Performance during Drought Depend upon Community Composition and the Greater Soil Environment

The increasing occurrence of drought is a global challenge that threatens food security through direct impacts to both plants and their interacting soil microorganisms. Plant growth promoting microbes are increasingly being harnessed to improve plant performance under stress. However, the magnitude of microbiome impacts on both structural and physiological plant traits under water limited and water replete conditions are not well-characterized. Using two microbiomes sourced from a ponderosa pine forest and an agricultural field, we performed a greenhouse experiment that used a crossed design to test the individual and combined effects of the water availability and the soil microbiome composition on plant performance. Specifically, we studied the structural and leaf functional traits of maize that are relevant to drought tolerance. We further examined how microbial relationships with plant phenotypes varied under different combinations of microbial composition and water availability. We found that water availability and microbial composition affected plant structural traits. Surprisingly, they did not alter leaf function. Maize grown in the forest-soil microbiome produced larger plants under well-watered and water-limited conditions, compared to an agricultural soil community. Although leaf functional traits were not significantly different between the watering and microbiome treatments, the bacterial composition and abundance explained significant variability in both plant structure and leaf function within individual treatments, especially water-limited plants. Our results suggest that bacteria-plant interactions that promote plant performance under stress depend upon the greater community composition and the abiotic environment.

59 BASIC BIOLOGICAL SCIENCES↗